Merge pull request #391 from broadinstitute/dp-terra

add generic upload_entities_tsv task

Author: dpark01

pipes/WDL/tasks/tasks_terra.wdl

@@ -30,7 +30,7 @@ task gcs_copy {
   }
 }
 
-task upload_entities_tsv {
+task upload_reads_assemblies_entities_tsv {
   input {
     String        workspace_name
     String        terra_project
@@ -65,6 +65,40 @@ task upload_entities_tsv {
   }
 }
 
+task upload_entities_tsv {
+  input {
+    String        workspace_name
+    String        terra_project
+    File          tsv_file
+
+    String        docker = "schaluvadi/pathogen-genomic-surveillance:api-wdl"
+  }
+  command {
+    set -e
+    python3<<CODE
+    import sys
+    from firecloud import api as fapi
+    response = fapi.upload_entities_tsv(
+      '~{terra_project}', '~{workspace_name}', '~{tsv_file}', model="flexible")
+    if response.status_code != 200:
+        print('ERROR UPLOADING: See full error message:')
+        print(response.text)
+        sys.exit(1)
+    else:
+        print("Upload complete. Check your workspace for new table!")
+    CODE
+  }
+  runtime {
+    docker: docker
+    memory: "2 GB"
+    cpu: 1
+    maxRetries: 0
+  }
+  output {
+    Array[String] stdout = read_lines(stdout())
+  }
+}
+
 task download_entities_tsv {
   input {
     String  terra_project

pipes/WDL/workflows/sarscov2_illumina_full.wdl

@@ -364,7 +364,7 @@ workflow sarscov2_illumina_full {
 
     # create data tables with assembly_meta_tsv if workspace name and project provided
     if (defined(workspace_name) && defined(terra_project)) {
-      call terra.upload_entities_tsv as data_tables {
+      call terra.upload_reads_assemblies_entities_tsv as data_tables {
         input:
           workspace_name                      = select_first([workspace_name]),
           terra_project                       = select_first([terra_project]),

pipes/WDL/workflows/terra_update_assemblies.wdl

@@ -9,9 +9,9 @@ workflow update_data_tables {
         email:  "viral-ngs@broadinstitute.org"
     }
 
-    call terra.upload_entities_tsv
+    call terra.upload_reads_assemblies_entities_tsv
 
     output {
-        Array[String] tables = upload_entities_tsv.tables
+        Array[String] tables = upload_reads_assemblies_entities_tsv.tables
     }
 }