diff --git a/include_notebooks/include_documentreference.ipynb b/include_notebooks/include_documentreference.ipynb
new file mode 100644
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--- /dev/null
+++ b/include_notebooks/include_documentreference.ipynb
@@ -0,0 +1,2560 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Warning message in system(\"timedatectl\", intern = TRUE):\n",
+ "“running command 'timedatectl' had status 1”\n",
+ "── \u001b[1mAttaching packages\u001b[22m ─────────────────────────────────────── tidyverse 1.3.1 ──\n",
+ "\n",
+ "\u001b[32m✔\u001b[39m \u001b[34mggplot2\u001b[39m 3.3.6 \u001b[32m✔\u001b[39m \u001b[34mpurrr \u001b[39m 0.3.4\n",
+ "\u001b[32m✔\u001b[39m \u001b[34mtibble \u001b[39m 3.1.7 \u001b[32m✔\u001b[39m \u001b[34mdplyr \u001b[39m 1.0.9\n",
+ "\u001b[32m✔\u001b[39m \u001b[34mtidyr \u001b[39m 1.2.0 \u001b[32m✔\u001b[39m \u001b[34mstringr\u001b[39m 1.4.0\n",
+ "\u001b[32m✔\u001b[39m \u001b[34mreadr \u001b[39m 2.1.2 \u001b[32m✔\u001b[39m \u001b[34mforcats\u001b[39m 0.5.1\n",
+ "\n",
+ "── \u001b[1mConflicts\u001b[22m ────────────────────────────────────────── tidyverse_conflicts() ──\n",
+ "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mfilter()\u001b[39m masks \u001b[34mstats\u001b[39m::filter()\n",
+ "\u001b[31m✖\u001b[39m \u001b[34mdplyr\u001b[39m::\u001b[32mlag()\u001b[39m masks \u001b[34mstats\u001b[39m::lag()\n",
+ "\n",
+ "\n",
+ "Attaching package: ‘jsonlite’\n",
+ "\n",
+ "\n",
+ "The following object is masked from ‘package:purrr’:\n",
+ "\n",
+ " flatten\n",
+ "\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "library(tidyverse)\n",
+ "library(httr)\n",
+ "library(jsonlite)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "INCLUDE_FHIR=\"https://include-api-fhir-service.includedcc.org/\"\n",
+ "cookie=gsub(\"\\n\",\"\",read_file(\"~/config/include_cookie\"))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "#Create some reading functions to query the fhir server and extract resource responses.\n",
+ "\n",
+ "simple_get = function(request) {\n",
+ " res=GET(request,add_headers(Cookie=sprintf(\"AWSELBAuthSessionCookie-0=%s\",cookie), ContentType=\"application/json\"))\n",
+ " con=content(res,as=\"parsed\",type=\"application/json\")\n",
+ " con\n",
+ "}\n",
+ "\n",
+ "default_get=function(request) {\n",
+ " simple_get(paste0(INCLUDE_FHIR,request))\n",
+ "}\n",
+ "\n",
+ "\n",
+ "get_all=function(request) {\n",
+ " next_request=paste0(INCLUDE_FHIR,request)\n",
+ " all_content=list()\n",
+ " while(next_request!=\"\") {\n",
+ " my_content=simple_get(next_request)\n",
+ " if(my_content$resourceType==\"Bundle\") {\n",
+ " all_content=append(all_content,lapply(my_content$entry,function(x){x$resource}))\n",
+ " next_request=paste0(sapply(my_content$link,function(x){ifelse(x$relation==\"next\",x$url,\"\")}),collapse = \"\")\n",
+ " }\n",
+ " else {\n",
+ " all_content=append(all_content,list(my_content))\n",
+ " next_request=\"\"\n",
+ " }\n",
+ " }\n",
+ " all_content\n",
+ "}\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "scrolled": true
+ },
+ "outputs": [
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+ "$lastUpdated\n",
+ ": '2022-03-18T23:56:17.258+00:00'\n",
+ "$source\n",
+ ": '#hS1qQMSxTSqxl8KQ'\n",
+ "$profile\n",
+ ": 1. 'http://hl7.org/fhir/StructureDefinition/ResearchStudy'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$identifier\n",
+ ": 1. $use\n",
+ ": 'official'\n",
+ "$value\n",
+ ": 'DS-COG-ALL'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. $system\n",
+ ": 'https://kf-api-dataservice.kidsfirstdrc.org/studies/'\n",
+ "$value\n",
+ ": 'SD_FYCR78W0'\n",
+ "\n",
+ "\n",
+ "\n",
+ "3. $system\n",
+ ": 'https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id='\n",
+ "$value\n",
+ ": 'phs002330.v1.p1'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$title\n",
+ ": 'INCLUDE: (Lupo) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome'\n",
+ "$status\n",
+ ": 'completed'\n",
+ "$category\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'http://snomed.info/sct'\n",
+ "$code\n",
+ ": '276720006'\n",
+ "$display\n",
+ ": 'Dysmorphism (disorder)'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. $system\n",
+ ": 'http://snomed.info/sct'\n",
+ "$code\n",
+ ": '86049000'\n",
+ "$display\n",
+ ": 'Malignant neoplasm, primary (morphologic abnormality)'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'CANCERANDBIRTHDEFECT'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$relatedArtifact\n",
+ ": 1. $type\n",
+ ": 'documentation'\n",
+ "$url\n",
+ ": 'https://includedcc.org/studies/gmkf-ds-x01'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$keyword\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'https://includedcc.org/fhir/code-systems/programs'\n",
+ "$code\n",
+ ": 'INCLUDE-KF'\n",
+ "$display\n",
+ ": 'INCLUDE/KF'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'INCLUDE'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. **$coding** = 1. **$code** = 'SDFYCR78W0'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$search\n",
+ ": **$mode** = 'match'\n",
+ "\n",
+ "\n",
+ "\n",
+ "3. $fullUrl\n",
+ ": 'https://include-api-fhir-service.includedcc.org/ResearchStudy/276232'\n",
+ "$resource\n",
+ ": $resourceType\n",
+ ": 'ResearchStudy'\n",
+ "$id\n",
+ ": '276232'\n",
+ "$meta\n",
+ ": $versionId\n",
+ ": '4'\n",
+ "$lastUpdated\n",
+ ": '2022-03-18T23:53:40.068+00:00'\n",
+ "$source\n",
+ ": '#NqZKaKuAnuiA2oD3'\n",
+ "$profile\n",
+ ": 1. 'http://hl7.org/fhir/StructureDefinition/ResearchStudy'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$identifier\n",
+ ": 1. $use\n",
+ ": 'official'\n",
+ "$value\n",
+ ": 'DS-PCGC'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. $system\n",
+ ": 'https://kf-api-dataservice.kidsfirstdrc.org/studies/'\n",
+ "$value\n",
+ ": 'SD_Y6VRG6MD'\n",
+ "\n",
+ "\n",
+ "\n",
+ "3. $system\n",
+ ": 'https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id='\n",
+ "$value\n",
+ ": 'phs002330.v1.p1'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$title\n",
+ ": 'INCLUDE: (PCGC) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome'\n",
+ "$status\n",
+ ": 'completed'\n",
+ "$category\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'http://snomed.info/sct'\n",
+ "$code\n",
+ ": '276720006'\n",
+ "$display\n",
+ ": 'Dysmorphism (disorder)'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'BIRTHDEFECT'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$relatedArtifact\n",
+ ": 1. $type\n",
+ ": 'documentation'\n",
+ "$url\n",
+ ": 'https://includedcc.org/studies/gmkf-ds-x01'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$keyword\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'https://includedcc.org/fhir/code-systems/programs'\n",
+ "$code\n",
+ ": 'INCLUDE-KF'\n",
+ "$display\n",
+ ": 'INCLUDE/KF'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'INCLUDE'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. **$coding** = 1. **$code** = 'SDY6VRG6MD'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$search\n",
+ ": **$mode** = 'match'\n",
+ "\n",
+ "\n",
+ "\n",
+ "4. $fullUrl\n",
+ ": 'https://include-api-fhir-service.includedcc.org/ResearchStudy/264848'\n",
+ "$resource\n",
+ ": $resourceType\n",
+ ": 'ResearchStudy'\n",
+ "$id\n",
+ ": '264848'\n",
+ "$meta\n",
+ ": $versionId\n",
+ ": '4'\n",
+ "$lastUpdated\n",
+ ": '2022-03-18T23:52:46.428+00:00'\n",
+ "$source\n",
+ ": '#Shp5BEo2bLs7S3Sk'\n",
+ "$profile\n",
+ ": 1. 'http://hl7.org/fhir/StructureDefinition/ResearchStudy'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$identifier\n",
+ ": 1. $use\n",
+ ": 'official'\n",
+ "$value\n",
+ ": 'DS360-CHD'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. $system\n",
+ ": 'https://kf-api-dataservice.kidsfirstdrc.org/studies/'\n",
+ "$value\n",
+ ": 'SD_65064P2Z'\n",
+ "\n",
+ "\n",
+ "\n",
+ "3. $system\n",
+ ": 'https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id='\n",
+ "$value\n",
+ ": 'phs002330.v1.p1'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$title\n",
+ ": 'INCLUDE: (Sherman) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome'\n",
+ "$status\n",
+ ": 'completed'\n",
+ "$category\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'http://snomed.info/sct'\n",
+ "$code\n",
+ ": '276720006'\n",
+ "$display\n",
+ ": 'Dysmorphism (disorder)'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'BIRTHDEFECT'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$relatedArtifact\n",
+ ": 1. $type\n",
+ ": 'documentation'\n",
+ "$url\n",
+ ": 'https://includedcc.org/studies/gmkf-ds-x01'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$keyword\n",
+ ": 1. $coding\n",
+ ": 1. $system\n",
+ ": 'https://includedcc.org/fhir/code-systems/programs'\n",
+ "$code\n",
+ ": 'INCLUDE-KF'\n",
+ "$display\n",
+ ": 'INCLUDE/KF'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$text\n",
+ ": 'INCLUDE'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. **$coding** = 1. **$code** = 'SD65064P2Z'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$search\n",
+ ": **$mode** = 'match'\n",
+ "\n",
+ "\n",
+ "\n",
+ "5. $fullUrl\n",
+ ": 'https://include-api-fhir-service.includedcc.org/ResearchStudy/19908'\n",
+ "$resource\n",
+ ": $resourceType\n",
+ ": 'ResearchStudy'\n",
+ "$id\n",
+ ": '19908'\n",
+ "$meta\n",
+ ": $versionId\n",
+ ": '3'\n",
+ "$lastUpdated\n",
+ ": '2022-03-17T22:09:38.053+00:00'\n",
+ "$source\n",
+ ": '#PQXswYZi3FTYGhdS'\n",
+ "$tag\n",
+ ": 1. $system\n",
+ ": 'https://include.org/htp/fhir/researchstudy'\n",
+ "$code\n",
+ ": 'HTP'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$identifier\n",
+ ": 1. $use\n",
+ ": 'official'\n",
+ "$system\n",
+ ": 'https://include.org/htp/fhir/researchstudy'\n",
+ "$value\n",
+ ": 'HTP'\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. $system\n",
+ ": 'https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id='\n",
+ "$value\n",
+ ": 'phs002330'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$title\n",
+ ": 'Crnic Institute Human Trisome Project'\n",
+ "$status\n",
+ ": 'completed'\n",
+ "$relatedArtifact\n",
+ ": 1. $type\n",
+ ": 'documentation'\n",
+ "$url\n",
+ ": 'https://includedcc.org/studies/human-trisome-project'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$keyword\n",
+ ": 1. **$coding** = 1. $system\n",
+ ": 'https://includedcc.org/fhir/code-systems/programs'\n",
+ "$version\n",
+ ": 'v1'\n",
+ "$code\n",
+ ": 'INCLUDE-KF'\n",
+ "$display\n",
+ ": 'INCLUDE/KF'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "2. **$coding** = 1. **$code** = 'HTP'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$description\n",
+ ": 'TBD'\n",
+ "$enrollment\n",
+ ": 1. **$reference** = 'Group/15367'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$search\n",
+ ": **$mode** = 'match'\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n"
+ ],
+ "text/plain": [
+ "$resourceType\n",
+ "[1] \"Bundle\"\n",
+ "\n",
+ "$id\n",
+ "[1] \"712ded52-8e11-49fd-b40e-7b8f5aa750a7\"\n",
+ "\n",
+ "$meta\n",
+ "$meta$lastUpdated\n",
+ "[1] \"2022-06-27T20:35:56.151+00:00\"\n",
+ "\n",
+ "\n",
+ "$type\n",
+ "[1] \"searchset\"\n",
+ "\n",
+ "$total\n",
+ "[1] 5\n",
+ "\n",
+ "$link\n",
+ "$link[[1]]\n",
+ "$link[[1]]$relation\n",
+ "[1] \"self\"\n",
+ "\n",
+ "$link[[1]]$url\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry\n",
+ "$entry[[1]]\n",
+ "$entry[[1]]$fullUrl\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy/258782\"\n",
+ "\n",
+ "$entry[[1]]$resource\n",
+ "$entry[[1]]$resource$resourceType\n",
+ "[1] \"ResearchStudy\"\n",
+ "\n",
+ "$entry[[1]]$resource$id\n",
+ "[1] \"258782\"\n",
+ "\n",
+ "$entry[[1]]$resource$meta\n",
+ "$entry[[1]]$resource$meta$versionId\n",
+ "[1] \"3\"\n",
+ "\n",
+ "$entry[[1]]$resource$meta$lastUpdated\n",
+ "[1] \"2022-05-24T18:07:03.253+00:00\"\n",
+ "\n",
+ "$entry[[1]]$resource$meta$source\n",
+ "[1] \"#N5kcXtbnx7TIz7Q7\"\n",
+ "\n",
+ "$entry[[1]]$resource$meta$profile\n",
+ "$entry[[1]]$resource$meta$profile[[1]]\n",
+ "[1] \"https://ncpi-fhir.github.io/ncpi-fhir-study-summary-ig/StructureDefinition/ncpi-research-study\"\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$meta$tag\n",
+ "$entry[[1]]$resource$meta$tag[[1]]\n",
+ "$entry[[1]]$resource$meta$tag[[1]]$system\n",
+ "[1] \"https://include.org/ds-connect/fhir/researchstudy\"\n",
+ "\n",
+ "$entry[[1]]$resource$meta$tag[[1]]$code\n",
+ "[1] \"DSC\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$identifier\n",
+ "$entry[[1]]$resource$identifier[[1]]\n",
+ "$entry[[1]]$resource$identifier[[1]]$use\n",
+ "[1] \"official\"\n",
+ "\n",
+ "$entry[[1]]$resource$identifier[[1]]$system\n",
+ "[1] \"https://include.org/ds-connect/fhir/researchstudy\"\n",
+ "\n",
+ "$entry[[1]]$resource$identifier[[1]]$value\n",
+ "[1] \"DSC\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$title\n",
+ "[1] \"DS-Connect\"\n",
+ "\n",
+ "$entry[[1]]$resource$status\n",
+ "[1] \"completed\"\n",
+ "\n",
+ "$entry[[1]]$resource$relatedArtifact\n",
+ "$entry[[1]]$resource$relatedArtifact[[1]]\n",
+ "$entry[[1]]$resource$relatedArtifact[[1]]$type\n",
+ "[1] \"documentation\"\n",
+ "\n",
+ "$entry[[1]]$resource$relatedArtifact[[1]]$url\n",
+ "[1] \"https://includedcc.org/studies/ds-connect\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$keyword\n",
+ "$entry[[1]]$resource$keyword[[1]]\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding[[1]]\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding[[1]]$system\n",
+ "[1] \"https://includedcc.org/fhir/code-systems/programs\"\n",
+ "\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding[[1]]$version\n",
+ "[1] \"v1\"\n",
+ "\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding[[1]]$code\n",
+ "[1] \"INCLUDE\"\n",
+ "\n",
+ "$entry[[1]]$resource$keyword[[1]]$coding[[1]]$display\n",
+ "[1] \"INCLUDE\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$keyword[[2]]\n",
+ "$entry[[1]]$resource$keyword[[2]]$coding\n",
+ "$entry[[1]]$resource$keyword[[2]]$coding[[1]]\n",
+ "$entry[[1]]$resource$keyword[[2]]$coding[[1]]$code\n",
+ "[1] \"DSC\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$resource$description\n",
+ "[1] \"TBD\"\n",
+ "\n",
+ "$entry[[1]]$resource$enrollment\n",
+ "$entry[[1]]$resource$enrollment[[1]]\n",
+ "$entry[[1]]$resource$enrollment[[1]]$reference\n",
+ "[1] \"Group/258781\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[1]]$search\n",
+ "$entry[[1]]$search$mode\n",
+ "[1] \"match\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]\n",
+ "$entry[[2]]$fullUrl\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy/286606\"\n",
+ "\n",
+ "$entry[[2]]$resource\n",
+ "$entry[[2]]$resource$resourceType\n",
+ "[1] \"ResearchStudy\"\n",
+ "\n",
+ "$entry[[2]]$resource$id\n",
+ "[1] \"286606\"\n",
+ "\n",
+ "$entry[[2]]$resource$meta\n",
+ "$entry[[2]]$resource$meta$versionId\n",
+ "[1] \"4\"\n",
+ "\n",
+ "$entry[[2]]$resource$meta$lastUpdated\n",
+ "[1] \"2022-03-18T23:56:17.258+00:00\"\n",
+ "\n",
+ "$entry[[2]]$resource$meta$source\n",
+ "[1] \"#hS1qQMSxTSqxl8KQ\"\n",
+ "\n",
+ "$entry[[2]]$resource$meta$profile\n",
+ "$entry[[2]]$resource$meta$profile[[1]]\n",
+ "[1] \"http://hl7.org/fhir/StructureDefinition/ResearchStudy\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$identifier\n",
+ "$entry[[2]]$resource$identifier[[1]]\n",
+ "$entry[[2]]$resource$identifier[[1]]$use\n",
+ "[1] \"official\"\n",
+ "\n",
+ "$entry[[2]]$resource$identifier[[1]]$value\n",
+ "[1] \"DS-COG-ALL\"\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$identifier[[2]]\n",
+ "$entry[[2]]$resource$identifier[[2]]$system\n",
+ "[1] \"https://kf-api-dataservice.kidsfirstdrc.org/studies/\"\n",
+ "\n",
+ "$entry[[2]]$resource$identifier[[2]]$value\n",
+ "[1] \"SD_FYCR78W0\"\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$identifier[[3]]\n",
+ "$entry[[2]]$resource$identifier[[3]]$system\n",
+ "[1] \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=\"\n",
+ "\n",
+ "$entry[[2]]$resource$identifier[[3]]$value\n",
+ "[1] \"phs002330.v1.p1\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$title\n",
+ "[1] \"INCLUDE: (Lupo) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome\"\n",
+ "\n",
+ "$entry[[2]]$resource$status\n",
+ "[1] \"completed\"\n",
+ "\n",
+ "$entry[[2]]$resource$category\n",
+ "$entry[[2]]$resource$category[[1]]\n",
+ "$entry[[2]]$resource$category[[1]]$coding\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[1]]\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[1]]$system\n",
+ "[1] \"http://snomed.info/sct\"\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[1]]$code\n",
+ "[1] \"276720006\"\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[1]]$display\n",
+ "[1] \"Dysmorphism (disorder)\"\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[2]]\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[2]]$system\n",
+ "[1] \"http://snomed.info/sct\"\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[2]]$code\n",
+ "[1] \"86049000\"\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$coding[[2]]$display\n",
+ "[1] \"Malignant neoplasm, primary (morphologic abnormality)\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$category[[1]]$text\n",
+ "[1] \"CANCERANDBIRTHDEFECT\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$relatedArtifact\n",
+ "$entry[[2]]$resource$relatedArtifact[[1]]\n",
+ "$entry[[2]]$resource$relatedArtifact[[1]]$type\n",
+ "[1] \"documentation\"\n",
+ "\n",
+ "$entry[[2]]$resource$relatedArtifact[[1]]$url\n",
+ "[1] \"https://includedcc.org/studies/gmkf-ds-x01\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$keyword\n",
+ "$entry[[2]]$resource$keyword[[1]]\n",
+ "$entry[[2]]$resource$keyword[[1]]$coding\n",
+ "$entry[[2]]$resource$keyword[[1]]$coding[[1]]\n",
+ "$entry[[2]]$resource$keyword[[1]]$coding[[1]]$system\n",
+ "[1] \"https://includedcc.org/fhir/code-systems/programs\"\n",
+ "\n",
+ "$entry[[2]]$resource$keyword[[1]]$coding[[1]]$code\n",
+ "[1] \"INCLUDE-KF\"\n",
+ "\n",
+ "$entry[[2]]$resource$keyword[[1]]$coding[[1]]$display\n",
+ "[1] \"INCLUDE/KF\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$keyword[[1]]$text\n",
+ "[1] \"INCLUDE\"\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$resource$keyword[[2]]\n",
+ "$entry[[2]]$resource$keyword[[2]]$coding\n",
+ "$entry[[2]]$resource$keyword[[2]]$coding[[1]]\n",
+ "$entry[[2]]$resource$keyword[[2]]$coding[[1]]$code\n",
+ "[1] \"SDFYCR78W0\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[2]]$search\n",
+ "$entry[[2]]$search$mode\n",
+ "[1] \"match\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]\n",
+ "$entry[[3]]$fullUrl\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy/276232\"\n",
+ "\n",
+ "$entry[[3]]$resource\n",
+ "$entry[[3]]$resource$resourceType\n",
+ "[1] \"ResearchStudy\"\n",
+ "\n",
+ "$entry[[3]]$resource$id\n",
+ "[1] \"276232\"\n",
+ "\n",
+ "$entry[[3]]$resource$meta\n",
+ "$entry[[3]]$resource$meta$versionId\n",
+ "[1] \"4\"\n",
+ "\n",
+ "$entry[[3]]$resource$meta$lastUpdated\n",
+ "[1] \"2022-03-18T23:53:40.068+00:00\"\n",
+ "\n",
+ "$entry[[3]]$resource$meta$source\n",
+ "[1] \"#NqZKaKuAnuiA2oD3\"\n",
+ "\n",
+ "$entry[[3]]$resource$meta$profile\n",
+ "$entry[[3]]$resource$meta$profile[[1]]\n",
+ "[1] \"http://hl7.org/fhir/StructureDefinition/ResearchStudy\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$identifier\n",
+ "$entry[[3]]$resource$identifier[[1]]\n",
+ "$entry[[3]]$resource$identifier[[1]]$use\n",
+ "[1] \"official\"\n",
+ "\n",
+ "$entry[[3]]$resource$identifier[[1]]$value\n",
+ "[1] \"DS-PCGC\"\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$identifier[[2]]\n",
+ "$entry[[3]]$resource$identifier[[2]]$system\n",
+ "[1] \"https://kf-api-dataservice.kidsfirstdrc.org/studies/\"\n",
+ "\n",
+ "$entry[[3]]$resource$identifier[[2]]$value\n",
+ "[1] \"SD_Y6VRG6MD\"\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$identifier[[3]]\n",
+ "$entry[[3]]$resource$identifier[[3]]$system\n",
+ "[1] \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=\"\n",
+ "\n",
+ "$entry[[3]]$resource$identifier[[3]]$value\n",
+ "[1] \"phs002330.v1.p1\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$title\n",
+ "[1] \"INCLUDE: (PCGC) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome\"\n",
+ "\n",
+ "$entry[[3]]$resource$status\n",
+ "[1] \"completed\"\n",
+ "\n",
+ "$entry[[3]]$resource$category\n",
+ "$entry[[3]]$resource$category[[1]]\n",
+ "$entry[[3]]$resource$category[[1]]$coding\n",
+ "$entry[[3]]$resource$category[[1]]$coding[[1]]\n",
+ "$entry[[3]]$resource$category[[1]]$coding[[1]]$system\n",
+ "[1] \"http://snomed.info/sct\"\n",
+ "\n",
+ "$entry[[3]]$resource$category[[1]]$coding[[1]]$code\n",
+ "[1] \"276720006\"\n",
+ "\n",
+ "$entry[[3]]$resource$category[[1]]$coding[[1]]$display\n",
+ "[1] \"Dysmorphism (disorder)\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$category[[1]]$text\n",
+ "[1] \"BIRTHDEFECT\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$relatedArtifact\n",
+ "$entry[[3]]$resource$relatedArtifact[[1]]\n",
+ "$entry[[3]]$resource$relatedArtifact[[1]]$type\n",
+ "[1] \"documentation\"\n",
+ "\n",
+ "$entry[[3]]$resource$relatedArtifact[[1]]$url\n",
+ "[1] \"https://includedcc.org/studies/gmkf-ds-x01\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$keyword\n",
+ "$entry[[3]]$resource$keyword[[1]]\n",
+ "$entry[[3]]$resource$keyword[[1]]$coding\n",
+ "$entry[[3]]$resource$keyword[[1]]$coding[[1]]\n",
+ "$entry[[3]]$resource$keyword[[1]]$coding[[1]]$system\n",
+ "[1] \"https://includedcc.org/fhir/code-systems/programs\"\n",
+ "\n",
+ "$entry[[3]]$resource$keyword[[1]]$coding[[1]]$code\n",
+ "[1] \"INCLUDE-KF\"\n",
+ "\n",
+ "$entry[[3]]$resource$keyword[[1]]$coding[[1]]$display\n",
+ "[1] \"INCLUDE/KF\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$keyword[[1]]$text\n",
+ "[1] \"INCLUDE\"\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$resource$keyword[[2]]\n",
+ "$entry[[3]]$resource$keyword[[2]]$coding\n",
+ "$entry[[3]]$resource$keyword[[2]]$coding[[1]]\n",
+ "$entry[[3]]$resource$keyword[[2]]$coding[[1]]$code\n",
+ "[1] \"SDY6VRG6MD\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[3]]$search\n",
+ "$entry[[3]]$search$mode\n",
+ "[1] \"match\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]\n",
+ "$entry[[4]]$fullUrl\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy/264848\"\n",
+ "\n",
+ "$entry[[4]]$resource\n",
+ "$entry[[4]]$resource$resourceType\n",
+ "[1] \"ResearchStudy\"\n",
+ "\n",
+ "$entry[[4]]$resource$id\n",
+ "[1] \"264848\"\n",
+ "\n",
+ "$entry[[4]]$resource$meta\n",
+ "$entry[[4]]$resource$meta$versionId\n",
+ "[1] \"4\"\n",
+ "\n",
+ "$entry[[4]]$resource$meta$lastUpdated\n",
+ "[1] \"2022-03-18T23:52:46.428+00:00\"\n",
+ "\n",
+ "$entry[[4]]$resource$meta$source\n",
+ "[1] \"#Shp5BEo2bLs7S3Sk\"\n",
+ "\n",
+ "$entry[[4]]$resource$meta$profile\n",
+ "$entry[[4]]$resource$meta$profile[[1]]\n",
+ "[1] \"http://hl7.org/fhir/StructureDefinition/ResearchStudy\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$identifier\n",
+ "$entry[[4]]$resource$identifier[[1]]\n",
+ "$entry[[4]]$resource$identifier[[1]]$use\n",
+ "[1] \"official\"\n",
+ "\n",
+ "$entry[[4]]$resource$identifier[[1]]$value\n",
+ "[1] \"DS360-CHD\"\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$identifier[[2]]\n",
+ "$entry[[4]]$resource$identifier[[2]]$system\n",
+ "[1] \"https://kf-api-dataservice.kidsfirstdrc.org/studies/\"\n",
+ "\n",
+ "$entry[[4]]$resource$identifier[[2]]$value\n",
+ "[1] \"SD_65064P2Z\"\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$identifier[[3]]\n",
+ "$entry[[4]]$resource$identifier[[3]]$system\n",
+ "[1] \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=\"\n",
+ "\n",
+ "$entry[[4]]$resource$identifier[[3]]$value\n",
+ "[1] \"phs002330.v1.p1\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$title\n",
+ "[1] \"INCLUDE: (Sherman) Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome\"\n",
+ "\n",
+ "$entry[[4]]$resource$status\n",
+ "[1] \"completed\"\n",
+ "\n",
+ "$entry[[4]]$resource$category\n",
+ "$entry[[4]]$resource$category[[1]]\n",
+ "$entry[[4]]$resource$category[[1]]$coding\n",
+ "$entry[[4]]$resource$category[[1]]$coding[[1]]\n",
+ "$entry[[4]]$resource$category[[1]]$coding[[1]]$system\n",
+ "[1] \"http://snomed.info/sct\"\n",
+ "\n",
+ "$entry[[4]]$resource$category[[1]]$coding[[1]]$code\n",
+ "[1] \"276720006\"\n",
+ "\n",
+ "$entry[[4]]$resource$category[[1]]$coding[[1]]$display\n",
+ "[1] \"Dysmorphism (disorder)\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$category[[1]]$text\n",
+ "[1] \"BIRTHDEFECT\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$relatedArtifact\n",
+ "$entry[[4]]$resource$relatedArtifact[[1]]\n",
+ "$entry[[4]]$resource$relatedArtifact[[1]]$type\n",
+ "[1] \"documentation\"\n",
+ "\n",
+ "$entry[[4]]$resource$relatedArtifact[[1]]$url\n",
+ "[1] \"https://includedcc.org/studies/gmkf-ds-x01\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$keyword\n",
+ "$entry[[4]]$resource$keyword[[1]]\n",
+ "$entry[[4]]$resource$keyword[[1]]$coding\n",
+ "$entry[[4]]$resource$keyword[[1]]$coding[[1]]\n",
+ "$entry[[4]]$resource$keyword[[1]]$coding[[1]]$system\n",
+ "[1] \"https://includedcc.org/fhir/code-systems/programs\"\n",
+ "\n",
+ "$entry[[4]]$resource$keyword[[1]]$coding[[1]]$code\n",
+ "[1] \"INCLUDE-KF\"\n",
+ "\n",
+ "$entry[[4]]$resource$keyword[[1]]$coding[[1]]$display\n",
+ "[1] \"INCLUDE/KF\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$keyword[[1]]$text\n",
+ "[1] \"INCLUDE\"\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$resource$keyword[[2]]\n",
+ "$entry[[4]]$resource$keyword[[2]]$coding\n",
+ "$entry[[4]]$resource$keyword[[2]]$coding[[1]]\n",
+ "$entry[[4]]$resource$keyword[[2]]$coding[[1]]$code\n",
+ "[1] \"SD65064P2Z\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[4]]$search\n",
+ "$entry[[4]]$search$mode\n",
+ "[1] \"match\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]\n",
+ "$entry[[5]]$fullUrl\n",
+ "[1] \"https://include-api-fhir-service.includedcc.org/ResearchStudy/19908\"\n",
+ "\n",
+ "$entry[[5]]$resource\n",
+ "$entry[[5]]$resource$resourceType\n",
+ "[1] \"ResearchStudy\"\n",
+ "\n",
+ "$entry[[5]]$resource$id\n",
+ "[1] \"19908\"\n",
+ "\n",
+ "$entry[[5]]$resource$meta\n",
+ "$entry[[5]]$resource$meta$versionId\n",
+ "[1] \"3\"\n",
+ "\n",
+ "$entry[[5]]$resource$meta$lastUpdated\n",
+ "[1] \"2022-03-17T22:09:38.053+00:00\"\n",
+ "\n",
+ "$entry[[5]]$resource$meta$source\n",
+ "[1] \"#PQXswYZi3FTYGhdS\"\n",
+ "\n",
+ "$entry[[5]]$resource$meta$tag\n",
+ "$entry[[5]]$resource$meta$tag[[1]]\n",
+ "$entry[[5]]$resource$meta$tag[[1]]$system\n",
+ "[1] \"https://include.org/htp/fhir/researchstudy\"\n",
+ "\n",
+ "$entry[[5]]$resource$meta$tag[[1]]$code\n",
+ "[1] \"HTP\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$identifier\n",
+ "$entry[[5]]$resource$identifier[[1]]\n",
+ "$entry[[5]]$resource$identifier[[1]]$use\n",
+ "[1] \"official\"\n",
+ "\n",
+ "$entry[[5]]$resource$identifier[[1]]$system\n",
+ "[1] \"https://include.org/htp/fhir/researchstudy\"\n",
+ "\n",
+ "$entry[[5]]$resource$identifier[[1]]$value\n",
+ "[1] \"HTP\"\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$identifier[[2]]\n",
+ "$entry[[5]]$resource$identifier[[2]]$system\n",
+ "[1] \"https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=\"\n",
+ "\n",
+ "$entry[[5]]$resource$identifier[[2]]$value\n",
+ "[1] \"phs002330\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$title\n",
+ "[1] \"Crnic Institute Human Trisome Project\"\n",
+ "\n",
+ "$entry[[5]]$resource$status\n",
+ "[1] \"completed\"\n",
+ "\n",
+ "$entry[[5]]$resource$relatedArtifact\n",
+ "$entry[[5]]$resource$relatedArtifact[[1]]\n",
+ "$entry[[5]]$resource$relatedArtifact[[1]]$type\n",
+ "[1] \"documentation\"\n",
+ "\n",
+ "$entry[[5]]$resource$relatedArtifact[[1]]$url\n",
+ "[1] \"https://includedcc.org/studies/human-trisome-project\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$keyword\n",
+ "$entry[[5]]$resource$keyword[[1]]\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding[[1]]\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding[[1]]$system\n",
+ "[1] \"https://includedcc.org/fhir/code-systems/programs\"\n",
+ "\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding[[1]]$version\n",
+ "[1] \"v1\"\n",
+ "\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding[[1]]$code\n",
+ "[1] \"INCLUDE-KF\"\n",
+ "\n",
+ "$entry[[5]]$resource$keyword[[1]]$coding[[1]]$display\n",
+ "[1] \"INCLUDE/KF\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$keyword[[2]]\n",
+ "$entry[[5]]$resource$keyword[[2]]$coding\n",
+ "$entry[[5]]$resource$keyword[[2]]$coding[[1]]\n",
+ "$entry[[5]]$resource$keyword[[2]]$coding[[1]]$code\n",
+ "[1] \"HTP\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$resource$description\n",
+ "[1] \"TBD\"\n",
+ "\n",
+ "$entry[[5]]$resource$enrollment\n",
+ "$entry[[5]]$resource$enrollment[[1]]\n",
+ "$entry[[5]]$resource$enrollment[[1]]$reference\n",
+ "[1] \"Group/15367\"\n",
+ "\n",
+ "\n",
+ "\n",
+ "\n",
+ "$entry[[5]]$search\n",
+ "$entry[[5]]$search$mode\n",
+ "[1] \"match\"\n",
+ "\n",
+ "\n",
+ "\n"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "default_get(\"ResearchStudy\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "all_files=get_all(\"DocumentReference?_tag=HTP&category=RNA-Seq&type=Gene-Expression,Gene-Expression-Quantifications&location:missing=false\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "1155"
+ ],
+ "text/latex": [
+ "1155"
+ ],
+ "text/markdown": [
+ "1155"
+ ],
+ "text/plain": [
+ "[1] 1155"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "length(all_files)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "filter_files=all_files[grepl(\"rsem.genes\",sapply(all_files,function(x){x$content[[1]]$attachment$title}))]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 25,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "385"
+ ],
+ "text/latex": [
+ "385"
+ ],
+ "text/markdown": [
+ "385"
+ ],
+ "text/plain": [
+ "[1] 385"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "length(filter_files)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 26,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "df = as_tibble_col(filter_files,\"resource\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "- 385
- 1
\n"
+ ],
+ "text/latex": [
+ "\\begin{enumerate*}\n",
+ "\\item 385\n",
+ "\\item 1\n",
+ "\\end{enumerate*}\n"
+ ],
+ "text/markdown": [
+ "1. 385\n",
+ "2. 1\n",
+ "\n",
+ "\n"
+ ],
+ "text/plain": [
+ "[1] 385 1"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "dim(df)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "opening file output connection.\n",
+ "\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Complete! Processed total of 385 rows.\n"
+ ]
+ },
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "closing file output connection.\n",
+ "\n"
+ ]
+ }
+ ],
+ "source": [
+ "stream_out(df, file(tmp <- tempfile()))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "[1] \"/tmp/RtmpSqDkLt/file1e0207e400c\"\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(tmp)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 30,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "system2(\"gsutil\", args=c(\"cp\", tmp, \"$WORKSPACE_BUCKET/DocumentReference/include.ndjson\"))"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "R",
+ "language": "R",
+ "name": "ir"
+ },
+ "language_info": {
+ "codemirror_mode": "r",
+ "file_extension": ".r",
+ "mimetype": "text/x-r-source",
+ "name": "R",
+ "pygments_lexer": "r",
+ "version": "4.2.0"
+ },
+ "toc": {
+ "base_numbering": 1,
+ "nav_menu": {},
+ "number_sections": true,
+ "sideBar": true,
+ "skip_h1_title": false,
+ "title_cell": "Table of Contents",
+ "title_sidebar": "Contents",
+ "toc_cell": false,
+ "toc_position": {},
+ "toc_section_display": true,
+ "toc_window_display": false
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}