Update get-template to handle filepaths or URLs in config.yml

Sage-Bionetworks · Mar 7, 2022 · c7991d1 · c7991d1
1 parent 7c87f97
commit c7991d1
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Showing 5 changed files with 101 additions and 10 deletions.
diff --git a/R/get-template.R b/R/get-template.R
@@ -6,7 +6,8 @@
 #' @param synID Synapse ID of an excel or csv file containing a metadata
 #'   template
 #' @param id The id of JSON metadata schema registered in Synapse or Synapse ID
-#' of an excel or csv file containing a metadata template
+#' of an excel or csv file containing a metadata template. Or a filepath or URL
+#' to a json schema.
 #' @inheritParams get_synapse_annotations
 #' @param ... Additional arguments passed to syn$get()
 #' @return Character vector of template column names
@@ -28,6 +29,10 @@ get_template <- function(id = NA, syn, synID = NA, ...) {
     if (grepl("^syn", id)) {
       return(get_template_keys_synID(syn = syn, synID = id, ...))
     }
+    ## Check if a schema file or URL was passed
+    if (identical(tolower(tools::file_ext(id)), "json") | grepl("/", id)) {
+      return(get_template_keys_schema(syn = syn, file = id))
+    }
     ## If not a synID, assume a schema id
     return(get_template_keys_schema(syn = syn, id = id))
   }

diff --git a/inst/config.yml b/inst/config.yml
@@ -1,6 +1,6 @@
 default:
   production: TRUE
-  app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-test/"
+  app_url: "https://shinypro.synapse.org/users/awilliams/dccvalidator/"
   parent: "syn20400157"
   path_to_markdown: "inst/using-the-dccvalidator-app-amp-ad.Rmd"
   study_table: "syn11363298"
@@ -19,14 +19,15 @@ default:
   templates:
     manifest_template: "syn20820080"
     individual_templates:
-      human: "syn12973254"
+      human: "awilliams.test-IndividualHumanMetadataTemplate"
       mouse or other animal model: "syn12973253"
     biospecimen_templates:
       mouse or other animal model: "syn12973252"
       human: "syn12973252"
       drosophila: "syn20673251"
     assay_templates:
-      rnaSeq: "sysbio.metadataTemplates-assay.rnaSeq"
+      rnaSeq: "awilliams.test-AssayRnaSeqMetadataTemplate"
+      16SrRNAseq: "awilliams.test-Assay16SrRNAseqMetadataTemplate"
   species_list:
     - "mouse or other animal model"
     - "human"
@@ -77,8 +78,9 @@ testing:
 
 
 amp-ad:
-  app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-ad/"
+  app_url: "https://shinypro.synapse.org/users/awilliams/dccvalidator/"
   parent: "syn21643404"
+  samples_table: "syn21578908"
   annotations_table: "syn21459391"
   annotations_link: "https://shinypro.synapse.org/users/kwoo/amp-ad-metadata-dictionary/"
   teams:
@@ -116,6 +118,7 @@ amp-ad:
       ATACseq: "syn22024364"
       autorad: "syn22087295"
       immunoassay: "syn22117582"
+      rnaSeq: "sysbio.metadataTemplates-assay.rnaSeq"
       proteomics: "syn12973255"
       single cell RNAseq: "syn21018360"
       wholeGenomeSeq: "syn21018358"
@@ -150,7 +153,7 @@ amp-ad:
   contact_email: "[email protected]"
 
 pec:
-  app_url: "https://shinypro.synapse.org/users/kmontgomery/apps_w_oauth/dccvalidator/"
+  app_url: "https://shinypro.synapse.org/users/awilliams/dccvalidator/"
   parent: "syn21763123"
   path_to_markdown: "inst/using-the-dccvalidator-pec.Rmd"
   study_table: "syn20968992"
@@ -219,7 +222,7 @@ pec:
   contact_email: "[email protected]"
 
 veoibd:
-  app_url: "https://shinypro.synapse.org/users/nkauer/dccvalidator-veoibd/"
+  app_url: "https://shinypro.synapse.org/users/awilliams/dccvalidator/"
   parent: "syn25556537"
   path_to_markdown: "inst/using-the-dccvalidator-veoibd.Rmd"
   study_table: "syn25557724"
@@ -279,3 +282,72 @@ veoibd:
     assay:
       - "specimenID"
   contact_email: "[email protected]"
+
+  amp-ad-test:
+    app_url: "https://shinypro.synapse.org/users/awilliams/dccmonitor"
+    annotations_link: "https://shinypro.synapse.org/users/kwoo/amp-ad-metadata-dictionary/"
+    consortium_fileview: "syn21448475"
+    samples_table: "syn21578908"
+    annotations_storage: "syn21698384"
+    annotations_table: "syn21459391"
+    annotation_keys:
+      - "age"
+      - "primaryDiagnosis"
+    teams:
+      - "3346847"
+    species_list:
+      - "human"
+      - "drosophila"
+      - "MODEL-AD mouse model"
+      - "other mouse or animal model"
+    templates:
+      individual_templates:
+        human: "https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schematic_schemas/json/amp.ad.data.IndividualHumanMetadataTemplate.schema.json"
+        other mouse or animal model: "syn27000468"
+        MODEL-AD mouse model: "syn21084071"
+      biospecimen_templates:
+        human:
+          in vivo, postmortem, other: "awilliams.test-BiospecimenMetadataTemplate"
+          in vitro: "awilliams.test-BiospecimenInvitroMetadataTemplate"
+        other mouse or animal model:
+          in vivo, postmortem, other: "syn12973252"
+          in vitro: "syn25955510"
+        MODEL-AD mouse model:
+          in vivo, postmortem, other: "syn12973252"
+          in vitro: "syn25955510"
+        drosophila: "syn20673251"
+      assay_templates:
+        ATACseq: "awilliams.test-AssayATACSeqMetadataTemplate"
+        autorad: "syn22087295"
+        rnaSeq: "awilliams.test-AssayRnaSeqMetadataTemplate"
+        immunoassay: "syn22117582"
+        proteomics: "syn12973255"
+        single cell RNAseq: "awilliams.test-AssayScrnaSeqMetadataTemplate"
+        wholeGenomeSeq: "awilliams.test-AssayWholeGenomeSeqMetadataTemplate"
+        wholeExomeSeq: "awilliams.test-AssayWholeExomeSeqMetadataTemplate"
+        NanoString: "awilliams.test-AssayNanostringMetadataTemplate"
+        snpArray: "awilliams.test-AssaySnpArrayMetadataTemplate"
+        STARRSeq: "awilliams.test-AssaySTARRSeqMetadataTemplate"
+        TMT quantitation: "awilliams.test-AssayTMTquantitationMetadataTemplate"
+        methylationArray: "awilliams.test-AssayMethylationArrayMetadataTemplate"
+        MRI: "awilliams.test-AssayMRIMetadataTemplate"
+        PET: "awilliams.test-AssayPETMetadataTemplate"
+        16SrRNAseq: "awilliams.test-Assay16SrRNAseqMetadataTemplate"
+        metabolomics: "awilliams.test-AssayMetabolomicsMetadataTemplate"
+        HI-C: "syn27000426"
+        ChIPSeq: "awilliams.test-AssayChIPSeqMetadataTemplate"
+        bisulfiteSeq: "awilliams.test-AssayBisulfiteSeqMetadataTemplate"
+    complete_columns:
+      manifest:
+        - "consortium"
+        - "study"
+        - "grant"
+        - "fileFormat"
+        - "parent"
+      individual:
+        - "individualID"
+      biospecimen:
+        - "individualID"
+        - "specimenID"
+      assay:
+        - "specimenID"
diff --git a/man/get_synapse_schema.Rd b/man/get_synapse_schema.Rd
diff --git a/man/get_template.Rd b/man/get_template.Rd
diff --git a/tests/testthat/test-get-template.R b/tests/testthat/test-get-template.R
@@ -65,6 +65,18 @@ test_that("get_template accepts synID with id param", {
   expect_equal(xlsx2, c("a", "b", "c", "d"))
 })
 
+test_that("get_template can correctly handles URLs and filepaths", {
+  gt <- get_template(id = "https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schematic_schemas/json/amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json",
+               syn = syn)
+  gu <- get_file_schema(file="https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schematic_schemas/json/amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json")
+  expect_identical(gt, names(gu$properties))
+
+  gt <- get_template(id = system.file("testdata",
+                      "amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json",
+                      package="dccvalidator"))
+  expect_identical(gt, names(gu$properties))
+})
+
 # test_that("get_template can get keys from a (simple) registered schema", {
 #   skip_if_not(logged_in(syn = syn))
 # 
@@ -103,7 +115,7 @@ test_that("get_template can get a schema file", {
       "specimenID", "platform", "assay", "readLength", "dnaBatch", "Component", 
       "assayTarget", "libraryBatch"))
 
-  schema_url <- get_file_schema(file="https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schema_metadata_templates/schematic_test/json/amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json")
+  schema_url <- get_file_schema(file="https://raw.githubusercontent.com/afwillia/sysbioDCCjsonschemas/schematic_workflow/schematic_schemas/json/amp.ad.data.Assay16SrRNAseqMetadataTemplate.schema.json")
   expect_equal(names(schema_url$properties),
      c("dnaExtractionMethod", "runType", "libraryPrep", "sequencingBatch",
        "specimenID", "platform", "assay", "readLength", "dnaBatch", "Component",