cookie: generic function to deal with http cookies

R/cookie.R

@@ -0,0 +1,137 @@
+#!/usr/bin/env Rscript
+
+#
+#  This file is part of the `OmnipathR` R package
+#
+#  Copyright
+#  2018-2023
+#  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
+#
+#  File author(s): Alberto Valdeolivas
+#                  Dénes Türei ([email protected])
+#                  Attila Gábor
+#
+#  Distributed under the MIT (Expat) License.
+#  See accompanying file `LICENSE` or find a copy at
+#      https://directory.fsf.org/wiki/License:Expat
+#
+#  Website: https://r.omnipathdb.org/
+#  Git repo: https://github.com/saezlab/OmnipathR
+#
+
+
+#' Acquire a cookie if necessary
+#'
+#' @param curl_verbose Logical. Perform CURL requests in verbose mode for
+#'     debugging purposes.
+#'
+#' @importFrom magrittr %>% %T>%
+#' @importFrom readr read_tsv cols
+#' @importFrom curl new_handle handle_setopt curl_fetch_memory handle_cookies
+#' @importFrom logger log_trace
+#' @export
+#'
+#' @return A list with cache file path, cookies and response headers.
+cookie <- function(
+    url,
+    init_url = NULL,
+    post = NULL,
+    payload = NULL,
+    init_post = NULL,
+    init_payload = NULL,
+    curl_verbose = FALSE
+){
+
+    .slow_doctest()
+
+    # NSE vs. R CMD check workaround
+    name <- value <- NULL
+
+    if(is.null(init_url)) {
+        init_url <- url
+        init_post %<>% if_null(post)
+        init_payload %<>% if_null(payload)
+    }
+
+    version <- omnipath_cache_latest_or_new(
+        url = url,
+        post = post,
+        payload = payload,
+        create = FALSE
+    )
+
+    result <- list(cache = version)
+
+    if(is.null(version) || version$status != CACHE_STATUS$READY){
+
+        handle <-
+            new_handle() %>%
+            handle_setopt(
+                url = init_url,
+                verbose = curl_verbose,
+                followlocation = TRUE,
+                httpheader = 'Content-Type: application/json;charset=utf-8',
+                postfields = payload,
+                post = TRUE
+            )
+
+        login_resp <- curl_fetch_memory(login_url, handle)
+
+        token <-
+            handle %>%
+            handle_cookies %>%
+            filter(name == 'access_token') %>%
+            pull(value)
+
+        # the token is also available in the response:
+        # token <-
+        #     login_resp$content %>%
+        #     rawToChar %>%
+        #     parse_json %>%
+        #     `$`(token)
+
+        log_trace('InBioMap token: %s', token)
+
+    }
+
+    # doing the actual download or reading from the cache
+    archive_extractor(
+        url_key = 'inbiomap',
+        path = 'InBio_Map_core_2016_09_12/core.psimitab',
+        reader = read_tsv,
+        reader_param = list(
+            col_types = cols(),
+            col_names = c(
+                'id_a',
+                'id_b',
+                'id_alt_a',
+                'id_alt_b',
+                'synonyms_a',
+                'synonyms_b',
+                'detection_methods',
+                'ref_first_authors',
+                'references',
+                'organism_a',
+                'organism_b',
+                'interaction_types',
+                'databases',
+                'database_ids',
+                'score',
+                'complex_expansion'
+            ),
+            progress = FALSE
+        ),
+        curl_verbose = curl_verbose,
+        # this is passed to curl::handle_setopt
+        httpheader = sprintf('Cookie: access_token=%s', token),
+        resource = 'InWeb InBioMap'
+    ) %T>%
+    load_success()
+
+}
+
+
+#' @noRd
+post_payload <- function(post = NULL, payload = NULL) {
+
+}