try API-less acquisition of workspace info; stub out create_or_update…

…_sample_tables regex introspection derived from: https://github.com/broadinstitute/gatk/blob/c00d4599acc7170ddb857b7fb3db1e0903162cea/scripts/variantstore/wdl/GvsUtils.wdl#L35-L40
broadinstitute · Oct 27, 2023 · bfc8495 · bfc8495
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diff --git a/github_actions_ci/version-wdl-runtimes.sh b/github_actions_ci/version-wdl-runtimes.sh
@@ -5,7 +5,7 @@
 # skip this replacement for any version string line with the comment "#skip-global-version-pin"
 #
 # requires $MODULE_VERSIONS to be set to point to a text file with equal-sign-separated values
-# export MODULE_VERSIONS="./requirements-modules.txt" && ./github_actions_ci/check-wdl-runtimes.sh
+# export MODULE_VERSIONS="./requirements-modules.txt" && ./github_actions_ci/version-wdl-runtimes.sh
 
 printf "Updating docker image tags in WDL files with those in ${MODULE_VERSIONS}\n\n"
 

diff --git a/pipes/WDL/tasks/tasks_terra.wdl b/pipes/WDL/tasks/tasks_terra.wdl
@@ -83,6 +83,21 @@ task check_terra_env {
 
       # === Determine Terra workspace name and namespace for the workspace responsible for this job
 
+      # Scrape out various workflow / workspace info from the localization and delocalization scripts.
+      #   from: https://github.com/broadinstitute/gatk/blob/ah_var_store/scripts/variantstore/wdl/GvsUtils.wdl#L35-L40
+      sed -n -E 's!.*gs://fc-(secure-)?([^\/]+).*!\2!p' /cromwell_root/gcs_delocalization.sh | sort -u 
+      sed -n -E 's!.*(gs://(fc-(secure-)?[^\/]+)).*!\1!p' /cromwell_root/gcs_delocalization.sh | sort -u 
+      sed -n -E 's!.*gs://fc-(secure-)?([^\/]+)/submissions/([^\/]+).*!\3!p' /cromwell_root/gcs_delocalization.sh | sort -u 
+      sed -n -E 's!.*gs://fc-(secure-)?([^\/]+)/submissions/([^\/]+)/([^\/]+)/([^\/]+).*!\5!p' /cromwell_root/gcs_delocalization.sh | sort -u 
+      sed -n -E 's!.*(terra-[0-9a-f]+).*# project to use if requester pays$!\1!p' /cromwell_root/gcs_localization.sh | sort -u 
+
+      # MORE DIRECT IF BUCKET PATH IS KNOWN:
+      #curl -X 'GET' \
+      #  'https://rawls.dsde-prod.broadinstitute.org/api/workspaces/id/8819db8a-7afb-4a27-97e2-6c314968b421?fields=workspace.name%2Cworkspace.namespace' \
+      #  -H 'accept: application/json' \
+      #  -H 'Authorization: Bearer ya29.a0AfB_byDnTCv4_f-qON3w2_z-zFv8Px1_sA1xy8n2Q4MD4suiWyi6YGCYNTs-QXI8VN50COKFT5FtrN05FpWtgPfGv8EZcAxBGNw3TRkYSIbDfbOgRzRVmHe2fmcompALhnHXbVC837qHqUeit1cD22rhwxZQX3EpP2APaCgYKAS0SARMSFQGOcNnCnzFNqCJPvZrC7iHFMed00w0171'
+
+
       # get list of workspaces, limiting the output to only the fields we need
       curl -s -X 'GET' \
       'https://api.firecloud.org/api/workspaces?fields=workspace.name%2Cworkspace.namespace%2Cworkspace.bucketName%2Cworkspace.googleProject' \
@@ -256,3 +271,39 @@ task download_entities_tsv {
   }
 }
 
+task create_or_update_sample_tables {
+  input {
+    String flowcell_run_id
+
+    String workspace_namespace
+    String workspace_name
+    String workspace_bucket
+
+    String  docker = "quay.io/broadinstitute/viral-core:2.2.2" #skip-global-version-pin
+  }
+
+  meta {
+    volatile: true
+  }
+
+  command <<<
+    python3<<CODE
+
+    workspace_project = '~{workspace_namespace}'
+    workspace_name    = '~{workspace_name}'
+    workspace_bucket  = '~{workspace_bucket}'
+    table_name        = ''
+
+    CODE
+  >>>
+  runtime {
+    docker: docker
+    memory: "2 GB"
+    cpu: 1
+    maxRetries: 2
+  }
+  output {
+    File stdout_log = stdout()
+    File stderr_log = stderr()
+  }
+}