From 29520835ccd2663cfbb1ac5321f346cedde663fa Mon Sep 17 00:00:00 2001 From: Felipe Date: Wed, 15 Sep 2021 13:29:46 +0000 Subject: [PATCH 01/44] update document Rd to Rmd --- DESCRIPTION | 1 + R/assets_download.R | 72 ++++++++-------- R/collections.R | 16 ++-- R/documents.R | 88 +++++++++---------- R/ext_query.R | 64 +++++++------- R/extensions.R | 98 ++++++++++----------- R/items.R | 42 ++++----- R/print.R | 38 ++++---- R/query.R | 28 +++--- R/request.R | 44 +++++----- R/rstac.R | 32 +++---- R/stac.R | 16 ++-- R/stac_search.R | 52 +++++------ R/utils.R | 192 ++++++++++++++++++++--------------------- man/assets_download.Rd | 10 +-- man/assets_list.Rd | 8 +- man/collections.Rd | 22 ++--- man/doc_query.Rd | 2 +- man/ext_query.Rd | 24 +++--- man/extensions.Rd | 6 +- man/items.Rd | 42 ++++----- man/items_fields.Rd | 2 +- man/items_functions.Rd | 6 +- man/items_group.Rd | 8 +- man/items_reap.Rd | 8 +- man/print.Rd | 34 ++++---- man/request.Rd | 10 +-- man/rstac.Rd | 46 +++++----- man/stac.Rd | 8 +- man/stac_search.Rd | 26 +++--- man/utilities.Rd | 4 +- 31 files changed, 525 insertions(+), 524 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bd3fb8f4..49909b78 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -28,3 +28,4 @@ Suggests: covr, testthat, vcr +Roxygen: list(markdown = TRUE) diff --git a/R/assets_download.R b/R/assets_download.R index 014984be..1c79e6be 100644 --- a/R/assets_download.R +++ b/R/assets_download.R @@ -1,33 +1,33 @@ #' @title Downloads assets via STAC API #' -#' @description The \code{assets_download} function downloads the assets +#' @description The `assets_download` function downloads the assets #' provided by the STAC API. #' -#' @param items a \code{STACItem} or \code{STACItemCollection} object -#' representing the result of \code{/stac/search}, +#' @param items a `STACItem` or `STACItemCollection` object +#' representing the result of `/stac/search`, #' \code{/collections/{collectionId}/items} or #' \code{/collections/{collectionId}/items/{itemId}} endpoints. #' -#' @param assets_name a \code{character} with the assets names to be filtered. +#' @param assets_name a `character` with the assets names to be filtered. #' -#' @param output_dir a \code{character} directory in which the assets will be +#' @param output_dir a `character` directory in which the assets will be #' saved. #' -#' @param overwrite a \code{logical} if TRUE will replaced the existing file, -#' if FALSE a warning message is shown. (\code{FALSE}, default). +#' @param overwrite a `logical` if TRUE will replaced the existing file, +#' if FALSE a warning message is shown. (`FALSE`, default). #' -#' @param items_max a \code{numeric} corresponding how many items will be +#' @param items_max a `numeric` corresponding how many items will be #' downloaded. #' -#' @param progress a \code{logical} indicating if a progress bar must be -#' shown or not. (\code{TRUE}, default). +#' @param progress a `logical` indicating if a progress bar must be +#' shown or not. (`TRUE`, default). #' -#' @param ... config parameters to be passed to \link[httr]{GET} or -#' \link[httr]{POST} methods, such as \link[httr]{add_headers} or -#' \link[httr]{set_cookies}. +#' @param ... config parameters to be passed to [GET][httr::GET] or +#' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or +#' [set_cookies][httr::set_cookies]. #' #' @seealso -#' \code{\link{stac_search}}, \code{\link{items}}, \code{\link{get_request}} +#' [stac_search()], [items()], [get_request()] #' #' @examples #' \dontrun{ @@ -38,7 +38,7 @@ #' assets_download(assets_name = "thumbnail", output_dir = ".") #' } #' -#' @return The same \code{STACItemCollection} or \code{STACItem} object, with +#' @return The same `STACItemCollection` or `STACItem` object, with #' the link pointing to the directory where the assets were saved. #' #' @export @@ -111,27 +111,27 @@ assets_download <- function(items, # helpers ---------------------------------------------------------------------- -#' @title Helper function of \code{assets_download} function +#' @title Helper function of `assets_download` function #' -#' @description the \code{.item_download} function downloads the assets of a -#' \code{STACItem} object. +#' @description the `.item_download` function downloads the assets of a +#' `STACItem` object. #' -#' @param stac_item a \code{stac_item} object expressing a STAC -#' search criteria provided by \code{stac_item} function. +#' @param stac_item a `stac_item` object expressing a STAC +#' search criteria provided by `stac_item` function. #' -#' @param assets_name a \code{character} with the assets names to be filtered. +#' @param assets_name a `character` with the assets names to be filtered. #' -#' @param output_dir a \code{character} directory in which the images will be +#' @param output_dir a `character` directory in which the images will be #' saved. #' -#' @param overwrite a \code{logical} if TRUE will replaced the existing file, +#' @param overwrite a `logical` if TRUE will replaced the existing file, #' if FALSE a warning message is shown. #' -#' @param ... config parameters to be passed to \link[httr]{GET} or -#' \link[httr]{POST} methods, such as \link[httr]{add_headers} or -#' \link[httr]{set_cookies}. +#' @param ... config parameters to be passed to [GET][httr::GET] or +#' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or +#' [set_cookies][httr::set_cookies]. #' -#' @return The same \code{stac_item} object, but with the link of the item +#' @return The same `stac_item` object, but with the link of the item #' pointing to the directory where the assets were saved. #' #' @noRd @@ -165,14 +165,14 @@ assets_download <- function(items, return(stac_item) } -#' @title Helper function of \code{assets_download} function +#' @title Helper function of `assets_download` function #' -#' @description The \code{.file_ext} is function to extract the extension +#' @description The `.file_ext` is function to extract the extension #' from a file #' -#' @param asset_url a \code{character} URL provided from a \code{stac_search}. +#' @param asset_url a `character` URL provided from a `stac_search`. #' -#' @return A \code{character} of the extracted file extension. +#' @return A `character` of the extracted file extension. #' #' @noRd .file_ext <- function(asset_url) { @@ -185,17 +185,17 @@ assets_download <- function(items, return(substring(asset_url[[1]], pos + 1)) } -#' @title Helper function of \code{assets_download} function +#' @title Helper function of `assets_download` function #' -#' @description The helper function \code{.select_assets} selects the names of +#' @description The helper function `.select_assets` selects the names of #' each asset provided by users #' -#' @param assets_list a \code{list} with the information of each item provided +#' @param assets_list a `list` with the information of each item provided #' by API STAC #' -#' @param assets_names a \code{character} with the assets names to be filtered. +#' @param assets_names a `character` with the assets names to be filtered. #' -#' @return A \code{list} in the same format as the list of assets, but with the +#' @return A `list` in the same format as the list of assets, but with the #' selected assets names. #' #' @noRd diff --git a/R/collections.R b/R/collections.R index 23e7183a..7d69a381 100644 --- a/R/collections.R +++ b/R/collections.R @@ -3,29 +3,29 @@ #' @rdname collections #' #' @description -#' The \code{collections} function implements the WFS3 \code{/collections} +#' The `collections` function implements the WFS3 `/collections` #' and \code{/collections/\{collectionId\}} endpoints. #' #' Each endpoint retrieves specific STAC objects: #' \itemize{ -#' \item \code{/collections}: Returns a list of STAC Collection published in +#' \item `/collections`: Returns a list of STAC Collection published in #' the STAC service #' \item \code{/collections/\{collectionId\}}: Returns a single STAC #' Collection object #' } #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param collection_id a \code{character} collection id to be retrieved. +#' @param collection_id a `character` collection id to be retrieved. #' #' @seealso -#' \code{\link{get_request}}, \code{\link{post_request}}, -#' \code{\link{items}} +#' [get_request()], [post_request()], +#' [items()] #' #' @return -#' A \code{RSTACQuery} object with the subclass \code{collections} for -#' \code{/collections/} endpoint, or a \code{collection_id} subclass for +#' A `RSTACQuery` object with the subclass `collections` for +#' `/collections/` endpoint, or a `collection_id` subclass for #' \code{/collections/{collection_id}} endpoint, containing all search field #' parameters to be provided to STAC API web service. #' diff --git a/R/documents.R b/R/documents.R index c07bb8e0..57976fcd 100644 --- a/R/documents.R +++ b/R/documents.R @@ -1,34 +1,34 @@ #' @title Document development functions #' #' @describeIn extensions -#' The \code{RSTACDocument()} function is a constructor of +#' The `RSTACDocument()` function is a constructor of #' STAC documents. Currently, there are five STAC documents defined: #' \itemize{ -#' \item \code{STACCatalog} -#' \item \code{STACCollection} -#' \item \code{STACCollectionList} -#' \item \code{STACItem} -#' \item \code{STACItemCollection} +#' \item `STACCatalog` +#' \item `STACCollection` +#' \item `STACCollectionList` +#' \item `STACItem` +#' \item `STACItemCollection` #' } #' #' Each document class is associated with STAC API endpoints. #' As soon as new STAC documents are proposed in the specification, new -#' classes can be created in the \code{rstac} package. +#' classes can be created in the `rstac` package. #' -#' Let \code{version} parameter \code{NULL} to detect version automatically. +#' Let `version` parameter `NULL` to detect version automatically. #' -#' @param content a \code{list} data structure representing the JSON file -#' received in HTTP response (see \code{\link{content_response}()} function) +#' @param content a `list` data structure representing the JSON file +#' received in HTTP response (see [content_response()] function) #' -#' @param q a \code{RSTACQuery} object expressing the STAC query used +#' @param q a `RSTACQuery` object expressing the STAC query used #' to retrieve the document. #' -#' @param subclass a \code{character} corresponding to the subclass of the +#' @param subclass a `character` corresponding to the subclass of the #' document to be created. #' #' @return -#' The \code{RSTACDocument()} function returns a \code{RSTACDocument} object -#' with subclass defined by \code{subclass} parameter. +#' The `RSTACDocument()` function returns a `RSTACDocument` object +#' with subclass defined by `subclass` parameter. #' #' @export RSTACDocument <- function(content, q, subclass) { @@ -56,9 +56,9 @@ check_subclass.RSTACDocument <- function(x, subclasses) { #' @title Document utils functions #' -#' @param d \code{RSTACDocument} object +#' @param d `RSTACDocument` object #' -#' @return a \code{RSTACQuery} object with the predecessor subclass with the +#' @return a `RSTACQuery` object with the predecessor subclass with the #' fields used in the request. #' #' @export @@ -92,36 +92,36 @@ stac_version.STACCollectionList <- function(x, ...) { #' @title STACItemCollection functions #' #' @description -#' The \code{items_length()} function shows how many items there are in -#' the \code{STACItemCollection} object. -#' The \code{items_matched()} function shows how many items matched the -#' search criteria. It supports \code{search:metadata} (v0.8.0), -#' \code{context} (v0.9.0), and \code{numberMatched} (OGC WFS3 core spec). -#' The \code{items_fetch()} function request all STAC Items through +#' The `items_length()` function shows how many items there are in +#' the `STACItemCollection` object. +#' The `items_matched()` function shows how many items matched the +#' search criteria. It supports `search:metadata` (v0.8.0), +#' `context` (v0.9.0), and `numberMatched` (OGC WFS3 core spec). +#' The `items_fetch()` function request all STAC Items through #' pagination. -#' The \code{items_datetime()} function retrieves a the \code{datetime} -#' field in \code{properties} from \code{STACItemCollection} and -#' \code{STACItem} objects. -#' The \code{items_bbox()} function retrieves a the \code{bbox} -#' field of a \code{STACItemCollection} or an \code{STACItem} object. -#' The \code{get_assets_name()} function returns the assets name from -#' \code{STACItemCollection} and \code{STACItem} objects. +#' The `items_datetime()` function retrieves a the `datetime` +#' field in `properties` from `STACItemCollection` and +#' `STACItem` objects. +#' The `items_bbox()` function retrieves a the `bbox` +#' field of a `STACItemCollection` or an `STACItem` object. +#' The `get_assets_name()` function returns the assets name from +#' `STACItemCollection` and `STACItem` objects. #' -#' @param items a \code{STACItemCollection} object. -#' @param matched_field a \code{character} vector with the path +#' @param items a `STACItemCollection` object. +#' @param matched_field a `character` vector with the path #' where the number of items returned in the named list is located starting from #' the initial node of the list. For example, if the information is at position -#' \code{items$meta$found} of the object, it must be passed as the following -#' parameter \code{c("meta", "found")}. +#' `items$meta$found` of the object, it must be passed as the following +#' parameter `c("meta", "found")`. #' #' @return -#' The \code{items_length()} returns an \code{integer} value. -#' The \code{items_matched()} returns an \code{integer} value. -#' If STAC web server does not support this extension, returns \code{NULL}. -#' The \code{items_fetch()} returns an \code{STACItemCollection} with all +#' The `items_length()` returns an `integer` value. +#' The `items_matched()` returns an `integer` value. +#' If STAC web server does not support this extension, returns `NULL`. +#' The `items_fetch()` returns an `STACItemCollection` with all #' matched items. -#' The \code{items_datetime()} returns a \code{list} of all items' datetime. -#' The \code{items_bbox()} returns a \code{list} with all items' +#' The `items_datetime()` returns a `list` of all items' datetime. +#' The `items_bbox()` returns a `list` with all items' #' bounding boxes. #' #' @examples @@ -190,12 +190,12 @@ items_matched <- function(items, matched_field = NULL) { return(matched) } -#' @param progress a \code{logical} indicating if a progress bar must be -#' shown or not. Defaults to \code{TRUE}. +#' @param progress a `logical` indicating if a progress bar must be +#' shown or not. Defaults to `TRUE`. #' -#' @param ... config parameters to be passed to \link[httr]{GET} or -#' \link[httr]{POST} methods, such as \link[httr]{add_headers} or -#' \link[httr]{set_cookies}. +#' @param ... config parameters to be passed to [GET][httr::GET] or +#' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or +#' [set_cookies][httr::set_cookies]. #' #' @examples #' \dontrun{ diff --git a/R/ext_query.R b/R/ext_query.R index d77be6c4..ee97fef7 100644 --- a/R/ext_query.R +++ b/R/ext_query.R @@ -1,58 +1,58 @@ #' @title Extension functions #' #' @description -#' The \code{ext_query()} is the \emph{exported function} of the STAC API -#' query extension. It can be used after a call to \code{stac_search()} +#' The `ext_query()` is the *exported function* of the STAC API +#' query extension. It can be used after a call to `stac_search()` #' function. It allows that additional fields and operators other than those -#' defined in \code{stac_search()} function be used to make a complex filter. +#' defined in `stac_search()` function be used to make a complex filter. #' #' The function accepts multiple filter criteria. Each filter entry is an -#' expression formed by \code{ }, where -#' \code{} refers to a valid item property. Supported \code{} +#' expression formed by ` `, where +#' `` refers to a valid item property. Supported `` #' depends on STAC API service implementation. The users must rely on service #' providers' documentation to know which properties can be used by this #' extension. #' -#' The \code{ext_query()} function allows the following \code{} +#' The `ext_query()` function allows the following `` #' \itemize{ -#' \item \code{==} corresponds to '\code{eq}' -#' \item \code{!=} corresponds to '\code{neq}' -#' \item \code{<} corresponds to '\code{lt}' -#' \item \code{<=} corresponds to '\code{lte}' -#' \item \code{>} corresponds to '\code{gt}' -#' \item \code{>=} corresponds to '\code{gte}' -#' \item \code{\%startsWith\%} corresponds to '\code{startsWith}' and implements +#' \item `==` corresponds to '`eq`' +#' \item `!=` corresponds to '`neq`' +#' \item `<` corresponds to '`lt`' +#' \item `<=` corresponds to '`lte`' +#' \item `>` corresponds to '`gt`' +#' \item `>=` corresponds to '`gte`' +#' \item `\%startsWith\%` corresponds to '`startsWith`' and implements #' a string prefix search operator. -#' \item \code{\%endsWith\%} corresponds to '\code{endsWith}' and implements a +#' \item `\%endsWith\%` corresponds to '`endsWith`' and implements a #' string suffix search operator. -#' \item \code{\%contains\%}: corresponds to '\code{contains}' and implements a +#' \item `\%contains\%`: corresponds to '`contains`' and implements a #' string infix search operator. -#' \item \code{\%in\%}: corresponds to '\code{in}' and implements a vector +#' \item `\%in\%`: corresponds to '`in`' and implements a vector #' search operator. #' } #' #' Besides this function, the following S3 generic methods were implemented #' to get things done for this extension: #' \itemize{ -#' \item The \code{endpoint()} for subclass \code{ext_query} -#' \item The \code{before_request()} for subclass \code{ext_query} -#' \item The \code{after_response()} for subclass \code{ext_query} +#' \item The `endpoint()` for subclass `ext_query` +#' \item The `before_request()` for subclass `ext_query` +#' \item The `after_response()` for subclass `ext_query` #' } -#' See source file \code{ext_query.R} for an example on how implement new +#' See source file `ext_query.R` for an example on how implement new #' extensions. #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param ... entries with format \code{ }. +#' @param ... entries with format ` `. #' -#' @seealso \code{\link{stac_search}}, \code{\link{post_request}}, -#' \code{\link{endpoint}}, \code{\link{before_request}}, -#' \code{\link{after_response}}, \code{\link{content_response}} +#' @seealso [stac_search()], [post_request()], +#' [endpoint()], [before_request()], +#' [after_response()], [content_response()] #' #' @return -#' A \code{RSTACQuery} object with the subclass \code{ext_query} containing -#' all request parameters to be passed to \code{post_request()} function. +#' A `RSTACQuery` object with the subclass `ext_query` containing +#' all request parameters to be passed to `post_request()` function. #' #' @examples #' \donttest{ @@ -161,10 +161,10 @@ parse_params.ext_query <- function(q, params) { #' @title Utility function #' -#' @param op a \code{character} with operation to be searched. -#' @param values a named \code{list} with all values. +#' @param op a `character` with operation to be searched. +#' @param values a named `list` with all values. #' -#' @return a \code{vector} with one operation value. +#' @return a `vector` with one operation value. #' #' @noRd .parse_values_op <- function(op, values) { @@ -183,9 +183,9 @@ parse_params.ext_query <- function(q, params) { #' @title Utility function #' -#' @param query a \code{list} with parameters to be provided in requests. +#' @param query a `list` with parameters to be provided in requests. #' -#' @return a \code{list} with parsed parameters. +#' @return a `list` with parsed parameters. #' #' @noRd .parse_values_keys <- function(query) { diff --git a/R/extensions.R b/R/extensions.R index 8114122c..f994bfaf 100644 --- a/R/extensions.R +++ b/R/extensions.R @@ -12,15 +12,15 @@ #' } #' Here, we will focus on the second type of extension. #' -#' To let \code{rstac} package perform some behavior according to an +#' To let `rstac` package perform some behavior according to an #' STAC API extension we need define some functions. These functions #' can be implemented in three environments: #' \enumerate{ -#' \item In \code{rstac} package by including new functions make a -#' GitHub pull request on \code{rstac} repository -#' (\url{https://github.com/brazil-data-cube/rstac}) -#' \item In a new package by using \code{rstac} as dependent package -#' \item In a script that loads \code{rstac} into the environment +#' \item In `rstac` package by including new functions make a +#' GitHub pull request on `rstac` repository +#' () +#' \item In a new package by using `rstac` as dependent package +#' \item In a script that loads `rstac` into the environment #' } #' All these places may impose specific requirements, however the core #' logic to implement an extension is the same. @@ -29,59 +29,59 @@ #' extensions. An extension must define a subclass name and implement all the #' following S3 generic methods for that subclass: #' \itemize{ -#' \item \code{endpoint()}: returns the endpoint value of the extension. +#' \item `endpoint()`: returns the endpoint value of the extension. #' Endpoints that vary between STAC API versions can be properly returned by -#' checking the \code{version} field of \code{RSTACQuery} object. -#' \item \code{before_request()}: allows handling query parameters before +#' checking the `version` field of `RSTACQuery` object. +#' \item `before_request()`: allows handling query parameters before #' submit them to the HTTP server; -#' \item \code{after_request()}: allows to check and parse document received +#' \item `after_request()`: allows to check and parse document received #' by the HTTP server; #' } #' -#' These methods will work 'behind the scenes' when a \code{RSTACQuery} object +#' These methods will work 'behind the scenes' when a `RSTACQuery` object #' representing a user query are passed to a request function -#' (e.g. \code{get_request()} or \code{post_request()}). The calling order is: +#' (e.g. `get_request()` or `post_request()`). The calling order is: #' \enumerate{ -#' \item begin of \code{get_request()} or \code{post_request()} +#' \item begin of `get_request()` or `post_request()` #' \item if STAC API version is not defined, try detect it -#' \item call \code{endpoint()} -#' \item call \code{before_request()} +#' \item call `endpoint()` +#' \item call `before_request()` #' \item send HTTP request #' \item receive HTTP response -#' \item \code{after_response()} -#' \item end of \code{get_request()} or \code{post_request()} +#' \item `after_response()` +#' \item end of `get_request()` or `post_request()` #' } #' #' Besides that, the extension must expose a function to receive user -#' parameters and return a \code{RSTACQuery} object with a subclass +#' parameters and return a `RSTACQuery` object with a subclass #' associated with the above S3 methods. This function must accept as its -#' first parameter a \code{RSTACQuery} object representing the actual query. +#' first parameter a `RSTACQuery` object representing the actual query. #' To keep the command flow consistency, the function needs to check the #' subclass of the input query. After that, it must set new or changes the #' input query parameters according to the user input and, finally, -#' return the new query as a \code{RSTACQuery} object. +#' return the new query as a `RSTACQuery` object. #' #' You can see examples on how to implement an STAC API extension by looking at -#' \code{stac.R}, \code{collections.R}, \code{items.R}, \code{stac_search.R}, -#' and \code{ext_query.R} source files. These files implement core STAC API +#' `stac.R`, `collections.R`, `items.R`, `stac_search.R`, +#' and `ext_query.R` source files. These files implement core STAC API #' endpoints, as well as the query API extension. #' -#' There are also some utility functions described in \strong{Functions} +#' There are also some utility functions described in **Functions** #' section bellow that can help the extension development. #' #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param res a \code{httr} \code{response} object. -#' @param params a \code{list} with params to add in request. +#' @param res a `httr` `response` object. +#' @param params a `list` with params to add in request. #' #' @return -#' A \code{character} endpoint value for \code{endpoint()} function. -#' A \code{RSTACQuery} object for \code{before_request()} and -#' \code{after_response()} functions. +#' A `character` endpoint value for `endpoint()` function. +#' A `RSTACQuery` object for `before_request()` and +#' `after_response()` functions. #' -#' @seealso \code{\link{ext_query}} +#' @seealso [ext_query()] #' #' @name extensions NULL @@ -118,20 +118,20 @@ parse_params <- function(q, params) { } #' @describeIn extensions -#' The \code{content_response} function checks if the request's +#' The `content_response` function checks if the request's #' response is in accordance with the allowed status codes and content-types. #' It returns the parsed content response. #' -#' @param res a \code{httr} \code{response} object. +#' @param res a `httr` `response` object. #' -#' @param status_codes a \code{character} vector with successful +#' @param status_codes a `character` vector with successful #' status codes. #' -#' @param content_types a \code{character} vector with all acceptable +#' @param content_types a `character` vector with all acceptable #' responses' content type. #' #' @return -#' The \code{content_response()} function returns a \code{list} data structure +#' The `content_response()` function returns a `list` data structure #' representing the JSON file received in HTTP response #' #' @export @@ -171,15 +171,15 @@ content_response <- function(res, status_codes, content_types) { } #' @describeIn extensions -#' The \code{check_query_verb()} function allows you to define which HTTP +#' The `check_query_verb()` function allows you to define which HTTP #' verbs are allowed. It is useful for establishing which verbs will be #' supported by an extension. #' -#' @param q a \code{RSTACQuery} object. +#' @param q a `RSTACQuery` object. #' -#' @param verbs a \code{character} vector with allowed HTTP request methods +#' @param verbs a `character` vector with allowed HTTP request methods #' -#' @param msg a \code{character} with a personalized error message +#' @param msg a `character` with a personalized error message #' #' @export check_query_verb <- function(q, verbs, msg = NULL) { @@ -193,14 +193,14 @@ check_query_verb <- function(q, verbs, msg = NULL) { } #' @describeIn extensions -#' The \code{check_subclass()} function specifies which type of query -#' objects (\code{RSTACQuery}) or document objects (\code{RSTACDocument}) +#' The `check_subclass()` function specifies which type of query +#' objects (`RSTACQuery`) or document objects (`RSTACDocument`) #' are expected in the function extension. #' -#' @param x either a \code{RSTACQuery} object expressing a STAC query -#' criteria or any \code{RSTACDocument}. +#' @param x either a `RSTACQuery` object expressing a STAC query +#' criteria or any `RSTACDocument`. #' -#' @param subclasses a \code{character} vector with all allowed S3 subclasses +#' @param subclasses a `character` vector with all allowed S3 subclasses #' #' @export check_subclass <- function(x, subclasses) { @@ -209,8 +209,8 @@ check_subclass <- function(x, subclasses) { } #' @describeIn extensions -#' The \code{subclass()} function returns a \code{character} representing the -#' subclass name of either \code{RSTACQuery} or \code{RSTACDocument} S3 classes. +#' The `subclass()` function returns a `character` representing the +#' subclass name of either `RSTACQuery` or `RSTACDocument` S3 classes. #' #' @export subclass <- function(x) { @@ -219,14 +219,14 @@ subclass <- function(x) { } #' @describeIn extensions -#' The \code{omit_query_params()} function was created to omit the paths that +#' The `omit_query_params()` function was created to omit the paths that #' are defined as query parameters to simplify the creation of a query. #' Therefore, use this method only in endpoints that specify a parameter in #' their paths. #' -#' @param q a \code{RSTACQuery} object. +#' @param q a `RSTACQuery` object. #' -#' @param names a \code{character} vector with the names do omit. +#' @param names a `character` vector with the names do omit. #' #' @export omit_query_params <- function(q, names) { diff --git a/R/items.R b/R/items.R index 44258d68..ca6d7f19 100644 --- a/R/items.R +++ b/R/items.R @@ -1,7 +1,7 @@ #' @title Endpoint functions #' #' @description -#' The \code{items} function implements WFS3 +#' The `items` function implements WFS3 #' \code{/collections/\{collectionId\}/items}, and #' \code{/collections/\{collectionId\}/items/\{featureId\}} endpoints. #' @@ -14,32 +14,32 @@ #' } #' #' The endpoint \code{/collections/\{collectionId\}/items} accepts the same -#' filters parameters of \code{\link{stac_search}} function. +#' filters parameters of [stac_search()] function. #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param feature_id a \code{character} with item id to be fetched. -#' Only works if the \code{collection_id} is informed. This is equivalent to +#' @param feature_id a `character` with item id to be fetched. +#' Only works if the `collection_id` is informed. This is equivalent to #' the endpoint \code{/collections/\{collectionId\}/items/\{featureId\}}. #' -#' @param datetime a \code{character} with a date-time or an interval. +#' @param datetime a `character` with a date-time or an interval. #' Date and time strings needs to conform RFC 3339. Intervals are -#' expressed by separating two date-time strings by \code{'/'} character. -#' Open intervals are expressed by using \code{'..'} in place of date-time. +#' expressed by separating two date-time strings by `'/'` character. +#' Open intervals are expressed by using `'..'` in place of date-time. #' #' Examples: #' \itemize{ -#' \item A date-time: \code{"2018-02-12T23:20:50Z"} -#' \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} -#' \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or -#' \code{"../2018-03-18T12:31:12Z"} +#' \item A date-time: `"2018-02-12T23:20:50Z"` +#' \item A closed interval: `"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"` +#' \item Open intervals: `"2018-02-12T00:00:00Z/.."` or +#' `"../2018-03-18T12:31:12Z"` #' } #' -#' Only features that have a \code{datetime} property that intersects -#' the interval or date-time informed in \code{datetime} are selected. +#' Only features that have a `datetime` property that intersects +#' the interval or date-time informed in `datetime` are selected. #' -#' @param bbox a \code{numeric} vector with only features that have a +#' @param bbox a `numeric` vector with only features that have a #' geometry that intersects the bounding box are selected. The bounding box is #' provided as four or six numbers, depending on whether the coordinate #' reference system includes a vertical axis (elevation or depth): @@ -51,24 +51,24 @@ #' \item Upper right corner, coordinate axis 3 (optional) } #' #' The coordinate reference system of the values is WGS84 -#' longitude/latitude (\url{http://www.opengis.net/def/crs/OGC/1.3/CRS84}). +#' longitude/latitude (). #' The values are in most cases the sequence of minimum longitude, #' minimum latitude, maximum longitude and maximum latitude. However, #' in cases where the box spans the antimeridian the first value #' (west-most box edge) is larger than the third value #' (east-most box edge). #' -#' @param limit an \code{integer} defining the maximum number of results +#' @param limit an `integer` defining the maximum number of results #' to return. If not informed it defaults to the service implementation. #' #' @seealso -#' \code{\link{get_request}}, \code{\link{post_request}}, -#' \code{\link{collections}} +#' [get_request()], [post_request()], +#' [collections()] #' #' @return -#' A \code{RSTACQuery} object with the subclass \code{items} for +#' A `RSTACQuery` object with the subclass `items` for #' \code{/collections/{collection_id}/items} endpoint, or a -#' \code{item_id} subclass for +#' `item_id` subclass for #' \code{/collections/{collection_id}/items/{feature_id}} endpoint, #' containing all search field parameters to be provided to STAC API web #' service. diff --git a/R/print.R b/R/print.R index 846eb972..70c7e22a 100644 --- a/R/print.R +++ b/R/print.R @@ -3,20 +3,20 @@ #' @description The print function covers all objects in the rstac package: #' #' \itemize{ -#' \item \code{\link{stac}}: returns a \code{STACCatalog} document from -#' \code{/stac} (v0.8.0) or \code{/} (v0.9.0 or v1.0.0) endpoint. -#' \item \code{\link{stac_search}}: returns a \code{STACItemCollection} -#' document from \code{/stac/search} (v0.8.0) or \code{/search} +#' \item [stac()]: returns a `STACCatalog` document from +#' `/stac` (v0.8.0) or `/` (v0.9.0 or v1.0.0) endpoint. +#' \item [stac_search()]: returns a `STACItemCollection` +#' document from `/stac/search` (v0.8.0) or `/search` #' (v0.9.0 or v1.0.0) endpoint containing all Items that match #' the provided search predicates. -#' \item \code{\link{collections}}: implements the \code{/collections} and +#' \item [collections()]: implements the `/collections` and #' \code{/collections/\{collectionId\}} endpoints. The former returns -#' a \code{STACCollectionList} document that lists all collections published -#' by the server, and the later returns a single \code{STACCollection} +#' a `STACCollectionList` document that lists all collections published +#' by the server, and the later returns a single `STACCollection` #' document that describes a unique collection. -#' \item \code{\link{items}}: retrieves a \code{STACItemCollection} document +#' \item [items()]: retrieves a `STACItemCollection` document #' from \code{/collections/\{collectionId\}/items} endpoint and a -#' \code{STACItem} document from +#' `STACItem` document from #' \code{/collections/\{collectionId\}/items/\{itemId\}} endpoints. #' } #' @@ -24,26 +24,26 @@ #' lightweight markup language. You can paste the output into any #' markdown editor for a better visualization. #' -#' Call \code{print()} function to print the rstac's objects. -#' You can determine how many items will be printed using \code{n} parameter. +#' Call `print()` function to print the rstac's objects. +#' You can determine how many items will be printed using `n` parameter. #' -#' @param x either a \code{RSTACQuery} object expressing a STAC query -#' criteria or any \code{RSTACDocument}. +#' @param x either a `RSTACQuery` object expressing a STAC query +#' criteria or any `RSTACDocument`. #' #' @param n number of entries to print. Each object has its own rule of -#' truncation: the \code{STACCollection} objects will print +#' truncation: the `STACCollection` objects will print #' 10 links by default. If the object has less than 20 collections, all -#' collections will be shown. In \code{STACItemCollection}, 10 features -#' will be printed by default. To show all entries, use \code{n = Inf}. +#' collections will be shown. In `STACItemCollection`, 10 features +#' will be printed by default. To show all entries, use `n = Inf`. #' #' @param ... other parameters passed in the functions. #' -#' @param tail A \code{logical} value indicating if last features in +#' @param tail A `logical` value indicating if last features in #' STACItemCollection object must be show. #' #' @seealso -#' \code{\link{stac}} \code{\link{stac_search}} \code{\link{collections}} -#' \code{\link{items}} +#' [stac()] [stac_search()] [collections()] +#' [items()] #' #' @examples #' \donttest{ diff --git a/R/query.R b/R/query.R index 5d02c533..9b08acdd 100644 --- a/R/query.R +++ b/R/query.R @@ -1,39 +1,39 @@ #' @title Query development functions #' #' @describeIn extensions -#' The \code{RSTACQuery()} function is a constructor of \code{RSTACQuery} -#' objects. Every extension must implement a subclass of \code{RSTACQuery} to -#' represent its queries. This is done by informing to the \code{subclass} +#' The `RSTACQuery()` function is a constructor of `RSTACQuery` +#' objects. Every extension must implement a subclass of `RSTACQuery` to +#' represent its queries. This is done by informing to the `subclass` #' parameter the extension's subclass name. #' -#' The \code{params} parameter is a named \code{list} where user parameters +#' The `params` parameter is a named `list` where user parameters #' must be stored. It is important to know if previous query parameters needs #' to be keeped in the new query. If so, it is recommended do use -#' \code{\link[utils]{modifyList}()} function to merge the old and new +#' [utils::modifyList()] function to merge the old and new #' query parameters. #' -#' If the \code{version} parameter is \code{NULL}, \code{rstac} will detect +#' If the `version` parameter is `NULL`, `rstac` will detect #' STAC API version automatically. #' #' In general, if you are implementing a new subclass, the parameters -#' \code{version} and \code{url} will be the same as the previous query. The -#' \code{params} parameter will be merged with previous query. And subclass +#' `version` and `url` will be the same as the previous query. The +#' `params` parameter will be merged with previous query. And subclass #' is the extension's subclass name. #' -#' @param version a \code{character} with the STAC version. +#' @param version a `character` with the STAC version. #' -#' @param base_url a \code{character} informing the base URL of a +#' @param base_url a `character` informing the base URL of a #' STAC web service. #' -#' @param params a named \code{list} with all URL query parameters to be +#' @param params a named `list` with all URL query parameters to be #' appended in the URL. #' -#' @param subclass a \code{character} corresponding to the subclass of the +#' @param subclass a `character` corresponding to the subclass of the #' object to be created. #' #' @return -#' The \code{RSTACQuery()} function returns a \code{STACQuery} object with -#' subclass defined by \code{subclass} parameter. +#' The `RSTACQuery()` function returns a `STACQuery` object with +#' subclass defined by `subclass` parameter. #' #' @export RSTACQuery <- function(version = NULL, base_url, params = list(), subclass) { diff --git a/R/request.R b/R/request.R index 394b03f3..9089d8d2 100644 --- a/R/request.R +++ b/R/request.R @@ -2,33 +2,33 @@ #' #' @rdname request #' -#' @description The \code{get_request} is function that makes HTTP GET +#' @description The `get_request` is function that makes HTTP GET #' requests to STAC web services, retrieves, and parse the data. #' -#' The \code{post_request} is function that makes HTTP POST +#' The `post_request` is function that makes HTTP POST #' requests to STAC web services, retrieves, and parse the data. #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param encode a \code{character} informing the request body -#' Content-Type. Accepted types are \code{'json'} (\code{'application/json'}), -#' \code{'form'} (\code{'application/x-www-form-urlencoded'}), -#' and \code{'multipart'} (\code{'multipart/form-data'}). Defaults to -#' \code{'json'}. +#' @param encode a `character` informing the request body +#' Content-Type. Accepted types are `'json'` (`'application/json'`), +#' `'form'` (`'application/x-www-form-urlencoded'`), +#' and `'multipart'` (`'multipart/form-data'`). Defaults to +#' `'json'`. #' -#' @param ... config parameters to be passed to \link[httr]{GET} or -#' \link[httr]{POST} methods, such as \link[httr]{add_headers} or -#' \link[httr]{set_cookies}. +#' @param ... config parameters to be passed to [GET][httr::GET] or +#' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or +#' [set_cookies][httr::set_cookies]. #' #' @seealso -#' \code{\link{stac}} \code{\link{stac_search}} \code{\link{collections}} -#' \code{\link{items}} +#' [stac()] [stac_search()] [collections()] +#' [items()] #' #' @return -#' Either a \code{STACCatalog}, \code{STACCollection}, -#' \code{STACCollectionList}, \code{STACItemCollection} or \code{STACItem} -#' object depending on the subclass and search fields parameters of \code{q} +#' Either a `STACCatalog`, `STACCollection`, +#' `STACCollectionList`, `STACItemCollection` or `STACItem` +#' object depending on the subclass and search fields parameters of `q` #' argument. #' #' @examples @@ -129,10 +129,10 @@ post_request <- function(q, ..., encode = c("json", "multipart", "form")) { } #' @describeIn extensions -#' The \code{.do_omit_query_params()} Function to make the omission of the -#' parameters that were omitted in function \code{omit_query_params()}. +#' The `.do_omit_query_params()` Function to make the omission of the +#' parameters that were omitted in function `omit_query_params()`. #' -#' @param q a \code{RSTACQuery} object. +#' @param q a `RSTACQuery` object. #' #' @noRd .do_omit_query_params <- function(q) { @@ -149,10 +149,10 @@ post_request <- function(q, ..., encode = c("json", "multipart", "form")) { } #' @describeIn extensions -#' The \code{.undo_omit_query_params()} function to undo the omission of -#' parameters that were omitted in function \code{omit_query_params()}. +#' The `.undo_omit_query_params()` function to undo the omission of +#' parameters that were omitted in function `omit_query_params()`. #' -#' @param q a \code{RSTACQuery} object. +#' @param q a `RSTACQuery` object. #' #' @noRd .undo_omit_query_params <- function(q) { diff --git a/R/rstac.R b/R/rstac.R index a61b9dee..02e7ee24 100644 --- a/R/rstac.R +++ b/R/rstac.R @@ -1,41 +1,41 @@ #' @title R client library for STAC (rstac) #' -#' @section The \code{rstac} functions: +#' @section The `rstac` functions: #' The rstac package provides two categories of functions: #' API endpoints and data access and organization. #' #' @section STAC API endpoints functions: #' \itemize{ -#' \item \code{\link{stac}}: implements STAC \code{/stac} endpoint for version -#' 0.8.1 or below, and \code{/} for versions 0.9.0 or higher. -#' \item \code{\link{collections}}: implements \code{/collections} +#' \item [stac()]: implements STAC `/stac` endpoint for version +#' 0.8.1 or below, and `/` for versions 0.9.0 or higher. +#' \item [collections()]: implements `/collections` #' and \code{/collections/\{collectionId\}} WFS3 endpoints. -#' \item \code{\link{items}}: implements +#' \item [items()]: implements #' \code{/collections/\{collectionId\}/items} and #' \code{/collections/\{collectionId\}/items/\{featureId\}} WFS3 endpoints. -#' \item \code{\link{stac_search}}: implements STAC \code{/stac/search} -#' endpoint for version 0.8.1 or below, and \code{/search} endpoint for +#' \item [stac_search()]: implements STAC `/stac/search` +#' endpoint for version 0.8.1 or below, and `/search` endpoint for #' versions 0.9.0 or higher. #' } #' #' @section Data access and organization functions: #' \itemize{ -#' \item \code{\link{get_request}}: makes HTTP GET requests to STAC web +#' \item [get_request()]: makes HTTP GET requests to STAC web #' service. -#' \item \code{\link{post_request}}: makes HTTP POST requests to STAC web +#' \item [post_request()]: makes HTTP POST requests to STAC web #' service. -#' \item \code{\link{items_matched}}: returns how many items matched the +#' \item [items_matched()]: returns how many items matched the #' search criteria. -#' \item \code{\link{items_length}}: informs how many items are +#' \item [items_length()]: informs how many items are #' stored locally. -#' \item \code{\link{items_fetch}}: fetches all matched items from service. -#' \item \code{\link{assets_download}}: download all assets in batch. +#' \item [items_fetch()]: fetches all matched items from service. +#' \item [assets_download()]: download all assets in batch. #' } #' #' @section Data types: -#' The package implements the follow S3 classes: \code{STACItemCollection}, -#' \code{STACItem}, \code{STACCatalog}, \code{STACCollectionList} and -#' \code{STACCollection}. These classes are regular lists representing the +#' The package implements the follow S3 classes: `STACItemCollection`, +#' `STACItem`, `STACCatalog`, `STACCollectionList` and +#' `STACCollection`. These classes are regular lists representing the #' corresponding JSON STAC objects. #' #' @name rstac diff --git a/R/stac.R b/R/stac.R index 16b82cf2..a9aeb00a 100644 --- a/R/stac.R +++ b/R/stac.R @@ -1,26 +1,26 @@ #' @title Endpoint functions #' -#' @description The \code{stac} function implements \code{/stac} API -#' endpoint (>=0.8.0), and \code{/} for versions 0.9.0 or higher. It prepares +#' @description The `stac` function implements `/stac` API +#' endpoint (>=0.8.0), and `/` for versions 0.9.0 or higher. It prepares #' search fields parameters to be provided to a STAC API web service. This #' endpoint should return a STAC Catalog document containing all published data #' catalogs. #' -#' @param base_url a \code{character} informing the base url of a +#' @param base_url a `character` informing the base url of a #' STAC web service. #' -#' @param force_version a \code{character} providing the version of the STAC +#' @param force_version a `character` providing the version of the STAC #' used. If not provided, the rstac package will make requests to try to find #' the version of STAC used. It is highly recommended that you inform the STAC #' version you are using. #' #' @seealso -#' \code{\link{stac_search}}, \code{\link{collections}}, -#' \code{\link{items}}, \code{\link{get_request}}, -#' \code{\link{post_request}} +#' [stac_search()], [collections()], +#' [items()], [get_request()], +#' [post_request()] #' #' @return -#' A \code{RSTACQuery} object with the subclass \code{stac} containing all +#' A `RSTACQuery` object with the subclass `stac` containing all #' request parameters to be provided to API service. #' #' @examples diff --git a/R/stac_search.R b/R/stac_search.R index 91df6edd..41342b92 100644 --- a/R/stac_search.R +++ b/R/stac_search.R @@ -1,44 +1,44 @@ #' @title Endpoint functions #' #' @description (This document is based on STAC specification documentation -#' \url{https://github.com/radiantearth/stac-spec/} +#' #' and reproduces some of its parts) #' -#' The \code{stac_search} function implements \code{/stac/search} API endpoint -#' (v0.8.1) and \code{/search} (v0.9.0 or v1.0.0). +#' The `stac_search` function implements `/stac/search` API endpoint +#' (v0.8.1) and `/search` (v0.9.0 or v1.0.0). #' It prepares query parameters used in search API request, a -#' \code{stac} object with all filter parameters to be provided to -#' \code{get_request} or \code{post_request} functions. The GeoJSON content -#' returned by these requests is a \code{STACItemCollection} object, a regular R -#' \code{list} representing a STAC Item Collection document. +#' `stac` object with all filter parameters to be provided to +#' `get_request` or `post_request` functions. The GeoJSON content +#' returned by these requests is a `STACItemCollection` object, a regular R +#' `list` representing a STAC Item Collection document. #' -#' @param q a \code{RSTACQuery} object expressing a STAC query +#' @param q a `RSTACQuery` object expressing a STAC query #' criteria. #' -#' @param collections a \code{character} vector of collection IDs to include in +#' @param collections a `character` vector of collection IDs to include in #' the search for items. Only items in one of the provided collections will be #' searched. #' -#' @param ids a \code{character} vector with item IDs. All other filter +#' @param ids a `character` vector with item IDs. All other filter #' parameters that further restrict the number of search results are ignored. #' -#' @param datetime a \code{character} with a date-time or an interval. Date +#' @param datetime a `character` with a date-time or an interval. Date #' and time strings needs to conform RFC 3339. Intervals are expressed by -#' separating two date-time strings by \code{'/'} character. Open intervals are -#' expressed by using \code{'..'} in place of date-time. +#' separating two date-time strings by `'/'` character. Open intervals are +#' expressed by using `'..'` in place of date-time. #' #' Examples: #' \itemize{ -#' \item A date-time: \code{"2018-02-12T23:20:50Z"} -#' \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} -#' \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or -#' \code{"../2018-03-18T12:31:12Z"} +#' \item A date-time: `"2018-02-12T23:20:50Z"` +#' \item A closed interval: `"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"` +#' \item Open intervals: `"2018-02-12T00:00:00Z/.."` or +#' `"../2018-03-18T12:31:12Z"` #' } #' -#' Only features that have a \code{datetime} property that intersects the -#' interval or date-time informed in \code{datetime} are selected. +#' Only features that have a `datetime` property that intersects the +#' interval or date-time informed in `datetime` are selected. #' -#' @param bbox a \code{numeric} vector with only features that have a +#' @param bbox a `numeric` vector with only features that have a #' geometry that intersects the bounding box are selected. The bounding box is #' provided as four or six numbers, depending on whether the coordinate #' reference system includes a vertical axis (elevation or depth): @@ -50,24 +50,24 @@ #' \item Upper right corner, coordinate axis 3 (optional) } #' #' The coordinate reference system of the values is WGS84 longitude/latitude -#' (\url{http://www.opengis.net/def/crs/OGC/1.3/CRS84}). The values are in +#' (). The values are in #' most cases the sequence of minimum longitude, minimum latitude, maximum #' longitude and maximum latitude. However, in cases where the box spans the #' antimeridian the first value (west-most box edge) is larger than the third #' value (east-most box edge). #' -#' @param intersects a \code{character} value expressing GeoJSON geometries +#' @param intersects a `character` value expressing GeoJSON geometries #' objects as specified in RFC 7946. Only returns items that intersect with #' the provided polygon. #' -#' @param limit an \code{integer} defining the maximum number of results +#' @param limit an `integer` defining the maximum number of results #' to return. If not informed it defaults to the service implementation. #' -#' @seealso \code{\link{stac}}, \code{\link{ext_query}}, -#' \code{\link{get_request}}, \code{\link{post_request}} +#' @seealso [stac()], [ext_query()], +#' [get_request()], [post_request()] #' #' @return -#' A \code{RSTACQuery} object with the subclass \code{search} containing all +#' A `RSTACQuery` object with the subclass `search` containing all #' search field parameters to be provided to STAC API web service. #' #' @examples diff --git a/R/utils.R b/R/utils.R index ccbaffcf..337c3ac9 100644 --- a/R/utils.R +++ b/R/utils.R @@ -1,6 +1,6 @@ #' @title Utility functions #' -#' @param bbox a \code{numeric} vector with only features that have a +#' @param bbox a `numeric` vector with only features that have a #' geometry that intersects the bounding box are selected. The bounding box is #' provided as four or six numbers, depending on whether the coordinate #' reference system includes a vertical axis (elevation or depth): @@ -12,8 +12,8 @@ #' \item Upper right corner, coordinate axis 3 (optional) } #' #' -#' @return A \code{numeric} with the bbox provided,or an error if the supplied -#' \code{bbox} does not meet the specifications. +#' @return A `numeric` with the bbox provided,or an error if the supplied +#' `bbox` does not meet the specifications. #' #' @noRd .parse_bbox <- function(bbox) { @@ -29,11 +29,11 @@ #' @title Utility functions #' -#' @param limit an \code{integer} defining the maximum number of results +#' @param limit an `integer` defining the maximum number of results #' to return. If not informed it defaults to the service implementation. #' -#' @return A \code{integer} with the limit provided,or an error if the supplied -#' \code{limit} has a length different from 1. +#' @return A `integer` with the limit provided,or an error if the supplied +#' `limit` has a length different from 1. #' #' @noRd .parse_limit <- function(limit) { @@ -53,12 +53,12 @@ #' @title Utility functions #' -#' @param feature_id a \code{character} with item id to be fetched. -#' Only works if the \code{collection_id} is informed. This is equivalent to +#' @param feature_id a `character` with item id to be fetched. +#' Only works if the `collection_id` is informed. This is equivalent to #' the endpoint \code{/collections/\{collectionId\}/items/\{featureId\}}. #' -#' @return A \code{character} with the parameter provided,or an error if the -#' supplied \code{feature_id} has a length different from 1. +#' @return A `character` with the parameter provided,or an error if the +#' supplied `feature_id` has a length different from 1. #' #' @noRd .parse_feature_id <- function(feature_id) { @@ -71,11 +71,11 @@ #' @title Utility functions #' -#' @param collections a \code{character} vector of collection IDs to include in +#' @param collections a `character` vector of collection IDs to include in #' the search for items. Only items in one of the provided collections will be #' searched. #' -#' @return A \code{list} of collections. +#' @return A `list` of collections. #' #' @noRd .parse_collections <- function(collections) { @@ -91,10 +91,10 @@ #' @title Utility functions #' -#' @param ids a \code{character} vector with item IDs. All other filter +#' @param ids a `character` vector with item IDs. All other filter #' parameters that further restrict the number of search results are ignored. #' -#' @return A \code{list} with the ids. +#' @return A `list` with the ids. #' #' @noRd .parse_ids <- function(ids) { @@ -110,11 +110,11 @@ #' @title Utility functions #' -#' @param intersects a \code{character} value expressing GeoJSON geometries +#' @param intersects a `character` value expressing GeoJSON geometries #' objects as specified in RFC 7946. Only returns items that intersect with #' the provided polygon. #' -#' @return A \code{character} with the validate polygon. +#' @return A `character` with the validate polygon. #' #' @noRd .parse_geometry <- function(geom) { @@ -125,10 +125,10 @@ #' @title Utility functions #' -#' @param items a \code{STACItemCollection} object representing the result -#' of \code{/stac/search} or \code{/collections/{collectionId}/items}. +#' @param items a `STACItemCollection` object representing the result +#' of `/stac/search` or \code{/collections/{collectionId}/items}. #' -#' @return A \code{numeric} with the length of a \code{STACItemCollection} +#' @return A `numeric` with the length of a `STACItemCollection` #' object. #' #' @noRd @@ -154,14 +154,14 @@ #' expressed using double-dots. #' Examples: #' \itemize{ -#' \item A date-time: \code{"2018-02-12T23:20:50Z"} -#' \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} -#' \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or -#' \code{"../2018-03-18T12:31:12Z"} +#' \item A date-time: `"2018-02-12T23:20:50Z"` +#' \item A closed interval: `"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"` +#' \item Open intervals: `"2018-02-12T00:00:00Z/.."` or +#' `"../2018-03-18T12:31:12Z"` #' } #' #' @return An error if the date does not follow the specified standards or the -#' date time provided as \code{character}. +#' date time provided as `character`. #' #' @noRd .parse_datetime <- function(datetime) { @@ -233,13 +233,13 @@ #' expressed using double-dots. #' Examples: #' \itemize{ -#' \item A date-time: \code{"2018-02-12T23:20:50Z"} -#' \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} -#' \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or -#' \code{"../2018-03-18T12:31:12Z"} +#' \item A date-time: `"2018-02-12T23:20:50Z"` +#' \item A closed interval: `"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"` +#' \item Open intervals: `"2018-02-12T00:00:00Z/.."` or +#' `"../2018-03-18T12:31:12Z"` #' } #' -#' @return A \code{logical} if TRUE the date time provided is correct, +#' @return A `logical` if TRUE the date time provided is correct, #' otherwise not. #' #' @noRd @@ -254,9 +254,9 @@ #' @title Utility functions #' -#' @param msg a \code{character} string with format error message. +#' @param msg a `character` string with format error message. #' -#' @param ... values to be passed to \code{msg} parameter. +#' @param ... values to be passed to `msg` parameter. #' #' @noRd .error <- function(msg, ...) { @@ -266,9 +266,9 @@ #' @title Utility functions #' -#' @param msg a \code{character} string with format text message. +#' @param msg a `character` string with format text message. #' -#' @param ... values to be passed to \code{msg} parameter. +#' @param ... values to be passed to `msg` parameter. #' #' @noRd .message <- function(msg, ...) { @@ -278,9 +278,9 @@ #' @title Utility functions #' -#' @param msg a \code{character} string with format warning message. +#' @param msg a `character` string with format warning message. #' -#' @param ... values to be passed to \code{msg} parameter. +#' @param ... values to be passed to `msg` parameter. #' #' @noRd .warning <- function(msg, ...) { @@ -290,9 +290,9 @@ #' @title Utility functions #' -#' @param obj an \code{object} to compare. +#' @param obj an `object` to compare. #' -#' @param expected a \code{character} with the expected classes. +#' @param expected a `character` with the expected classes. #' #' @noRd .check_obj <- function(obj, expected) { @@ -313,28 +313,28 @@ #' @rdname http_request #' #' @description -#' \code{.make_url} is a helper function to generate url. The returned -#' url is formed by appending \code{endpoint} at the end of base url -#' informed by \code{url} parameter. If \code{endpoint} has multiple elements -#' it will be collapsed using \code{'/'} character. +#' `.make_url` is a helper function to generate url. The returned +#' url is formed by appending `endpoint` at the end of base url +#' informed by `url` parameter. If `endpoint` has multiple elements +#' it will be collapsed using `'/'` character. #' -#' Note that \code{.make_url} function differs from standards of relative URI +#' Note that `.make_url` function differs from standards of relative URI #' path resolution (RFC 3986). Any existing path in base url #' is maintained in the final url, and a simple string contatenation is made #' whithout including any character separator. For this reason, this function #' does not support the query and fragment URI components in the base url. #' -#' @param url a \code{character} informing the base url of a +#' @param url a `character` informing the base url of a #' STAC web service. #' -#' @param endpoint a \code{character} a path to be appended in the final +#' @param endpoint a `character` a path to be appended in the final #' url. #' -#' @param params a named \code{list} with all url query parameters to be +#' @param params a named `list` with all url query parameters to be #' appended in the url. #' #' @return -#' \code{.make_url} returns an url to access STAC endpoints. +#' `.make_url` returns an url to access STAC endpoints. #' #' @noRd .make_url <- function(url, endpoint = "", params = list()) { @@ -362,9 +362,9 @@ #' @title Utility functions #' -#' @param params a \code{list} of parameters received from stac objects. +#' @param params a `list` of parameters received from stac objects. #' -#' @return a \code{character} representing the encode parameters of the query. +#' @return a `character` representing the encode parameters of the query. #' #' @noRd .querystring_encode <- function(params) { @@ -378,9 +378,9 @@ #' @title Utility functions #' -#' @param querystring a \code{character} with the query to be decoded. +#' @param querystring a `character` with the query to be decoded. #' -#' @return a \code{list} with the query params. +#' @return a `list` with the query params. #' #' @noRd .querystring_decode <- function(querystring) { @@ -399,9 +399,9 @@ #' @title Utility functions #' -#' @param params a \code{list} with the parameters of query. +#' @param params a `list` with the parameters of query. #' -#' @return a \code{list} with the query parameters. +#' @return a `list` with the query parameters. #' #' @noRd .validate_query <- function(params) { @@ -419,18 +419,18 @@ #' @title Utility functions #' #' @description -#' These function retrieves information about either \code{rstac} queries -#' (\code{RSTACQuery} objects) or \code{rstac} documents -#' (\code{RSTACDocument} objects). +#' These function retrieves information about either `rstac` queries +#' (`RSTACQuery` objects) or `rstac` documents +#' (`RSTACDocument` objects). #' -#' @param x either a \code{RSTACQuery} object expressing a STAC query -#' criteria or any \code{RSTACDocument}. +#' @param x either a `RSTACQuery` object expressing a STAC query +#' criteria or any `RSTACDocument`. #' -#' @param ... config parameters to be passed to \link[httr]{GET} -#' method, such as \link[httr]{add_headers} or \link[httr]{set_cookies}. +#' @param ... config parameters to be passed to [GET][httr::GET] +#' method, such as [add_headers][httr::add_headers] or [set_cookies][httr::set_cookies]. #' #' @return -#' The \code{stac_version()} function returns a \code{character} STAC API +#' The `stac_version()` function returns a `character` STAC API #' version. #' #' @name utilities @@ -443,25 +443,25 @@ stac_version <- function(x, ...) { #' @title Utility functions #' -#' @description This function returns the \code{date}, \code{band} and -#' \code{URL} fields for each assets of an \code{STACItemCollection} object. +#' @description This function returns the `date`, `band` and +#' `URL` fields for each assets of an `STACItemCollection` object. #' For the URL you can add the GDAL library drivers for the following schemes: #' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). #' -#' @param items a \code{STACItemCollection} object representing -#' the result of \code{/stac/search}, \code{/collections/{collectionId}/items}. +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. #' -#' @param assets_names a \code{character} with the assets names to be -#' filtered. If \code{NULL} (default) all assets will be returned. +#' @param assets_names a `character` with the assets names to be +#' filtered. If `NULL` (default) all assets will be returned. #' -#' @param sort a \code{logical} if true the dates will be sorted +#' @param sort a `logical` if true the dates will be sorted #' in increasing order. By default, the dates are sorted. #' -#' @param gdal_vsi_resolution a \code{logical} if true, gdal drivers are +#' @param gdal_vsi_resolution a `logical` if true, gdal drivers are #' included in the URL of each asset. The following schemes are supported: #' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). #' -#' @return a \code{list} with the attributes of date, bands and paths. +#' @return a `list` with the attributes of date, bands and paths. #' #' @examples #' \donttest{ @@ -520,20 +520,20 @@ assets_list <- function(items, assets_names = NULL, sort = TRUE, #' @title Utility functions #' #' @description This function returns the values of a field of the -#' \code{STACItemCollections} object. If the values of the specified field are +#' `STACItemCollections` object. If the values of the specified field are #' not atomic the return will be in list form, if they are, it will be returned #' in vector form. #' -#' @param items a \code{STACItemCollection} object representing -#' the result of \code{/stac/search}, \code{/collections/{collectionId}/items}. +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. #' #' @param ... a named way to provide fields names to get the -#' subfields values from the \code{RSTACDocument} objects. +#' subfields values from the `RSTACDocument` objects. #' -#' @param field a \code{character} with the names of the field to -#' get the subfields values from the \code{RSTACDocument} objects. +#' @param field a `character` with the names of the field to +#' get the subfields values from the `RSTACDocument` objects. #' -#' @return a \code{vector} if the supplied field is atomic, or a list if not. +#' @return a `vector` if the supplied field is atomic, or a list if not. #' #' @examples #' \donttest{ @@ -574,19 +574,19 @@ items_reap <- function(items, ..., field = NULL) { #' @title Utility functions #' -#' @description This function returns the subfields of the \code{feature} -#' field of a \code{STACItemCollection} object. +#' @description This function returns the subfields of the `feature` +#' field of a `STACItemCollection` object. #' -#' @param items a \code{STACItemCollection} object representing -#' the result of \code{/stac/search}, \code{/collections/{collectionId}/items}. +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. #' #' @param ... a named way to provide field names to get the subfields values -#' from the \code{RSTACDocument} objects. +#' from the `RSTACDocument` objects. #' -#' @param field a \code{character} with the names of the field to get the -#' subfields values from the \code{RSTACDocument} objects. +#' @param field a `character` with the names of the field to get the +#' subfields values from the `RSTACDocument` objects. #' -#' @return A \code{character} with the subfields of the \code{feature} field. +#' @return A `character` with the subfields of the `feature` field. #' #' @examples #' \donttest{ @@ -619,23 +619,23 @@ items_fields <- function(items, ..., field = NULL) { #' @title Utility functions #' #' @description This function groups the items contained within the -#' \code{STACItemCollection} object according to some specified fields. Each +#' `STACItemCollection` object according to some specified fields. Each #' index in the returned list contains items belonging to the same group. #' -#' @param items a \code{STACItemCollection} object representing the result of -#' \code{/stac/search}, \code{/collections/{collectionId}/items}. +#' @param items a `STACItemCollection` object representing the result of +#' `/stac/search`, \code{/collections/{collectionId}/items}. #' #' @param ... a named way to provide field names to get the subfields values -#' from the \code{RSTACDocument} objects. +#' from the `RSTACDocument` objects. #' -#' @param field a \code{character} with the names of the field to get the -#' subfields values from the \code{RSTACDocument} objects. +#' @param field a `character` with the names of the field to get the +#' subfields values from the `RSTACDocument` objects. #' -#' @param index a \code{character} with the indexes to be grouped. It can be -#' used with the function \link{items_reap}. +#' @param index a `character` with the indexes to be grouped. It can be +#' used with the function [items_reap]. #' -#' @return A \code{list} in which each index corresponds to a group with its -#' corresponding \code{STACItemCollection} objects. +#' @return A `list` in which each index corresponds to a group with its +#' corresponding `STACItemCollection` objects. #' #' @examples #' \donttest{ @@ -696,7 +696,7 @@ items_group <- function(items, ..., field = NULL, index = NULL) { #' @title Utility functions #' -#' @param bbox a \code{numeric} vector with only features that have a +#' @param bbox a `numeric` vector with only features that have a #' geometry that intersects the bounding box are selected. The bounding box is #' provided as four or six numbers, depending on whether the coordinate #' reference system includes a vertical axis (elevation or depth): @@ -707,7 +707,7 @@ items_group <- function(items, ..., field = NULL, index = NULL) { #' \item Upper right corner, coordinate axis 2 #' \item Upper right corner, coordinate axis 3 (optional) }. #' -#' @return A \code{character} with \code{bbox} formatted based on min and max +#' @return A `character` with `bbox` formatted based on min and max #' values. #' #' @noRd diff --git a/man/assets_download.Rd b/man/assets_download.Rd index 2204f592..10f96c33 100644 --- a/man/assets_download.Rd +++ b/man/assets_download.Rd @@ -16,7 +16,7 @@ assets_download( } \arguments{ \item{items}{a \code{STACItem} or \code{STACItemCollection} object -representing the result of \code{/stac/search}, +representing the result of \verb{/stac/search}, \code{/collections/{collectionId}/items} or \code{/collections/{collectionId}/items/{itemId}} endpoints.} @@ -34,9 +34,9 @@ downloaded.} \item{progress}{a \code{logical} indicating if a progress bar must be shown or not. (\code{TRUE}, default).} -\item{...}{config parameters to be passed to \link[httr]{GET} or -\link[httr]{POST} methods, such as \link[httr]{add_headers} or -\link[httr]{set_cookies}.} +\item{...}{config parameters to be passed to \link[httr:GET]{GET} or +\link[httr:POST]{POST} methods, such as \link[httr:add_headers]{add_headers} or +\link[httr:set_cookies]{set_cookies}.} } \value{ The same \code{STACItemCollection} or \code{STACItem} object, with @@ -57,5 +57,5 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } \seealso{ -\code{\link{stac_search}}, \code{\link{items}}, \code{\link{get_request}} +\code{\link[=stac_search]{stac_search()}}, \code{\link[=items]{items()}}, \code{\link[=get_request]{get_request()}} } diff --git a/man/assets_list.Rd b/man/assets_list.Rd index 379c2f0c..8e2d20e1 100644 --- a/man/assets_list.Rd +++ b/man/assets_list.Rd @@ -13,7 +13,7 @@ assets_list( } \arguments{ \item{items}{a \code{STACItemCollection} object representing -the result of \code{/stac/search}, \code{/collections/{collectionId}/items}.} +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} \item{assets_names}{a \code{character} with the assets names to be filtered. If \code{NULL} (default) all assets will be returned.} @@ -30,9 +30,9 @@ a \code{list} with the attributes of date, bands and paths. } \description{ This function returns the \code{date}, \code{band} and - \code{URL} fields for each assets of an \code{STACItemCollection} object. - For the URL you can add the GDAL library drivers for the following schemes: - HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). +\code{URL} fields for each assets of an \code{STACItemCollection} object. +For the URL you can add the GDAL library drivers for the following schemes: +HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). } \examples{ \donttest{ diff --git a/man/collections.Rd b/man/collections.Rd index 34af1e93..2047d52c 100644 --- a/man/collections.Rd +++ b/man/collections.Rd @@ -14,20 +14,20 @@ criteria.} } \value{ A \code{RSTACQuery} object with the subclass \code{collections} for - \code{/collections/} endpoint, or a \code{collection_id} subclass for - \code{/collections/{collection_id}} endpoint, containing all search field - parameters to be provided to STAC API web service. +\verb{/collections/} endpoint, or a \code{collection_id} subclass for +\code{/collections/{collection_id}} endpoint, containing all search field +parameters to be provided to STAC API web service. } \description{ -The \code{collections} function implements the WFS3 \code{/collections} - and \code{/collections/\{collectionId\}} endpoints. +The \code{collections} function implements the WFS3 \verb{/collections} +and \code{/collections/\{collectionId\}} endpoints. Each endpoint retrieves specific STAC objects: \itemize{ - \item \code{/collections}: Returns a list of STAC Collection published in - the STAC service - \item \code{/collections/\{collectionId\}}: Returns a single STAC - Collection object +\item \verb{/collections}: Returns a list of STAC Collection published in +the STAC service +\item \code{/collections/\{collectionId\}}: Returns a single STAC +Collection object } } \examples{ @@ -42,6 +42,6 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } } \seealso{ -\code{\link{get_request}}, \code{\link{post_request}}, - \code{\link{items}} +\code{\link[=get_request]{get_request()}}, \code{\link[=post_request]{post_request()}}, +\code{\link[=items]{items()}} } diff --git a/man/doc_query.Rd b/man/doc_query.Rd index 6ba52dca..ed526286 100644 --- a/man/doc_query.Rd +++ b/man/doc_query.Rd @@ -11,7 +11,7 @@ doc_query(d) } \value{ a \code{RSTACQuery} object with the predecessor subclass with the - fields used in the request. +fields used in the request. } \description{ Document utils functions diff --git a/man/ext_query.Rd b/man/ext_query.Rd index 57ac95d0..afa358a0 100644 --- a/man/ext_query.Rd +++ b/man/ext_query.Rd @@ -10,11 +10,11 @@ ext_query(q, ...) \item{q}{a \code{RSTACQuery} object expressing a STAC query criteria.} -\item{...}{entries with format \code{ }.} +\item{...}{entries with format \verb{ }.} } \value{ A \code{RSTACQuery} object with the subclass \code{ext_query} containing - all request parameters to be passed to \code{post_request()} function. +all request parameters to be passed to \code{post_request()} function. } \description{ The \code{ext_query()} is the \emph{exported function} of the STAC API @@ -23,13 +23,13 @@ function. It allows that additional fields and operators other than those defined in \code{stac_search()} function be used to make a complex filter. The function accepts multiple filter criteria. Each filter entry is an -expression formed by \code{ }, where -\code{} refers to a valid item property. Supported \code{} +expression formed by \verb{ }, where +\verb{} refers to a valid item property. Supported \verb{} depends on STAC API service implementation. The users must rely on service providers' documentation to know which properties can be used by this extension. -The \code{ext_query()} function allows the following \code{} +The \code{ext_query()} function allows the following \verb{} \itemize{ \item \code{==} corresponds to '\code{eq}' \item \code{!=} corresponds to '\code{neq}' @@ -37,13 +37,13 @@ The \code{ext_query()} function allows the following \code{} \item \code{<=} corresponds to '\code{lte}' \item \code{>} corresponds to '\code{gt}' \item \code{>=} corresponds to '\code{gte}' -\item \code{\%startsWith\%} corresponds to '\code{startsWith}' and implements +\item \verb{\\\%startsWith\\\%} corresponds to '\code{startsWith}' and implements a string prefix search operator. -\item \code{\%endsWith\%} corresponds to '\code{endsWith}' and implements a +\item \verb{\\\%endsWith\\\%} corresponds to '\code{endsWith}' and implements a string suffix search operator. -\item \code{\%contains\%}: corresponds to '\code{contains}' and implements a +\item \verb{\\\%contains\\\%}: corresponds to '\code{contains}' and implements a string infix search operator. -\item \code{\%in\%}: corresponds to '\code{in}' and implements a vector +\item \verb{\\\%in\\\%}: corresponds to '\verb{in}' and implements a vector search operator. } @@ -67,7 +67,7 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } \seealso{ -\code{\link{stac_search}}, \code{\link{post_request}}, -\code{\link{endpoint}}, \code{\link{before_request}}, -\code{\link{after_response}}, \code{\link{content_response}} +\code{\link[=stac_search]{stac_search()}}, \code{\link[=post_request]{post_request()}}, +\code{\link[=endpoint]{endpoint()}}, \code{\link[=before_request]{before_request()}}, +\code{\link[=after_response]{after_response()}}, \code{\link[=content_response]{content_response()}} } diff --git a/man/extensions.Rd b/man/extensions.Rd index 1e5c490a..5b453cb5 100644 --- a/man/extensions.Rd +++ b/man/extensions.Rd @@ -39,7 +39,7 @@ RSTACQuery(version = NULL, base_url, params = list(), subclass) } \arguments{ \item{content}{a \code{list} data structure representing the JSON file -received in HTTP response (see \code{\link{content_response}()} function)} +received in HTTP response (see \code{\link[=content_response]{content_response()}} function)} \item{q}{a \code{RSTACQuery} object.} @@ -202,7 +202,7 @@ parameter the extension's subclass name. The \code{params} parameter is a named \code{list} where user parameters must be stored. It is important to know if previous query parameters needs to be keeped in the new query. If so, it is recommended do use -\code{\link[utils]{modifyList}()} function to merge the old and new +\code{\link[utils:modifyList]{utils::modifyList()}} function to merge the old and new query parameters. If the \code{version} parameter is \code{NULL}, \code{rstac} will detect @@ -215,5 +215,5 @@ is the extension's subclass name. }} \seealso{ -\code{\link{ext_query}} +\code{\link[=ext_query]{ext_query()}} } diff --git a/man/items.Rd b/man/items.Rd index 4a122d22..1704e88b 100644 --- a/man/items.Rd +++ b/man/items.Rd @@ -21,10 +21,10 @@ Open intervals are expressed by using \code{'..'} in place of date-time. Examples: \itemize{ - \item A date-time: \code{"2018-02-12T23:20:50Z"} - \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} - \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or - \code{"../2018-03-18T12:31:12Z"} +\item A date-time: \code{"2018-02-12T23:20:50Z"} +\item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} +\item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or +\code{"../2018-03-18T12:31:12Z"} } Only features that have a \code{datetime} property that intersects @@ -35,11 +35,11 @@ geometry that intersects the bounding box are selected. The bounding box is provided as four or six numbers, depending on whether the coordinate reference system includes a vertical axis (elevation or depth): \itemize{ \item Lower left corner, coordinate axis 1 - \item Lower left corner, coordinate axis 2 - \item Lower left corner, coordinate axis 3 (optional) - \item Upper right corner, coordinate axis 1 - \item Upper right corner, coordinate axis 2 - \item Upper right corner, coordinate axis 3 (optional) } +\item Lower left corner, coordinate axis 2 +\item Lower left corner, coordinate axis 3 (optional) +\item Upper right corner, coordinate axis 1 +\item Upper right corner, coordinate axis 2 +\item Upper right corner, coordinate axis 3 (optional) } The coordinate reference system of the values is WGS84 longitude/latitude (\url{http://www.opengis.net/def/crs/OGC/1.3/CRS84}). @@ -54,11 +54,11 @@ to return. If not informed it defaults to the service implementation.} } \value{ A \code{RSTACQuery} object with the subclass \code{items} for - \code{/collections/{collection_id}/items} endpoint, or a - \code{item_id} subclass for - \code{/collections/{collection_id}/items/{feature_id}} endpoint, - containing all search field parameters to be provided to STAC API web - service. +\code{/collections/{collection_id}/items} endpoint, or a +\code{item_id} subclass for +\code{/collections/{collection_id}/items/{feature_id}} endpoint, +containing all search field parameters to be provided to STAC API web +service. } \description{ The \code{items} function implements WFS3 @@ -67,14 +67,14 @@ The \code{items} function implements WFS3 Each endpoint retrieves specific STAC objects: \itemize{ - \item \code{/collections/\{collectionId\}/items}: Returns a STAC Items - collection (GeoJSON) - \item \code{/collections/\{collectionId\}/items/\{itemId\}}: Returns a - STAC Item (GeoJSON Feature) +\item \code{/collections/\{collectionId\}/items}: Returns a STAC Items +collection (GeoJSON) +\item \code{/collections/\{collectionId\}/items/\{itemId\}}: Returns a +STAC Item (GeoJSON Feature) } The endpoint \code{/collections/\{collectionId\}/items} accepts the same -filters parameters of \code{\link{stac_search}} function. +filters parameters of \code{\link[=stac_search]{stac_search()}} function. } \examples{ \donttest{ @@ -91,6 +91,6 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } \seealso{ -\code{\link{get_request}}, \code{\link{post_request}}, - \code{\link{collections}} +\code{\link[=get_request]{get_request()}}, \code{\link[=post_request]{post_request()}}, +\code{\link[=collections]{collections()}} } diff --git a/man/items_fields.Rd b/man/items_fields.Rd index b5542ea6..08d3635e 100644 --- a/man/items_fields.Rd +++ b/man/items_fields.Rd @@ -8,7 +8,7 @@ items_fields(items, ..., field = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing -the result of \code{/stac/search}, \code{/collections/{collectionId}/items}.} +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} \item{...}{a named way to provide field names to get the subfields values from the \code{RSTACDocument} objects.} diff --git a/man/items_functions.Rd b/man/items_functions.Rd index c16f4726..08ee5c0c 100644 --- a/man/items_functions.Rd +++ b/man/items_functions.Rd @@ -31,9 +31,9 @@ the initial node of the list. For example, if the information is at position \code{items$meta$found} of the object, it must be passed as the following parameter \code{c("meta", "found")}.} -\item{...}{config parameters to be passed to \link[httr]{GET} or -\link[httr]{POST} methods, such as \link[httr]{add_headers} or -\link[httr]{set_cookies}.} +\item{...}{config parameters to be passed to \link[httr:GET]{GET} or +\link[httr:POST]{POST} methods, such as \link[httr:add_headers]{add_headers} or +\link[httr:set_cookies]{set_cookies}.} \item{progress}{a \code{logical} indicating if a progress bar must be shown or not. Defaults to \code{TRUE}.} diff --git a/man/items_group.Rd b/man/items_group.Rd index bf88dff0..c08b65e9 100644 --- a/man/items_group.Rd +++ b/man/items_group.Rd @@ -8,7 +8,7 @@ items_group(items, ..., field = NULL, index = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing the result of -\code{/stac/search}, \code{/collections/{collectionId}/items}.} +\verb{/stac/search}, \code{/collections/{collectionId}/items}.} \item{...}{a named way to provide field names to get the subfields values from the \code{RSTACDocument} objects.} @@ -21,12 +21,12 @@ used with the function \link{items_reap}.} } \value{ A \code{list} in which each index corresponds to a group with its - corresponding \code{STACItemCollection} objects. +corresponding \code{STACItemCollection} objects. } \description{ This function groups the items contained within the - \code{STACItemCollection} object according to some specified fields. Each - index in the returned list contains items belonging to the same group. +\code{STACItemCollection} object according to some specified fields. Each +index in the returned list contains items belonging to the same group. } \examples{ \donttest{ diff --git a/man/items_reap.Rd b/man/items_reap.Rd index 8a0b891f..e7182159 100644 --- a/man/items_reap.Rd +++ b/man/items_reap.Rd @@ -8,7 +8,7 @@ items_reap(items, ..., field = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing -the result of \code{/stac/search}, \code{/collections/{collectionId}/items}.} +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} \item{...}{a named way to provide fields names to get the subfields values from the \code{RSTACDocument} objects.} @@ -21,9 +21,9 @@ a \code{vector} if the supplied field is atomic, or a list if not. } \description{ This function returns the values of a field of the - \code{STACItemCollections} object. If the values of the specified field are - not atomic the return will be in list form, if they are, it will be returned - in vector form. +\code{STACItemCollections} object. If the values of the specified field are +not atomic the return will be in list form, if they are, it will be returned +in vector form. } \examples{ \donttest{ diff --git a/man/print.Rd b/man/print.Rd index d4d12334..d0e1ffab 100644 --- a/man/print.Rd +++ b/man/print.Rd @@ -41,21 +41,21 @@ STACItemCollection object must be show.} The print function covers all objects in the rstac package: \itemize{ -\item \code{\link{stac}}: returns a \code{STACCatalog} document from - \code{/stac} (v0.8.0) or \code{/} (v0.9.0 or v1.0.0) endpoint. -\item \code{\link{stac_search}}: returns a \code{STACItemCollection} - document from \code{/stac/search} (v0.8.0) or \code{/search} - (v0.9.0 or v1.0.0) endpoint containing all Items that match - the provided search predicates. -\item \code{\link{collections}}: implements the \code{/collections} and - \code{/collections/\{collectionId\}} endpoints. The former returns - a \code{STACCollectionList} document that lists all collections published - by the server, and the later returns a single \code{STACCollection} - document that describes a unique collection. -\item \code{\link{items}}: retrieves a \code{STACItemCollection} document - from \code{/collections/\{collectionId\}/items} endpoint and a - \code{STACItem} document from - \code{/collections/\{collectionId\}/items/\{itemId\}} endpoints. +\item \code{\link[=stac]{stac()}}: returns a \code{STACCatalog} document from +\verb{/stac} (v0.8.0) or \code{/} (v0.9.0 or v1.0.0) endpoint. +\item \code{\link[=stac_search]{stac_search()}}: returns a \code{STACItemCollection} +document from \verb{/stac/search} (v0.8.0) or \verb{/search} +(v0.9.0 or v1.0.0) endpoint containing all Items that match +the provided search predicates. +\item \code{\link[=collections]{collections()}}: implements the \verb{/collections} and +\code{/collections/\{collectionId\}} endpoints. The former returns +a \code{STACCollectionList} document that lists all collections published +by the server, and the later returns a single \code{STACCollection} +document that describes a unique collection. +\item \code{\link[=items]{items()}}: retrieves a \code{STACItemCollection} document +from \code{/collections/\{collectionId\}/items} endpoint and a +\code{STACItem} document from +\code{/collections/\{collectionId\}/items/\{itemId\}} endpoints. } The rstac package objects visualization is based on markdown, a @@ -92,6 +92,6 @@ print(obj_rstac) } } \seealso{ -\code{\link{stac}} \code{\link{stac_search}} \code{\link{collections}} -\code{\link{items}} +\code{\link[=stac]{stac()}} \code{\link[=stac_search]{stac_search()}} \code{\link[=collections]{collections()}} +\code{\link[=items]{items()}} } diff --git a/man/request.Rd b/man/request.Rd index 81776833..792385a8 100644 --- a/man/request.Rd +++ b/man/request.Rd @@ -13,9 +13,9 @@ post_request(q, ..., encode = c("json", "multipart", "form")) \item{q}{a \code{RSTACQuery} object expressing a STAC query criteria.} -\item{...}{config parameters to be passed to \link[httr]{GET} or -\link[httr]{POST} methods, such as \link[httr]{add_headers} or -\link[httr]{set_cookies}.} +\item{...}{config parameters to be passed to \link[httr:GET]{GET} or +\link[httr:POST]{POST} methods, such as \link[httr:add_headers]{add_headers} or +\link[httr:set_cookies]{set_cookies}.} \item{encode}{a \code{character} informing the request body Content-Type. Accepted types are \code{'json'} (\code{'application/json'}), @@ -47,6 +47,6 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } } \seealso{ -\code{\link{stac}} \code{\link{stac_search}} \code{\link{collections}} -\code{\link{items}} +\code{\link[=stac]{stac()}} \code{\link[=stac_search]{stac_search()}} \code{\link[=collections]{collections()}} +\code{\link[=items]{items()}} } diff --git a/man/rstac.Rd b/man/rstac.Rd index c4294683..938600c9 100644 --- a/man/rstac.Rd +++ b/man/rstac.Rd @@ -20,41 +20,41 @@ API endpoints and data access and organization. \section{STAC API endpoints functions}{ \itemize{ - \item \code{\link{stac}}: implements STAC \code{/stac} endpoint for version - 0.8.1 or below, and \code{/} for versions 0.9.0 or higher. - \item \code{\link{collections}}: implements \code{/collections} - and \code{/collections/\{collectionId\}} WFS3 endpoints. - \item \code{\link{items}}: implements - \code{/collections/\{collectionId\}/items} and - \code{/collections/\{collectionId\}/items/\{featureId\}} WFS3 endpoints. - \item \code{\link{stac_search}}: implements STAC \code{/stac/search} - endpoint for version 0.8.1 or below, and \code{/search} endpoint for - versions 0.9.0 or higher. +\item \code{\link[=stac]{stac()}}: implements STAC \verb{/stac} endpoint for version +0.8.1 or below, and \code{/} for versions 0.9.0 or higher. +\item \code{\link[=collections]{collections()}}: implements \verb{/collections} +and \code{/collections/\{collectionId\}} WFS3 endpoints. +\item \code{\link[=items]{items()}}: implements +\code{/collections/\{collectionId\}/items} and +\code{/collections/\{collectionId\}/items/\{featureId\}} WFS3 endpoints. +\item \code{\link[=stac_search]{stac_search()}}: implements STAC \verb{/stac/search} +endpoint for version 0.8.1 or below, and \verb{/search} endpoint for +versions 0.9.0 or higher. } } \section{Data access and organization functions}{ \itemize{ - \item \code{\link{get_request}}: makes HTTP GET requests to STAC web - service. - \item \code{\link{post_request}}: makes HTTP POST requests to STAC web - service. - \item \code{\link{items_matched}}: returns how many items matched the - search criteria. - \item \code{\link{items_length}}: informs how many items are - stored locally. - \item \code{\link{items_fetch}}: fetches all matched items from service. - \item \code{\link{assets_download}}: download all assets in batch. +\item \code{\link[=get_request]{get_request()}}: makes HTTP GET requests to STAC web +service. +\item \code{\link[=post_request]{post_request()}}: makes HTTP POST requests to STAC web +service. +\item \code{\link[=items_matched]{items_matched()}}: returns how many items matched the +search criteria. +\item \code{\link[=items_length]{items_length()}}: informs how many items are +stored locally. +\item \code{\link[=items_fetch]{items_fetch()}}: fetches all matched items from service. +\item \code{\link[=assets_download]{assets_download()}}: download all assets in batch. } } \section{Data types}{ The package implements the follow S3 classes: \code{STACItemCollection}, - \code{STACItem}, \code{STACCatalog}, \code{STACCollectionList} and - \code{STACCollection}. These classes are regular lists representing the - corresponding JSON STAC objects. +\code{STACItem}, \code{STACCatalog}, \code{STACCollectionList} and +\code{STACCollection}. These classes are regular lists representing the +corresponding JSON STAC objects. } \seealso{ diff --git a/man/stac.Rd b/man/stac.Rd index 9c5e2833..85c1ea1c 100644 --- a/man/stac.Rd +++ b/man/stac.Rd @@ -20,7 +20,7 @@ A \code{RSTACQuery} object with the subclass \code{stac} containing all request parameters to be provided to API service. } \description{ -The \code{stac} function implements \code{/stac} API +The \code{stac} function implements \verb{/stac} API endpoint (>=0.8.0), and \code{/} for versions 0.9.0 or higher. It prepares search fields parameters to be provided to a STAC API web service. This endpoint should return a STAC Catalog document containing all published data @@ -34,7 +34,7 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } \seealso{ -\code{\link{stac_search}}, \code{\link{collections}}, -\code{\link{items}}, \code{\link{get_request}}, -\code{\link{post_request}} +\code{\link[=stac_search]{stac_search()}}, \code{\link[=collections]{collections()}}, +\code{\link[=items]{items()}}, \code{\link[=get_request]{get_request()}}, +\code{\link[=post_request]{post_request()}} } diff --git a/man/stac_search.Rd b/man/stac_search.Rd index c25a9e08..4d0445fb 100644 --- a/man/stac_search.Rd +++ b/man/stac_search.Rd @@ -30,11 +30,11 @@ geometry that intersects the bounding box are selected. The bounding box is provided as four or six numbers, depending on whether the coordinate reference system includes a vertical axis (elevation or depth): \itemize{ \item Lower left corner, coordinate axis 1 - \item Lower left corner, coordinate axis 2 - \item Lower left corner, coordinate axis 3 (optional) - \item Upper right corner, coordinate axis 1 - \item Upper right corner, coordinate axis 2 - \item Upper right corner, coordinate axis 3 (optional) } +\item Lower left corner, coordinate axis 2 +\item Lower left corner, coordinate axis 3 (optional) +\item Upper right corner, coordinate axis 1 +\item Upper right corner, coordinate axis 2 +\item Upper right corner, coordinate axis 3 (optional) } The coordinate reference system of the values is WGS84 longitude/latitude (\url{http://www.opengis.net/def/crs/OGC/1.3/CRS84}). The values are in @@ -44,16 +44,16 @@ antimeridian the first value (west-most box edge) is larger than the third value (east-most box edge).} \item{datetime}{a \code{character} with a date-time or an interval. Date - and time strings needs to conform RFC 3339. Intervals are expressed by - separating two date-time strings by \code{'/'} character. Open intervals are - expressed by using \code{'..'} in place of date-time. +and time strings needs to conform RFC 3339. Intervals are expressed by +separating two date-time strings by \code{'/'} character. Open intervals are +expressed by using \code{'..'} in place of date-time. Examples: \itemize{ \item A date-time: \code{"2018-02-12T23:20:50Z"} \item A closed interval: \code{"2018-02-12T00:00:00Z/2018-03-18T12:31:12Z"} \item Open intervals: \code{"2018-02-12T00:00:00Z/.."} or - \code{"../2018-03-18T12:31:12Z"} +\code{"../2018-03-18T12:31:12Z"} } Only features that have a \code{datetime} property that intersects the @@ -75,8 +75,8 @@ search field parameters to be provided to STAC API web service. \url{https://github.com/radiantearth/stac-spec/} and reproduces some of its parts) -The \code{stac_search} function implements \code{/stac/search} API endpoint -(v0.8.1) and \code{/search} (v0.9.0 or v1.0.0). +The \code{stac_search} function implements \verb{/stac/search} API endpoint +(v0.8.1) and \verb{/search} (v0.9.0 or v1.0.0). It prepares query parameters used in search API request, a \code{stac} object with all filter parameters to be provided to \code{get_request} or \code{post_request} functions. The GeoJSON content @@ -100,6 +100,6 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% } \seealso{ -\code{\link{stac}}, \code{\link{ext_query}}, -\code{\link{get_request}}, \code{\link{post_request}} +\code{\link[=stac]{stac()}}, \code{\link[=ext_query]{ext_query()}}, +\code{\link[=get_request]{get_request()}}, \code{\link[=post_request]{post_request()}} } diff --git a/man/utilities.Rd b/man/utilities.Rd index d4eefcda..797a827d 100644 --- a/man/utilities.Rd +++ b/man/utilities.Rd @@ -11,8 +11,8 @@ stac_version(x, ...) \item{x}{either a \code{RSTACQuery} object expressing a STAC query criteria or any \code{RSTACDocument}.} -\item{...}{config parameters to be passed to \link[httr]{GET} -method, such as \link[httr]{add_headers} or \link[httr]{set_cookies}.} +\item{...}{config parameters to be passed to \link[httr:GET]{GET} +method, such as \link[httr:add_headers]{add_headers} or \link[httr:set_cookies]{set_cookies}.} } \value{ The \code{stac_version()} function returns a \code{character} STAC API From 923948a3a5b14c497cd26fd15baef63fdb3b440c Mon Sep 17 00:00:00 2001 From: Felipe Date: Wed, 15 Sep 2021 13:51:23 +0000 Subject: [PATCH 02/44] refactoring assets_download code and depricated 'assets_name' parameter --- R/assets_download.R | 108 ++++++++++++++++++++++++----------------- man/assets_download.Rd | 29 +++++++---- 2 files changed, 84 insertions(+), 53 deletions(-) diff --git a/R/assets_download.R b/R/assets_download.R index 1c79e6be..0e521f3b 100644 --- a/R/assets_download.R +++ b/R/assets_download.R @@ -8,19 +8,27 @@ #' \code{/collections/{collectionId}/items} or #' \code{/collections/{collectionId}/items/{itemId}} endpoints. #' -#' @param assets_name a `character` with the assets names to be filtered. +#' @param assets_name `r lifecycle::badge('deprecated')` +#' use `asset_names` parameter instead. +#' +#' @param asset_names a `character` with the assets names to be filtered. +#' #' #' @param output_dir a `character` directory in which the assets will be #' saved. #' #' @param overwrite a `logical` if TRUE will replaced the existing file, -#' if FALSE a warning message is shown. (`FALSE`, default). +#' if FALSE a warning message is shown. #' #' @param items_max a `numeric` corresponding how many items will be #' downloaded. #' #' @param progress a `logical` indicating if a progress bar must be -#' shown or not. (`TRUE`, default). +#' shown or not. Defaults to `TRUE`. +#' +#' @param fn a `function` to handle the list of assets for each item. +#' Using this function you can change the hrefs for each asset, as well as use +#' another request verb, such as POST. #' #' @param ... config parameters to be passed to [GET][httr::GET] or #' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or @@ -32,36 +40,54 @@ #' @examples #' \dontrun{ #' stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1") %>% -#' stac_search(limit = 2) %>% +#' stac_search(collections = "CB4_64_16D_STK-1", +#' datetime = "2019-06-01/2019-08-01") %>% +#' stac_search() %>% #' get_request() %>% -#' assets_download(assets_name = "thumbnail", output_dir = ".") +#' assets_download(assets_name = "thumbnail", output_dir = ".", +#' overwrite = FALSE) #' } #' #' @return The same `STACItemCollection` or `STACItem` object, with -#' the link pointing to the directory where the assets were saved. +#' the link of the item pointing to the directory where the assets were saved. #' #' @export assets_download <- function(items, - assets_name, + asset_names = NULL, output_dir = ".", overwrite = FALSE, items_max = Inf, - progress = TRUE, - ...) { + progress = TRUE, + fn = NULL, ..., + assets_name = deprecated()) { #check the object subclass check_subclass(items, subclasses = c("STACItemCollection", "STACItem")) + if (lifecycle::is_present(assets_name)) { + + # signal the deprecation to the user + lifecycle::deprecate_soft("0.9.1-5", + "rstac::assets_download(assets_name = )", + "rstac::assets_download(asset_names = )") + + # deal with the deprecated argument for compatibility + asset_names <- assets_name + } + # check output dir if (!dir.exists(output_dir)) .error(paste("The directory provided does not exist.", "Please specify a valid directory.")) + + if (is.null(asset_names)) + asset_names <- items_fields(items, "assets") + # if the object is a STACItem if (subclass(items) == "STACItem") { items <- .item_download(stac_item = items, - assets_name = assets_name, + asset_names = asset_names, output_dir = output_dir, overwrite = overwrite, ...) return(items) @@ -100,7 +126,8 @@ assets_download <- function(items, items$features[[i]] <- .item_download(stac_item = items$features[[i]], assets_name = assets_name, output_dir = output_dir, - overwrite = overwrite, ...) + overwrite = overwrite, + fn = fn, ...) } # close progress bar if (progress) @@ -109,25 +136,23 @@ assets_download <- function(items, return(items) } -# helpers ---------------------------------------------------------------------- - #' @title Helper function of `assets_download` function #' #' @description the `.item_download` function downloads the assets of a -#' `STACItem` object. +#' stac_item #' #' @param stac_item a `stac_item` object expressing a STAC #' search criteria provided by `stac_item` function. #' -#' @param assets_name a `character` with the assets names to be filtered. +#' @param asset_names a `character` with the assets names to be filtered. #' #' @param output_dir a `character` directory in which the images will be #' saved. #' -#' @param overwrite a `logical` if TRUE will replaced the existing file, +#' @param overwrite a `logical` if TRUE will replaced the existing file, #' if FALSE a warning message is shown. #' -#' @param ... config parameters to be passed to [GET][httr::GET] or +#' @param ... config parameters to be passed to [GET][httr::GET] or #' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or #' [set_cookies][httr::set_cookies]. #' @@ -135,33 +160,33 @@ assets_download <- function(items, #' pointing to the directory where the assets were saved. #' #' @noRd -.item_download <- function(stac_item, assets_name, output_dir, overwrite, ...) { +.item_download <- function(stac_item, asset_names, output_dir, + overwrite, ..., fn) { - feat_id <- stac_item[["id"]] - assets <- .select_assets(stac_item[["assets"]], assets_name) + assets <- .select_assets(stac_item[["assets"]], assets_name) - for (i in seq_along(assets)) { - # store the names of assets - asset_name <- names(assets[i]) - asset_href <- assets[[i]]$href - file_ext <- .file_ext(asset_href) + stac_item[["assets"]] <- lapply(assets, function(asset){ + + if (!is.null(fn)) + return(fn(asset)) # create a full path name - dest_file <- sprintf("%s/%s_%s.%s", output_dir, feat_id, asset_name, - file_ext) + dest_file <- paste0(output_dir, "/", + gsub(".*/([^?]*)\\??.*$", "\\1", asset$href)) tryCatch({ - httr::GET(url = asset_href, + httr::GET(url = asset$href, httr::write_disk(path = dest_file, overwrite = overwrite), ...) - }, error = function(error) { - .warning(paste("\n", error, "in ", asset_href)) + }, error = function(e){ + .error("Error while downloading %s. \n%s", asset$href, e$message) }) - if (file.exists(dest_file)) { - stac_item[["assets"]][[asset_name]]$href <- dest_file - } - } + asset$href <- dest_file + + asset + }) + return(stac_item) } @@ -193,24 +218,19 @@ assets_download <- function(items, #' @param assets_list a `list` with the information of each item provided #' by API STAC #' -#' @param assets_names a `character` with the assets names to be filtered. +#' @param asset_names a `character` with the assets names to be filtered. #' #' @return A `list` in the same format as the list of assets, but with the #' selected assets names. #' #' @noRd -.select_assets <- function(assets, assets_names) { - - # If not provided the assets name, by default all assets will be used - if (missing(assets_names)) { - return(assets) - } +.select_assets <- function(assets, asset_names) { - if (!all(assets_names %in% names(assets))) { + if (!all(asset_names %in% names(assets))) { .error(paste("The provided assets names do not match with the", "assets names in the document.")) } - assets <- assets[names(assets) %in% assets_names] + assets <- assets[names(assets) %in% asset_names] return(assets) } diff --git a/man/assets_download.Rd b/man/assets_download.Rd index 10f96c33..ac84d668 100644 --- a/man/assets_download.Rd +++ b/man/assets_download.Rd @@ -6,12 +6,14 @@ \usage{ assets_download( items, - assets_name, + asset_names = NULL, output_dir = ".", overwrite = FALSE, items_max = Inf, progress = TRUE, - ... + fn = NULL, + ..., + assets_name = deprecated() ) } \arguments{ @@ -20,27 +22,34 @@ representing the result of \verb{/stac/search}, \code{/collections/{collectionId}/items} or \code{/collections/{collectionId}/items/{itemId}} endpoints.} -\item{assets_name}{a \code{character} with the assets names to be filtered.} +\item{asset_names}{a \code{character} with the assets names to be filtered.} \item{output_dir}{a \code{character} directory in which the assets will be saved.} \item{overwrite}{a \code{logical} if TRUE will replaced the existing file, -if FALSE a warning message is shown. (\code{FALSE}, default).} +if FALSE a warning message is shown.} \item{items_max}{a \code{numeric} corresponding how many items will be downloaded.} \item{progress}{a \code{logical} indicating if a progress bar must be -shown or not. (\code{TRUE}, default).} +shown or not. Defaults to \code{TRUE}.} + +\item{fn}{a \code{function} to handle the list of assets for each item. +Using this function you can change the hrefs for each asset, as well as use +another request verb, such as POST.} \item{...}{config parameters to be passed to \link[httr:GET]{GET} or \link[httr:POST]{POST} methods, such as \link[httr:add_headers]{add_headers} or \link[httr:set_cookies]{set_cookies}.} + +\item{assets_name}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} +use \code{asset_names} parameter instead.} } \value{ The same \code{STACItemCollection} or \code{STACItem} object, with -the link pointing to the directory where the assets were saved. +the link of the item pointing to the directory where the assets were saved. } \description{ The \code{assets_download} function downloads the assets @@ -49,10 +58,12 @@ provided by the STAC API. \examples{ \dontrun{ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1") \%>\% - stac_search(limit = 2) \%>\% + stac_search(collections = "CB4_64_16D_STK-1", + datetime = "2019-06-01/2019-08-01") \%>\% + stac_search() \%>\% get_request() \%>\% - assets_download(assets_name = "thumbnail", output_dir = ".") + assets_download(assets_name = "thumbnail", output_dir = ".", + overwrite = FALSE) } } From 2cae5ec69e0a405c0aa72347dc38e30f8a7c9f48 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 04:33:52 +0000 Subject: [PATCH 03/44] update version patch to 0.9.1-5 --- DESCRIPTION | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 49909b78..cd7c7f6c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rstac Title: Client Library for SpatioTemporal Asset Catalog -Version: 0.9.1-4 +Version: 0.9.1-5 Authors@R: c(person("Brazil Data Cube Team", email = "brazildatacube@inpe.br", @@ -23,7 +23,8 @@ Imports: crayon, utils, magrittr, - jsonlite + jsonlite, + lifecycle Suggests: covr, testthat, From de0450ee497dd36ce00eba85a121c3aa58cc9b1b Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 04:34:46 +0000 Subject: [PATCH 04/44] add lifecycle package function in imports --- NAMESPACE | 1 + R/rstac.R | 1 + 2 files changed, 2 insertions(+) diff --git a/NAMESPACE b/NAMESPACE index ef332978..cf348d06 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -80,6 +80,7 @@ importFrom(httr,http_type) importFrom(httr,status_code) importFrom(httr,write_disk) importFrom(jsonlite,validate) +importFrom(lifecycle,deprecated) importFrom(magrittr,"%>%") importFrom(utils,URLdecode) importFrom(utils,modifyList) diff --git a/R/rstac.R b/R/rstac.R index 02e7ee24..204707ca 100644 --- a/R/rstac.R +++ b/R/rstac.R @@ -58,4 +58,5 @@ NULL #' @importFrom crayon bold #' @importFrom utils modifyList URLdecode #' @importFrom jsonlite validate +#' @importFrom lifecycle deprecated NULL From 0f854255b35535f6782ddd3e1438e2b51eb09fcd Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:01:03 +0000 Subject: [PATCH 05/44] deprecated 'assets_names' in assets_list function --- R/utils.R | 32 ++++++++++++++++++++++++-------- man/assets_list.Rd | 13 +++++++++---- 2 files changed, 33 insertions(+), 12 deletions(-) diff --git a/R/utils.R b/R/utils.R index 337c3ac9..f1f24cae 100644 --- a/R/utils.R +++ b/R/utils.R @@ -451,8 +451,11 @@ stac_version <- function(x, ...) { #' @param items a `STACItemCollection` object representing #' the result of `/stac/search`, \code{/collections/{collectionId}/items}. #' -#' @param assets_names a `character` with the assets names to be -#' filtered. If `NULL` (default) all assets will be returned. +#' @param assets_names `r lifecycle::badge('deprecated')` +#' use `asset_names` parameter instead. +#' +#' @param asset_names a `character` with the assets names to be +#' filtered. If `NULL` (default) all assets will be returned.. #' #' @param sort a `logical` if true the dates will be sorted #' in increasing order. By default, the dates are sorted. @@ -476,20 +479,33 @@ stac_version <- function(x, ...) { #' } #' #' @export -assets_list <- function(items, assets_names = NULL, sort = TRUE, - gdal_vsi_resolution = TRUE) { +assets_list <- function(items, asset_names = NULL, + sort = TRUE, gdal_vsi_resolution = TRUE, ..., + assets_names = deprecated()) { + + + if (lifecycle::is_present(assets_names)) { + + # Signal the deprecation to the user + lifecycle::deprecate_soft("0.9.1-5", + "rstac::assets_download(assets_names = )", + "rstac::assets_download(asset_names = )") + + # Deal with the deprecated argument for compatibility + asset_names <- assets_names + } - if (is.null(assets_names)) - assets_names <- items_fields(items, "assets") + if (is.null(asset_names)) + asset_names <- items_fields(items, "assets") timeline <- items_reap(items, field = c("properties", "datetime")) index <- seq_along(timeline) if (sort) index <- order(timeline) timeline <- timeline[index] - assets <- list(date = rep(timeline, length(unique(assets_names)))) + assets <- list(date = rep(timeline, length(unique(asset_names)))) - for (b in assets_names) { + for (b in asset_names) { href <- items_reap(items, field = c("assets", b, "href"))[index] diff --git a/man/assets_list.Rd b/man/assets_list.Rd index 8e2d20e1..b1abf03a 100644 --- a/man/assets_list.Rd +++ b/man/assets_list.Rd @@ -6,17 +6,19 @@ \usage{ assets_list( items, - assets_names = NULL, + asset_names = NULL, sort = TRUE, - gdal_vsi_resolution = TRUE + gdal_vsi_resolution = TRUE, + ..., + assets_names = deprecated() ) } \arguments{ \item{items}{a \code{STACItemCollection} object representing the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} -\item{assets_names}{a \code{character} with the assets names to be -filtered. If \code{NULL} (default) all assets will be returned.} +\item{asset_names}{a \code{character} with the assets names to be +filtered. If \code{NULL} (default) all assets will be returned..} \item{sort}{a \code{logical} if true the dates will be sorted in increasing order. By default, the dates are sorted.} @@ -24,6 +26,9 @@ in increasing order. By default, the dates are sorted.} \item{gdal_vsi_resolution}{a \code{logical} if true, gdal drivers are included in the URL of each asset. The following schemes are supported: HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage).} + +\item{assets_names}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} +use \code{asset_names} parameter instead.} } \value{ a \code{list} with the attributes of date, bands and paths. From f263012dbbd4bf053629a877ac05228d99e51479 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:05:04 +0000 Subject: [PATCH 06/44] add filter function. Closes (#56) --- R/utils.R | 68 +++++++++++++++++++++++++++++++++++++++++++++ man/items_filter.Rd | 47 +++++++++++++++++++++++++++++++ 2 files changed, 115 insertions(+) create mode 100644 man/items_filter.Rd diff --git a/R/utils.R b/R/utils.R index f1f24cae..b88a1aa4 100644 --- a/R/utils.R +++ b/R/utils.R @@ -533,6 +533,74 @@ assets_list <- function(items, asset_names = NULL, assets } +#' @title Utility functions +#' +#' @description This function filters for the attributes contained in the STAC +#' properties. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param ... expressions used to filter items of a `STACItemCollection` +#' object. +#' @param fn a `function` that will be used to filter the attributes +#' listed in the properties. +#' +#' @return a `STACItemCollection` object with the filtered properties. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_filter(`eo:cloud_cover` < 10) +#' +#' # Example with AWS STAC +#' items <- stac("https://earth-search.aws.element84.com/v0") %>% +#' stac_search(collections = "sentinel-s2-l2a-cogs", +#' bbox = c(-48.206,-14.195,-45.067,-12.272), +#' datetime = "2018-06-01/2018-06-30", +#' limit = 500) %>% +#' post_request() +#' +#' items %>% +#' items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) +#' } +#' +#' @export +items_filter <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + sel <- vapply(items$features, function(f) { + eval(dots[[i]], envir = f$properties) + }, logical(1)) + + items$features <- items$features[sel] + } + } + + if (!is.null(fn)) { + + sel <- vapply(items$features, function(f) { + fn(f$properties) + }, logical(1)) + + items$features <- items$features[sel] + } + + items +} + #' @title Utility functions #' #' @description This function returns the values of a field of the diff --git a/man/items_filter.Rd b/man/items_filter.Rd new file mode 100644 index 00000000..9a7c3ee5 --- /dev/null +++ b/man/items_filter.Rd @@ -0,0 +1,47 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{items_filter} +\alias{items_filter} +\title{Utility functions} +\usage{ +items_filter(items, ..., fn = NULL) +} +\arguments{ +\item{items}{a \code{STACItemCollection} object representing +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} + +\item{...}{expressions used to filter items of a \code{STACItemCollection} +object.} + +\item{fn}{a \code{function} that will be used to filter the attributes +listed in the properties.} +} +\value{ +a \code{STACItemCollection} object with the filtered properties. +} +\description{ +This function filters for the attributes contained in the STAC +properties. +} +\examples{ +\donttest{ +# STACItemCollection object +stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_filter(`eo:cloud_cover` < 10) + +# Example with AWS STAC +items <- stac("https://earth-search.aws.element84.com/v0") \%>\% + stac_search(collections = "sentinel-s2-l2a-cogs", + bbox = c(-48.206,-14.195,-45.067,-12.272), + datetime = "2018-06-01/2018-06-30", + limit = 500) \%>\% + post_request() + + items \%>\% + items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) +} + +} From 518cde21f751c64902823da7535a48b62d471d6a Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:09:14 +0000 Subject: [PATCH 07/44] add signature function. Related to #36 --- R/signatures.R | 182 +++++++++++++++++++++++++++++++++ R/utils.R | 54 ++++++++++ man/items_sign.Rd | 40 ++++++++ man/sign_bdc.Rd | 23 +++++ man/sign_planetary_computer.Rd | 21 ++++ 5 files changed, 320 insertions(+) create mode 100644 R/signatures.R create mode 100644 man/items_sign.Rd create mode 100644 man/sign_bdc.Rd create mode 100644 man/sign_planetary_computer.Rd diff --git a/R/signatures.R b/R/signatures.R new file mode 100644 index 00000000..f7a6e2d4 --- /dev/null +++ b/R/signatures.R @@ -0,0 +1,182 @@ +#' @title Signature in hrefs provided by the STAC from the Brazil Data Cube +#' project. +#' +#' @description To sign the hrefs with your token you need to store it in an +#' environment variable in `BDC_ACCESS_KEY`or use `acess_token` parameter. +#' +#' @param access_token a `character` with the access token parameter to access +#' Brazil Data Cube assets. +#' +#' @param ... additional parameters can be supplied to the `GET` +#' function of the `httr` package. +#' +#' @return a `function` that signs each item assets. +#' +#' @export +sign_bdc <- function(access_token = NULL, ...) { + + token <- list() + + # parse href to separate each query element, this will be used to dont + # append the same token for an asset + parse <- function(obj_req) { + + token_str <- paste0("?access_token=", obj_req[["token"]]) + obj_req[["token_value"]] <- httr::parse_url(token_str)[["query"]] + + obj_req + } + + new_token <- function(item) { + + token[["default"]] <<- list("token" = access_token) + + if (is.null(access_token)) { + + if (!nzchar(Sys.getenv("BDC_ACCESS_KEY"))) + .error("No token informed in 'BDC_ACCESS_KEY' enviroment variable.") + + token[["default"]] <<- list("token" = Sys.getenv("BDC_ACCESS_KEY")) + } + + token[["default"]] <<- parse(token[["default"]]) + } + + exists_token <- function(item) { + "default" %in% names(token) + } + + get_token_value <- function(item) { + token[["default"]][["token_value"]] + } + + # in the current implementation bdc tokens do not expire + get_token_expiry <- function(item) { + return(NULL) + } + + is_token_expired <- function(item) { + return(FALSE) + } + + sign_asset <- function(asset, token) { + + asset_url <- httr::parse_url(asset[["href"]]) + + # if the href is already sign it will not be modified + asset_url$query <- .modify_list(asset_url$query, token) + + asset[["href"]] <- httr::build_url(asset_url) + asset + } + + sign_item <- function(item) { + + if (!exists_token(item) || is_token_expired(item)) + new_token(item) + + item[["assets"]] <- lapply(item[["assets"]], sign_asset, + get_token_value(item)) + + return(item) + } + + return(sign_item) +} + +#' @title Signature in hrefs provided by the STAC from Microsoft's Planetary +#' Computer. +#' +#' @description To perform the signing of the hrefs a request is sent to +#' Planetary Computer servers and the returned content corresponds to the +#' token that will be used in the href. +#' +#' @param ... additional parameters can be supplied to the `GET` function +#' of the `httr` package. +#' +#' @return a `function` that signs each item assets. +#' +#' @export +sign_planetary_computer <- function(...) { + + default_endpoint <- "https://planetarycomputer.microsoft.com/api/sas/v1/token" + default_max_timeleft <- 300 + + token <- list() + + # parse href to separate each query element, this will be used to dont + # append the same token for an asset + parse <- function(obj_req) { + + # transform to a datetime object + obj_req[["msft:expiry"]] <- strptime(obj_req[["msft:expiry"]], + "%Y-%m-%dT%H:%M:%SZ") + + token_str <- paste0("?", obj_req[["token"]]) + obj_req[["token_value"]] <- httr::parse_url(token_str)[["query"]] + + obj_req + } + + new_token <- function(item) { + + url <- paste0(default_endpoint, "/", item$collection) + + tryCatch({ + res_content <- httr::content(httr::GET(url, ...), encoding = "UTF-8") + }, + error = function(e) { + .error("Request error. %s", e$message) + }) + + if (!"token" %in% names(res_content)) + .error("No collection found with id '%s'", item$collection) + + token[[item$collection]] <<- parse(res_content) + } + + exists_token <- function(item) { + item$collection %in% names(token) + } + + get_token_value <- function(item) { + token[[item$collection]][["token_value"]] + } + + get_token_expiry <- function(item) { + token[[item$collection]][["msft:expiry"]] + } + + is_token_expired <- function(item) { + + difftime_token <- difftime(get_token_expiry(item), + as.POSIXlt(Sys.time(), tz = "UTC"), + units = "secs") + + difftime_token < default_max_timeleft + } + + sign_asset <- function(asset, token) { + + asset_url <- httr::parse_url(asset[["href"]]) + + # if the href is already sign it will not be modified + asset_url$query <- .modify_list(asset_url$query, token) + + asset[["href"]] <- httr::build_url(asset_url) + asset + } + + sign_item <- function(item) { + + if (!exists_token(item) || is_token_expired(item)) + new_token(item) + + item[["assets"]] <- lapply(item[["assets"]], sign_asset, + get_token_value(item)) + + return(item) + } + + return(sign_item) +} diff --git a/R/utils.R b/R/utils.R index b88a1aa4..9737a047 100644 --- a/R/utils.R +++ b/R/utils.R @@ -778,6 +778,60 @@ items_group <- function(items, ..., field = NULL, index = NULL) { }) } +#' @title Utility functions +#' +#' @description A utility function to create signatures in hrefs of each +#' asset in the STAC items. To create the signatures, the provided function +#' must return a function, being a factory function, so the manufactured +#' function will sign the hrefs returning one feature per interaction. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param sign_fn a `function` to assign each assets in STAC items. +#' +#' @return A `STACItemCollection` object with the signed assets according to the +#' supplied parameter function. +#' @examples +#' \dontrun{ +#' +#' # Defining BDC token +#' Sys.setenv("BDC_ACCESS_KEY" = ) +#' +#' # STACItem object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_sign(sign_fn = sign_bdc) +#' +#' } +#' +#' @export +items_sign <- function(items, sign_fn = NULL) { + + if (is.null(sign_fn)) { + return(items) + } + + if (!is.null(items_matched(items))) { + if (items_length(items) != items_matched(items)) + .warning(paste("The number of items in this object does not match the", + "total number of items in the item. If you want to get", + "all items, use `items_fetch()`")) + } + + # assign each item obj + items[["features"]] <- lapply(items[["features"]], function(item){ + + item <- sign_fn(item) + + item + }) + + items +} + #' @title Utility functions #' #' @param bbox a `numeric` vector with only features that have a diff --git a/man/items_sign.Rd b/man/items_sign.Rd new file mode 100644 index 00000000..89832c22 --- /dev/null +++ b/man/items_sign.Rd @@ -0,0 +1,40 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/utils.R +\name{items_sign} +\alias{items_sign} +\title{Utility functions} +\usage{ +items_sign(items, sign_fn = NULL) +} +\arguments{ +\item{items}{a \code{STACItemCollection} object representing +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} + +\item{sign_fn}{a \code{function} to assign each assets in STAC items.} +} +\value{ +A \code{STACItemCollection} object with the signed assets according to the +supplied parameter function. +} +\description{ +A utility function to create signatures in hrefs of each +asset in the STAC items. To create the signatures, the provided function +must return a function, being a factory function, so the manufactured +function will sign the hrefs returning one feature per interaction. +} +\examples{ +\dontrun{ + +# Defining BDC token +Sys.setenv("BDC_ACCESS_KEY" = ) + +# STACItem object +stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_sign(sign_fn = sign_bdc) + +} + +} diff --git a/man/sign_bdc.Rd b/man/sign_bdc.Rd new file mode 100644 index 00000000..06806206 --- /dev/null +++ b/man/sign_bdc.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/signatures.R +\name{sign_bdc} +\alias{sign_bdc} +\title{Signature in hrefs provided by the STAC from the Brazil Data Cube +project.} +\usage{ +sign_bdc(access_token = NULL, ...) +} +\arguments{ +\item{access_token}{a \code{character} with the access token parameter to access +Brazil Data Cube assets.} + +\item{...}{additional parameters can be supplied to the \code{GET} +function of the \code{httr} package.} +} +\value{ +a \code{function} that signs each item assets. +} +\description{ +To sign the hrefs with your token you need to store it in an +environment variable in \code{BDC_ACCESS_KEY}or use \code{acess_token} parameter. +} diff --git a/man/sign_planetary_computer.Rd b/man/sign_planetary_computer.Rd new file mode 100644 index 00000000..99f393ca --- /dev/null +++ b/man/sign_planetary_computer.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/signatures.R +\name{sign_planetary_computer} +\alias{sign_planetary_computer} +\title{Signature in hrefs provided by the STAC from Microsoft's Planetary +Computer.} +\usage{ +sign_planetary_computer(...) +} +\arguments{ +\item{...}{additional parameters can be supplied to the \code{GET} function +of the \code{httr} package.} +} +\value{ +a \code{function} that signs each item assets. +} +\description{ +To perform the signing of the hrefs a request is sent to +Planetary Computer servers and the returned content corresponds to the +token that will be used in the href. +} From fffcd1980f485b648544051eacd54c0a9bba7f79 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:10:02 +0000 Subject: [PATCH 08/44] add utilitary function --- R/utils.R | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/R/utils.R b/R/utils.R index 9737a047..5463827a 100644 --- a/R/utils.R +++ b/R/utils.R @@ -859,3 +859,22 @@ items_sign <- function(items, sign_fn = NULL) { return(paste(c("xmin:", "ymin:", "zmin:", "xmax:", "ymax:", "zmax:"), sprintf("%.5f", bbox), collapse = ", ")) } + +#' @title Utility functions +#' +#' @description Function similar to modifyList of utils, however it is checked +#' if the left parameter is null. +#' +#' @param x a `list` to be compared in left side. +#' +#' @param y a `list` to be compared in right side. +#' +#' @return a `list` with modified values. +#' +#' @noRd +.modify_list <- function(x, y) { + + if (is.null(x)) + x <- list() + utils::modifyList(x, y, keep.null = TRUE) +} From 37fc123bb22ba90c9b723faa22543165b8e27924 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:10:26 +0000 Subject: [PATCH 09/44] update documentation --- NAMESPACE | 6 +++++- R/rstac.R | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/NAMESPACE b/NAMESPACE index cf348d06..d073fdeb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -60,13 +60,17 @@ export(items_bbox) export(items_datetime) export(items_fetch) export(items_fields) +export(items_filter) export(items_group) export(items_length) export(items_matched) export(items_reap) +export(items_sign) export(omit_query_params) export(parse_params) export(post_request) +export(sign_bdc) +export(sign_planetary_computer) export(stac) export(stac_search) export(stac_version) @@ -79,7 +83,7 @@ importFrom(httr,content) importFrom(httr,http_type) importFrom(httr,status_code) importFrom(httr,write_disk) -importFrom(jsonlite,validate) +importFrom(jsonlite,fromJSON) importFrom(lifecycle,deprecated) importFrom(magrittr,"%>%") importFrom(utils,URLdecode) diff --git a/R/rstac.R b/R/rstac.R index 204707ca..09b167de 100644 --- a/R/rstac.R +++ b/R/rstac.R @@ -57,6 +57,6 @@ NULL #' http_type #' @importFrom crayon bold #' @importFrom utils modifyList URLdecode -#' @importFrom jsonlite validate +#' @importFrom jsonlite fromJSON #' @importFrom lifecycle deprecated NULL From 67695240b730e3460bd7608879aa83e5eccb2366 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:33:18 +0000 Subject: [PATCH 10/44] fix bug in asset_download parameter --- R/assets_download.R | 6 +++--- R/utils.R | 2 +- man/assets_download.Rd | 2 +- man/assets_list.Rd | 1 - 4 files changed, 5 insertions(+), 6 deletions(-) diff --git a/R/assets_download.R b/R/assets_download.R index 0e521f3b..9e96c544 100644 --- a/R/assets_download.R +++ b/R/assets_download.R @@ -44,7 +44,7 @@ #' datetime = "2019-06-01/2019-08-01") %>% #' stac_search() %>% #' get_request() %>% -#' assets_download(assets_name = "thumbnail", output_dir = ".", +#' assets_download(asset_names = "thumbnail", output_dir = ".", #' overwrite = FALSE) #' } #' @@ -124,7 +124,7 @@ assets_download <- function(items, utils::setTxtProgressBar(pb, i) items$features[[i]] <- .item_download(stac_item = items$features[[i]], - assets_name = assets_name, + asset_names = asset_names, output_dir = output_dir, overwrite = overwrite, fn = fn, ...) @@ -163,7 +163,7 @@ assets_download <- function(items, .item_download <- function(stac_item, asset_names, output_dir, overwrite, ..., fn) { - assets <- .select_assets(stac_item[["assets"]], assets_name) + assets <- .select_assets(stac_item[["assets"]], asset_names) stac_item[["assets"]] <- lapply(assets, function(asset){ diff --git a/R/utils.R b/R/utils.R index 5463827a..928b1512 100644 --- a/R/utils.R +++ b/R/utils.R @@ -480,7 +480,7 @@ stac_version <- function(x, ...) { #' #' @export assets_list <- function(items, asset_names = NULL, - sort = TRUE, gdal_vsi_resolution = TRUE, ..., + sort = TRUE, gdal_vsi_resolution = TRUE, assets_names = deprecated()) { diff --git a/man/assets_download.Rd b/man/assets_download.Rd index ac84d668..1f01090a 100644 --- a/man/assets_download.Rd +++ b/man/assets_download.Rd @@ -62,7 +62,7 @@ stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% datetime = "2019-06-01/2019-08-01") \%>\% stac_search() \%>\% get_request() \%>\% - assets_download(assets_name = "thumbnail", output_dir = ".", + assets_download(asset_names = "thumbnail", output_dir = ".", overwrite = FALSE) } diff --git a/man/assets_list.Rd b/man/assets_list.Rd index b1abf03a..bd6f8052 100644 --- a/man/assets_list.Rd +++ b/man/assets_list.Rd @@ -9,7 +9,6 @@ assets_list( asset_names = NULL, sort = TRUE, gdal_vsi_resolution = TRUE, - ..., assets_names = deprecated() ) } From d5f65800373467891b26e590884c20e1742203b9 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 16 Sep 2021 05:33:30 +0000 Subject: [PATCH 11/44] update tests --- tests/testthat/test-assets_download.R | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-assets_download.R b/tests/testthat/test-assets_download.R index 1f347a79..17470911 100644 --- a/tests/testthat/test-assets_download.R +++ b/tests/testthat/test-assets_download.R @@ -14,13 +14,13 @@ testthat::test_that("assets download", { bbox = c(-47.02148, -12.98314, -42.53906, -17.35063), limit = 0) %>% get_request() %>% - assets_download(assets_name = c("blue", "evi"))) + assets_download(asset_names = c("blue", "evi"))) # error - given another object testthat::expect_error( stac("http://brazildatacube.dpi.inpe.br/stac/") %>% get_request(.) %>% - assets_download(., assets_name = c("blue", "evi"))) + assets_download(., asset_names = c("blue", "evi"))) # error - wrong path testthat::expect_error( @@ -30,7 +30,7 @@ testthat::test_that("assets download", { datetime = "2019-09-01/2019-11-01", limit = 1) %>% get_request() %>% - assets_download(assets_name = c("thumbnail"), + assets_download(asset_names = c("thumbnail"), output_dir = "./non-existing-dir/")) # verify output object @@ -42,7 +42,7 @@ testthat::test_that("assets download", { datetime = "2019-09-01/2019-11-01", limit = 1) %>% get_request() %>% - assets_download(assets_name = c("thumbnail"), output_dir = ".") + assets_download(asset_names = c("thumbnail"), output_dir = ".") subclass(x) }, expected = "STACItemCollection") From 7389d9c847ac10dd3c6860e100c902a5fa02b9af Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:03:38 +0000 Subject: [PATCH 12/44] add assets name and not fetched info in print --- R/print.R | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/R/print.R b/R/print.R index 70c7e22a..5090c07f 100644 --- a/R/print.R +++ b/R/print.R @@ -163,8 +163,15 @@ print.STACItemCollection <- function(x, n = 10, ..., tail = FALSE) { matched <- suppressWarnings(items_matched(x)) if (!is.null(matched)) cat("-", crayon::bold("matched feature(s):"), matched, fill = TRUE) - cat("-", crayon::bold("features"), - sprintf("(%s item(s)):", length(x$features)), fill = TRUE) + + if (!is.null(matched)) + cat("-", crayon::bold("features"), + sprintf("(%s item(s) / %s not fetched):", + length(x$features), matched - length(x$features)), fill = TRUE) + else + cat("-", crayon::bold("features"), + sprintf("(%s item(s)):", length(x$features)), fill = TRUE) + if (missing(n) && length(x$features) < 2 * n) n <- length(x$features) n <- min(n, length(x$features)) @@ -180,7 +187,11 @@ print.STACItemCollection <- function(x, n = 10, ..., tail = FALSE) { if (n != length(x$features)) cat(sprintf(" - ... with %s more feature(s).", length(x$features) - n), fill = TRUE) - cat("-", crayon::bold("field(s):"), + + cat("-", crayon::bold("assets:"), + paste0(items_assets(x, simplify = TRUE), collapse = ", "), + fill = TRUE) + cat("-", crayon::bold("other field(s):"), paste0(names(x), collapse = ", "), fill = TRUE) invisible(x) } @@ -198,8 +209,9 @@ print.STACItem <- function(x, ...) { cat("-", crayon::bold("bbox:"), .format_bbox(x$bbox), fill = TRUE) cat("-", crayon::bold("datetime:"), x$properties$datetime, fill = TRUE) cat("-", crayon::bold("assets:"), - paste0("'", names(x$assets), "'", collapse = ", "), fill = TRUE) - cat("-", crayon::bold("field(s):"), paste0(names(x), collapse = ", "), + paste0(items_assets(x, simplify = TRUE), collapse = ", "), + fill = TRUE) + cat("-", crayon::bold("other field(s):"), paste0(names(x), collapse = ", "), fill = TRUE) invisible(x) } From 3e894d4c75c80b9f6307070e2a495a3c168a594c Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:04:35 +0000 Subject: [PATCH 13/44] add items function in documents.R --- R/documents.R | 644 +++++++++++++++++++-- man/{assets_list.Rd => assets_function.Rd} | 18 +- man/figures/lifecycle-archived.svg | 1 + man/figures/lifecycle-defunct.svg | 1 + man/figures/lifecycle-deprecated.svg | 1 + man/figures/lifecycle-experimental.svg | 1 + man/figures/lifecycle-maturing.svg | 1 + man/figures/lifecycle-questioning.svg | 1 + man/figures/lifecycle-stable.svg | 1 + man/figures/lifecycle-superseded.svg | 1 + man/items_bands.Rd | 27 + man/items_filter.Rd | 2 +- man/items_functions.Rd | 82 ++- man/items_group.Rd | 2 +- man/items_reap.Rd | 2 +- man/items_sign.Rd | 2 +- man/{items_fields.Rd => items_utils.Rd} | 11 +- 17 files changed, 728 insertions(+), 70 deletions(-) rename man/{assets_list.Rd => assets_function.Rd} (82%) create mode 100644 man/figures/lifecycle-archived.svg create mode 100644 man/figures/lifecycle-defunct.svg create mode 100644 man/figures/lifecycle-deprecated.svg create mode 100644 man/figures/lifecycle-experimental.svg create mode 100644 man/figures/lifecycle-maturing.svg create mode 100644 man/figures/lifecycle-questioning.svg create mode 100644 man/figures/lifecycle-stable.svg create mode 100644 man/figures/lifecycle-superseded.svg create mode 100644 man/items_bands.Rd rename man/{items_fields.Rd => items_utils.Rd} (78%) diff --git a/R/documents.R b/R/documents.R index 57976fcd..43256f47 100644 --- a/R/documents.R +++ b/R/documents.R @@ -77,8 +77,6 @@ stac_version.RSTACDocument <- function(x, ...) { x$stac_version } -####STACCollectionList#### - #' @export stac_version.STACCollectionList <- function(x, ...) { @@ -89,22 +87,29 @@ stac_version.STACCollectionList <- function(x, ...) { return(x$collections[[1]]$stac_version) } +####Items function#### + #' @title STACItemCollection functions #' #' @description #' The `items_length()` function shows how many items there are in #' the `STACItemCollection` object. +#' #' The `items_matched()` function shows how many items matched the #' search criteria. It supports `search:metadata` (v0.8.0), #' `context` (v0.9.0), and `numberMatched` (OGC WFS3 core spec). +#' #' The `items_fetch()` function request all STAC Items through #' pagination. +#' #' The `items_datetime()` function retrieves a the `datetime` #' field in `properties` from `STACItemCollection` and #' `STACItem` objects. +#' #' The `items_bbox()` function retrieves a the `bbox` #' field of a `STACItemCollection` or an `STACItem` object. -#' The `get_assets_name()` function returns the assets name from +#' +#' The `item_assets()` function returns the assets name from #' `STACItemCollection` and `STACItem` objects. #' #' @param items a `STACItemCollection` object. @@ -113,8 +118,24 @@ stac_version.STACCollectionList <- function(x, ...) { #' the initial node of the list. For example, if the information is at position #' `items$meta$found` of the object, it must be passed as the following #' parameter `c("meta", "found")`. +#' @param simplify a `logical` should return only the assets name of the +#' first item? if not a `list` with all assets name will be returned. Default +#' is `FALSE`. +#' @param ... additional arguments. See details. +#' @param progress a `logical` indicating if a progress bar must be +#' shown or not. Defaults to `TRUE`. +#' +#' @details +#' For `items_fetch` ellipsis is used to pass additional `httr` options to +#' [GET][httr::GET] or [POST][httr::POST] methods, such as +#' [add_headers][httr::add_headers] or [set_cookies][httr::set_cookies]. +#' +#' For `items_filter` function is used to pass logical expressions. #' #' @return +#' The `items_assets()` if simplify is `TRUE`, returns a `character` value with +#' all assets names of the first item. Otherwise, returns a `list` with assets +#' name for each item. #' The `items_length()` returns an `integer` value. #' The `items_matched()` returns an `integer` value. #' If STAC web server does not support this extension, returns `NULL`. @@ -129,13 +150,14 @@ stac_version.STACCollectionList <- function(x, ...) { #' #' x <- stac("http://brazildatacube.dpi.inpe.br/stac") %>% #' stac_search(collections = "CB4_64_16D_STK-1") %>% -#' stac_search() %>% +#' stac_search(limit = 500) %>% #' get_request() #' #' x %>% items_length() #' x %>% items_matched() #' x %>% items_datetime() #' x %>% items_bbox() +#' x %>% items_fetch() #' } #' #' @name items_functions @@ -143,8 +165,21 @@ stac_version.STACCollectionList <- function(x, ...) { #' @export items_length <- function(items) { - # Check object class - check_subclass(items, "STACItemCollection") + UseMethod("items_length", items) +} + +#' @rdname items_functions +#' +#' @export +items_length.STACItem <- function(items) { + + return(1) +} + +#' @rdname items_functions +#' +#' @export +items_length.STACItemCollection <- function(items) { return(length(items$features)) } @@ -152,10 +187,23 @@ items_length <- function(items) { #' @rdname items_functions #' #' @export -items_matched <- function(items, matched_field = NULL) { +items_matched <- function(items, ...) { + + UseMethod("items_matched", items) +} - # Check object class - check_subclass(items, "STACItemCollection") +#' @rdname items_functions +#' +#' @export +items_matched.STACItem <- function(items, ...) { + + return(1) +} + +#' @rdname items_functions +#' +#' @export +items_matched.STACItemCollection <- function(items, ..., matched_field = NULL) { matched <- NULL @@ -190,31 +238,28 @@ items_matched <- function(items, matched_field = NULL) { return(matched) } -#' @param progress a `logical` indicating if a progress bar must be -#' shown or not. Defaults to `TRUE`. -#' -#' @param ... config parameters to be passed to [GET][httr::GET] or -#' [POST][httr::POST] methods, such as [add_headers][httr::add_headers] or -#' [set_cookies][httr::set_cookies]. -#' -#' @examples -#' \dontrun{ -#' x <- -#' stac("http://brazildatacube.dpi.inpe.br/stac") %>% -#' stac_search(collections = "CB4_64_16D_STK-1") %>% -#' stac_search(limit = 500) %>% -#' get_request() -#' -#' x %>% items_fetch() -#' } +#' @rdname items_functions #' +#' @export +items_fetch <- function(items, ...) { + + UseMethod("items_fetch", items) +} + #' @rdname items_functions #' #' @export -items_fetch <- function(items, ..., progress = TRUE, matched_field = NULL) { +items_fetch.STACItem <- function(items, ...) { + + return(items) +} - # Check object class - check_subclass(items, "STACItemCollection") +#' @rdname items_functions +#' +#' @export +items_fetch.STACItemCollection <- function(items, ..., + progress = TRUE, + matched_field = NULL) { matched <- items_matched(items, matched_field) @@ -344,11 +389,21 @@ items_fetch <- function(items, ..., progress = TRUE, matched_field = NULL) { #' @export items_datetime <- function(items) { - # Check object class - check_subclass(items, c("STACItemCollection", "STACItem")) + UseMethod("items_datetime", items) +} - if (subclass(items) == "STACItem") - return(items$properties[["datetime"]]) +#' @rdname items_functions +#' +#' @export +items_datetime.STACItem <- function(items) { + + return(items$properties[["datetime"]]) +} + +#' @rdname items_functions +#' +#' @export +items_datetime.STACItemCollection <- function(items) { lapply(items$features, `[[`, c("properties", "datetime")) } @@ -358,11 +413,21 @@ items_datetime <- function(items) { #' @export items_bbox <- function(items) { - # Check object class - check_subclass(items, c("STACItemCollection", "STACItem")) + UseMethod("items_bbox", items) +} + +#' @rdname items_functions +#' +#' @export +items_bbox.STACItem <- function(items) { - if (subclass(items) == "STACItem") - return(items[["bbox"]]) + return(items[["bbox"]]) +} + +#' @rdname items_functions +#' +#' @export +items_bbox.STACItemCollection <- function(items) { lapply(items$features, `[[`, c("bbox")) } @@ -370,13 +435,508 @@ items_bbox <- function(items) { #' @rdname items_functions #' #' @export -items_bands <- function(items) { +items_assets <- function(items, ...) { - # Check object class - check_subclass(items, c("STACItemCollection", "STACItem")) + UseMethod("items_assets", items) +} - if (subclass(items) == "STACItem") - return(names(items[["assets"]])) +#' @rdname items_functions +#' +#' @export +items_assets.STACItem <- function(items, ...) { + + return(items_fields(items, "assets")) +} + +#' @rdname items_functions +#' +#' @export +items_assets.STACItemCollection <- function(items, ..., simplify = FALSE) { + if (simplify) + return(items_fields(items, "assets")) lapply(lapply(items$features, `[[`, c("assets")), names) } + + +#' @title Utility functions +#' +#' @description This function filters for the attributes contained in the STAC +#' properties. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param ... expressions used to filter items of a `STACItemCollection` +#' object. +#' @param fn a `function` that will be used to filter the attributes +#' listed in the properties. +#' +#' @return a `STACItemCollection` object with the filtered properties. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_filter(`eo:cloud_cover` < 10) +#' +#' # Example with AWS STAC +#' items <- stac("https://earth-search.aws.element84.com/v0") %>% +#' stac_search(collections = "sentinel-s2-l2a-cogs", +#' bbox = c(-48.206,-14.195,-45.067,-12.272), +#' datetime = "2018-06-01/2018-06-30", +#' limit = 500) %>% +#' post_request() +#' +#' items %>% +#' items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) +#' } +#' +#' @export +items_filter <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + sel <- vapply(items$features, function(f) { + eval(dots[[i]], envir = f$properties) + }, logical(1)) + + items$features <- items$features[sel] + } + } + + if (!is.null(fn)) { + + sel <- vapply(items$features, function(f) { + fn(f$properties) + }, logical(1)) + + items$features <- items$features[sel] + } + + items +} + +#' @title Utility functions +#' +#' @description This function returns the values of a field of the +#' `STACItemCollections` object. If the values of the specified field are +#' not atomic the return will be in list form, if they are, it will be returned +#' in vector form. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param ... a named way to provide fields names to get the +#' subfields values from the `RSTACDocument` objects. +#' +#' @param field a `character` with the names of the field to +#' get the subfields values from the `RSTACDocument` objects. +#' +#' @return a `vector` if the supplied field is atomic, or a list if not. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% items_reap(field = c("properties", "datetime")) +#' } +#' +#' @export +items_reap <- function(items, ..., field = NULL) { + + # checks if the object is STACItemCollections + if (items_length(items) == 0) return(NULL) + + dots <- substitute(list(...))[-1] + if (!is.character(dots)) dots <- as.character(dots) + + if (length(dots) > 0 && length(field) > 0) + .error("Only one of the parameters '...' or 'field' must be supplied.") + + if (length(field) == 0 && length(dots) == 0) + return(items$features) + + values <- lapply(items$features, `[[`, c(dots, field)) + + if (all(vapply(values, is.null, logical(1)))) + .error("The provided field does not exist.") + + if (all(vapply(values, is.atomic, logical(1)))) + return(unlist(values)) + values +} + +#' @title Utility functions +#' +#' @description This function returns the subfields of the `feature` +#' field of a `STACItemCollection` object. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param ... a named way to provide field names to get the subfields values +#' from the `RSTACDocument` objects. +#' +#' @param field a `character` with the names of the field to get the +#' subfields values from the `RSTACDocument` objects. +#' +#' @return A `character` with the subfields of the `feature` field. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 10, +#' datetime = "2017-08-01/2018-03-01") %>% +#' get_request() +#' +#' stac_item %>% items_fields(field = c("properties")) +#' } +#' +#' @name items_utils +#' +#' @export +items_fields <- function(items, ..., field = NULL) { + UseMethod("items_fields", items) +} + +#' @rdname items_utils +#' +#' @export +items_fields.STACItemCollection <- function(items, ..., field = NULL) { + + dots <- substitute(list(...))[-1] + if (!is.character(dots)) dots <- as.character(dots) + + if (length(field) > 0 && length(dots) > 0) + .error("Only one of the parameters '...' or 'field' must be supplied.") + + if (length(field) == 0 && length(dots) == 0) + return(names(items$features[[1]])) + names(items$features[[1]][[c(dots, field)]]) +} + +#' @rdname items_utils +#' +#' @export +items_fields.STACItem <- function(items, ..., field = NULL) { + + dots <- substitute(list(...))[-1] + if (!is.character(dots)) dots <- as.character(dots) + + if (length(field) > 0 && length(dots) > 0) + .error("Only one of the parameters '...' or 'field' must be supplied.") + + if (length(field) == 0 && length(dots) == 0) + return(names(items)) + names(items[[c(dots, field)]]) +} + +#' @title Utility functions +#' +#' @description This function groups the items contained within the +#' `STACItemCollection` object according to some specified fields. Each +#' index in the returned list contains items belonging to the same group. +#' +#' @param items a `STACItemCollection` object representing the result of +#' `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param ... a named way to provide field names to get the subfields values +#' from the `RSTACDocument` objects. +#' +#' @param field a `character` with the names of the field to get the +#' subfields values from the `RSTACDocument` objects. +#' +#' @param index a `character` with the indexes to be grouped. It can be +#' used with the function [items_reap]. +#' +#' @return A `list` in which each index corresponds to a group with its +#' corresponding `STACItemCollection` objects. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% items_group(., field = c("properties", "bdc:tiles")) +#' } +#' +#' @export +items_group <- function(items, ..., field = NULL, index = NULL) { + + # checks if the object is STACItemCollections + if (items_length(items) == 0) return(list(items)) + + dots <- substitute(list(...))[-1] + if (!is.character(dots)) dots <- as.character(dots) + + if (length(index) == 0 && length(field) == 0 && length(dots) == 0) + .error(paste("Either parameters 'index', 'field' or '...' parameters must", + "be supplied.")) + + if (length(index) > 0 && (length(field) > 0 || length(dots) > 0)) + .error(paste("Only one of the parameters '...','index' or 'field' should", + "be supplied.")) + + if (is.null(index)) { + index <- items_reap(items, ..., field = field) + + if (!is.atomic(index)) + .error("The field must be atomic vector.") + } else { + + if (items_matched(items) > items_length(items)) + .warning(paste("The number of matched items is greater than the number", + "of items length on your object. Considere to use", + "the 'items_fetch()' function before this operation.")) + } + + if (items_length(items) != length(index)) + .error(paste("The length of the field provided for grouping must contain", + "the same size as the length of the items.")) + + features <- unname(tapply(X = items$features, + INDEX = index, + FUN = c, simplify = FALSE)) + + lapply(features, function(x){ + items$features <- x + + items + }) +} + +#' @title Utility functions +#' +#' @description A utility function to create signatures in hrefs of each +#' asset in the STAC items. To create the signatures, the provided function +#' must return a function, being a factory function, so the manufactured +#' function will sign the hrefs returning one feature per interaction. +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param sign_fn a `function` to assign each assets in STAC items. +#' +#' @return A `STACItemCollection` object with the signed assets according to the +#' supplied parameter function. +#' @examples +#' \dontrun{ +#' +#' # Defining BDC token +#' Sys.setenv("BDC_ACCESS_KEY" = ) +#' +#' # STACItem object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_sign(sign_fn = sign_bdc) +#' +#' } +#' +#' @export +items_sign <- function(items, sign_fn = NULL) { + + if (is.null(sign_fn)) { + return(items) + } + + if (!is.null(items_matched(items))) { + if (items_length(items) != items_matched(items)) + .warning(paste("The number of items in this object does not match the", + "total number of items in the item. If you want to get", + "all items, use `items_fetch()`")) + } + + # assign each item obj + items[["features"]] <- lapply(items[["features"]], function(item){ + + item <- sign_fn(item) + + item + }) + + items +} + +####Assets function#### + +#' @title Assets functions +#' +#' @description This function returns the `date`, `band` and +#' `URL` fields for each assets of an `STACItemCollection` object. +#' For the URL you can add the GDAL library drivers for the following schemes: +#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param assets_names `r lifecycle::badge('deprecated')` +#' use `asset_names` parameter instead. +#' +#' @param asset_names a `character` with the assets names to be +#' filtered. If `NULL` (default) all assets will be returned.. +#' +#' @param sort a `logical` if true the dates will be sorted +#' in increasing order. By default, the dates are sorted. +#' +#' @param gdal_vsi_resolution a `logical` if true, gdal drivers are +#' included in the URL of each asset. The following schemes are supported: +#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). +#' +#' @param ... additional arguments. See details. +#' +#' @param fn a `function` that will be used to filter the attributes +#' listed in the properties. +#' +#' @return a `list` with the attributes of date, bands and paths. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% assets_list(assets_names = c("EVI", "NDVI")) +#' } +#' +#' @name assets_function +NULL + +#' @rdname assets_function +#' @export +assets_list <- function(items, asset_names = NULL, + sort = TRUE, gdal_vsi_resolution = TRUE, + assets_names = deprecated()) { + + + if (lifecycle::is_present(assets_names)) { + + # Signal the deprecation to the user + lifecycle::deprecate_soft("0.9.1-5", + "rstac::assets_download(assets_names = )", + "rstac::assets_download(asset_names = )") + + # Deal with the deprecated argument for compatibility + asset_names <- assets_names + } + + if (is.null(asset_names)) + asset_names <- items_fields(items, "assets") + + timeline <- items_reap(items, field = c("properties", "datetime")) + index <- seq_along(timeline) + if (sort) index <- order(timeline) + + timeline <- timeline[index] + assets <- list(date = rep(timeline, length(unique(asset_names)))) + + for (b in asset_names) { + + href <- items_reap(items, field = c("assets", b, "href"))[index] + + if (gdal_vsi_resolution) { + + # for http or https schema + paste_index <- grepl("^http|[s]://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsicurl", href[paste_index], sep = "/") + + # for S3 schema + paste_index <- grepl("^s3://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsis3", gsub("^s3://(.*)$", "\\1", + href[paste_index]), sep = "/") + # for gs schema + paste_index <- grepl("^gs://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsigs", gsub("^gs://(.*)$", "\\1", + href[paste_index]), sep = "/") + } + assets$band <- c(rep(b, length(href)), assets$band) + assets$path <- c(href, assets$path) + } + assets +} + +#' @rdname assets_function +#' +#' @export +assets_select <- function(items, asset_names) { + + if (!all(asset_names %in% items_assets(items, simplify = TRUE))) + .error("Invalid 'asset_names' parameter.") + + items$features <- lapply(items$features, function(item) { + item$assets <- item$assets[asset_names] + + item + }) + + items +} + +#' @rdname assets_function +#' +#' @export +assets_filter <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + items$features <- lapply(items$features, function(item) { + + sel <- vapply(item$assets, function(asset) { + eval(dots[[i]], envir = asset) + }, logical(1)) + + item$assets <- item$assets[sel] + + item + }) + } + } + + if (!is.null(fn)) { + + items$features <- lapply(items$features, function(item) { + + sel <- vapply(item$assets, function(asset) { fn(asset) }, logical(1)) + + item$assets <- item$assets[sel] + item + }) + } + + items +} diff --git a/man/assets_list.Rd b/man/assets_function.Rd similarity index 82% rename from man/assets_list.Rd rename to man/assets_function.Rd index bd6f8052..e4055178 100644 --- a/man/assets_list.Rd +++ b/man/assets_function.Rd @@ -1,8 +1,11 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{assets_list} +% Please edit documentation in R/documents.R +\name{assets_function} +\alias{assets_function} \alias{assets_list} -\title{Utility functions} +\alias{assets_select} +\alias{assets_filter} +\title{Assets functions} \usage{ assets_list( items, @@ -11,6 +14,10 @@ assets_list( gdal_vsi_resolution = TRUE, assets_names = deprecated() ) + +assets_select(items, asset_names) + +assets_filter(items, ..., fn = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing @@ -28,6 +35,11 @@ HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage).} \item{assets_names}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} use \code{asset_names} parameter instead.} + +\item{...}{additional arguments. See details.} + +\item{fn}{a \code{function} that will be used to filter the attributes +listed in the properties.} } \value{ a \code{list} with the attributes of date, bands and paths. diff --git a/man/figures/lifecycle-archived.svg b/man/figures/lifecycle-archived.svg new file mode 100644 index 00000000..48f72a6f --- /dev/null +++ b/man/figures/lifecycle-archived.svg @@ -0,0 +1 @@ + lifecyclelifecyclearchivedarchived \ No newline at end of file diff --git a/man/figures/lifecycle-defunct.svg b/man/figures/lifecycle-defunct.svg new file mode 100644 index 00000000..01452e5f --- /dev/null +++ b/man/figures/lifecycle-defunct.svg @@ -0,0 +1 @@ +lifecyclelifecycledefunctdefunct \ No newline at end of file diff --git a/man/figures/lifecycle-deprecated.svg b/man/figures/lifecycle-deprecated.svg new file mode 100644 index 00000000..4baaee01 --- /dev/null +++ b/man/figures/lifecycle-deprecated.svg @@ -0,0 +1 @@ +lifecyclelifecycledeprecateddeprecated \ No newline at end of file diff --git a/man/figures/lifecycle-experimental.svg b/man/figures/lifecycle-experimental.svg new file mode 100644 index 00000000..d1d060e9 --- /dev/null +++ b/man/figures/lifecycle-experimental.svg @@ -0,0 +1 @@ +lifecyclelifecycleexperimentalexperimental \ No newline at end of file diff --git a/man/figures/lifecycle-maturing.svg b/man/figures/lifecycle-maturing.svg new file mode 100644 index 00000000..df713101 --- /dev/null +++ b/man/figures/lifecycle-maturing.svg @@ -0,0 +1 @@ +lifecyclelifecyclematuringmaturing \ No newline at end of file diff --git a/man/figures/lifecycle-questioning.svg b/man/figures/lifecycle-questioning.svg new file mode 100644 index 00000000..08ee0c90 --- /dev/null +++ b/man/figures/lifecycle-questioning.svg @@ -0,0 +1 @@ +lifecyclelifecyclequestioningquestioning \ No newline at end of file diff --git a/man/figures/lifecycle-stable.svg b/man/figures/lifecycle-stable.svg new file mode 100644 index 00000000..e015dc81 --- /dev/null +++ b/man/figures/lifecycle-stable.svg @@ -0,0 +1 @@ +lifecyclelifecyclestablestable \ No newline at end of file diff --git a/man/figures/lifecycle-superseded.svg b/man/figures/lifecycle-superseded.svg new file mode 100644 index 00000000..75f24f55 --- /dev/null +++ b/man/figures/lifecycle-superseded.svg @@ -0,0 +1 @@ + lifecyclelifecyclesupersededsuperseded \ No newline at end of file diff --git a/man/items_bands.Rd b/man/items_bands.Rd new file mode 100644 index 00000000..11dd8618 --- /dev/null +++ b/man/items_bands.Rd @@ -0,0 +1,27 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/deprec-functions.R +\name{items_bands} +\alias{items_bands} +\title{STACItemCollection function} +\usage{ +items_bands(items) +} +\arguments{ +\item{items}{a \code{STACItemCollection} or \code{STACItem} object.} +} +\description{ +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Use \code{\link{items_assets}()} function +instead. +} +\examples{ +\dontrun{ + +x <- stac("http://brazildatacube.dpi.inpe.br/stac") \%>\% + stac_search(collections = "CB4_64_16D_STK-1") \%>\% + stac_search() \%>\% + get_request() + +x \%>\% items_assets() +} + +} diff --git a/man/items_filter.Rd b/man/items_filter.Rd index 9a7c3ee5..2775a820 100644 --- a/man/items_filter.Rd +++ b/man/items_filter.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R +% Please edit documentation in R/documents.R \name{items_filter} \alias{items_filter} \title{Utility functions} diff --git a/man/items_functions.Rd b/man/items_functions.Rd index 08ee5c0c..721f9e93 100644 --- a/man/items_functions.Rd +++ b/man/items_functions.Rd @@ -3,42 +3,83 @@ \name{items_functions} \alias{items_functions} \alias{items_length} +\alias{items_length.STACItem} +\alias{items_length.STACItemCollection} \alias{items_matched} +\alias{items_matched.STACItem} +\alias{items_matched.STACItemCollection} \alias{items_fetch} +\alias{items_fetch.STACItem} +\alias{items_fetch.STACItemCollection} \alias{items_datetime} +\alias{items_datetime.STACItem} +\alias{items_datetime.STACItemCollection} \alias{items_bbox} -\alias{items_bands} +\alias{items_bbox.STACItem} +\alias{items_bbox.STACItemCollection} +\alias{items_assets} +\alias{items_assets.STACItem} +\alias{items_assets.STACItemCollection} \title{STACItemCollection functions} \usage{ items_length(items) -items_matched(items, matched_field = NULL) +\method{items_length}{STACItem}(items) -items_fetch(items, ..., progress = TRUE, matched_field = NULL) +\method{items_length}{STACItemCollection}(items) + +items_matched(items, ...) + +\method{items_matched}{STACItem}(items, ...) + +\method{items_matched}{STACItemCollection}(items, ..., matched_field = NULL) + +items_fetch(items, ...) + +\method{items_fetch}{STACItem}(items, ...) + +\method{items_fetch}{STACItemCollection}(items, ..., progress = TRUE, matched_field = NULL) items_datetime(items) +\method{items_datetime}{STACItem}(items) + +\method{items_datetime}{STACItemCollection}(items) + items_bbox(items) -items_bands(items) +\method{items_bbox}{STACItem}(items) + +\method{items_bbox}{STACItemCollection}(items) + +items_assets(items, ...) + +\method{items_assets}{STACItem}(items, ...) + +\method{items_assets}{STACItemCollection}(items, ..., simplify = FALSE) } \arguments{ \item{items}{a \code{STACItemCollection} object.} +\item{...}{additional arguments. See details.} + \item{matched_field}{a \code{character} vector with the path where the number of items returned in the named list is located starting from the initial node of the list. For example, if the information is at position \code{items$meta$found} of the object, it must be passed as the following parameter \code{c("meta", "found")}.} -\item{...}{config parameters to be passed to \link[httr:GET]{GET} or -\link[httr:POST]{POST} methods, such as \link[httr:add_headers]{add_headers} or -\link[httr:set_cookies]{set_cookies}.} - \item{progress}{a \code{logical} indicating if a progress bar must be shown or not. Defaults to \code{TRUE}.} + +\item{simplify}{a \code{logical} should return only the assets name of the +first item? if not a \code{list} with all assets name will be returned. Default +is \code{FALSE}.} } \value{ +The \code{items_assets()} if simplify is \code{TRUE}, returns a \code{character} value with +all assets names of the first item. Otherwise, returns a \code{list} with assets +name for each item. The \code{items_length()} returns an \code{integer} value. The \code{items_matched()} returns an \code{integer} value. If STAC web server does not support this extension, returns \code{NULL}. @@ -51,40 +92,43 @@ bounding boxes. \description{ The \code{items_length()} function shows how many items there are in the \code{STACItemCollection} object. + The \code{items_matched()} function shows how many items matched the search criteria. It supports \code{search:metadata} (v0.8.0), \code{context} (v0.9.0), and \code{numberMatched} (OGC WFS3 core spec). + The \code{items_fetch()} function request all STAC Items through pagination. + The \code{items_datetime()} function retrieves a the \code{datetime} field in \code{properties} from \code{STACItemCollection} and \code{STACItem} objects. + The \code{items_bbox()} function retrieves a the \code{bbox} field of a \code{STACItemCollection} or an \code{STACItem} object. -The \code{get_assets_name()} function returns the assets name from + +The \code{item_assets()} function returns the assets name from \code{STACItemCollection} and \code{STACItem} objects. } +\details{ +For \code{items_fetch} ellipsis is used to pass additional \code{httr} options to +\link[httr:GET]{GET} or \link[httr:POST]{POST} methods, such as +\link[httr:add_headers]{add_headers} or \link[httr:set_cookies]{set_cookies}. + +For \code{items_filter} function is used to pass logical expressions. +} \examples{ \dontrun{ x <- stac("http://brazildatacube.dpi.inpe.br/stac") \%>\% stac_search(collections = "CB4_64_16D_STK-1") \%>\% - stac_search() \%>\% + stac_search(limit = 500) \%>\% get_request() x \%>\% items_length() x \%>\% items_matched() x \%>\% items_datetime() x \%>\% items_bbox() -} - -\dontrun{ -x <- - stac("http://brazildatacube.dpi.inpe.br/stac") \%>\% - stac_search(collections = "CB4_64_16D_STK-1") \%>\% - stac_search(limit = 500) \%>\% - get_request() - x \%>\% items_fetch() } diff --git a/man/items_group.Rd b/man/items_group.Rd index c08b65e9..eb9d6c2d 100644 --- a/man/items_group.Rd +++ b/man/items_group.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R +% Please edit documentation in R/documents.R \name{items_group} \alias{items_group} \title{Utility functions} diff --git a/man/items_reap.Rd b/man/items_reap.Rd index e7182159..a993515d 100644 --- a/man/items_reap.Rd +++ b/man/items_reap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R +% Please edit documentation in R/documents.R \name{items_reap} \alias{items_reap} \title{Utility functions} diff --git a/man/items_sign.Rd b/man/items_sign.Rd index 89832c22..7edcb69a 100644 --- a/man/items_sign.Rd +++ b/man/items_sign.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R +% Please edit documentation in R/documents.R \name{items_sign} \alias{items_sign} \title{Utility functions} diff --git a/man/items_fields.Rd b/man/items_utils.Rd similarity index 78% rename from man/items_fields.Rd rename to man/items_utils.Rd index 08d3635e..1e83e2ea 100644 --- a/man/items_fields.Rd +++ b/man/items_utils.Rd @@ -1,10 +1,17 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/utils.R -\name{items_fields} +% Please edit documentation in R/documents.R +\name{items_utils} +\alias{items_utils} \alias{items_fields} +\alias{items_fields.STACItemCollection} +\alias{items_fields.STACItem} \title{Utility functions} \usage{ items_fields(items, ..., field = NULL) + +\method{items_fields}{STACItemCollection}(items, ..., field = NULL) + +\method{items_fields}{STACItem}(items, ..., field = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing From d8b884bb0c535e4ff5cc3747b8fcb921d04cf28e Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:04:57 +0000 Subject: [PATCH 14/44] add assets_select and assets_filter functions --- R/utils.R | 391 ------------------------------------------------------ 1 file changed, 391 deletions(-) diff --git a/R/utils.R b/R/utils.R index 928b1512..b6510436 100644 --- a/R/utils.R +++ b/R/utils.R @@ -441,397 +441,6 @@ stac_version <- function(x, ...) { UseMethod("stac_version") } -#' @title Utility functions -#' -#' @description This function returns the `date`, `band` and -#' `URL` fields for each assets of an `STACItemCollection` object. -#' For the URL you can add the GDAL library drivers for the following schemes: -#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param assets_names `r lifecycle::badge('deprecated')` -#' use `asset_names` parameter instead. -#' -#' @param asset_names a `character` with the assets names to be -#' filtered. If `NULL` (default) all assets will be returned.. -#' -#' @param sort a `logical` if true the dates will be sorted -#' in increasing order. By default, the dates are sorted. -#' -#' @param gdal_vsi_resolution a `logical` if true, gdal drivers are -#' included in the URL of each asset. The following schemes are supported: -#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). -#' -#' @return a `list` with the attributes of date, bands and paths. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% assets_list(assets_names = c("EVI", "NDVI")) -#' } -#' -#' @export -assets_list <- function(items, asset_names = NULL, - sort = TRUE, gdal_vsi_resolution = TRUE, - assets_names = deprecated()) { - - - if (lifecycle::is_present(assets_names)) { - - # Signal the deprecation to the user - lifecycle::deprecate_soft("0.9.1-5", - "rstac::assets_download(assets_names = )", - "rstac::assets_download(asset_names = )") - - # Deal with the deprecated argument for compatibility - asset_names <- assets_names - } - - if (is.null(asset_names)) - asset_names <- items_fields(items, "assets") - - timeline <- items_reap(items, field = c("properties", "datetime")) - index <- seq_along(timeline) - if (sort) index <- order(timeline) - - timeline <- timeline[index] - assets <- list(date = rep(timeline, length(unique(asset_names)))) - - for (b in asset_names) { - - href <- items_reap(items, field = c("assets", b, "href"))[index] - - if (gdal_vsi_resolution) { - - # for http or https schema - paste_index <- grepl("^http|[s]://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsicurl", href[paste_index], sep = "/") - - # for S3 schema - paste_index <- grepl("^s3://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsis3", gsub("^s3://(.*)$", "\\1", - href[paste_index]), sep = "/") - # for gs schema - paste_index <- grepl("^gs://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsigs", gsub("^gs://(.*)$", "\\1", - href[paste_index]), sep = "/") - } - assets$band <- c(rep(b, length(href)), assets$band) - assets$path <- c(href, assets$path) - } - assets -} - -#' @title Utility functions -#' -#' @description This function filters for the attributes contained in the STAC -#' properties. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... expressions used to filter items of a `STACItemCollection` -#' object. -#' @param fn a `function` that will be used to filter the attributes -#' listed in the properties. -#' -#' @return a `STACItemCollection` object with the filtered properties. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_filter(`eo:cloud_cover` < 10) -#' -#' # Example with AWS STAC -#' items <- stac("https://earth-search.aws.element84.com/v0") %>% -#' stac_search(collections = "sentinel-s2-l2a-cogs", -#' bbox = c(-48.206,-14.195,-45.067,-12.272), -#' datetime = "2018-06-01/2018-06-30", -#' limit = 500) %>% -#' post_request() -#' -#' items %>% -#' items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) -#' } -#' -#' @export -items_filter <- function(items, ..., fn = NULL) { - - dots <- substitute(list(...))[-1] - - if (length(dots) > 0) { - - if (!is.null(names(dots))) - .error("Invalid filter arguments.") - - for (i in seq_along(dots)) { - - sel <- vapply(items$features, function(f) { - eval(dots[[i]], envir = f$properties) - }, logical(1)) - - items$features <- items$features[sel] - } - } - - if (!is.null(fn)) { - - sel <- vapply(items$features, function(f) { - fn(f$properties) - }, logical(1)) - - items$features <- items$features[sel] - } - - items -} - -#' @title Utility functions -#' -#' @description This function returns the values of a field of the -#' `STACItemCollections` object. If the values of the specified field are -#' not atomic the return will be in list form, if they are, it will be returned -#' in vector form. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... a named way to provide fields names to get the -#' subfields values from the `RSTACDocument` objects. -#' -#' @param field a `character` with the names of the field to -#' get the subfields values from the `RSTACDocument` objects. -#' -#' @return a `vector` if the supplied field is atomic, or a list if not. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% items_reap(field = c("properties", "datetime")) -#' } -#' -#' @export -items_reap <- function(items, ..., field = NULL) { - - # checks if the object is STACItemCollections - if (items_length(items) == 0) return(NULL) - - dots <- substitute(list(...))[-1] - if (!is.character(dots)) dots <- as.character(dots) - - if (length(dots) > 0 && length(field) > 0) - .error("Only one of the parameters '...' or 'field' must be supplied.") - - if (length(field) == 0 && length(dots) == 0) - return(items$features) - - values <- lapply(items$features, `[[`, c(dots, field)) - - if (all(vapply(values, is.null, logical(1)))) - .error("The provided field does not exist.") - - if (all(vapply(values, is.atomic, logical(1)))) - return(unlist(values)) - values -} - -#' @title Utility functions -#' -#' @description This function returns the subfields of the `feature` -#' field of a `STACItemCollection` object. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... a named way to provide field names to get the subfields values -#' from the `RSTACDocument` objects. -#' -#' @param field a `character` with the names of the field to get the -#' subfields values from the `RSTACDocument` objects. -#' -#' @return A `character` with the subfields of the `feature` field. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 10, -#' datetime = "2017-08-01/2018-03-01") %>% -#' get_request() -#' -#' stac_item %>% items_fields(field = c("properties")) -#' } -#' -#' @export -items_fields <- function(items, ..., field = NULL) { - - # checks if the object is STACItemCollections - if (items_length(items) == 0) return(NULL) - - dots <- substitute(list(...))[-1] - if (!is.character(dots)) dots <- as.character(dots) - - if (length(field) > 0 && length(dots) > 0) - .error("Only one of the parameters '...' or 'field' must be supplied.") - - if (length(field) == 0 && length(dots) == 0) - return(names(items$features[[1]])) - names(items$features[[1]][[c(dots, field)]]) -} - -#' @title Utility functions -#' -#' @description This function groups the items contained within the -#' `STACItemCollection` object according to some specified fields. Each -#' index in the returned list contains items belonging to the same group. -#' -#' @param items a `STACItemCollection` object representing the result of -#' `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... a named way to provide field names to get the subfields values -#' from the `RSTACDocument` objects. -#' -#' @param field a `character` with the names of the field to get the -#' subfields values from the `RSTACDocument` objects. -#' -#' @param index a `character` with the indexes to be grouped. It can be -#' used with the function [items_reap]. -#' -#' @return A `list` in which each index corresponds to a group with its -#' corresponding `STACItemCollection` objects. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% items_group(., field = c("properties", "bdc:tiles")) -#' } -#' -#' @export -items_group <- function(items, ..., field = NULL, index = NULL) { - - # checks if the object is STACItemCollections - if (items_length(items) == 0) return(list(items)) - - dots <- substitute(list(...))[-1] - if (!is.character(dots)) dots <- as.character(dots) - - if (length(index) == 0 && length(field) == 0 && length(dots) == 0) - .error(paste("Either parameters 'index', 'field' or '...' parameters must", - "be supplied.")) - - if (length(index) > 0 && (length(field) > 0 || length(dots) > 0)) - .error(paste("Only one of the parameters '...','index' or 'field' should", - "be supplied.")) - - if (is.null(index)) { - index <- items_reap(items, ..., field = field) - - if (!is.atomic(index)) - .error("The field must be atomic vector.") - } else { - - if (items_matched(items) > items_length(items)) - .warning(paste("The number of matched items is greater than the number", - "of items length on your object. Considere to use", - "the 'items_fetch()' function before this operation.")) - } - - if (items_length(items) != length(index)) - .error(paste("The length of the field provided for grouping must contain", - "the same size as the length of the items.")) - - features <- unname(tapply(X = items$features, - INDEX = index, - FUN = c, simplify = FALSE)) - - lapply(features, function(x){ - items$features <- x - - items - }) -} - -#' @title Utility functions -#' -#' @description A utility function to create signatures in hrefs of each -#' asset in the STAC items. To create the signatures, the provided function -#' must return a function, being a factory function, so the manufactured -#' function will sign the hrefs returning one feature per interaction. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param sign_fn a `function` to assign each assets in STAC items. -#' -#' @return A `STACItemCollection` object with the signed assets according to the -#' supplied parameter function. -#' @examples -#' \dontrun{ -#' -#' # Defining BDC token -#' Sys.setenv("BDC_ACCESS_KEY" = ) -#' -#' # STACItem object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_sign(sign_fn = sign_bdc) -#' -#' } -#' -#' @export -items_sign <- function(items, sign_fn = NULL) { - - if (is.null(sign_fn)) { - return(items) - } - - if (!is.null(items_matched(items))) { - if (items_length(items) != items_matched(items)) - .warning(paste("The number of items in this object does not match the", - "total number of items in the item. If you want to get", - "all items, use `items_fetch()`")) - } - - # assign each item obj - items[["features"]] <- lapply(items[["features"]], function(item){ - - item <- sign_fn(item) - - item - }) - - items -} - #' @title Utility functions #' #' @param bbox a `numeric` vector with only features that have a From d766697f3e4ec30010e1b7586255a39fd1b7c3a5 Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:05:47 +0000 Subject: [PATCH 15/44] update tests --- tests/fixtures/stac_item_obj.yml | 130 ++++++-- tests/fixtures/stac_search_obj.yml | 292 ++++++++++++----- tests/fixtures/tests_examples.yml | 444 ++++++++++++++++++++++++-- tests/testthat/test-internals.R | 52 ++- tests/testthat/test-items_functions.R | 8 +- 5 files changed, 749 insertions(+), 177 deletions(-) diff --git a/tests/fixtures/stac_item_obj.yml b/tests/fixtures/stac_item_obj.yml index 7a842848..2ea444f7 100644 --- a/tests/fixtures/stac_item_obj.yml +++ b/tests/fixtures/stac_item_obj.yml @@ -24,7 +24,7 @@ http_interactions: file: no string: | {"assets":{"blue":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_blue.tif"},"evi":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_evi.tif"},"ndvi":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_ndvi.tif"},"nir":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_nir.tif"},"red":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_red.tif"},"reliability":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_reliability.tif"},"swir2":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754_swir2.tif"},"thumbnail":{"href":"http://brazildatacube.dpi.inpe.br/Repository/Archive/MOD13Q1/2019-08/MOD13Q1.A2019241.h13v09.006.2019262164754/MOD13Q1.2019-08-29.h13v09.006.2019262164754.png"}},"bbox":[-50.7713305942872,-10.0,-40.0,0.0],"collection":"MOD13Q1","geometry":{"coordinates":[[[[-50,0],[-40,0],[-40.617064475,-10],[-50.771330594,-10],[-50,0]]]],"type":"MultiPolygon"},"id":"MOD13Q1.A2019241.h13v09.006.2019262164754","links":[{"href":"http://brazildatacube.dpi.inpe.br/bdc-stac/0.8.0/collections/MOD13Q1/items/MOD13Q1.A2019241.h13v09.006.2019262164754","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/bdc-stac/0.8.0/collections/MOD13Q1","rel":"parent"},{"href":"http://brazildatacube.dpi.inpe.br/bdc-stac/0.8.0/collections/MOD13Q1","rel":"collection"},{"href":"http://brazildatacube.dpi.inpe.br/bdc-stac/0.8.0/stac","rel":"root"}],"properties":{"bdc:tile":"013009","datetime":"2019-08-29"},"stac_version":"0.8.0","type":"Feature"} - 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profile=cloud-optimized","eo:bands":[3]},"thumbnail":{"href":"http://brazildatacube.dpi.inpe.br/dev/Repository/Warped/CB4_64/020022/2019-12-31/CB4_64_020022_2019-12-31.png","type":"image/png"}},"links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1/items/CB4_64_020022_2019-12-31","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"parent"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"collection"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/stac","rel":"root"}]}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1163,7 +1163,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1191,7 +1191,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1219,7 +1219,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1247,7 +1247,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1275,7 +1275,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1303,7 +1303,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1331,7 +1331,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1359,7 +1359,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1387,7 +1387,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1415,7 +1415,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1443,7 +1443,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1471,7 +1471,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-07-09 16:04:25 GMT + recorded_at: 2021-09-17 00:18:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1499,7 +1499,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cube Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/stac/","rel":"self","type":"application/json","title":"Link to this document"},{"href":"http://brazildatacube.dpi.inpe.br/stac/docs","rel":"service-doc","type":"text/html","title":"API documentation in HTML"},{"href":"http://brazildatacube.dpi.inpe.br/stac/conformance","rel":"conformance","type":"application/json","title":"OGC API conformance classes implemented by the server"},{"href":"http://brazildatacube.dpi.inpe.br/stac/collections","rel":"data","type":"application/json","title":"Information about image collections"},{"href":"http://brazildatacube.dpi.inpe.br/stac/search","rel":"search","type":"application/json","title":"STAC-Search 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+lat_0=-12 +lon_0=-54 +lat_1=-2 +lat_2=-22 +x_0=5000000 +y_0=10000000 +ellps=GRS80 +units=m +no_defs ","bdc:temporal_composition":null,"links":[{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4MUX_20-1","rel":"self","type":"application/json","title":"Link to this document"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4MUX_20-1/items","rel":"items","type":"application/json","title":"Items of the collection CB4MUX_20-1"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections","rel":"parent","type":"application/json","title":"Link to catalog collections"},{"href":"https://brazildatacube.dpi.inpe.br/stac/","rel":"root","type":"application/json","title":"API landing page (root catalog)"}]},{"id":"LCC_L8_30_1M_STK_Cerrado-1","stac_version":"0.9.0","stac_extensions":["commons","datacube","version"],"title":"LCC Landsat-8 1M STK Cerrado","version":1,"deprecated":false,"description":"This is a land cover classification map of Brazilian Cerrado, from August 2017 to August 2018. This classification was made on top of Landsat-8 monthly cubes with spatial resolution of 30 meters using the best pixel composition function (Stack). The classification model was trained using 67359 sample points spread across the whole Cerrado biome (Annual Crop: 9390, Dune Beach: 35, Forest: 5439, Pasture: 19697, Savanna: 30014, Semi-Perennial Crop: 1161, Silviculture: 1268, Water: 355). The spectral band used were B1, B2, B3, B4, B5, B6, and B7 along with the vegetation indices EVI and NDVI; the clouded observation were identified using the Fmask4 algorithm and estimated using linear interpolation. The classification algorithm was Multi-Layer Perceptron (Deep Learning).","license":"","properties":{"eo:gsd":30.0,"eo:bands":[{"name":"lcc","common_name":"lcc","description":"This is a classification.","min":1.0,"max":8.0,"nodata":255.0,"scale":1.0,"center_wavelength":null,"full_width_half_max":null,"data_type":"uint8"}],"instruments":["OLI"],"platform":"LANDSAT-8"},"extent":{"spatial":{"bbox":[[-54.356031,-17.015976,-44.846777,-7.085732]]},"temporal":{"interval":[["2017-08-01T00:00:00","2018-08-31T00:00:00"]]}},"bdc:metadata":{"ows":{"url":"http://brazildatacube.dpi.inpe.br/bdc/geoserver/bdc_lcc/ows","layerName":"LCC_L8_30_1M_STK_Cerrado"},"sources":[{"name":"Landsat-8 - OLI - Cube Stack 16 days - v001","stacUri":"https://brazildatacube.dpi.inpe.br/stac/collections/LC8_30_16D_STK-1","descriptionUri":"https://brazil-data-cube.github.io/products/cube_col/LC8_30_16D_STK.html"}],"datacite":{"id":"LCC_L8_30_1M_STK_Cerrado","dates":[{"date":"2021"}],"sizes":[],"state":"unfindable","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"agency":"INPE","titles":{"lang":"en","title":"LCC Landsat-8 1M STK Cerrado - Annual Crop, Dune Beach, Forest, Pasture, Savanna, Semi-Perennial Crop, Silviculture, Water"},"formats":[],"version":"1.","creators":[{"@type":"ResearchGroup","familyName":"BDC Team"}],"language":"en","subjects":[{"lang":"en","subject":"LANDSAT-8"},{"lang":"en","subject":"OLI"},{"lang":"en","subject":"Data Cube"},{"lang":"en","subject":"Brazil"},{"lang":"en","subject":"Classification"},{"lang":"en","subject":"Machine Learning"},{"lang":"en","subject":"MLP (multi-layer perceptrons)"}],"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/"}],"contributors":[{"name":"National Institute for Space Research (INPE)","nameType":"Organizational","contributorType":"HostingInstitution"},{"name":"Brazil Data Cube Team","contributorType":"ResearchGroup"}],"descriptions":[{"lang":"en","description":"This land cover classification refers to a study area in Goi\u00e1s state, in the Cerrado biome. 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This algorithm delivers the surface reflectance data from CBERS-4B Level-4 images. The methodology includes the integration of MODIS-MCD19A2 and VIIRS-EDR products as input atmospheric information (aerosol optical depth and water vapor). The results were evaluated using 616 Landsat-8 OLI surface reflectance imagery and AERONET data. These findings confirm that (i) CMPAC is a suitable tool for estimating surface reflectance of CBERS MUX data, and (ii) ancillary products support the application of atmospheric correction by filling the gap of atmospheric information. More information about the method is available in the following paper (Martins et al. 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profile=cloud-optimized","roles":["data"],"created":"2020-09-14T19:53:42","updated":"2020-09-14T19:53:42","bdc:size":7738587,"bdc:chunk_size":{"x":256,"y":256},"bdc:raster_size":{"x":10504,"y":6865},"checksum:multihash":"122020cbf5b902a9a6e43faf73344bb8d219aa5eb631d43b433ec73a86713eb2fd00","eo:bands":[8]}},"links":[{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4_64_16D_STK-1/items/CB4_64_16D_STK_v001_022021_2018-02-18_2018-03-05","rel":"self"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4_64_16D_STK-1","rel":"parent"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4_64_16D_STK-1","rel":"collection"},{"href":"https://brazildatacube.dpi.inpe.br/stac/","rel":"root"}]}]} + recorded_at: 2021-09-17 00:18:31 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 diff --git a/tests/testthat/test-internals.R b/tests/testthat/test-internals.R index 71e03e33..6be1eaf0 100644 --- a/tests/testthat/test-internals.R +++ b/tests/testthat/test-internals.R @@ -1,37 +1,33 @@ -context("test_internal_functions") - testthat::test_that("internals functions", { - vcr::use_cassette("test_internal_functions", { - # skip cran check test - testthat::skip_on_cran() + # skip cran check test + testthat::skip_on_cran() - stac_obj <- rstac::stac("https://brazildatacube.dpi.inpe.br/stac/") + stac_obj <- rstac::stac("https://brazildatacube.dpi.inpe.br/stac/") - # check_subclass object - testthat::expect_null( - object = check_subclass(stac_obj, subclasses = c("stac")) - ) + # check_subclass object + testthat::expect_null( + object = check_subclass(stac_obj, subclasses = c("stac")) + ) - # subclass object - testthat::expect_equal( - object = subclass(stac_obj), - expected = "stac" - ) + # subclass object + testthat::expect_equal( + object = subclass(stac_obj), + expected = "stac" + ) - # .error function - testthat::expect_error( - .error("error function") - ) + # .error function + testthat::expect_error( + .error("error function") + ) - # .warning function - testthat::expect_warning( - .warning("warning function") - ) + # .warning function + testthat::expect_warning( + .warning("warning function") + ) - # .message function - testthat::expect_message( - .message("message function") - ) - }) + # .message function + testthat::expect_message( + .message("message function") + ) }) diff --git a/tests/testthat/test-items_functions.R b/tests/testthat/test-items_functions.R index a4d2f17c..fc42b3ec 100644 --- a/tests/testthat/test-items_functions.R +++ b/tests/testthat/test-items_functions.R @@ -69,16 +69,16 @@ testthat::test_that("items functions", { ) ) - # items_bands--------------------------------------------------------------- + # items_assets--------------------------------------------------------------- # STACItemCollection - testthat::expect_length(items_bands(res), n = 10) + testthat::expect_length(items_assets(res), n = 10) # STACItem - testthat::expect_vector(items_bands(item_stac), ptype = character()) + testthat::expect_vector(items_assets(item_stac), ptype = character()) # provide wrong object testthat::expect_error( - object = items_bands( + object = items_assets( rstac::stac("https://brazildatacube.dpi.inpe.br/stac/") %>% collections(collection_id = "CB4_64_16D_STK-1") %>% get_request() From d9923b617d06e2eceaf1e7e283349d4919fbedf0 Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:06:00 +0000 Subject: [PATCH 16/44] update docs --- NAMESPACE | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/NAMESPACE b/NAMESPACE index d073fdeb..21ddf8cc 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -26,6 +26,20 @@ S3method(endpoint,item_id) S3method(endpoint,items) S3method(endpoint,search) S3method(endpoint,stac) +S3method(items_assets,STACItem) +S3method(items_assets,STACItemCollection) +S3method(items_bbox,STACItem) +S3method(items_bbox,STACItemCollection) +S3method(items_datetime,STACItem) +S3method(items_datetime,STACItemCollection) +S3method(items_fetch,STACItem) +S3method(items_fetch,STACItemCollection) +S3method(items_fields,STACItem) +S3method(items_fields,STACItemCollection) +S3method(items_length,STACItem) +S3method(items_length,STACItemCollection) +S3method(items_matched,STACItem) +S3method(items_matched,STACItemCollection) S3method(parse_params,ext_query) S3method(parse_params,search) S3method(print,RSTACQuery) @@ -44,7 +58,9 @@ export(RSTACDocument) export(RSTACQuery) export(after_response) export(assets_download) +export(assets_filter) export(assets_list) +export(assets_select) export(before_request) export(check_query_verb) export(check_subclass) @@ -55,6 +71,7 @@ export(endpoint) export(ext_query) export(get_request) export(items) +export(items_assets) export(items_bands) export(items_bbox) export(items_datetime) From 0cb3284cc0e07597c122b38a7f088230f8b8736b Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 17 Sep 2021 01:16:05 +0000 Subject: [PATCH 17/44] deprecate items_bands function. (closes #57) --- R/deprec-functions.R | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 R/deprec-functions.R diff --git a/R/deprec-functions.R b/R/deprec-functions.R new file mode 100644 index 00000000..92590360 --- /dev/null +++ b/R/deprec-functions.R @@ -0,0 +1,29 @@ +#' @title STACItemCollection function +#' +#' @description +#' `r lifecycle::badge('deprecated')` Use \code{\link{items_assets}()} function +#' instead. +#' +#' @param items a `STACItemCollection` or `STACItem` object. +#' +#' @examples +#' \dontrun{ +#' +#' x <- stac("http://brazildatacube.dpi.inpe.br/stac") %>% +#' stac_search(collections = "CB4_64_16D_STK-1") %>% +#' stac_search() %>% +#' get_request() +#' +#' x %>% items_assets() +#' } +#' +#' @export +items_bands <- function(items) { + + # signal the deprecation to the user + lifecycle::deprecate_soft("0.9.1-5", + "rstac::items_bands(items = )", + "rstac::items_assets(items = )") + + return(items_assets(items)) +} From 0fe6a018f6d74f39709ac3d405229f3592f574fc Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 21:24:40 +0000 Subject: [PATCH 18/44] add tests for assets functions --- tests/fixtures/assets_functions.yml | 129 ++++++++ tests/fixtures/bdc_signatures.yml | 130 +++++++++ tests/fixtures/ms_signatures.yml | 389 +++++++++++++++++++++++++ tests/testthat/test-assets_download.R | 50 ---- tests/testthat/test-assets_functions.R | 140 +++++++++ tests/testthat/test-signatures.R | 141 +++++++++ 6 files changed, 929 insertions(+), 50 deletions(-) create mode 100644 tests/fixtures/assets_functions.yml create mode 100644 tests/fixtures/bdc_signatures.yml create mode 100644 tests/fixtures/ms_signatures.yml delete mode 100644 tests/testthat/test-assets_download.R create mode 100644 tests/testthat/test-assets_functions.R create mode 100644 tests/testthat/test-signatures.R diff --git a/tests/fixtures/assets_functions.yml b/tests/fixtures/assets_functions.yml new file mode 100644 index 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'{"msft:expiry":"2021-09-24T15:15:35Z","token":"st=2021-09-23T14%3A30%3A35Z&se=2021-09-24T15%3A15%3A35Z&sp=rl&sv=2020-02-10&sr=c&skoid=c85c15d6-d1ae-42d4-af60-e2ca0f81359b&sktid=72f988bf-86f1-41af-91ab-2d7cd011db47&skt=2021-09-24T13%3A30%3A35Z&ske=2021-09-25T14%3A30%3A35Z&sks=b&skv=2020-02-10&sig=NYfop6ohW296ldSJxu5kr/WYgp0VuyXRUVqVEvz07Oc%3D"}' + recorded_at: 2021-09-24 14:30:36 GMT + recorded_with: vcr/1.0.2, webmockr/0.8.0 +- request: + method: get + uri: https://planetarycomputer.microsoft.com/api/sas/v1/token/landsat-8-c2-l2 + body: + encoding: '' + string: '' + headers: + Accept: application/json, text/xml, application/xml, */* + response: + status: + status_code: 200 + category: Success + reason: OK + message: 'Success: (200) OK' + headers: + content-length: '347' + content-type: application/json + strict-transport-security: max-age=15724800; includeSubDomains + request-context: appId=cid-v1:75161b1b-6883-4b66-9410-715040c44427 + x-cache: CONFIG_NOCACHE + x-azure-ref: 0C+FNYQAAAABzwWAcEd0MSKrq6eJFzGrqUklPMDNFREdFMDcwOQA5MjdhYmZhNi0xOWY2LTRhZjEtYTA5ZC1jOTU5ZDlhMWU2NDQ= + date: Fri, 24 Sep 2021 14:30:36 GMT + body: + encoding: UTF-8 + file: no + string: '{"msft:expiry":"2021-09-24T15:15:36Z","token":"st=2021-09-23T14%3A30%3A36Z&se=2021-09-24T15%3A15%3A36Z&sp=rl&sv=2020-02-10&sr=c&skoid=c85c15d6-d1ae-42d4-af60-e2ca0f81359b&sktid=72f988bf-86f1-41af-91ab-2d7cd011db47&skt=2021-09-24T13%3A30%3A36Z&ske=2021-09-25T14%3A30%3A36Z&sks=b&skv=2020-02-10&sig=GyDxbOy%2BeiVWGwtAQTU47PVrTVzX8cgWVA5ziCc1mMU%3D"}' + recorded_at: 2021-09-24 14:30:36 GMT + recorded_with: vcr/1.0.2, webmockr/0.8.0 diff --git a/tests/testthat/test-assets_download.R b/tests/testthat/test-assets_download.R deleted file mode 100644 index 17470911..00000000 --- a/tests/testthat/test-assets_download.R +++ /dev/null @@ -1,50 +0,0 @@ -context("test_assets_download") - -testthat::test_that("assets download", { - vcr::use_cassette("assets_download", { - # skip cran check test - testthat::skip_on_cran() - - # error - zero items - testthat::expect_error( - rstac::stac("http://brazildatacube.dpi.inpe.br/stac/") %>% - stac_search( - collections = "CB4_64_16D_STK-1", - datetime = "2019-09-01/2019-11-01", - bbox = c(-47.02148, -12.98314, -42.53906, -17.35063), - limit = 0) %>% - get_request() %>% - assets_download(asset_names = c("blue", "evi"))) - - # error - given another object - testthat::expect_error( - stac("http://brazildatacube.dpi.inpe.br/stac/") %>% - get_request(.) %>% - assets_download(., asset_names = c("blue", "evi"))) - - # error - wrong path - testthat::expect_error( - stac("http://brazildatacube.dpi.inpe.br/stac/") %>% - stac_search( - collections = "CB4_64_16D_STK-1", - datetime = "2019-09-01/2019-11-01", - limit = 1) %>% - get_request() %>% - assets_download(asset_names = c("thumbnail"), - output_dir = "./non-existing-dir/")) - - # verify output object - testthat::expect_equal( - object = { - x <- stac("http://brazildatacube.dpi.inpe.br/dev/bdc-stac/") %>% - stac_search( - collections = "CB4_64_16D_STK-1", - datetime = "2019-09-01/2019-11-01", - limit = 1) %>% - get_request() %>% - assets_download(asset_names = c("thumbnail"), output_dir = ".") - subclass(x) - }, - expected = "STACItemCollection") - }) -}) diff --git a/tests/testthat/test-assets_functions.R b/tests/testthat/test-assets_functions.R new file mode 100644 index 00000000..df457a11 --- /dev/null +++ b/tests/testthat/test-assets_functions.R @@ -0,0 +1,140 @@ +testthat::test_that("assets functions", { + vcr::use_cassette("assets_download", { + # skip cran check test + testthat::skip_on_cran() + + # error - zero items + testthat::expect_error( + rstac::stac("http://brazildatacube.dpi.inpe.br/stac/") %>% + stac_search( + collections = "CB4_64_16D_STK-1", + datetime = "2019-09-01/2019-11-01", + bbox = c(-47.02148, -12.98314, -42.53906, -17.35063), + limit = 0) %>% + get_request() %>% + assets_download(asset_names = c("blue", "evi"))) + + # error - given another object + testthat::expect_error( + stac("http://brazildatacube.dpi.inpe.br/stac/") %>% + get_request(.) %>% + assets_download(., asset_names = c("blue", "evi"))) + + # error - wrong path + testthat::expect_error( + stac("http://brazildatacube.dpi.inpe.br/stac/") %>% + stac_search( + collections = "CB4_64_16D_STK-1", + datetime = "2019-09-01/2019-11-01", + limit = 1) %>% + get_request() %>% + assets_download(asset_names = c("thumbnail"), + output_dir = "./non-existing-dir/")) + + # verify output object + testthat::expect_equal( + object = { + x <- stac("http://brazildatacube.dpi.inpe.br/dev/bdc-stac/") %>% + stac_search( + collections = "CB4_64_16D_STK-1", + datetime = "2019-09-01/2019-11-01", + limit = 1) %>% + get_request() %>% + assets_download(asset_names = c("thumbnail"), output_dir = ".") + subclass(x) + }, + expected = "STACItemCollection") + }) + + vcr::use_cassette("assets_functions", { + + stac_items <- stac("https://brazildatacube.dpi.inpe.br/stac") %>% + stac_search(collections = "CB4_64_16D_STK-1") %>% + stac_search(limit = 2) %>% + get_request() + + stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% + collections("CB4_64_16D_STK-1") %>% + items("CB4_64_16D_STK_v001_022023_2020-07-11_2020-07-26") %>% + get_request() + + # ---- assets_select ----# + + # an error is expected if a non-existent asset is provided for + # STACItemCollection obj + testthat::expect_error(assets_select(stac_items, asset_names = "DDDDD")) + + # an error is expected if a non-existent asset is provided for + # STACItem obj + testthat::expect_error(assets_select(stac_item, asset_names = "DDDDD")) + + # return the same object after select? + testthat::expect_s3_class( + object = assets_select(stac_items, asset_names = "BAND13"), + class = c("STACItemCollection", "RSTACDocument") + ) + + # return the same object after select? + testthat::expect_s3_class( + object = assets_select(stac_item, asset_names = "BAND13"), + class = c("STACItem", "RSTACDocument") + ) + + # were the asset selected? + testthat::expect_equal( + object = items_assets(assets_select(stac_items, asset_names = "BAND13"), + simplify = TRUE), + expected = "BAND13" + ) + + # were the asset selected? + testthat::expect_equal( + object = items_assets(assets_select(stac_item, asset_names = "BAND13")), + expected = "BAND13" + ) + + # ---- assets_filter ----# + + # return the same object after filter? + testthat::expect_s3_class( + object = assets_filter(stac_items, `eo:bands` < 6), + class = c("STACItemCollection", "RSTACDocument") + ) + + # return the same object after filter? + testthat::expect_s3_class( + object = assets_filter(stac_item, `eo:bands` < 6), + class = c("STACItem", "RSTACDocument") + ) + + # return the same object after filter? + testthat::expect_s3_class( + object = assets_filter(stac_items, fn = function(x) { + if ("eo:bands" %in% names(x)) + return(x$`eo:bands` < 6) + return(TRUE) + }), + class = c("STACItemCollection", "RSTACDocument") + ) + + # return the same object after filter? + testthat::expect_s3_class( + object = assets_filter(stac_items, fn = function(x) { + if ("eo:bands" %in% names(x)) + return(x$`eo:bands` < 6) + return(TRUE) + }), + class = c("STACItem", "RSTACDocument") + ) + + # an error is expected if the ellipses is named + testthat::expect_error( + assets_filter(stac_items, j = "a" < 20) + ) + + # an error is expected if the ellipses is named + testthat::expect_error( + assets_filter(stac_item, j = "a" < 20) + ) + }) +}) diff --git a/tests/testthat/test-signatures.R b/tests/testthat/test-signatures.R new file mode 100644 index 00000000..c8438d22 --- /dev/null +++ b/tests/testthat/test-signatures.R @@ -0,0 +1,141 @@ +testthat::test_that("signature functions", { + vcr::use_cassette("bdc_signatures",{ + + #--- BDC provider ----# + + # stac item collection from bdc + stac_items <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% + stac_search(collections = "CB4_64_16D_STK-1", + limit = 1) %>% + ext_query("bdc:tile" == "021027") %>% + post_request() + + # stac item from bdc + stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% + collections("CB4_64_16D_STK-1") %>% + items("CB4_64_16D_STK_v001_022023_2020-07-11_2020-07-26") %>% + get_request() + + # return the same object after signature? + testthat::expect_s3_class( + object = items_sign(stac_items, sign_bdc("AAAA-BBB")), + class = c("STACItemCollection", "RSTACDocument") + ) + + # return the same object after signature? + testthat::expect_s3_class( + object = stac_item %>% items_sign(sign_bdc("AAAA-BBB")), + class = c("STACItem", "RSTACDocument") + ) + + items_signed <- items_sign(stac_items, sign_bdc("AAAA-BBB")) + href_items <- items_signed$features[[1]]$assets[[1]]$href + + # is the token being added at the end of the url? + testthat::expect_equal( + gsub("^([^?]+)(\\?.*)?$", "\\2", href_items), "?access_token=AAAA-BBB" + ) + + item_signed <- items_sign(stac_item, sign_bdc("AAAA-BBB")) + href_item <- item_signed$assets[[1]]$href + + # is the token being added at the end of the url? + testthat::expect_equal( + gsub("^([^?]+)(\\?.*)?$", "\\2", href_item), "?access_token=AAAA-BBB" + ) + + Sys.setenv("BDC_ACCESS_KEY" = "CCCC-DDD") + items_signed <- items_sign(stac_items, sign_bdc()) + href_items <- items_signed$features[[1]]$assets[[1]]$href + + # is the token being added at the end of the url with env var? + testthat::expect_equal( + gsub("^([^?]+)(\\?.*)?$", "\\2", href_items), "?access_token=CCCC-DDD" + ) + + item_signed <- items_sign(stac_item, sign_bdc()) + href_item <- item_signed$assets[[1]]$href + + # is the token being added at the end of the url with env var? + testthat::expect_equal( + gsub("^([^?]+)(\\?.*)?$", "\\2", href_item), "?access_token=CCCC-DDD" + ) + + Sys.setenv("BDC_ACCESS_KEY" = "") + + # an error is expected if no option is provided + testthat::expect_error( + items_sign(stac_items, sign_bdc()) + ) + + # an error is expected if no option is provided + testthat::expect_error( + items_sign(stac_item, sign_bdc()) + ) + }) + + vcr::use_cassette("ms_signatures",{ + + #--- MS provider ----# + + # stac item collection from ms + stac_items <- + stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% + stac_search(collections = "landsat-8-c2-l2", + bbox = c(-47.02148, -12.98314, -42.53906, -17.35063), + limit = 1) %>% + get_request() + + # stac item from ms + stac_item <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% + collections("landsat-8-c2-l2") %>% + items("LC08_L2SP_217072_20210909_02_T1") %>% + get_request() + + # return the same object after signature? + testthat::expect_s3_class( + object = suppressWarnings( + items_sign(stac_items, sign_planetary_computer) + ), + class = c("STACItemCollection", "RSTACDocument") + ) + + # return the same object after signature? + testthat::expect_s3_class( + object = suppressWarnings( + items_sign(stac_item, sign_planetary_computer()) + ), + class = c("STACItem", "RSTACDocument") + ) + + items_signed <- suppressWarnings( + items_sign(stac_items, sign_planetary_computer()) + ) + href_items <- items_signed$features[[1]]$assets[[1]]$href + + # is the token being added at the end of the url? + testthat::expect_match( + object = href_items, + regexp = "se" + ) + + item_signed <- suppressWarnings( + items_sign(stac_item, sign_planetary_computer()) + ) + href_item <- item_signed$assets[[1]]$href + + # is the token being added at the end of the url? + testthat::expect_match( + object = href_item, + regexp = "se" + ) + + # provided wrong url + testthat::expect_error( + object = suppressWarnings( + items_sign(stac_items, + sign_planetary_computer(token_url = "test")) + ) + ) + }) +}) From 87820b2f68511cf2e8177c902488601eef1fe99b Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 21:25:27 +0000 Subject: [PATCH 19/44] introduces 'items_next' function --- R/documents.R | 289 +++++++++++++++++++++++++++++++++++++------------- 1 file changed, 214 insertions(+), 75 deletions(-) diff --git a/R/documents.R b/R/documents.R index 43256f47..562d498b 100644 --- a/R/documents.R +++ b/R/documents.R @@ -148,7 +148,7 @@ stac_version.STACCollectionList <- function(x, ...) { #' @examples #' \dontrun{ #' -#' x <- stac("http://brazildatacube.dpi.inpe.br/stac") %>% +#' x <- stac("https://brazildatacube.dpi.inpe.br/stac") %>% #' stac_search(collections = "CB4_64_16D_STK-1") %>% #' stac_search(limit = 500) %>% #' get_request() @@ -280,108 +280,144 @@ items_fetch.STACItemCollection <- function(items, ..., .error(paste("Length of returned items (%s) is different", "from matched items (%s)."), items_length(items), matched) - q <- doc_query(items) - if (is.null(q)) break + content <- items_next(items) - # get url of the next page - next_url <- Filter(function(x) x$rel == "next", items$links) - if (length(next_url) == 0) break - next_url <- next_url[[1]] + if (!is.null(content)) + items <- content + else + break - # create a new stac object with params from the next url - # check for body implementation in next link - if (q$verb == "POST" && all(c("body", "method") %in% names(next_url))) { + # update progress bar + if (progress) + utils::setTxtProgressBar(pb, items_length(content)) + } - # TODO: check if spec can enforce that the same provided base url - # must be used to proceed pagination. - # For security concerns, here, the original base_url will be used in - # subsequent requests of pagination + # close progress bar + if (progress) { + utils::setTxtProgressBar(pb, matched) + close(pb) + } - # # update query base_url and verb to the returned one - # q$base_url <- next_url$href + return(items) +} - # erase current parameters if merge == FALSE - if (!is.null(next_url$merge) && !next_url$merge) { - q$params <- list() - } +#' @rdname items_functions +#' +#' @export +items_next <- function(items, ...) { - # get parameters - params <- next_url$body + UseMethod("items_next", items) +} - } else { +#' @rdname items_functions +#' +#' @export +items_next.STACItem <- function(items, ...) { - # TODO: check if spec can enforce that the same provided base url - # must be used to proceed pagination. - # For security concerns, here, the original base_url will be used in - # subsequent requests of pagination + return(items) +} - # # update query base_url and verb to the returned one - # q$base_url <- gsub("^([^?]+)(\\?.*)?$", "\\1", next_url$href) +#' @rdname items_functions +#' +#' @export +items_next.STACItemCollection <- function(items, ...) { - # get next link parameters from url - params <- .querystring_decode(substring( - gsub("^([^?]+)(\\?.*)?$", "\\2", next_url$href), 2)) + matched <- items_matched(items) - # verify if query params is valid - params <- .validate_query(params = params) - } + q <- doc_query(items) + if (is.null(q)) + return(NULL) - # parse params - params <- parse_params(q, params = params) + # get url of the next page + next_url <- Filter(function(x) x$rel == "next", items$links) + if (length(next_url) == 0) + return(NULL) - next_stac <- RSTACQuery(version = q$version, - base_url = q$base_url, - params = utils::modifyList(q$params, params), - subclass = subclass(q)) + next_url <- next_url[[1]] - # call request - if (q$verb == "GET") { + # create a new stac object with params from the next url + # check for body implementation in next link + if (q$verb == "POST" && all(c("body", "method") %in% names(next_url))) { - content <- get_request(next_stac, ...) - } else if (q$verb == "POST") { + # TODO: check if spec can enforce that the same provided base url + # must be used to proceed pagination. + # For security concerns, here, the original base_url will be used in + # subsequent requests of pagination - content <- post_request(next_stac, ..., encode = q$encode) - } else { + # # update query base_url and verb to the returned one + # q$base_url <- next_url$href - .error("Invalid HTTP method.") + # erase current parameters if merge == FALSE + if (!is.null(next_url$merge) && !next_url$merge) { + q$params <- list() } - # check content response - check_subclass(content, "STACItemCollection") + # get parameters + params <- next_url$body - # check pagination length - if (!is.null(q$params[["limit"]]) && - items_length(content) > as.numeric(q$params[["limit"]])) { + } else { - .error("STAC invalid retrieved page length.") - } + # TODO: check if spec can enforce that the same provided base url + # must be used to proceed pagination. + # For security concerns, here, the original base_url will be used in + # subsequent requests of pagination - # check if result length is valid - if (!is.null(matched) && !is.null(q$params[["limit"]]) && - (items_length(content) != as.numeric(q$params[["limit"]])) && - (items_length(content) + items_length(items) != matched)) { + # # update query base_url and verb to the returned one + # q$base_url <- gsub("^([^?]+)(\\?.*)?$", "\\1", next_url$href) - .error("STAC pagination error.") - } + # get next link parameters from url + params <- .querystring_decode(substring( + gsub("^([^?]+)(\\?.*)?$", "\\2", next_url$href), 2)) - # merge features result into resulting content - content$features <- c(items$features, content$features) + # verify if query params is valid + params <- .validate_query(params = params) + } - # update progress bar - if (progress) - utils::setTxtProgressBar(pb, items_length(content)) + # parse params + params <- parse_params(q, params = params) + + next_stac <- RSTACQuery(version = q$version, + base_url = q$base_url, + params = utils::modifyList(q$params, params), + subclass = subclass(q)) + + # call request + if (q$verb == "GET") { - # prepares next iteration - items <- content + content <- get_request(next_stac, ...) + } else if (q$verb == "POST") { + + content <- post_request(next_stac, ..., encode = q$encode) + } else { + + .error("Invalid HTTP method.") } - # close progress bar - if (progress) { - utils::setTxtProgressBar(pb, matched) - close(pb) + # check content response + check_subclass(content, "STACItemCollection") + + # check pagination length + if (!is.null(q$params[["limit"]]) && + items_length(content) > as.numeric(q$params[["limit"]])) { + + .error("STAC invalid retrieved page length.") } - return(items) + # check if result length is valid + if (!is.null(matched) && !is.null(q$params[["limit"]]) && + (items_length(content) != as.numeric(q$params[["limit"]])) && + (items_length(content) + items_length(items) != matched)) { + + .error("STAC pagination error.") + } + + # merge features result into resulting content + content$features <- c(items$features, content$features) + + # prepares next iteration + items <- content + + items } #' @rdname items_functions @@ -498,6 +534,9 @@ items_assets.STACItemCollection <- function(items, ..., simplify = FALSE) { #' @export items_filter <- function(items, ..., fn = NULL) { + # check items parameter + check_subclass(items, "STACItemCollection") + dots <- substitute(list(...))[-1] if (length(dots) > 0) { @@ -755,8 +794,21 @@ items_group <- function(items, ..., field = NULL, index = NULL) { #' #' } #' +#' @name items_assign_change +NULL + +#' @rdname items_assign_change +#' #' @export -items_sign <- function(items, sign_fn = NULL) { +items_sign <- function(items, sign_fn = NULL, ...) { + + UseMethod("items_sign", items) +} + +#' @rdname items_assign_change +#' +#' @export +items_sign.STACItemCollection <- function(items, sign_fn = NULL) { if (is.null(sign_fn)) { return(items) @@ -764,7 +816,7 @@ items_sign <- function(items, sign_fn = NULL) { if (!is.null(items_matched(items))) { if (items_length(items) != items_matched(items)) - .warning(paste("The number of items in this object does not match the", + .message(paste("The number of items in this object does not match the", "total number of items in the item. If you want to get", "all items, use `items_fetch()`")) } @@ -780,6 +832,20 @@ items_sign <- function(items, sign_fn = NULL) { items } +#' @rdname items_assign_change +#' +#' @export +items_sign.STACItem <- function(items, sign_fn = NULL) { + + if (is.null(sign_fn)) { + return(items) + } + + items <- sign_fn(items) + + items +} + ####Assets function#### #' @title Assets functions @@ -888,6 +954,14 @@ assets_list <- function(items, asset_names = NULL, #' @export assets_select <- function(items, asset_names) { + UseMethod("assets_select", items) +} + +#' @rdname assets_function +#' +#' @export +assets_select.STACItemCollection <- function(items, asset_names) { + if (!all(asset_names %in% items_assets(items, simplify = TRUE))) .error("Invalid 'asset_names' parameter.") @@ -900,11 +974,32 @@ assets_select <- function(items, asset_names) { items } +#' @rdname assets_function +#' +#' @export +assets_select.STACItem <- function(items, asset_names) { + + if (!all(asset_names %in% items_assets(items))) + .error("Invalid 'asset_names' parameter.") + + items$assets <- items$assets[asset_names] + + items +} + #' @rdname assets_function #' #' @export assets_filter <- function(items, ..., fn = NULL) { + UseMethod("assets_filter", items) +} + +#' @rdname assets_function +#' +#' @export +assets_filter.STACItemCollection <- function(items, ..., fn = NULL) { + dots <- substitute(list(...))[-1] if (length(dots) > 0) { @@ -917,6 +1012,12 @@ assets_filter <- function(items, ..., fn = NULL) { items$features <- lapply(items$features, function(item) { sel <- vapply(item$assets, function(asset) { + + # is the searched key in the asset's name? + key <- as.character(dots[[i]][[2]]) + if (!key %in% names(asset)) + return(TRUE) + eval(dots[[i]], envir = asset) }, logical(1)) @@ -940,3 +1041,41 @@ assets_filter <- function(items, ..., fn = NULL) { items } + +#' @rdname assets_function +#' +#' @export +assets_filter.STACItem <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + sel <- vapply(items$assets, function(asset) { + + # is the searched key in the asset's name? + key <- as.character(dots[[i]][[2]]) + if (!key %in% names(asset)) + return(TRUE) + + eval(dots[[i]], envir = asset) + }, logical(1)) + + items$assets <- items$assets[sel] + } + } + + if (!is.null(fn)) { + + sel <- vapply(items$assets, function(asset) { fn(asset) }, logical(1)) + + items$assets <- items$assets[sel] + } + + items +} From cdb18df15589571a41ac934d6914d805919fbff0 Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 21:26:00 +0000 Subject: [PATCH 20/44] add examples for ms planetary --- R/signatures.R | 38 ++++++++++++++++++++++++++++++++++++-- 1 file changed, 36 insertions(+), 2 deletions(-) diff --git a/R/signatures.R b/R/signatures.R index f7a6e2d4..4b6ff883 100644 --- a/R/signatures.R +++ b/R/signatures.R @@ -12,6 +12,20 @@ #' #' @return a `function` that signs each item assets. #' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", +#' datetime = "2019-06-01/2019-08-01") %>% +#' stac_search() %>% +#' get_request() +#' +#' # signing each item href +#' stac_obj %>% items_sign(sign_fn = sign_bdc()) +#' +#' } +#' #' @export sign_bdc <- function(access_token = NULL, ...) { @@ -91,15 +105,35 @@ sign_bdc <- function(access_token = NULL, ...) { #' Planetary Computer servers and the returned content corresponds to the #' token that will be used in the href. #' -#' @param ... additional parameters can be supplied to the `GET` function +#' @param ... additional parameters can be supplied to the `GET` function #' of the `httr` package. +#' @param token_url a `character` with the URL that generates the tokens +#' in the Microsoft service. +#' By default is used: +#' `"https://planetarycomputer.microsoft.com/api/sas/v1/token"` #' #' @return a `function` that signs each item assets. #' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% +#' stac_search(collections = "sentinel-2-l2a", +#' bbox = c(-47.02148, -12.98314, -42.53906,-17.35063)) %>% +#' get_request() +#' +#' # signing each item href +#' stac_obj %>% items_sign(sign_fn = sign_planetary_computer()) +#' +#' } +#' #' @export -sign_planetary_computer <- function(...) { +sign_planetary_computer <- function(..., token_url = NULL) { default_endpoint <- "https://planetarycomputer.microsoft.com/api/sas/v1/token" + if (!is.null(token_url)) + default_endpoint <- token_url + default_max_timeleft <- 300 token <- list() From d602cab12065c0662b3e135d656cf81dd0731be3 Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 21:26:17 +0000 Subject: [PATCH 21/44] update documentation --- DESCRIPTION | 2 +- NAMESPACE | 9 ++++++++ man/assets_function.Rd | 12 +++++++++++ man/{items_sign.Rd => items_assign_change.Rd} | 11 ++++++++-- man/items_functions.Rd | 11 +++++++++- man/sign_bdc.Rd | 15 +++++++++++++ man/sign_planetary_computer.Rd | 21 ++++++++++++++++++- 7 files changed, 76 insertions(+), 5 deletions(-) rename man/{items_sign.Rd => items_assign_change.Rd} (80%) diff --git a/DESCRIPTION b/DESCRIPTION index cd7c7f6c..aefd4f7a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -15,7 +15,7 @@ License: MIT + file LICENSE URL: https://github.com/brazil-data-cube/rstac BugReports: https://github.com/brazil-data-cube/rstac/issues Encoding: UTF-8 -RoxygenNote: 7.1.1 +RoxygenNote: 7.1.2 Depends: R (>= 3.5) Imports: diff --git a/NAMESPACE b/NAMESPACE index 21ddf8cc..de7d2f42 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,6 +8,10 @@ S3method(after_response,item_id) S3method(after_response,items) S3method(after_response,search) S3method(after_response,stac) +S3method(assets_filter,STACItem) +S3method(assets_filter,STACItemCollection) +S3method(assets_select,STACItem) +S3method(assets_select,STACItemCollection) S3method(before_request,RSTACQuery) S3method(before_request,collection_id) S3method(before_request,collections) @@ -40,6 +44,10 @@ S3method(items_length,STACItem) S3method(items_length,STACItemCollection) S3method(items_matched,STACItem) S3method(items_matched,STACItemCollection) +S3method(items_next,STACItem) +S3method(items_next,STACItemCollection) +S3method(items_sign,STACItem) +S3method(items_sign,STACItemCollection) S3method(parse_params,ext_query) S3method(parse_params,search) S3method(print,RSTACQuery) @@ -81,6 +89,7 @@ export(items_filter) export(items_group) export(items_length) export(items_matched) +export(items_next) export(items_reap) export(items_sign) export(omit_query_params) diff --git a/man/assets_function.Rd b/man/assets_function.Rd index e4055178..f8e892b9 100644 --- a/man/assets_function.Rd +++ b/man/assets_function.Rd @@ -4,7 +4,11 @@ \alias{assets_function} \alias{assets_list} \alias{assets_select} +\alias{assets_select.STACItemCollection} +\alias{assets_select.STACItem} \alias{assets_filter} +\alias{assets_filter.STACItemCollection} +\alias{assets_filter.STACItem} \title{Assets functions} \usage{ assets_list( @@ -17,7 +21,15 @@ assets_list( assets_select(items, asset_names) +\method{assets_select}{STACItemCollection}(items, asset_names) + +\method{assets_select}{STACItem}(items, asset_names) + assets_filter(items, ..., fn = NULL) + +\method{assets_filter}{STACItemCollection}(items, ..., fn = NULL) + +\method{assets_filter}{STACItem}(items, ..., fn = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing diff --git a/man/items_sign.Rd b/man/items_assign_change.Rd similarity index 80% rename from man/items_sign.Rd rename to man/items_assign_change.Rd index 7edcb69a..62eb9a51 100644 --- a/man/items_sign.Rd +++ b/man/items_assign_change.Rd @@ -1,10 +1,17 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/documents.R -\name{items_sign} +\name{items_assign_change} +\alias{items_assign_change} \alias{items_sign} +\alias{items_sign.STACItemCollection} +\alias{items_sign.STACItem} \title{Utility functions} \usage{ -items_sign(items, sign_fn = NULL) +items_sign(items, sign_fn = NULL, ...) + +\method{items_sign}{STACItemCollection}(items, sign_fn = NULL) + +\method{items_sign}{STACItem}(items, sign_fn = NULL) } \arguments{ \item{items}{a \code{STACItemCollection} object representing diff --git a/man/items_functions.Rd b/man/items_functions.Rd index 721f9e93..9560aa42 100644 --- a/man/items_functions.Rd +++ b/man/items_functions.Rd @@ -11,6 +11,9 @@ \alias{items_fetch} \alias{items_fetch.STACItem} \alias{items_fetch.STACItemCollection} +\alias{items_next} +\alias{items_next.STACItem} +\alias{items_next.STACItemCollection} \alias{items_datetime} \alias{items_datetime.STACItem} \alias{items_datetime.STACItemCollection} @@ -40,6 +43,12 @@ items_fetch(items, ...) \method{items_fetch}{STACItemCollection}(items, ..., progress = TRUE, matched_field = NULL) +items_next(items, ...) + +\method{items_next}{STACItem}(items, ...) + +\method{items_next}{STACItemCollection}(items, ...) + items_datetime(items) \method{items_datetime}{STACItem}(items) @@ -120,7 +129,7 @@ For \code{items_filter} function is used to pass logical expressions. \examples{ \dontrun{ -x <- stac("http://brazildatacube.dpi.inpe.br/stac") \%>\% +x <- stac("https://brazildatacube.dpi.inpe.br/stac") \%>\% stac_search(collections = "CB4_64_16D_STK-1") \%>\% stac_search(limit = 500) \%>\% get_request() diff --git a/man/sign_bdc.Rd b/man/sign_bdc.Rd index 06806206..a91916ac 100644 --- a/man/sign_bdc.Rd +++ b/man/sign_bdc.Rd @@ -21,3 +21,18 @@ a \code{function} that signs each item assets. To sign the hrefs with your token you need to store it in an environment variable in \code{BDC_ACCESS_KEY}or use \code{acess_token} parameter. } +\examples{ +\donttest{ +# STACItemCollection object +stac_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", + datetime = "2019-06-01/2019-08-01") \%>\% + stac_search() \%>\% + get_request() + +# signing each item href +stac_obj \%>\% items_sign(sign_fn = sign_bdc()) + +} + +} diff --git a/man/sign_planetary_computer.Rd b/man/sign_planetary_computer.Rd index 99f393ca..7a073f72 100644 --- a/man/sign_planetary_computer.Rd +++ b/man/sign_planetary_computer.Rd @@ -5,11 +5,16 @@ \title{Signature in hrefs provided by the STAC from Microsoft's Planetary Computer.} \usage{ -sign_planetary_computer(...) +sign_planetary_computer(..., token_url = NULL) } \arguments{ \item{...}{additional parameters can be supplied to the \code{GET} function of the \code{httr} package.} + +\item{token_url}{a \code{character} with the URL that generates the tokens +in the Microsoft service. +By default is used: +\code{"https://planetarycomputer.microsoft.com/api/sas/v1/token"}} } \value{ a \code{function} that signs each item assets. @@ -19,3 +24,17 @@ To perform the signing of the hrefs a request is sent to Planetary Computer servers and the returned content corresponds to the token that will be used in the href. } +\examples{ +\donttest{ +# STACItemCollection object +stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") \%>\% + stac_search(collections = "sentinel-2-l2a", + bbox = c(-47.02148, -12.98314, -42.53906,-17.35063)) \%>\% + get_request() + +# signing each item href +stac_obj \%>\% items_sign(sign_fn = sign_planetary_computer()) + +} + +} From 271d4c99f62dfd6c6225b788eadb6dd12b8e5b0c Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 22:50:41 +0000 Subject: [PATCH 22/44] closes #69 --- R/{assets_download.R => assets-funs.R} | 236 ++++++++++++++++ R/{collections.R => collections-query.R} | 0 R/{deprec-functions.R => deprec-funs.R} | 0 R/document-funs.R | 88 ++++++ R/{documents.R => items-funs.R} | 327 +---------------------- R/{items.R => items-query.R} | 0 R/{query.R => query-funs.R} | 0 R/{stac.R => stac-query.R} | 0 man/assets_download.Rd | 2 +- man/assets_function.Rd | 2 +- man/collections.Rd | 2 +- man/doc_query.Rd | 4 +- man/extensions.Rd | 2 +- man/items.Rd | 2 +- man/items_assign_change.Rd | 2 +- man/items_bands.Rd | 2 +- man/items_filter.Rd | 2 +- man/items_functions.Rd | 2 +- man/items_group.Rd | 2 +- man/items_reap.Rd | 2 +- man/items_utils.Rd | 2 +- man/stac.Rd | 2 +- tests/testthat/test-assets_functions.R | 4 +- 23 files changed, 342 insertions(+), 343 deletions(-) rename R/{assets_download.R => assets-funs.R} (55%) rename R/{collections.R => collections-query.R} (100%) rename R/{deprec-functions.R => deprec-funs.R} (100%) create mode 100644 R/document-funs.R rename R/{documents.R => items-funs.R} (71%) rename R/{items.R => items-query.R} (100%) rename R/{query.R => query-funs.R} (100%) rename R/{stac.R => stac-query.R} (100%) diff --git a/R/assets_download.R b/R/assets-funs.R similarity index 55% rename from R/assets_download.R rename to R/assets-funs.R index 9e96c544..97c60b01 100644 --- a/R/assets_download.R +++ b/R/assets-funs.R @@ -234,3 +234,239 @@ assets_download <- function(items, return(assets) } + +#' @title Assets functions +#' +#' @description This function returns the `date`, `band` and +#' `URL` fields for each assets of an `STACItemCollection` object. +#' For the URL you can add the GDAL library drivers for the following schemes: +#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). +#' +#' @param items a `STACItemCollection` object representing +#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. +#' +#' @param assets_names `r lifecycle::badge('deprecated')` +#' use `asset_names` parameter instead. +#' +#' @param asset_names a `character` with the assets names to be +#' filtered. If `NULL` (default) all assets will be returned.. +#' +#' @param sort a `logical` if true the dates will be sorted +#' in increasing order. By default, the dates are sorted. +#' +#' @param gdal_vsi_resolution a `logical` if true, gdal drivers are +#' included in the URL of each asset. The following schemes are supported: +#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). +#' +#' @param ... additional arguments. See details. +#' +#' @param fn a `function` that will be used to filter the attributes +#' listed in the properties. +#' +#' @return a `list` with the attributes of date, bands and paths. +#' +#' @examples +#' \donttest{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% assets_list(assets_names = c("EVI", "NDVI")) +#' } +#' +#' @name assets_function +NULL + +#' @rdname assets_function +#' @export +assets_list <- function(items, asset_names = NULL, + sort = TRUE, gdal_vsi_resolution = TRUE, + assets_names = deprecated()) { + + + if (lifecycle::is_present(assets_names)) { + + # Signal the deprecation to the user + lifecycle::deprecate_soft("0.9.1-5", + "rstac::assets_download(assets_names = )", + "rstac::assets_download(asset_names = )") + + # Deal with the deprecated argument for compatibility + asset_names <- assets_names + } + + if (is.null(asset_names)) + asset_names <- items_fields(items, "assets") + + timeline <- items_reap(items, field = c("properties", "datetime")) + index <- seq_along(timeline) + if (sort) index <- order(timeline) + + timeline <- timeline[index] + assets <- list(date = rep(timeline, length(unique(asset_names)))) + + for (b in asset_names) { + + href <- items_reap(items, field = c("assets", b, "href"))[index] + + if (gdal_vsi_resolution) { + + # for http or https schema + paste_index <- grepl("^http|[s]://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsicurl", href[paste_index], sep = "/") + + # for S3 schema + paste_index <- grepl("^s3://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsis3", gsub("^s3://(.*)$", "\\1", + href[paste_index]), sep = "/") + # for gs schema + paste_index <- grepl("^gs://.*", href) + if (any(paste_index)) + href[paste_index] <- paste("/vsigs", gsub("^gs://(.*)$", "\\1", + href[paste_index]), sep = "/") + } + assets$band <- c(rep(b, length(href)), assets$band) + assets$path <- c(href, assets$path) + } + assets +} + +#' @rdname assets_function +#' +#' @export +assets_select <- function(items, asset_names) { + + UseMethod("assets_select", items) +} + +#' @rdname assets_function +#' +#' @export +assets_select.STACItemCollection <- function(items, asset_names) { + + if (!all(asset_names %in% items_assets(items, simplify = TRUE))) + .error("Invalid 'asset_names' parameter.") + + items$features <- lapply(items$features, function(item) { + item$assets <- item$assets[asset_names] + + item + }) + + items +} + +#' @rdname assets_function +#' +#' @export +assets_select.STACItem <- function(items, asset_names) { + + if (!all(asset_names %in% items_assets(items))) + .error("Invalid 'asset_names' parameter.") + + items$assets <- items$assets[asset_names] + + items +} + +#' @rdname assets_function +#' +#' @export +assets_filter <- function(items, ..., fn = NULL) { + + UseMethod("assets_filter", items) +} + +#' @rdname assets_function +#' +#' @export +assets_filter.STACItemCollection <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + items$features <- lapply(items$features, function(item) { + + sel <- vapply(item$assets, function(asset) { + + tryCatch({ + eval(dots[[i]], envir = asset, enclos = baseenv()) + }, error = function(e) { NA }) + }, logical(1)) + + if (all(is.na(sel))) + .error("Invalid condition arguments.") + + sel[is.na(sel)] <- FALSE + + item$assets <- item$assets[sel] + + item + }) + } + } + + if (!is.null(fn)) { + + items$features <- lapply(items$features, function(item) { + + sel <- vapply(item$assets, function(asset) { fn(asset) }, logical(1)) + + item$assets <- item$assets[sel] + item + }) + } + + items +} + +#' @rdname assets_function +#' +#' @export +assets_filter.STACItem <- function(items, ..., fn = NULL) { + + dots <- substitute(list(...))[-1] + + if (length(dots) > 0) { + + if (!is.null(names(dots))) + .error("Invalid filter arguments.") + + for (i in seq_along(dots)) { + + sel <- vapply(items$assets, function(asset) { + + tryCatch({ + eval(dots[[i]], envir = asset, enclos = baseenv()) + }, error = function(e) { NA }) + }, logical(1)) + + if (all(is.na(sel))) + .error("Invalid condition arguments.") + + sel[is.na(sel)] <- FALSE + + items$assets <- items$assets[sel] + } + } + + if (!is.null(fn)) { + + sel <- vapply(items$assets, function(asset) { fn(asset) }, logical(1)) + + items$assets <- items$assets[sel] + } + + items +} diff --git a/R/collections.R b/R/collections-query.R similarity index 100% rename from R/collections.R rename to R/collections-query.R diff --git a/R/deprec-functions.R b/R/deprec-funs.R similarity index 100% rename from R/deprec-functions.R rename to R/deprec-funs.R diff --git a/R/document-funs.R b/R/document-funs.R new file mode 100644 index 00000000..758fdb3f --- /dev/null +++ b/R/document-funs.R @@ -0,0 +1,88 @@ +#' @title Document development functions +#' +#' @describeIn extensions +#' The `RSTACDocument()` function is a constructor of +#' STAC documents. Currently, there are five STAC documents defined: +#' \itemize{ +#' \item `STACCatalog` +#' \item `STACCollection` +#' \item `STACCollectionList` +#' \item `STACItem` +#' \item `STACItemCollection` +#' } +#' +#' Each document class is associated with STAC API endpoints. +#' As soon as new STAC documents are proposed in the specification, new +#' classes can be created in the `rstac` package. +#' +#' Let `version` parameter `NULL` to detect version automatically. +#' +#' @param content a `list` data structure representing the JSON file +#' received in HTTP response (see [content_response()] function) +#' +#' @param q a `RSTACQuery` object expressing the STAC query used +#' to retrieve the document. +#' +#' @param subclass a `character` corresponding to the subclass of the +#' document to be created. +#' +#' @return +#' The `RSTACDocument()` function returns a `RSTACDocument` object +#' with subclass defined by `subclass` parameter. +#' +#' @export +RSTACDocument <- function(content, q, subclass) { + + structure( + content, + query = q, + class = c(subclass, "RSTACDocument", "list") + ) +} + +#' @export +subclass.RSTACDocument <- function(x) { + + class(x)[[1]] +} + +#' @export +check_subclass.RSTACDocument <- function(x, subclasses) { + + if (!subclass(x) %in% subclasses) + .error("Expecting %s document(s).", + paste0("`", subclasses, "`", collapse = " or ")) +} + +#' @title Document utils functions +#' +#' @param d an `RSTACDocument` object +#' +#' @return a `RSTACQuery` object with the predecessor subclass with the +#' fields used in the request. +#' +#' @export +doc_query <- function(d) { + + .check_obj(d, "RSTACDocument") + + attr(d, "query") +} + +#' @export +stac_version.RSTACDocument <- function(x, ...) { + + if (is.null(x$stac_version)) + return(stac_version(doc_query(x))) + x$stac_version +} + +#' @export +stac_version.STACCollectionList <- function(x, ...) { + + q <- doc_query(x) + if (!is.null(q)) + return(stac_version(q)) + if (length(x$collections) > 0) + return(x$collections[[1]]$stac_version) +} diff --git a/R/documents.R b/R/items-funs.R similarity index 71% rename from R/documents.R rename to R/items-funs.R index 562d498b..175b4e81 100644 --- a/R/documents.R +++ b/R/items-funs.R @@ -1,94 +1,3 @@ -#' @title Document development functions -#' -#' @describeIn extensions -#' The `RSTACDocument()` function is a constructor of -#' STAC documents. Currently, there are five STAC documents defined: -#' \itemize{ -#' \item `STACCatalog` -#' \item `STACCollection` -#' \item `STACCollectionList` -#' \item `STACItem` -#' \item `STACItemCollection` -#' } -#' -#' Each document class is associated with STAC API endpoints. -#' As soon as new STAC documents are proposed in the specification, new -#' classes can be created in the `rstac` package. -#' -#' Let `version` parameter `NULL` to detect version automatically. -#' -#' @param content a `list` data structure representing the JSON file -#' received in HTTP response (see [content_response()] function) -#' -#' @param q a `RSTACQuery` object expressing the STAC query used -#' to retrieve the document. -#' -#' @param subclass a `character` corresponding to the subclass of the -#' document to be created. -#' -#' @return -#' The `RSTACDocument()` function returns a `RSTACDocument` object -#' with subclass defined by `subclass` parameter. -#' -#' @export -RSTACDocument <- function(content, q, subclass) { - - structure( - content, - query = q, - class = c(subclass, "RSTACDocument", "list") - ) -} - -#' @export -subclass.RSTACDocument <- function(x) { - - class(x)[[1]] -} - -#' @export -check_subclass.RSTACDocument <- function(x, subclasses) { - - if (!subclass(x) %in% subclasses) - .error("Expecting %s document(s).", - paste0("`", subclasses, "`", collapse = " or ")) -} - -#' @title Document utils functions -#' -#' @param d `RSTACDocument` object -#' -#' @return a `RSTACQuery` object with the predecessor subclass with the -#' fields used in the request. -#' -#' @export -doc_query <- function(d) { - - .check_obj(d, "RSTACDocument") - - attr(d, "query") -} - -#' @export -stac_version.RSTACDocument <- function(x, ...) { - - if (is.null(x$stac_version)) - return(stac_version(doc_query(x))) - x$stac_version -} - -#' @export -stac_version.STACCollectionList <- function(x, ...) { - - q <- doc_query(x) - if (!is.null(q)) - return(stac_version(q)) - if (length(x$collections) > 0) - return(x$collections[[1]]$stac_version) -} - -####Items function#### - #' @title STACItemCollection functions #' #' @description @@ -283,7 +192,7 @@ items_fetch.STACItemCollection <- function(items, ..., content <- items_next(items) if (!is.null(content)) - items <- content + items <- content else break @@ -845,237 +754,3 @@ items_sign.STACItem <- function(items, sign_fn = NULL) { items } - -####Assets function#### - -#' @title Assets functions -#' -#' @description This function returns the `date`, `band` and -#' `URL` fields for each assets of an `STACItemCollection` object. -#' For the URL you can add the GDAL library drivers for the following schemes: -#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param assets_names `r lifecycle::badge('deprecated')` -#' use `asset_names` parameter instead. -#' -#' @param asset_names a `character` with the assets names to be -#' filtered. If `NULL` (default) all assets will be returned.. -#' -#' @param sort a `logical` if true the dates will be sorted -#' in increasing order. By default, the dates are sorted. -#' -#' @param gdal_vsi_resolution a `logical` if true, gdal drivers are -#' included in the URL of each asset. The following schemes are supported: -#' HTTP/HTTPS files, S3 (AWS S3) and GS (Google Cloud Storage). -#' -#' @param ... additional arguments. See details. -#' -#' @param fn a `function` that will be used to filter the attributes -#' listed in the properties. -#' -#' @return a `list` with the attributes of date, bands and paths. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% assets_list(assets_names = c("EVI", "NDVI")) -#' } -#' -#' @name assets_function -NULL - -#' @rdname assets_function -#' @export -assets_list <- function(items, asset_names = NULL, - sort = TRUE, gdal_vsi_resolution = TRUE, - assets_names = deprecated()) { - - - if (lifecycle::is_present(assets_names)) { - - # Signal the deprecation to the user - lifecycle::deprecate_soft("0.9.1-5", - "rstac::assets_download(assets_names = )", - "rstac::assets_download(asset_names = )") - - # Deal with the deprecated argument for compatibility - asset_names <- assets_names - } - - if (is.null(asset_names)) - asset_names <- items_fields(items, "assets") - - timeline <- items_reap(items, field = c("properties", "datetime")) - index <- seq_along(timeline) - if (sort) index <- order(timeline) - - timeline <- timeline[index] - assets <- list(date = rep(timeline, length(unique(asset_names)))) - - for (b in asset_names) { - - href <- items_reap(items, field = c("assets", b, "href"))[index] - - if (gdal_vsi_resolution) { - - # for http or https schema - paste_index <- grepl("^http|[s]://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsicurl", href[paste_index], sep = "/") - - # for S3 schema - paste_index <- grepl("^s3://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsis3", gsub("^s3://(.*)$", "\\1", - href[paste_index]), sep = "/") - # for gs schema - paste_index <- grepl("^gs://.*", href) - if (any(paste_index)) - href[paste_index] <- paste("/vsigs", gsub("^gs://(.*)$", "\\1", - href[paste_index]), sep = "/") - } - assets$band <- c(rep(b, length(href)), assets$band) - assets$path <- c(href, assets$path) - } - assets -} - -#' @rdname assets_function -#' -#' @export -assets_select <- function(items, asset_names) { - - UseMethod("assets_select", items) -} - -#' @rdname assets_function -#' -#' @export -assets_select.STACItemCollection <- function(items, asset_names) { - - if (!all(asset_names %in% items_assets(items, simplify = TRUE))) - .error("Invalid 'asset_names' parameter.") - - items$features <- lapply(items$features, function(item) { - item$assets <- item$assets[asset_names] - - item - }) - - items -} - -#' @rdname assets_function -#' -#' @export -assets_select.STACItem <- function(items, asset_names) { - - if (!all(asset_names %in% items_assets(items))) - .error("Invalid 'asset_names' parameter.") - - items$assets <- items$assets[asset_names] - - items -} - -#' @rdname assets_function -#' -#' @export -assets_filter <- function(items, ..., fn = NULL) { - - UseMethod("assets_filter", items) -} - -#' @rdname assets_function -#' -#' @export -assets_filter.STACItemCollection <- function(items, ..., fn = NULL) { - - dots <- substitute(list(...))[-1] - - if (length(dots) > 0) { - - if (!is.null(names(dots))) - .error("Invalid filter arguments.") - - for (i in seq_along(dots)) { - - items$features <- lapply(items$features, function(item) { - - sel <- vapply(item$assets, function(asset) { - - # is the searched key in the asset's name? - key <- as.character(dots[[i]][[2]]) - if (!key %in% names(asset)) - return(TRUE) - - eval(dots[[i]], envir = asset) - }, logical(1)) - - item$assets <- item$assets[sel] - - item - }) - } - } - - if (!is.null(fn)) { - - items$features <- lapply(items$features, function(item) { - - sel <- vapply(item$assets, function(asset) { fn(asset) }, logical(1)) - - item$assets <- item$assets[sel] - item - }) - } - - items -} - -#' @rdname assets_function -#' -#' @export -assets_filter.STACItem <- function(items, ..., fn = NULL) { - - dots <- substitute(list(...))[-1] - - if (length(dots) > 0) { - - if (!is.null(names(dots))) - .error("Invalid filter arguments.") - - for (i in seq_along(dots)) { - - sel <- vapply(items$assets, function(asset) { - - # is the searched key in the asset's name? - key <- as.character(dots[[i]][[2]]) - if (!key %in% names(asset)) - return(TRUE) - - eval(dots[[i]], envir = asset) - }, logical(1)) - - items$assets <- items$assets[sel] - } - } - - if (!is.null(fn)) { - - sel <- vapply(items$assets, function(asset) { fn(asset) }, logical(1)) - - items$assets <- items$assets[sel] - } - - items -} diff --git a/R/items.R b/R/items-query.R similarity index 100% rename from R/items.R rename to R/items-query.R diff --git a/R/query.R b/R/query-funs.R similarity index 100% rename from R/query.R rename to R/query-funs.R diff --git a/R/stac.R b/R/stac-query.R similarity index 100% rename from R/stac.R rename to R/stac-query.R diff --git a/man/assets_download.Rd b/man/assets_download.Rd index 1f01090a..96d5450c 100644 --- a/man/assets_download.Rd +++ b/man/assets_download.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/assets_download.R +% Please edit documentation in R/assets-funs.R \name{assets_download} \alias{assets_download} \title{Downloads assets via STAC API} diff --git a/man/assets_function.Rd b/man/assets_function.Rd index f8e892b9..e9379304 100644 --- a/man/assets_function.Rd +++ b/man/assets_function.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/assets-funs.R \name{assets_function} \alias{assets_function} \alias{assets_list} diff --git a/man/collections.Rd b/man/collections.Rd index 2047d52c..1e597b0d 100644 --- a/man/collections.Rd +++ b/man/collections.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/collections.R +% Please edit documentation in R/collections-query.R \name{collections} \alias{collections} \title{Endpoint functions} diff --git a/man/doc_query.Rd b/man/doc_query.Rd index ed526286..8e2abb69 100644 --- a/man/doc_query.Rd +++ b/man/doc_query.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/document-funs.R \name{doc_query} \alias{doc_query} \title{Document utils functions} @@ -7,7 +7,7 @@ doc_query(d) } \arguments{ -\item{d}{\code{RSTACDocument} object} +\item{d}{an \code{RSTACDocument} object} } \value{ a \code{RSTACQuery} object with the predecessor subclass with the diff --git a/man/extensions.Rd b/man/extensions.Rd index 5b453cb5..3add62fa 100644 --- a/man/extensions.Rd +++ b/man/extensions.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R, R/extensions.R, R/query.R +% Please edit documentation in R/document-funs.R, R/extensions.R, R/query-funs.R \name{RSTACDocument} \alias{RSTACDocument} \alias{extensions} diff --git a/man/items.Rd b/man/items.Rd index 1704e88b..a00b7acb 100644 --- a/man/items.Rd +++ b/man/items.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items.R +% Please edit documentation in R/items-query.R \name{items} \alias{items} \title{Endpoint functions} diff --git a/man/items_assign_change.Rd b/man/items_assign_change.Rd index 62eb9a51..262633c3 100644 --- a/man/items_assign_change.Rd +++ b/man/items_assign_change.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_assign_change} \alias{items_assign_change} \alias{items_sign} diff --git a/man/items_bands.Rd b/man/items_bands.Rd index 11dd8618..c1a5fd83 100644 --- a/man/items_bands.Rd +++ b/man/items_bands.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/deprec-functions.R +% Please edit documentation in R/deprec-funs.R \name{items_bands} \alias{items_bands} \title{STACItemCollection function} diff --git a/man/items_filter.Rd b/man/items_filter.Rd index 2775a820..fc61f014 100644 --- a/man/items_filter.Rd +++ b/man/items_filter.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_filter} \alias{items_filter} \title{Utility functions} diff --git a/man/items_functions.Rd b/man/items_functions.Rd index 9560aa42..f3ca61df 100644 --- a/man/items_functions.Rd +++ b/man/items_functions.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_functions} \alias{items_functions} \alias{items_length} diff --git a/man/items_group.Rd b/man/items_group.Rd index eb9d6c2d..007c337e 100644 --- a/man/items_group.Rd +++ b/man/items_group.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_group} \alias{items_group} \title{Utility functions} diff --git a/man/items_reap.Rd b/man/items_reap.Rd index a993515d..e32432e9 100644 --- a/man/items_reap.Rd +++ b/man/items_reap.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_reap} \alias{items_reap} \title{Utility functions} diff --git a/man/items_utils.Rd b/man/items_utils.Rd index 1e83e2ea..022963f6 100644 --- a/man/items_utils.Rd +++ b/man/items_utils.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/documents.R +% Please edit documentation in R/items-funs.R \name{items_utils} \alias{items_utils} \alias{items_fields} diff --git a/man/stac.Rd b/man/stac.Rd index 85c1ea1c..55386e60 100644 --- a/man/stac.Rd +++ b/man/stac.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/stac.R +% Please edit documentation in R/stac-query.R \name{stac} \alias{stac} \title{Endpoint functions} diff --git a/tests/testthat/test-assets_functions.R b/tests/testthat/test-assets_functions.R index df457a11..c95f8f6e 100644 --- a/tests/testthat/test-assets_functions.R +++ b/tests/testthat/test-assets_functions.R @@ -112,7 +112,7 @@ testthat::test_that("assets functions", { object = assets_filter(stac_items, fn = function(x) { if ("eo:bands" %in% names(x)) return(x$`eo:bands` < 6) - return(TRUE) + return(FALSE) }), class = c("STACItemCollection", "RSTACDocument") ) @@ -122,7 +122,7 @@ testthat::test_that("assets functions", { object = assets_filter(stac_items, fn = function(x) { if ("eo:bands" %in% names(x)) return(x$`eo:bands` < 6) - return(TRUE) + return(FALSE) }), class = c("STACItem", "RSTACDocument") ) From c170551e8d1320103c4eb504f2965a8f2eeb7746 Mon Sep 17 00:00:00 2001 From: Felipe Date: Fri, 24 Sep 2021 23:19:10 +0000 Subject: [PATCH 23/44] closes #19 --- NEWS.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/NEWS.md b/NEWS.md index 768622f6..b5ca5cc6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -22,6 +22,21 @@ * Change version 0.9.0 to 0.9.0-2 in DESCRIPTION * Fix assets without extension in assets_download function +# rstac 0.9.0-1 (Released 2020-10-20) + +* Update ext_query function +* Add magrittr package in depends +* Add function items_bands +* Introduces items_bbox and items_datetime functions +* Update print.R file +* Fix items_fetch +* Update 'assets_download.R' and others functions +* Add function 'get_assets_name' +* Add overwrite and items_max parameter; solve issue #10 +* Fix bug in stac_matched and update documentation +* Change function name '.verify_datime()' to 'parse_datetime()' +* Rename extension_query -> ext_query + # rstac 0.9.0 (Released 2020-09-18) * Fix issue from CRAN. From 2b34d53844a065574f432353c04aaa9c987aebd1 Mon Sep 17 00:00:00 2001 From: Rolf Simoes Date: Fri, 22 Oct 2021 21:51:07 -0300 Subject: [PATCH 24/44] Solve #73 --- DESCRIPTION | 3 ++- README.Rmd | 10 +++++++++ README.md | 62 ++++++++++++++++++++++++++++++--------------------- inst/CITATION | 22 ++++++++++++++++++ man/rstac.Rd | 5 +---- 5 files changed, 72 insertions(+), 30 deletions(-) create mode 100644 inst/CITATION diff --git a/DESCRIPTION b/DESCRIPTION index aefd4f7a..f247bc47 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,8 @@ Authors@R: Description: Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification - (). + (). For further details see + DOI: 10.1109/IGARSS47720.2021.9553518 License: MIT + file LICENSE URL: https://github.com/brazil-data-cube/rstac BugReports: https://github.com/brazil-data-cube/rstac/issues diff --git a/README.Rmd b/README.Rmd index 904bac3e..b76aec6d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -189,3 +189,13 @@ You can get a full explanation about each STAC (v1.0.0) endpoint at [STAC API sp documentation with examples on how to use each endpoint and other functions available in the `rstac` package can be obtained by typing `?rstac` in R console. + +## Citation + +To cite rstac in publications use: + +R. Simoes, F. C. de Souza, M. Zaglia, G. R. de Queiroz, R. D. C. dos Santos + and K. R. Ferreira, "Rstac: An R Package to Access Spatiotemporal Asset + Catalog Satellite Imagery," 2021 IEEE International Geoscience and Remote + Sensing Symposium IGARSS, 2021, pp. 7674-7677, doi: + 10.1109/IGARSS47720.2021.9553518. diff --git a/README.md b/README.md index a0b5f0bb..009d8fda 100644 --- a/README.md +++ b/README.md @@ -29,7 +29,7 @@ geospatial information assets. The specification can be consulted in . R client library for STAC (`rstac`) was designed to fully support STAC -API v1.0.0. It also supports earlier versions (\>= v0.8.0). +API v1.0.0. It also supports earlier versions (>= v0.8.0). ## Installation @@ -61,15 +61,15 @@ library(magrittr) # for pipe (%>%) in examples `rstac` implements the following STAC endpoints: | **STAC** endpoints | `rstac` functions | API version | -| :------------------------------------------- | :--------------------------- | :---------- | -| `/` | `stac()` | \>= 0.9.0 | -| `/stac` | `stac()` | \< 0.9.0 | -| `/collections` | `collections()` | \>= 0.9.0 | -| `/collections/{collectionId}` | `collections(collection_id)` | \>= 0.9.0 | -| `/collections/{collectionId}/items` | `items()` | \>= 0.9.0 | -| `/collections/{collectionId}/items/{itemId}` | `items(feature_id)` | \>= 0.9.0 | -| `/search` | `stac_search()` | \>= 0.9.0 | -| `/stac/search` | `stac_search()` | \< 0.9.0 | +|:---------------------------------------------|:-----------------------------|:------------| +| `/` | `stac()` | >= 0.9.0 | +| `/stac` | `stac()` | < 0.9.0 | +| `/collections` | `collections()` | >= 0.9.0 | +| `/collections/{collectionId}` | `collections(collection_id)` | >= 0.9.0 | +| `/collections/{collectionId}/items` | `items()` | >= 0.9.0 | +| `/collections/{collectionId}/items/{itemId}` | `items(feature_id)` | >= 0.9.0 | +| `/search` | `stac_search()` | >= 0.9.0 | +| `/stac/search` | `stac_search()` | < 0.9.0 | These functions can be used to retrieve information from a STAC API service. The code bellow creates a `stac` object and list the available @@ -107,19 +107,21 @@ it_obj <- s_obj %>% it_obj #> ###STACItemCollection -#> - matched feature(s): 236 -#> - features (10 item(s)): -#> - CB4_64_16D_STK_v001_022024_2021-02-02_2021-02-17 -#> - CB4_64_16D_STK_v001_022025_2021-02-02_2021-02-17 -#> - CB4_64_16D_STK_v001_022024_2021-01-17_2021-02-01 -#> - CB4_64_16D_STK_v001_022025_2021-01-17_2021-02-01 -#> - CB4_64_16D_STK_v001_022024_2021-01-01_2021-01-16 -#> - CB4_64_16D_STK_v001_022025_2021-01-01_2021-01-16 -#> - CB4_64_16D_STK_v001_022024_2020-12-18_2020-12-31 -#> - CB4_64_16D_STK_v001_022025_2020-12-18_2020-12-31 -#> - CB4_64_16D_STK_v001_022024_2020-12-02_2020-12-17 -#> - CB4_64_16D_STK_v001_022025_2020-12-02_2020-12-17 -#> - field(s): type, links, context, features +#> - matched feature(s): 264 +#> - features (10 item(s) / 254 not fetched): +#> - CB4_64_16D_STK_v001_022024_2021-09-14_2021-09-29 +#> - CB4_64_16D_STK_v001_022025_2021-09-14_2021-09-29 +#> - CB4_64_16D_STK_v001_022024_2021-08-29_2021-09-13 +#> - CB4_64_16D_STK_v001_022025_2021-08-29_2021-09-13 +#> - CB4_64_16D_STK_v001_022024_2021-08-13_2021-08-28 +#> - CB4_64_16D_STK_v001_022025_2021-08-13_2021-08-28 +#> - CB4_64_16D_STK_v001_022024_2021-07-28_2021-08-12 +#> - CB4_64_16D_STK_v001_022025_2021-07-28_2021-08-12 +#> - CB4_64_16D_STK_v001_022024_2021-07-12_2021-07-27 +#> - CB4_64_16D_STK_v001_022025_2021-07-12_2021-07-27 +#> - assets: +#> EVI, NDVI, CMASK, BAND13, BAND14, BAND15, BAND16, CLEAROB, TOTALOB, thumbnail, PROVENANCE +#> - other field(s): type, links, context, features ``` The `rstac` uses the [httr](https://github.com/r-lib/httr) package to @@ -148,7 +150,7 @@ criteria: ``` r # it_obj variable from the last code example it_obj %>% items_matched() -#> [1] 236 +#> [1] 264 ``` However, if we count how many items there are in `it_obj` variable, we @@ -165,7 +167,7 @@ it_obj %>% items_length() # (but don't stored them back in it_obj) it_obj %>% items_fetch(progress = FALSE) %>% items_length() -#> [1] 236 +#> [1] 264 ``` ### Download assets @@ -218,3 +220,13 @@ spec](https://github.com/radiantearth/stac-api-spec/tree/master/ogcapi-features) A detailed documentation with examples on how to use each endpoint and other functions available in the `rstac` package can be obtained by typing `?rstac` in R console. + +## Citation + +To cite rstac in publications use: + +R. Simoes, F. C. de Souza, M. Zaglia, G. R. de Queiroz, R. D. C. dos +Santos and K. R. Ferreira, “Rstac: An R Package to Access Spatiotemporal +Asset Catalog Satellite Imagery,” 2021 IEEE International Geoscience and +Remote Sensing Symposium IGARSS, 2021, pp. 7674-7677, doi: +10.1109/IGARSS47720.2021.9553518. diff --git a/inst/CITATION b/inst/CITATION new file mode 100644 index 00000000..38e75097 --- /dev/null +++ b/inst/CITATION @@ -0,0 +1,22 @@ +citHeader("To cite rstac in publications use:") + +citEntry(entry = "InProceedings", + title = "Rstac: An R Package to Access Spatiotemporal Asset Catalog Satellite Imagery", + author = personList(as.person("Rolf Simoes"), + as.person("Felipe Souza"), + as.person("Matheus Zaglia"), + as.person("Gilberto Ribeiro Queiroz"), + as.person("Rafael Santos"), + as.person("Karine Ferreira")), + booktitle = "2021 IEEE International Geoscience and Remote Sensing Symposium IGARSS", + year = "2021", + pages = "7674-7677", + doi = "10.1109/IGARSS47720.2021.9553518", + textVersion = + paste("R. Simoes, F. C. de Souza, M. Zaglia, G. R. de Queiroz,", + "R. D. C. dos Santos and K. R. Ferreira, \"Rstac: An R", + "Package to Access Spatiotemporal Asset Catalog Satellite", + "Imagery,\" 2021 IEEE International Geoscience and Remote", + "Sensing Symposium IGARSS, 2021, pp. 7674-7677, doi:", + "10.1109/IGARSS47720.2021.9553518.") +) diff --git a/man/rstac.Rd b/man/rstac.Rd index 938600c9..dd260c58 100644 --- a/man/rstac.Rd +++ b/man/rstac.Rd @@ -6,10 +6,7 @@ \alias{rstac-package} \title{R client library for STAC (rstac)} \description{ -Provides functions to access, search and download spacetime earth - observation data via SpatioTemporal Asset Catalog (STAC). This package - supports the version 1.0.0 of the STAC specification - (). +Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). For further details see DOI: 10.1109/IGARSS47720.2021.9553518 } \section{The \code{rstac} functions}{ From 952d4abd459928eba59dea7e32b55445c9a137ad Mon Sep 17 00:00:00 2001 From: Rolf Simoes Date: Fri, 22 Oct 2021 21:54:42 -0300 Subject: [PATCH 25/44] update README.md --- README.Rmd | 2 +- README.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/README.Rmd b/README.Rmd index b76aec6d..e880e7f1 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,7 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) -[![Build Status](https://drone.dpi.inpe.br/api/badges/brazil-data-cube/rstac/status.svg)](https://drone.dpi.inpe.br/brazil-data-cube/rstac) + [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) [![Software Life Cycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![CRAN status](https://www.r-pkg.org/badges/version/rstac)](https://cran.r-project.org/package=rstac) diff --git a/README.md b/README.md index 009d8fda..24cb2ca5 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,7 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) -[![Build -Status](https://drone.dpi.inpe.br/api/badges/brazil-data-cube/rstac/status.svg)](https://drone.dpi.inpe.br/brazil-data-cube/rstac) + [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) From f67bf171e418f0d657a9f8a8ce0ddbd129441246 Mon Sep 17 00:00:00 2001 From: Felipe Date: Sat, 23 Oct 2021 02:55:51 +0000 Subject: [PATCH 26/44] update R code --- R/deprec-funs.R | 4 ++-- R/signatures.R | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/R/deprec-funs.R b/R/deprec-funs.R index 92590360..d3dd7584 100644 --- a/R/deprec-funs.R +++ b/R/deprec-funs.R @@ -22,8 +22,8 @@ items_bands <- function(items) { # signal the deprecation to the user lifecycle::deprecate_soft("0.9.1-5", - "rstac::items_bands(items = )", - "rstac::items_assets(items = )") + "rstac::items_bands()", + "rstac::items_assets()") return(items_assets(items)) } diff --git a/R/signatures.R b/R/signatures.R index 4b6ff883..ad22d569 100644 --- a/R/signatures.R +++ b/R/signatures.R @@ -119,7 +119,7 @@ sign_bdc <- function(access_token = NULL, ...) { #' # STACItemCollection object #' stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% #' stac_search(collections = "sentinel-2-l2a", -#' bbox = c(-47.02148, -12.98314, -42.53906,-17.35063)) %>% +#' bbox = c(-47.02148, -42.53906, -12.98314, -17.35063)) %>% #' get_request() #' #' # signing each item href From b1b662f76848bbd9abaf8b2b7e7983410a8f721e Mon Sep 17 00:00:00 2001 From: Felipe Date: Sat, 23 Oct 2021 02:56:27 +0000 Subject: [PATCH 27/44] closes #68 --- tests/testthat/test-items_functions.R | 53 ++++++++++++++++++++++++++- tests/testthat/test-signatures.R | 4 +- 2 files changed, 53 insertions(+), 4 deletions(-) diff --git a/tests/testthat/test-items_functions.R b/tests/testthat/test-items_functions.R index fc42b3ec..6e044809 100644 --- a/tests/testthat/test-items_functions.R +++ b/tests/testthat/test-items_functions.R @@ -1,5 +1,3 @@ -context("test_items_functions") - testthat::test_that("items functions", { vcr::use_cassette("items_functions", { # skip cran check test @@ -91,5 +89,56 @@ testthat::test_that("items functions", { # ok - return a numeric testthat::expect_true(is.numeric(items_matched(res))) + + # items_filter-------------------------------------------------------------- + testthat::expect_s3_class( + object = items_filter(res, fn = function(x) {x[["eo:cloud_cover"]] < 10}), + class = "STACItemCollection" + ) + + testthat::expect_s3_class( + object = items_filter(res, `eo:cloud_cover` < 10), + class = "STACItemCollection" + ) + + testthat::expect_s3_class( + object = items_filter(res), + class = "STACItemCollection" + ) + + testthat::expect_error( + object = items_filter(item_stac, `eo:cloud_cover` < 10) + ) + + testthat::expect_error( + object = items_filter(res, list(`eo:cloud_cover` < 10)) + ) + + # items_assets-------------------------------------------------------------- + testthat::expect_equal( + object = class(items_assets(res)), + expected = "list" + ) + + testthat::expect_equal( + object = class(items_assets(item_stac)), + expected = "character" + ) + + # items_next---------------------------------------------------------------- + testthat::expect_s3_class( + object = items_next(item_stac), + class = "STACItem" + ) + + testthat::expect_s3_class( + object = items_next(res), + class = "STACItemCollection" + ) + + testthat::expect_equal( + object = items_length(items_next(res)), + expected = 20 + ) }) }) diff --git a/tests/testthat/test-signatures.R b/tests/testthat/test-signatures.R index c8438d22..5513041a 100644 --- a/tests/testthat/test-signatures.R +++ b/tests/testthat/test-signatures.R @@ -81,8 +81,8 @@ testthat::test_that("signature functions", { # stac item collection from ms stac_items <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% - stac_search(collections = "landsat-8-c2-l2", - bbox = c(-47.02148, -12.98314, -42.53906, -17.35063), + stac_search(collections = "sentinel-2-l2a", + bbox = c(-47.02148, -42.53906, -12.98314, -17.35063), limit = 1) %>% get_request() From 124f687e17587c763392f7f68901666fd1eeefa8 Mon Sep 17 00:00:00 2001 From: Felipe Date: Sat, 23 Oct 2021 02:56:43 +0000 Subject: [PATCH 28/44] update fixture --- tests/fixtures/items_functions.yml | 88 ++- tests/fixtures/ms_signatures.yml | 208 ++++++- tests/fixtures/stac_item_obj.yml | 198 +++++-- tests/fixtures/stac_search_obj.yml | 428 ++++++++++++--- tests/fixtures/tests_examples.yml | 852 +++++++++++++++++++++++++++-- 5 files changed, 1592 insertions(+), 182 deletions(-) diff --git a/tests/fixtures/items_functions.yml b/tests/fixtures/items_functions.yml index 6e20920d..5296a3b4 100644 --- a/tests/fixtures/items_functions.yml +++ b/tests/fixtures/items_functions.yml @@ -29,7 +29,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cube Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"https://brazildatacube.dpi.inpe.br/stac/","rel":"self","type":"application/json","title":"Link to this 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recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -61,7 +61,7 @@ http_interactions: file: no string: | 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profile=cloud-optimized","eo:bands":[3]},"thumbnail":{"href":"http://brazildatacube.dpi.inpe.br/dev/Repository/Warped/CB4_64/020022/2019-12-31/CB4_64_020022_2019-12-31.png","type":"image/png"}},"links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1/items/CB4_64_020022_2019-12-31","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"parent"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"collection"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/stac","rel":"root"}]}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1163,7 +1163,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1191,7 +1191,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1219,7 +1219,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1247,7 +1247,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1275,7 +1275,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1303,7 +1303,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1331,7 +1331,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1359,7 +1359,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1387,7 +1387,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1415,7 +1415,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1443,7 +1443,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1471,7 +1471,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cubes Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/","rel":"self"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/docs","rel":"service"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/conformance","rel":"conformance"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections","rel":"data"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/search","rel":"search"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64_16D_STK-1","rel":"child","title":"CB4_64_16D_STK-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4_64-1","rel":"child","title":"CB4_64-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/CB4-MUX-L4-SR-CMPAC-1","rel":"child","title":"CB4-MUX-L4-SR-CMPAC-1"},{"href":"http://brazildatacube.dpi.inpe.br/dev/bdc-stac/collections/RF.ANL-1","rel":"child","title":"RF.ANL-1"}]} - recorded_at: 2021-09-17 00:18:41 GMT + recorded_at: 2021-10-23 02:54:41 GMT recorded_with: vcr/1.0.2, webmockr/0.8.0 - request: method: get @@ -1499,7 +1499,7 @@ http_interactions: file: no string: | {"description":"Brazil Data Cube Catalog","id":"bdc","stac_version":"0.9.0","links":[{"href":"http://brazildatacube.dpi.inpe.br/stac/","rel":"self","type":"application/json","title":"Link to this document"},{"href":"http://brazildatacube.dpi.inpe.br/stac/docs","rel":"service-doc","type":"text/html","title":"API documentation in HTML"},{"href":"http://brazildatacube.dpi.inpe.br/stac/conformance","rel":"conformance","type":"application/json","title":"OGC API conformance classes implemented by the server"},{"href":"http://brazildatacube.dpi.inpe.br/stac/collections","rel":"data","type":"application/json","title":"Information about image collections"},{"href":"http://brazildatacube.dpi.inpe.br/stac/search","rel":"search","type":"application/json","title":"STAC-Search 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+lat_0=-12 +lon_0=-54 +lat_1=-2 +lat_2=-22 +x_0=5000000 +y_0=10000000 +ellps=GRS80 +units=m +no_defs ","bdc:temporal_composition":null,"links":[{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4MUX_20-1","rel":"self","type":"application/json","title":"Link to this document"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections/CB4MUX_20-1/items","rel":"items","type":"application/json","title":"Items of the collection CB4MUX_20-1"},{"href":"https://brazildatacube.dpi.inpe.br/stac/collections","rel":"parent","type":"application/json","title":"Link to catalog collections"},{"href":"https://brazildatacube.dpi.inpe.br/stac/","rel":"root","type":"application/json","title":"API landing page (root catalog)"}]},{"id":"LCC_L8_30_1M_STK_Cerrado-1","stac_version":"0.9.0","stac_extensions":["commons","datacube","version"],"title":"LCC Landsat-8 1M STK Cerrado","version":1,"deprecated":false,"description":"This is a land cover classification map of Brazilian Cerrado, from August 2017 to August 2018. This classification was made on top of Landsat-8 monthly cubes with spatial resolution of 30 meters using the best pixel composition function (Stack). The classification model was trained using 67359 sample points spread across the whole Cerrado biome (Annual Crop: 9390, Dune Beach: 35, Forest: 5439, Pasture: 19697, Savanna: 30014, Semi-Perennial Crop: 1161, Silviculture: 1268, Water: 355). The spectral band used were B1, B2, B3, B4, B5, B6, and B7 along with the vegetation indices EVI and NDVI; the clouded observation were identified using the Fmask4 algorithm and estimated using linear interpolation. The classification algorithm was Multi-Layer Perceptron (Deep Learning).","license":"","properties":{"eo:gsd":30.0,"eo:bands":[{"name":"lcc","common_name":"lcc","description":"This is a classification.","min":1.0,"max":8.0,"nodata":255.0,"scale":1.0,"center_wavelength":null,"full_width_half_max":null,"data_type":"uint8"}],"instruments":["OLI"],"platform":"LANDSAT-8"},"extent":{"spatial":{"bbox":[[-54.356031,-17.015976,-44.846777,-7.085732]]},"temporal":{"interval":[["2017-08-01T00:00:00","2018-08-31T00:00:00"]]}},"bdc:metadata":{"ows":{"url":"http://brazildatacube.dpi.inpe.br/bdc/geoserver/bdc_lcc/ows","layerName":"LCC_L8_30_1M_STK_Cerrado"},"sources":[{"name":"Landsat-8 - OLI - Cube Stack 16 days - v001","stacUri":"https://brazildatacube.dpi.inpe.br/stac/collections/LC8_30_16D_STK-1","descriptionUri":"https://brazil-data-cube.github.io/products/cube_col/LC8_30_16D_STK.html"}],"datacite":{"id":"LCC_L8_30_1M_STK_Cerrado","dates":[{"date":"2021"}],"sizes":[],"state":"unfindable","types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"agency":"INPE","titles":{"lang":"en","title":"LCC Landsat-8 1M STK Cerrado - Annual Crop, Dune Beach, Forest, Pasture, Savanna, Semi-Perennial Crop, Silviculture, Water"},"formats":[],"version":"1.","creators":[{"@type":"ResearchGroup","familyName":"BDC Team"}],"language":"en","subjects":[{"lang":"en","subject":"LANDSAT-8"},{"lang":"en","subject":"OLI"},{"lang":"en","subject":"Data Cube"},{"lang":"en","subject":"Brazil"},{"lang":"en","subject":"Classification"},{"lang":"en","subject":"Machine Learning"},{"lang":"en","subject":"MLP (multi-layer perceptrons)"}],"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/"}],"contributors":[{"name":"National Institute for Space Research (INPE)","nameType":"Organizational","contributorType":"HostingInstitution"},{"name":"Brazil Data Cube Team","contributorType":"ResearchGroup"}],"descriptions":[{"lang":"en","description":"This land cover classification refers to a study area in Goi\u00e1s state, in the Cerrado biome. 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This algorithm delivers the surface reflectance data from CBERS-4B Level-4 images. The methodology includes the integration of MODIS-MCD19A2 and VIIRS-EDR products as input atmospheric information (aerosol optical depth and water vapor). The results were evaluated using 616 Landsat-8 OLI surface reflectance imagery and AERONET data. These findings confirm that (i) CMPAC is a suitable tool for estimating surface reflectance of CBERS MUX data, and (ii) ancillary products support the application of atmospheric correction by filling the gap of atmospheric information. More information about the method is available in the following paper (Martins et al. 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R/items-funs.R | 343 +++++++++++++++++++------------------ man/items_assign_change.Rd | 47 ----- man/items_filter.Rd | 47 ----- man/items_functions.Rd | 221 +++++++++++++++++++++--- man/items_group.Rd | 43 ----- man/items_reap.Rd | 40 ----- man/items_utils.Rd | 44 ----- 7 files changed, 371 insertions(+), 414 deletions(-) delete mode 100644 man/items_assign_change.Rd delete mode 100644 man/items_filter.Rd delete mode 100644 man/items_group.Rd delete mode 100644 man/items_reap.Rd delete mode 100644 man/items_utils.Rd diff --git a/R/items-funs.R b/R/items-funs.R index 175b4e81..10f4572f 100644 --- a/R/items-funs.R +++ b/R/items-funs.R @@ -1,66 +1,142 @@ #' @title STACItemCollection functions #' #' @description -#' The `items_length()` function shows how many items there are in +#' These functions provide support to work with +#' `STACItemCollection` and `STACItem` objects. +#' +#' \itemize{ +#' \item `items_length()`: shows how many items there are in #' the `STACItemCollection` object. #' -#' The `items_matched()` function shows how many items matched the +#' \item `items_matched()`: shows how many items matched the #' search criteria. It supports `search:metadata` (v0.8.0), #' `context` (v0.9.0), and `numberMatched` (OGC WFS3 core spec). #' -#' The `items_fetch()` function request all STAC Items through +#' \item `items_fetch()`: request all STAC Items through #' pagination. #' -#' The `items_datetime()` function retrieves a the `datetime` +#' \item `items_next()`: fetches a new page from STAC service. +#' +#' \item `items_datetime()`: retrieves a the `datetime` #' field in `properties` from `STACItemCollection` and #' `STACItem` objects. #' -#' The `items_bbox()` function retrieves a the `bbox` +#' \item `items_bbox()`: retrieves a the `bbox` #' field of a `STACItemCollection` or an `STACItem` object. #' -#' The `item_assets()` function returns the assets name from +#' \item `item_assets()`: returns the assets name from #' `STACItemCollection` and `STACItem` objects. #' +#' \item `items_filter()`: selects only items that match some +#' criteria. +#' +#' \item `items_reap()`: extract key values by traversing all items +#' in an `STACItemCollection` object. +#' +#' \item `items_fields()`: lists field names inside an item. +#' +#' \item `items_group()`: organizes items as elements of a list using +#' some criteria. +#' +#' \item `items_sign()`: allow access assets by preparing its url. +#' } +#' #' @param items a `STACItemCollection` object. +#' #' @param matched_field a `character` vector with the path #' where the number of items returned in the named list is located starting from #' the initial node of the list. For example, if the information is at position #' `items$meta$found` of the object, it must be passed as the following #' parameter `c("meta", "found")`. +#' +#' @param progress a `logical` indicating if a progress bar must be +#' shown or not. Defaults to `TRUE`. +#' #' @param simplify a `logical` should return only the assets name of the #' first item? if not a `list` with all assets name will be returned. Default #' is `FALSE`. +#' +#' @param filter_fn a `function` that receives an item that should +#' evaluate a `logical` value. +#' +#' @param field a `character` with the names of the field to +#' get the subfields values. +#' +#' @param index an `atomic` vector with values as group index +#' +#' @param sign_fn a `function` that receives an item as parameter +#' and returns an item signed. +#' #' @param ... additional arguments. See details. -#' @param progress a `logical` indicating if a progress bar must be -#' shown or not. Defaults to `TRUE`. #' #' @details -#' For `items_fetch` ellipsis is used to pass additional `httr` options to -#' [GET][httr::GET] or [POST][httr::POST] methods, such as -#' [add_headers][httr::add_headers] or [set_cookies][httr::set_cookies]. +#' Ellipsis argument (`...`) appears in different items function and +#' has distinct purposes: +#' \itemize{ +#' \item `items_matched()` and `items_assets()`: ellipsis is not used. #' -#' For `items_filter` function is used to pass logical expressions. +#' \item `items_fetch()` and `items_next()`: ellipsis is used to pass +#' additional `httr` options to [GET][httr::GET] or [POST][httr::POST] +#' methods, such as [add_headers][httr::add_headers] or +#' [set_cookies][httr::set_cookies]. +#' +#' \item `items_filter()`: ellipsis is used to pass logical +#' expressions using keys in `properties` field as filter criteria. +#' +#' \item `items_reap()`, `items_fields()`, and `items_group()`: ellipsis can +#' be used to provide fields names to get the subfields values from +#' the `STACItemCollection` objects. +#' +#' \item `items_sign()`: in a near future, ellipsis will be used to append +#' key value pairs to url query string of an asset. +#' } +#' +#' `items_sign()` has `sign_fn` parameter that must be a function that +#' receives as argument an item and returns an signed item. `rstac` provides +#' `sign_bdc()` and `sign_planetary_computer()` functions to access Brazil +#' Data Cube products and Microsoft Planetary Computer catalogs, respectively. #' #' @return -#' The `items_assets()` if simplify is `TRUE`, returns a `character` value with -#' all assets names of the first item. Otherwise, returns a `list` with assets -#' name for each item. -#' The `items_length()` returns an `integer` value. -#' The `items_matched()` returns an `integer` value. -#' If STAC web server does not support this extension, returns `NULL`. -#' The `items_fetch()` returns an `STACItemCollection` with all -#' matched items. -#' The `items_datetime()` returns a `list` of all items' datetime. -#' The `items_bbox()` returns a `list` with all items' -#' bounding boxes. +#' +#' \itemize{ +#' \item `items_length()`: an `integer` value. +#' +#' \item `items_matched()`: returns an `integer` value if STAC web server does +#' support this extension, otherwise returns `NULL`. +#' +#' \item `items_fetch()`: an `STACItemCollection` with all matched items. +#' +#' \item `items_next()`: fetches a new page from STAC service. +#' +#' \item `items_datetime()`: a `list` of all items' datetime. +#' +#' \item `items_bbox()`: returns a `list` with all items' bounding boxes. +#' +#' \item `item_assets()`: if simplify is `TRUE`, returns a `character` +#' value with all assets names of the first item. Otherwise, returns a +#' `list` with assets name for each item. +#' +#' \item `items_filter()`: a `STACItemCollection` object. +#' +#' \item `items_reap()`: a `vector` if the supplied field is atomic, +#' otherwise or a `list`. +#' +#' \item `items_fields()`: a `character` vector. +#' +#' \item `items_group()`: a `list` of `STACItemCollection` objects. +#' +#' \item `items_sign()`: a `STACItemCollection` object with signed assets url +#' } +#' #' #' @examples +#' #' \dontrun{ #' #' x <- stac("https://brazildatacube.dpi.inpe.br/stac") %>% -#' stac_search(collections = "CB4_64_16D_STK-1") %>% -#' stac_search(limit = 500) %>% -#' get_request() +#' stac_search(collections = "CB4_64_16D_STK-1") %>% +#' stac_search(limit = 500) %>% +#' get_request() #' #' x %>% items_length() #' x %>% items_matched() @@ -69,7 +145,65 @@ #' x %>% items_fetch() #' } #' +#' \dontrun{ +#' +#' # Defining BDC token +#' Sys.setenv("BDC_ACCESS_KEY" = ) +#' +#' # STACItem object +#' stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_sign(sign_fn = sign_bdc()) +#' +#' } +#' +#' \dontrun{ +#' +#' # STACItemCollection object +#' stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_filter(`eo:cloud_cover` < 10) +#' +#' # Example with AWS STAC +#' stac("https://earth-search.aws.element84.com/v0") %>% +#' stac_search(collections = "sentinel-s2-l2a-cogs", +#' bbox = c(-48.206,-14.195,-45.067,-12.272), +#' datetime = "2018-06-01/2018-06-30", +#' limit = 500) %>% +#' post_request() %>% +#' items_filter(filter_fn = function(x) {x[["eo:cloud_cover"]] < 10}) +#' } +#' +#' \dontrun{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% items_reap(field = c("properties", "datetime")) +#' } +#' +#' \dontrun{ +#' # STACItemCollection object +#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% +#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, +#' datetime = "2017-08-01/2018-03-01", +#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% +#' get_request() %>% items_fetch(progress = FALSE) +#' +#' stac_item %>% items_group(., field = c("properties", "bdc:tiles")) +#' } +#' #' @name items_functions +NULL + +#' @rdname items_functions #' #' @export items_length <- function(items) { @@ -189,7 +323,7 @@ items_fetch.STACItemCollection <- function(items, ..., .error(paste("Length of returned items (%s) is different", "from matched items (%s)."), items_length(items), matched) - content <- items_next(items) + content <- items_next(items, ...) if (!is.null(content)) items <- content @@ -404,44 +538,10 @@ items_assets.STACItemCollection <- function(items, ..., simplify = FALSE) { } -#' @title Utility functions -#' -#' @description This function filters for the attributes contained in the STAC -#' properties. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... expressions used to filter items of a `STACItemCollection` -#' object. -#' @param fn a `function` that will be used to filter the attributes -#' listed in the properties. -#' -#' @return a `STACItemCollection` object with the filtered properties. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_filter(`eo:cloud_cover` < 10) -#' -#' # Example with AWS STAC -#' items <- stac("https://earth-search.aws.element84.com/v0") %>% -#' stac_search(collections = "sentinel-s2-l2a-cogs", -#' bbox = c(-48.206,-14.195,-45.067,-12.272), -#' datetime = "2018-06-01/2018-06-30", -#' limit = 500) %>% -#' post_request() -#' -#' items %>% -#' items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) -#' } +#' @rdname items_functions #' #' @export -items_filter <- function(items, ..., fn = NULL) { +items_filter <- function(items, ..., filter_fn = NULL) { # check items parameter check_subclass(items, "STACItemCollection") @@ -463,10 +563,10 @@ items_filter <- function(items, ..., fn = NULL) { } } - if (!is.null(fn)) { + if (!is.null(filter_fn)) { sel <- vapply(items$features, function(f) { - fn(f$properties) + filter_fn(f$properties) }, logical(1)) items$features <- items$features[sel] @@ -475,35 +575,7 @@ items_filter <- function(items, ..., fn = NULL) { items } -#' @title Utility functions -#' -#' @description This function returns the values of a field of the -#' `STACItemCollections` object. If the values of the specified field are -#' not atomic the return will be in list form, if they are, it will be returned -#' in vector form. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... a named way to provide fields names to get the -#' subfields values from the `RSTACDocument` objects. -#' -#' @param field a `character` with the names of the field to -#' get the subfields values from the `RSTACDocument` objects. -#' -#' @return a `vector` if the supplied field is atomic, or a list if not. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% items_reap(field = c("properties", "datetime")) -#' } +#' @rdname items_functions #' #' @export items_reap <- function(items, ..., field = NULL) { @@ -557,14 +629,14 @@ items_reap <- function(items, ..., field = NULL) { #' stac_item %>% items_fields(field = c("properties")) #' } #' -#' @name items_utils +#' @rdname items_functions #' #' @export items_fields <- function(items, ..., field = NULL) { UseMethod("items_fields", items) } -#' @rdname items_utils +#' @rdname items_functions #' #' @export items_fields.STACItemCollection <- function(items, ..., field = NULL) { @@ -580,7 +652,7 @@ items_fields.STACItemCollection <- function(items, ..., field = NULL) { names(items$features[[1]][[c(dots, field)]]) } -#' @rdname items_utils +#' @rdname items_functions #' #' @export items_fields.STACItem <- function(items, ..., field = NULL) { @@ -596,38 +668,7 @@ items_fields.STACItem <- function(items, ..., field = NULL) { names(items[[c(dots, field)]]) } -#' @title Utility functions -#' -#' @description This function groups the items contained within the -#' `STACItemCollection` object according to some specified fields. Each -#' index in the returned list contains items belonging to the same group. -#' -#' @param items a `STACItemCollection` object representing the result of -#' `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param ... a named way to provide field names to get the subfields values -#' from the `RSTACDocument` objects. -#' -#' @param field a `character` with the names of the field to get the -#' subfields values from the `RSTACDocument` objects. -#' -#' @param index a `character` with the indexes to be grouped. It can be -#' used with the function [items_reap]. -#' -#' @return A `list` in which each index corresponds to a group with its -#' corresponding `STACItemCollection` objects. -#' -#' @examples -#' \donttest{ -#' # STACItemCollection object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_fetch(progress = FALSE) -#' -#' stac_item %>% items_group(., field = c("properties", "bdc:tiles")) -#' } +#' @rdname items_functions #' #' @export items_group <- function(items, ..., field = NULL, index = NULL) { @@ -674,50 +715,18 @@ items_group <- function(items, ..., field = NULL, index = NULL) { }) } -#' @title Utility functions -#' -#' @description A utility function to create signatures in hrefs of each -#' asset in the STAC items. To create the signatures, the provided function -#' must return a function, being a factory function, so the manufactured -#' function will sign the hrefs returning one feature per interaction. -#' -#' @param items a `STACItemCollection` object representing -#' the result of `/stac/search`, \code{/collections/{collectionId}/items}. -#' -#' @param sign_fn a `function` to assign each assets in STAC items. -#' -#' @return A `STACItemCollection` object with the signed assets according to the -#' supplied parameter function. -#' @examples -#' \dontrun{ -#' -#' # Defining BDC token -#' Sys.setenv("BDC_ACCESS_KEY" = ) -#' -#' # STACItem object -#' stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% -#' stac_search(collections = "CB4_64_16D_STK-1", limit = 100, -#' datetime = "2017-08-01/2018-03-01", -#' bbox = c(-48.206,-14.195,-45.067,-12.272)) %>% -#' get_request() %>% items_sign(sign_fn = sign_bdc) -#' -#' } -#' -#' @name items_assign_change -NULL - -#' @rdname items_assign_change +#' @rdname items_functions #' #' @export -items_sign <- function(items, sign_fn = NULL, ...) { +items_sign <- function(items, ..., sign_fn = NULL) { UseMethod("items_sign", items) } -#' @rdname items_assign_change +#' @rdname items_functions #' #' @export -items_sign.STACItemCollection <- function(items, sign_fn = NULL) { +items_sign.STACItemCollection <- function(items, ..., sign_fn = NULL) { if (is.null(sign_fn)) { return(items) @@ -741,10 +750,10 @@ items_sign.STACItemCollection <- function(items, sign_fn = NULL) { items } -#' @rdname items_assign_change +#' @rdname items_functions #' #' @export -items_sign.STACItem <- function(items, sign_fn = NULL) { +items_sign.STACItem <- function(items, ..., sign_fn = NULL) { if (is.null(sign_fn)) { return(items) diff --git a/man/items_assign_change.Rd b/man/items_assign_change.Rd deleted file mode 100644 index 262633c3..00000000 --- a/man/items_assign_change.Rd +++ /dev/null @@ -1,47 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items-funs.R -\name{items_assign_change} -\alias{items_assign_change} -\alias{items_sign} -\alias{items_sign.STACItemCollection} -\alias{items_sign.STACItem} -\title{Utility functions} -\usage{ -items_sign(items, sign_fn = NULL, ...) - -\method{items_sign}{STACItemCollection}(items, sign_fn = NULL) - -\method{items_sign}{STACItem}(items, sign_fn = NULL) -} -\arguments{ -\item{items}{a \code{STACItemCollection} object representing -the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} - -\item{sign_fn}{a \code{function} to assign each assets in STAC items.} -} -\value{ -A \code{STACItemCollection} object with the signed assets according to the -supplied parameter function. -} -\description{ -A utility function to create signatures in hrefs of each -asset in the STAC items. To create the signatures, the provided function -must return a function, being a factory function, so the manufactured -function will sign the hrefs returning one feature per interaction. -} -\examples{ -\dontrun{ - -# Defining BDC token -Sys.setenv("BDC_ACCESS_KEY" = ) - -# STACItem object -stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1", limit = 100, - datetime = "2017-08-01/2018-03-01", - bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% - get_request() \%>\% items_sign(sign_fn = sign_bdc) - -} - -} diff --git a/man/items_filter.Rd b/man/items_filter.Rd deleted file mode 100644 index fc61f014..00000000 --- a/man/items_filter.Rd +++ /dev/null @@ -1,47 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items-funs.R -\name{items_filter} -\alias{items_filter} -\title{Utility functions} -\usage{ -items_filter(items, ..., fn = NULL) -} -\arguments{ -\item{items}{a \code{STACItemCollection} object representing -the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} - -\item{...}{expressions used to filter items of a \code{STACItemCollection} -object.} - -\item{fn}{a \code{function} that will be used to filter the attributes -listed in the properties.} -} -\value{ -a \code{STACItemCollection} object with the filtered properties. -} -\description{ -This function filters for the attributes contained in the STAC -properties. -} -\examples{ -\donttest{ -# STACItemCollection object -stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1", limit = 100, - datetime = "2017-08-01/2018-03-01", - bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% - get_request() \%>\% items_filter(`eo:cloud_cover` < 10) - -# Example with AWS STAC -items <- stac("https://earth-search.aws.element84.com/v0") \%>\% - stac_search(collections = "sentinel-s2-l2a-cogs", - bbox = c(-48.206,-14.195,-45.067,-12.272), - datetime = "2018-06-01/2018-06-30", - limit = 500) \%>\% - post_request() - - items \%>\% - items_filter(fn = function(x) {x[["eo:cloud_cover"]] < 10}) -} - -} diff --git a/man/items_functions.Rd b/man/items_functions.Rd index f3ca61df..5cb7d434 100644 --- a/man/items_functions.Rd +++ b/man/items_functions.Rd @@ -23,6 +23,15 @@ \alias{items_assets} \alias{items_assets.STACItem} \alias{items_assets.STACItemCollection} +\alias{items_filter} +\alias{items_reap} +\alias{items_fields} +\alias{items_fields.STACItemCollection} +\alias{items_fields.STACItem} +\alias{items_group} +\alias{items_sign} +\alias{items_sign.STACItemCollection} +\alias{items_sign.STACItem} \title{STACItemCollection functions} \usage{ items_length(items) @@ -66,11 +75,31 @@ items_assets(items, ...) \method{items_assets}{STACItem}(items, ...) \method{items_assets}{STACItemCollection}(items, ..., simplify = FALSE) + +items_filter(items, ..., filter_fn = NULL) + +items_reap(items, ..., field = NULL) + +items_fields(items, ..., field = NULL) + +\method{items_fields}{STACItemCollection}(items, ..., field = NULL) + +\method{items_fields}{STACItem}(items, ..., field = NULL) + +items_group(items, ..., field = NULL, index = NULL) + +items_sign(items, ..., sign_fn = NULL) + +\method{items_sign}{STACItemCollection}(items, ..., sign_fn = NULL) + +\method{items_sign}{STACItem}(items, ..., sign_fn = NULL) } \arguments{ -\item{items}{a \code{STACItemCollection} object.} +\item{items}{a \code{STACItemCollection} object representing +the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} -\item{...}{additional arguments. See details.} +\item{...}{a named way to provide field names to get the subfields values +from the \code{RSTACDocument} objects.} \item{matched_field}{a \code{character} vector with the path where the number of items returned in the named list is located starting from @@ -84,55 +113,130 @@ shown or not. Defaults to \code{TRUE}.} \item{simplify}{a \code{logical} should return only the assets name of the first item? if not a \code{list} with all assets name will be returned. Default is \code{FALSE}.} + +\item{filter_fn}{a \code{function} that receives an item that should +evaluate a \code{logical} value.} + +\item{field}{a \code{character} with the names of the field to get the +subfields values from the \code{RSTACDocument} objects.} + +\item{index}{an \code{atomic} vector with values as group index} + +\item{sign_fn}{a \code{function} that receives an item as parameter +and returns an item signed.} } \value{ -The \code{items_assets()} if simplify is \code{TRUE}, returns a \code{character} value with -all assets names of the first item. Otherwise, returns a \code{list} with assets -name for each item. -The \code{items_length()} returns an \code{integer} value. -The \code{items_matched()} returns an \code{integer} value. -If STAC web server does not support this extension, returns \code{NULL}. -The \code{items_fetch()} returns an \code{STACItemCollection} with all -matched items. -The \code{items_datetime()} returns a \code{list} of all items' datetime. -The \code{items_bbox()} returns a \code{list} with all items' -bounding boxes. +\itemize{ +\item \code{items_length()}: an \code{integer} value. + +\item \code{items_matched()}: returns an \code{integer} value if STAC web server does +support this extension, otherwise returns \code{NULL}. + +\item \code{items_fetch()}: an \code{STACItemCollection} with all matched items. + +\item \code{items_next()}: fetches a new page from STAC service. + +\item \code{items_datetime()}: a \code{list} of all items' datetime. + +\item \code{items_bbox()}: returns a \code{list} with all items' bounding boxes. + +\item \code{item_assets()}: if simplify is \code{TRUE}, returns a \code{character} +value with all assets names of the first item. Otherwise, returns a +\code{list} with assets name for each item. + +\item \code{items_filter()}: a \code{STACItemCollection} object. + +\item \code{items_reap()}: a \code{vector} if the supplied field is atomic, +otherwise or a \code{list}. + +\item \code{items_fields()}: a \code{character} vector. + +\item \code{items_group()}: a \code{list} of \code{STACItemCollection} objects. + +\item \code{items_sign()}: a \code{STACItemCollection} object with signed assets url +} + +A \code{character} with the subfields of the \code{feature} field. } \description{ -The \code{items_length()} function shows how many items there are in +These functions provide support to work with +\code{STACItemCollection} and \code{STACItem} objects. + +\itemize{ +\item \code{items_length()}: shows how many items there are in the \code{STACItemCollection} object. -The \code{items_matched()} function shows how many items matched the +\item \code{items_matched()}: shows how many items matched the search criteria. It supports \code{search:metadata} (v0.8.0), \code{context} (v0.9.0), and \code{numberMatched} (OGC WFS3 core spec). -The \code{items_fetch()} function request all STAC Items through +\item \code{items_fetch()}: request all STAC Items through pagination. -The \code{items_datetime()} function retrieves a the \code{datetime} +\item \code{items_next()}: fetches a new page from STAC service. + +\item \code{items_datetime()}: retrieves a the \code{datetime} field in \code{properties} from \code{STACItemCollection} and \code{STACItem} objects. -The \code{items_bbox()} function retrieves a the \code{bbox} +\item \code{items_bbox()}: retrieves a the \code{bbox} field of a \code{STACItemCollection} or an \code{STACItem} object. -The \code{item_assets()} function returns the assets name from +\item \code{item_assets()}: returns the assets name from \code{STACItemCollection} and \code{STACItem} objects. + +\item \code{items_filter()}: selects only items that match some +criteria. + +\item \code{items_reap()}: extract key values by traversing all items +in an \code{STACItemCollection} object. + +\item \code{items_fields()}: lists field names inside an item. + +\item \code{items_group()}: organizes items as elements of a list using +some criteria. + +\item \code{items_sign()}: allow access assets by preparing its url. +} + +This function returns the subfields of the \code{feature} +field of a \code{STACItemCollection} object. } \details{ -For \code{items_fetch} ellipsis is used to pass additional \code{httr} options to -\link[httr:GET]{GET} or \link[httr:POST]{POST} methods, such as -\link[httr:add_headers]{add_headers} or \link[httr:set_cookies]{set_cookies}. +Ellipsis argument (\code{...}) appears in different items function and +has distinct purposes: +\itemize{ +\item \code{items_matched()} and \code{items_assets()}: ellipsis is not used. + +\item \code{items_fetch()} and \code{items_next()}: ellipsis is used to pass +additional \code{httr} options to \link[httr:GET]{GET} or \link[httr:POST]{POST} +methods, such as \link[httr:add_headers]{add_headers} or +\link[httr:set_cookies]{set_cookies}. + +\item \code{items_filter()}: ellipsis is used to pass logical +expressions using keys in \code{properties} field as filter criteria. + +\item \code{items_reap()}, \code{items_fields()}, and \code{items_group()}: ellipsis can +be used to provide fields names to get the subfields values from +the \code{STACItemCollection} objects. -For \code{items_filter} function is used to pass logical expressions. +\item \code{items_sign()}: in a near future, ellipsis will be used to append +key value pairs to url query string of an asset. +} + +\code{items_sign()} has \code{sign_fn} parameter that must be a function that +receives as argument an item and returns an signed item. \code{rstac} provides +\code{sign_bdc()} and \code{sign_planetary_computer()} functions to access Brazil +Data Cube products and Microsoft Planetary Computer catalogs, respectively. } \examples{ + \dontrun{ x <- stac("https://brazildatacube.dpi.inpe.br/stac") \%>\% - stac_search(collections = "CB4_64_16D_STK-1") \%>\% - stac_search(limit = 500) \%>\% - get_request() + stac_search(collections = "CB4_64_16D_STK-1") \%>\% + stac_search(limit = 500) \%>\% + get_request() x \%>\% items_length() x \%>\% items_matched() @@ -141,4 +245,69 @@ x \%>\% items_bbox() x \%>\% items_fetch() } +\dontrun{ + +# Defining BDC token +Sys.setenv("BDC_ACCESS_KEY" = ) + +# STACItem object +stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_sign(sign_fn = sign_bdc()) + +} + +\dontrun{ + +# STACItemCollection object +stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_filter(`eo:cloud_cover` < 10) + +# Example with AWS STAC +stac("https://earth-search.aws.element84.com/v0") \%>\% + stac_search(collections = "sentinel-s2-l2a-cogs", + bbox = c(-48.206,-14.195,-45.067,-12.272), + datetime = "2018-06-01/2018-06-30", + limit = 500) \%>\% + post_request() \%>\% + items_filter(filter_fn = function(x) {x[["eo:cloud_cover"]] < 10}) +} + +\dontrun{ +# STACItemCollection object +stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_fetch(progress = FALSE) + +stac_item \%>\% items_reap(field = c("properties", "datetime")) +} + +\dontrun{ +# STACItemCollection object +stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 100, + datetime = "2017-08-01/2018-03-01", + bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% + get_request() \%>\% items_fetch(progress = FALSE) + + stac_item \%>\% items_group(., field = c("properties", "bdc:tiles")) +} + +\donttest{ +# STACItemCollection object +stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% + stac_search(collections = "CB4_64_16D_STK-1", limit = 10, + datetime = "2017-08-01/2018-03-01") \%>\% + get_request() + +stac_item \%>\% items_fields(field = c("properties")) +} + } diff --git a/man/items_group.Rd b/man/items_group.Rd deleted file mode 100644 index 007c337e..00000000 --- a/man/items_group.Rd +++ /dev/null @@ -1,43 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items-funs.R -\name{items_group} -\alias{items_group} -\title{Utility functions} -\usage{ -items_group(items, ..., field = NULL, index = NULL) -} -\arguments{ -\item{items}{a \code{STACItemCollection} object representing the result of -\verb{/stac/search}, \code{/collections/{collectionId}/items}.} - -\item{...}{a named way to provide field names to get the subfields values -from the \code{RSTACDocument} objects.} - -\item{field}{a \code{character} with the names of the field to get the -subfields values from the \code{RSTACDocument} objects.} - -\item{index}{a \code{character} with the indexes to be grouped. It can be -used with the function \link{items_reap}.} -} -\value{ -A \code{list} in which each index corresponds to a group with its -corresponding \code{STACItemCollection} objects. -} -\description{ -This function groups the items contained within the -\code{STACItemCollection} object according to some specified fields. Each -index in the returned list contains items belonging to the same group. -} -\examples{ -\donttest{ -# STACItemCollection object -stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1", limit = 100, - datetime = "2017-08-01/2018-03-01", - bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% - get_request() \%>\% items_fetch(progress = FALSE) - - stac_item \%>\% items_group(., field = c("properties", "bdc:tiles")) -} - -} diff --git a/man/items_reap.Rd b/man/items_reap.Rd deleted file mode 100644 index e32432e9..00000000 --- a/man/items_reap.Rd +++ /dev/null @@ -1,40 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items-funs.R -\name{items_reap} -\alias{items_reap} -\title{Utility functions} -\usage{ -items_reap(items, ..., field = NULL) -} -\arguments{ -\item{items}{a \code{STACItemCollection} object representing -the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} - -\item{...}{a named way to provide fields names to get the -subfields values from the \code{RSTACDocument} objects.} - -\item{field}{a \code{character} with the names of the field to -get the subfields values from the \code{RSTACDocument} objects.} -} -\value{ -a \code{vector} if the supplied field is atomic, or a list if not. -} -\description{ -This function returns the values of a field of the -\code{STACItemCollections} object. If the values of the specified field are -not atomic the return will be in list form, if they are, it will be returned -in vector form. -} -\examples{ -\donttest{ -# STACItemCollection object -stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1", limit = 100, - datetime = "2017-08-01/2018-03-01", - bbox = c(-48.206,-14.195,-45.067,-12.272)) \%>\% - get_request() \%>\% items_fetch(progress = FALSE) - -stac_item \%>\% items_reap(field = c("properties", "datetime")) -} - -} diff --git a/man/items_utils.Rd b/man/items_utils.Rd deleted file mode 100644 index 022963f6..00000000 --- a/man/items_utils.Rd +++ /dev/null @@ -1,44 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/items-funs.R -\name{items_utils} -\alias{items_utils} -\alias{items_fields} -\alias{items_fields.STACItemCollection} -\alias{items_fields.STACItem} -\title{Utility functions} -\usage{ -items_fields(items, ..., field = NULL) - -\method{items_fields}{STACItemCollection}(items, ..., field = NULL) - -\method{items_fields}{STACItem}(items, ..., field = NULL) -} -\arguments{ -\item{items}{a \code{STACItemCollection} object representing -the result of \verb{/stac/search}, \code{/collections/{collectionId}/items}.} - -\item{...}{a named way to provide field names to get the subfields values -from the \code{RSTACDocument} objects.} - -\item{field}{a \code{character} with the names of the field to get the -subfields values from the \code{RSTACDocument} objects.} -} -\value{ -A \code{character} with the subfields of the \code{feature} field. -} -\description{ -This function returns the subfields of the \code{feature} -field of a \code{STACItemCollection} object. -} -\examples{ -\donttest{ -# STACItemCollection object -stac_item <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% - stac_search(collections = "CB4_64_16D_STK-1", limit = 10, - datetime = "2017-08-01/2018-03-01") \%>\% - get_request() - -stac_item \%>\% items_fields(field = c("properties")) -} - -} From 2756fef7142011c032472d4a5a12e9f987998a2d Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:10:46 +0000 Subject: [PATCH 30/44] fix bug in docs --- R/items-funs.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/items-funs.R b/R/items-funs.R index 175b4e81..de0d2443 100644 --- a/R/items-funs.R +++ b/R/items-funs.R @@ -709,7 +709,7 @@ NULL #' @rdname items_assign_change #' #' @export -items_sign <- function(items, sign_fn = NULL, ...) { +items_sign <- function(items, sign_fn = NULL) { UseMethod("items_sign", items) } From 7a7cefd8c7ca626413eb62e6691672b709d7b3fe Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:10:55 +0000 Subject: [PATCH 31/44] update docs --- man/items_assign_change.Rd | 2 +- man/rstac.Rd | 5 +---- man/sign_planetary_computer.Rd | 2 +- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/man/items_assign_change.Rd b/man/items_assign_change.Rd index 262633c3..f597f1f6 100644 --- a/man/items_assign_change.Rd +++ b/man/items_assign_change.Rd @@ -7,7 +7,7 @@ \alias{items_sign.STACItem} \title{Utility functions} \usage{ -items_sign(items, sign_fn = NULL, ...) +items_sign(items, sign_fn = NULL) \method{items_sign}{STACItemCollection}(items, sign_fn = NULL) diff --git a/man/rstac.Rd b/man/rstac.Rd index 938600c9..1ba109e4 100644 --- a/man/rstac.Rd +++ b/man/rstac.Rd @@ -6,10 +6,7 @@ \alias{rstac-package} \title{R client library for STAC (rstac)} \description{ -Provides functions to access, search and download spacetime earth - observation data via SpatioTemporal Asset Catalog (STAC). This package - supports the version 1.0.0 of the STAC specification - (). +Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). } \section{The \code{rstac} functions}{ diff --git a/man/sign_planetary_computer.Rd b/man/sign_planetary_computer.Rd index 7a073f72..5ec11785 100644 --- a/man/sign_planetary_computer.Rd +++ b/man/sign_planetary_computer.Rd @@ -29,7 +29,7 @@ token that will be used in the href. # STACItemCollection object stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") \%>\% stac_search(collections = "sentinel-2-l2a", - bbox = c(-47.02148, -12.98314, -42.53906,-17.35063)) \%>\% + bbox = c(-47.02148, -42.53906, -12.98314, -17.35063)) \%>\% get_request() # signing each item href From a084a86d25babfad3a28b3c5316a362f78228720 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:23:10 +0000 Subject: [PATCH 32/44] change donttest to dontrun in sign functions --- R/signatures.R | 6 +++--- man/sign_bdc.Rd | 4 ++-- man/sign_planetary_computer.Rd | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/signatures.R b/R/signatures.R index ad22d569..083528ed 100644 --- a/R/signatures.R +++ b/R/signatures.R @@ -13,7 +13,7 @@ #' @return a `function` that signs each item assets. #' #' @examples -#' \donttest{ +#' \dontrun{ #' # STACItemCollection object #' stac_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/") %>% #' stac_search(collections = "CB4_64_16D_STK-1", @@ -22,7 +22,7 @@ #' get_request() #' #' # signing each item href -#' stac_obj %>% items_sign(sign_fn = sign_bdc()) +#' stac_obj %>% items_sign(sign_fn = sign_bdc(access_token = "123")) #' #' } #' @@ -115,7 +115,7 @@ sign_bdc <- function(access_token = NULL, ...) { #' @return a `function` that signs each item assets. #' #' @examples -#' \donttest{ +#' \dontrun{ #' # STACItemCollection object #' stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") %>% #' stac_search(collections = "sentinel-2-l2a", diff --git a/man/sign_bdc.Rd b/man/sign_bdc.Rd index a91916ac..5427ba95 100644 --- a/man/sign_bdc.Rd +++ b/man/sign_bdc.Rd @@ -22,7 +22,7 @@ To sign the hrefs with your token you need to store it in an environment variable in \code{BDC_ACCESS_KEY}or use \code{acess_token} parameter. } \examples{ -\donttest{ +\dontrun{ # STACItemCollection object stac_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% stac_search(collections = "CB4_64_16D_STK-1", @@ -31,7 +31,7 @@ stac_obj <- stac("https://brazildatacube.dpi.inpe.br/stac/") \%>\% get_request() # signing each item href -stac_obj \%>\% items_sign(sign_fn = sign_bdc()) +stac_obj \%>\% items_sign(sign_fn = sign_bdc(access_token = "123")) } diff --git a/man/sign_planetary_computer.Rd b/man/sign_planetary_computer.Rd index 5ec11785..c5712e05 100644 --- a/man/sign_planetary_computer.Rd +++ b/man/sign_planetary_computer.Rd @@ -25,7 +25,7 @@ Planetary Computer servers and the returned content corresponds to the token that will be used in the href. } \examples{ -\donttest{ +\dontrun{ # STACItemCollection object stac_obj <- stac("https://planetarycomputer.microsoft.com/api/stac/v1/") \%>\% stac_search(collections = "sentinel-2-l2a", From c4b69f50aa0256b26fa6c4b597ad509d21d685de Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:23:52 +0000 Subject: [PATCH 33/44] update tests --- tests/testthat/test-items_functions.R | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/tests/testthat/test-items_functions.R b/tests/testthat/test-items_functions.R index 6e044809..00b74e60 100644 --- a/tests/testthat/test-items_functions.R +++ b/tests/testthat/test-items_functions.R @@ -125,6 +125,17 @@ testthat::test_that("items functions", { expected = "character" ) + # items_bands--------------------------------------------------------------- + testthat::expect_equal( + object = class(items_bands(res)), + expected = "list" + ) + + testthat::expect_equal( + object = class(items_bands(item_stac)), + expected = "character" + ) + # items_next---------------------------------------------------------------- testthat::expect_s3_class( object = items_next(item_stac), From 22fe19c853d147ebd10db577125042ea535470b3 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:30:42 +0000 Subject: [PATCH 34/44] update drone file --- .drone.yml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/.drone.yml b/.drone.yml index 89ebb54b..472fcee3 100644 --- a/.drone.yml +++ b/.drone.yml @@ -19,13 +19,3 @@ steps: when: event: - push - -- name: discord-notify - image: brazildatacube/bdc-drone-discord - settings: - webhook: - from_secret: discord_webhook - when: - status: - - failure - - success From 360ceedfac12e5304ba8a3863076a19a16a8d457 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 18:33:27 +0000 Subject: [PATCH 35/44] update README --- README.Rmd | 3 ++- README.md | 55 ++++++++++++++++++++++++++++-------------------------- 2 files changed, 31 insertions(+), 27 deletions(-) diff --git a/README.Rmd b/README.Rmd index 904bac3e..ce10cf53 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,8 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) -[![Build Status](https://drone.dpi.inpe.br/api/badges/brazil-data-cube/rstac/status.svg)](https://drone.dpi.inpe.br/brazil-data-cube/rstac) + +[![Build Status](https://cloud.drone.io/api/badges/OldLipe/rstac/status.svg)](https://cloud.drone.io/OldLipe/rstac) [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) [![Software Life Cycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![CRAN status](https://www.r-pkg.org/badges/version/rstac)](https://cran.r-project.org/package=rstac) diff --git a/README.md b/README.md index a0b5f0bb..30524bcd 100644 --- a/README.md +++ b/README.md @@ -9,8 +9,9 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) + [![Build -Status](https://drone.dpi.inpe.br/api/badges/brazil-data-cube/rstac/status.svg)](https://drone.dpi.inpe.br/brazil-data-cube/rstac) +Status](https://cloud.drone.io/api/badges/OldLipe/rstac/status.svg)](https://cloud.drone.io/OldLipe/rstac) [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) @@ -29,7 +30,7 @@ geospatial information assets. The specification can be consulted in . R client library for STAC (`rstac`) was designed to fully support STAC -API v1.0.0. It also supports earlier versions (\>= v0.8.0). +API v1.0.0. It also supports earlier versions (>= v0.8.0). ## Installation @@ -61,15 +62,15 @@ library(magrittr) # for pipe (%>%) in examples `rstac` implements the following STAC endpoints: | **STAC** endpoints | `rstac` functions | API version | -| :------------------------------------------- | :--------------------------- | :---------- | -| `/` | `stac()` | \>= 0.9.0 | -| `/stac` | `stac()` | \< 0.9.0 | -| `/collections` | `collections()` | \>= 0.9.0 | -| `/collections/{collectionId}` | `collections(collection_id)` | \>= 0.9.0 | -| `/collections/{collectionId}/items` | `items()` | \>= 0.9.0 | -| `/collections/{collectionId}/items/{itemId}` | `items(feature_id)` | \>= 0.9.0 | -| `/search` | `stac_search()` | \>= 0.9.0 | -| `/stac/search` | `stac_search()` | \< 0.9.0 | +|:---------------------------------------------|:-----------------------------|:------------| +| `/` | `stac()` | >= 0.9.0 | +| `/stac` | `stac()` | < 0.9.0 | +| `/collections` | `collections()` | >= 0.9.0 | +| `/collections/{collectionId}` | `collections(collection_id)` | >= 0.9.0 | +| `/collections/{collectionId}/items` | `items()` | >= 0.9.0 | +| `/collections/{collectionId}/items/{itemId}` | `items(feature_id)` | >= 0.9.0 | +| `/search` | `stac_search()` | >= 0.9.0 | +| `/stac/search` | `stac_search()` | < 0.9.0 | These functions can be used to retrieve information from a STAC API service. The code bellow creates a `stac` object and list the available @@ -107,19 +108,21 @@ it_obj <- s_obj %>% it_obj #> ###STACItemCollection -#> - matched feature(s): 236 -#> - features (10 item(s)): -#> - CB4_64_16D_STK_v001_022024_2021-02-02_2021-02-17 -#> - CB4_64_16D_STK_v001_022025_2021-02-02_2021-02-17 -#> - CB4_64_16D_STK_v001_022024_2021-01-17_2021-02-01 -#> - CB4_64_16D_STK_v001_022025_2021-01-17_2021-02-01 -#> - CB4_64_16D_STK_v001_022024_2021-01-01_2021-01-16 -#> - CB4_64_16D_STK_v001_022025_2021-01-01_2021-01-16 -#> - CB4_64_16D_STK_v001_022024_2020-12-18_2020-12-31 -#> - CB4_64_16D_STK_v001_022025_2020-12-18_2020-12-31 -#> - CB4_64_16D_STK_v001_022024_2020-12-02_2020-12-17 -#> - CB4_64_16D_STK_v001_022025_2020-12-02_2020-12-17 -#> - field(s): type, links, context, features +#> - matched feature(s): 264 +#> - features (10 item(s) / 254 not fetched): +#> - CB4_64_16D_STK_v001_022024_2021-09-14_2021-09-29 +#> - CB4_64_16D_STK_v001_022025_2021-09-14_2021-09-29 +#> - CB4_64_16D_STK_v001_022024_2021-08-29_2021-09-13 +#> - CB4_64_16D_STK_v001_022025_2021-08-29_2021-09-13 +#> - CB4_64_16D_STK_v001_022024_2021-08-13_2021-08-28 +#> - CB4_64_16D_STK_v001_022025_2021-08-13_2021-08-28 +#> - CB4_64_16D_STK_v001_022024_2021-07-28_2021-08-12 +#> - CB4_64_16D_STK_v001_022025_2021-07-28_2021-08-12 +#> - CB4_64_16D_STK_v001_022024_2021-07-12_2021-07-27 +#> - CB4_64_16D_STK_v001_022025_2021-07-12_2021-07-27 +#> - assets: +#> EVI, NDVI, CMASK, BAND13, BAND14, BAND15, BAND16, CLEAROB, TOTALOB, thumbnail, PROVENANCE +#> - other field(s): type, links, context, features ``` The `rstac` uses the [httr](https://github.com/r-lib/httr) package to @@ -148,7 +151,7 @@ criteria: ``` r # it_obj variable from the last code example it_obj %>% items_matched() -#> [1] 236 +#> [1] 264 ``` However, if we count how many items there are in `it_obj` variable, we @@ -165,7 +168,7 @@ it_obj %>% items_length() # (but don't stored them back in it_obj) it_obj %>% items_fetch(progress = FALSE) %>% items_length() -#> [1] 236 +#> [1] 264 ``` ### Download assets From f6c83174740d03ca1ee6dbc5140e2e05d06e78fb Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 20:03:04 +0000 Subject: [PATCH 36/44] update tests --- tests/testthat/test-items_functions.R | 4 +++- tests/testthat/test-signatures.R | 24 ++++++++++++------------ 2 files changed, 15 insertions(+), 13 deletions(-) diff --git a/tests/testthat/test-items_functions.R b/tests/testthat/test-items_functions.R index 00b74e60..564fa4f0 100644 --- a/tests/testthat/test-items_functions.R +++ b/tests/testthat/test-items_functions.R @@ -92,7 +92,9 @@ testthat::test_that("items functions", { # items_filter-------------------------------------------------------------- testthat::expect_s3_class( - object = items_filter(res, fn = function(x) {x[["eo:cloud_cover"]] < 10}), + object = items_filter( + res, filter_fn = function(x) {x[["eo:cloud_cover"]] < 10} + ), class = "STACItemCollection" ) diff --git a/tests/testthat/test-signatures.R b/tests/testthat/test-signatures.R index 5513041a..f6cce07b 100644 --- a/tests/testthat/test-signatures.R +++ b/tests/testthat/test-signatures.R @@ -18,17 +18,17 @@ testthat::test_that("signature functions", { # return the same object after signature? testthat::expect_s3_class( - object = items_sign(stac_items, sign_bdc("AAAA-BBB")), + object = items_sign(stac_items, sign_fn = sign_bdc("AAAA-BBB")), class = c("STACItemCollection", "RSTACDocument") ) # return the same object after signature? testthat::expect_s3_class( - object = stac_item %>% items_sign(sign_bdc("AAAA-BBB")), + object = stac_item %>% items_sign(sign_fn = sign_bdc("AAAA-BBB")), class = c("STACItem", "RSTACDocument") ) - items_signed <- items_sign(stac_items, sign_bdc("AAAA-BBB")) + items_signed <- items_sign(stac_items, sign_fn = sign_bdc("AAAA-BBB")) href_items <- items_signed$features[[1]]$assets[[1]]$href # is the token being added at the end of the url? @@ -36,7 +36,7 @@ testthat::test_that("signature functions", { gsub("^([^?]+)(\\?.*)?$", "\\2", href_items), "?access_token=AAAA-BBB" ) - item_signed <- items_sign(stac_item, sign_bdc("AAAA-BBB")) + item_signed <- items_sign(stac_item, sign_fn =sign_bdc("AAAA-BBB")) href_item <- item_signed$assets[[1]]$href # is the token being added at the end of the url? @@ -45,7 +45,7 @@ testthat::test_that("signature functions", { ) Sys.setenv("BDC_ACCESS_KEY" = "CCCC-DDD") - items_signed <- items_sign(stac_items, sign_bdc()) + items_signed <- items_sign(stac_items, sign_fn = sign_bdc()) href_items <- items_signed$features[[1]]$assets[[1]]$href # is the token being added at the end of the url with env var? @@ -53,7 +53,7 @@ testthat::test_that("signature functions", { gsub("^([^?]+)(\\?.*)?$", "\\2", href_items), "?access_token=CCCC-DDD" ) - item_signed <- items_sign(stac_item, sign_bdc()) + item_signed <- items_sign(stac_item, sign_fn = sign_bdc()) href_item <- item_signed$assets[[1]]$href # is the token being added at the end of the url with env var? @@ -65,12 +65,12 @@ testthat::test_that("signature functions", { # an error is expected if no option is provided testthat::expect_error( - items_sign(stac_items, sign_bdc()) + items_sign(stac_items, sign_fn = sign_bdc()) ) # an error is expected if no option is provided testthat::expect_error( - items_sign(stac_item, sign_bdc()) + items_sign(stac_item, sign_fn = sign_bdc()) ) }) @@ -103,13 +103,13 @@ testthat::test_that("signature functions", { # return the same object after signature? testthat::expect_s3_class( object = suppressWarnings( - items_sign(stac_item, sign_planetary_computer()) + items_sign(stac_item, sign_fn = sign_planetary_computer()) ), class = c("STACItem", "RSTACDocument") ) items_signed <- suppressWarnings( - items_sign(stac_items, sign_planetary_computer()) + items_sign(stac_items, sign_fn = sign_planetary_computer()) ) href_items <- items_signed$features[[1]]$assets[[1]]$href @@ -120,7 +120,7 @@ testthat::test_that("signature functions", { ) item_signed <- suppressWarnings( - items_sign(stac_item, sign_planetary_computer()) + items_sign(stac_item, sign_fn = sign_planetary_computer()) ) href_item <- item_signed$assets[[1]]$href @@ -134,7 +134,7 @@ testthat::test_that("signature functions", { testthat::expect_error( object = suppressWarnings( items_sign(stac_items, - sign_planetary_computer(token_url = "test")) + sign_fn = sign_planetary_computer(token_url = "test")) ) ) }) From d0ede0c4ef94e015af82071914aefc2bdaaf8767 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 20:03:18 +0000 Subject: [PATCH 37/44] update DESCRIPTION --- DESCRIPTION | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f247bc47..fe328d04 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,10 +8,10 @@ Authors@R: person(given = "National Institute for Space Research (INPE)", role = c("cph"))) Description: Provides functions to access, search and download spacetime earth - observation data via SpatioTemporal Asset Catalog (STAC). This package + observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification - (). For further details see - DOI: 10.1109/IGARSS47720.2021.9553518 + (). + For further details see Simoes et al. (2021) . License: MIT + file LICENSE URL: https://github.com/brazil-data-cube/rstac BugReports: https://github.com/brazil-data-cube/rstac/issues From 1a47cb1aa39df9e5a0eca75efcc43fe61e321f8c Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 20:03:30 +0000 Subject: [PATCH 38/44] update docs --- man/rstac.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/man/rstac.Rd b/man/rstac.Rd index dd260c58..aa6a91b2 100644 --- a/man/rstac.Rd +++ b/man/rstac.Rd @@ -6,7 +6,7 @@ \alias{rstac-package} \title{R client library for STAC (rstac)} \description{ -Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). For further details see DOI: 10.1109/IGARSS47720.2021.9553518 +Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). For further details see Simoes et al. (2021) . } \section{The \code{rstac} functions}{ From 3eff80626360218891215cd3916c2f0916f098d3 Mon Sep 17 00:00:00 2001 From: Felipe Date: Thu, 28 Oct 2021 21:47:37 +0000 Subject: [PATCH 39/44] update README --- README.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/README.md b/README.md index 6ee496e9..579bdda1 100644 --- a/README.md +++ b/README.md @@ -10,11 +10,8 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) -<<<<<<< HEAD [![Build Status](https://cloud.drone.io/api/badges/OldLipe/rstac/status.svg)](https://cloud.drone.io/OldLipe/rstac) -======= ->>>>>>> 9c35257931cbefd90b5169050b6b677458bcd357 [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) From 63b91d2e75dd6034336a80a902eb1e08129bbe9d Mon Sep 17 00:00:00 2001 From: Felipe Date: Sat, 30 Oct 2021 23:57:55 +0000 Subject: [PATCH 40/44] Update README --- README.Rmd | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 3ababbf7..fd0e638d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -22,7 +22,7 @@ R Client Library for SpatioTemporal Asset Catalog (rstac) [![Software License](https://img.shields.io/badge/license-MIT-green)](https://github.com/brazil-data-cube/rstac/blob/master/LICENSE) [![Build Status](https://cloud.drone.io/api/badges/OldLipe/rstac/status.svg)](https://cloud.drone.io/OldLipe/rstac) -[![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) +[![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) [![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://app.codecov.io/gh/brazil-data-cube/rstac) [![Software Life Cycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![CRAN status](https://www.r-pkg.org/badges/version/rstac)](https://cran.r-project.org/package=rstac) [![STAC API](https://img.shields.io/badge/STAC%20API-v1.0.0-informational)](https://github.com/radiantearth/stac-api-spec) diff --git a/README.md b/README.md index 579bdda1..d261bc1d 100644 --- a/README.md +++ b/README.md @@ -14,7 +14,7 @@ License](https://img.shields.io/badge/license-MIT-green)](https://github.com/bra Status](https://cloud.drone.io/api/badges/OldLipe/rstac/status.svg)](https://cloud.drone.io/OldLipe/rstac) [![Build status](https://ci.appveyor.com/api/projects/status/73w7h6u46l1587jj?svg=true)](https://ci.appveyor.com/project/OldLipe/rstac) -[![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://codecov.io/gh/brazil-data-cube/rstac) +[![codecov](https://codecov.io/gh/brazil-data-cube/rstac/branch/master/graph/badge.svg?token=ILQLPW19UT)](https://app.codecov.io/gh/brazil-data-cube/rstac) [![Software Life Cycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) [![CRAN From 0a4183c92c90831b011319bdb6276fb3fb6687b1 Mon Sep 17 00:00:00 2001 From: Felipe Date: Sun, 31 Oct 2021 00:10:03 +0000 Subject: [PATCH 41/44] update DESCRIPTION --- DESCRIPTION | 2 +- man/rstac.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index fe328d04..5e1e694e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,7 +10,7 @@ Authors@R: Description: Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification - (). + (). For further details see Simoes et al. (2021) . License: MIT + file LICENSE URL: https://github.com/brazil-data-cube/rstac diff --git a/man/rstac.Rd b/man/rstac.Rd index aa6a91b2..dbea6245 100644 --- a/man/rstac.Rd +++ b/man/rstac.Rd @@ -6,7 +6,7 @@ \alias{rstac-package} \title{R client library for STAC (rstac)} \description{ -Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). For further details see Simoes et al. (2021) . +Provides functions to access, search and download spacetime earth observation data via SpatioTemporal Asset Catalog (STAC). This package supports the version 1.0.0 of the STAC specification (). For further details see Simoes et al. (2021) . } \section{The \code{rstac} functions}{ From fdadacec43a651801024da16f80f51b251000b22 Mon Sep 17 00:00:00 2001 From: Felipe Date: Mon, 1 Nov 2021 02:43:31 +0000 Subject: [PATCH 42/44] Closes #79 --- NEWS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/NEWS.md b/NEWS.md index b5ca5cc6..de69ebdb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,13 @@ # rstac (development version) +# rstac 0.9.1-5 (Released 2021-11-01) + +* Add the `rstac` reference paper in README +* Add feature name on print items objects +* Create `items_next` function +* Adjust download helpers to access data from Microsoft's Planetary Computer +* Update news.md of v0.9.0-1 + # rstac 0.9.1-4 (Released 2021-09-14) * Fix typos From f72c5b83c5cac8ccf60880b690dcdd2b9717631e Mon Sep 17 00:00:00 2001 From: Felipe Date: Mon, 1 Nov 2021 14:59:41 +0000 Subject: [PATCH 43/44] Closes #18 --- NEWS.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/NEWS.md b/NEWS.md index de69ebdb..4f4b0d99 100644 --- a/NEWS.md +++ b/NEWS.md @@ -32,18 +32,18 @@ # rstac 0.9.0-1 (Released 2020-10-20) -* Update ext_query function -* Add magrittr package in depends +* Update `ext_query` function +* Add `magrittr` package in depends * Add function items_bands -* Introduces items_bbox and items_datetime functions +* Introduces `items_bbox` and `items_datetime` functions * Update print.R file * Fix items_fetch -* Update 'assets_download.R' and others functions +* Update `assets_download.R` and others functions * Add function 'get_assets_name' * Add overwrite and items_max parameter; solve issue #10 * Fix bug in stac_matched and update documentation -* Change function name '.verify_datime()' to 'parse_datetime()' -* Rename extension_query -> ext_query +* Change function name `.verify_datime()'` to `parse_datetime()` +* Rename function `extension_query` to `ext_query` # rstac 0.9.0 (Released 2020-09-18) From 585440891a0b0dbc129062858f45a49012948ebc Mon Sep 17 00:00:00 2001 From: Felipe Date: Mon, 1 Nov 2021 15:22:19 +0000 Subject: [PATCH 44/44] Closes #79 --- NEWS.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 4f4b0d99..740e56e8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -2,9 +2,17 @@ # rstac 0.9.1-5 (Released 2021-11-01) +* Add support to `lifecycle` package +* Documentation has been changed from `Rd` to `markdown` +* New functions that support assets and items manipulation have been added: `assets_select`, `assets_filter`, and `items_filter` +* The documentation was reviewed +* New examples and tests were added +* `rstac` now supports signatures in `href` using the `items_sign` function +* Function `items_bands()` was changed to `items_assets()` +* Parameters `assets_name` and `assets_names` are now called `asset_names` * Add the `rstac` reference paper in README * Add feature name on print items objects -* Create `items_next` function +* Create `items_next` function to do a single pagination request * Adjust download helpers to access data from Microsoft's Planetary Computer * Update news.md of v0.9.0-1