Merge pull request #54 from DNAstack/Handle-expressions-with-parenthe…

…ses-in-wdl-ci-BIOS-540

Handle expressions with parentheses

README.md

@@ -15,7 +15,7 @@ If any step of the action fails, the check will fail; however if some task tests
 # GitHub action usage
 
 ```yaml
-- uses: dnastack/[email protected].0
+- uses: dnastack/[email protected].1
   with:
     # Configuration file where tests can be found
     # Default: wdl-ci.config.json
@@ -91,7 +91,7 @@ jobs:
         with:
           submodules: true
       - name: wdl-ci
-        uses: dnastack/[email protected].0
+        uses: dnastack/[email protected].1
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -119,7 +119,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].0
+        uses: dnastack/[email protected].1
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -149,7 +149,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/[email protected].0
+        uses: dnastack/[email protected].1
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}

action.yml

@@ -53,19 +53,19 @@ runs:
           echo "WDL_CI_CUSTOM_TEST_WDL_DIR"=${{ inputs.wdl-ci-custom-test-wdl-dir }} >> $GITHUB_ENV
         fi
     - name: lint
-      uses: docker://dnastack/wdl-ci:v2.0.0
+      uses: docker://dnastack/wdl-ci:v2.0.1
       with:
         args: lint ${{ inputs.suppress-lint-errors && '--suppress-lint-errors' || '' }}
     - name: detect-changes
-      uses: docker://dnastack/wdl-ci:v2.0.0
+      uses: docker://dnastack/wdl-ci:v2.0.1
       with:
         args: detect-changes
     - name: submit
-      uses: docker://dnastack/wdl-ci:v2.0.0
+      uses: docker://dnastack/wdl-ci:v2.0.1
       with:
         args: submit
     - name: monitor
-      uses: docker://dnastack/wdl-ci:v2.0.0
+      uses: docker://dnastack/wdl-ci:v2.0.1
       with:
         args: monitor --update-digests
       # If a test fails, still update task digests for any tests that succeeded
@@ -79,6 +79,6 @@ runs:
         default_author: github_actions
     - name: cleanup
       if: always()
-      uses: docker://dnastack/wdl-ci:v2.0.0
+      uses: docker://dnastack/wdl-ci:v2.0.1
       with:
         args: cleanup

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "wdl-testing-cli"
 description = "DNAstack WDL testing CLI"
-version = "2.0.0"
+version = "2.0.1"
 authors = [
     { name = "DNAstack", email = "[email protected]" }
 ]

src/wdlci/cli/submit.py

@@ -104,6 +104,7 @@ def submit_handler(kwargs):
                         try:
                             write_workflow(
                                 workflow_name,
+                                doc,
                                 doc_main_task,
                                 output_tests,
                                 test_key,
@@ -170,9 +171,9 @@ def submit_handler(kwargs):
                         output_test_val_hydrated = HydrateParams.hydrate(
                             source_params, output_test_val, update_key=False
                         )
-                        output_tests_hydrated[
-                            output_test_key_hydrated
-                        ] = output_test_val_hydrated
+                        output_tests_hydrated[output_test_key_hydrated] = (
+                            output_test_val_hydrated
+                        )
 
                     workflow_id = submission_state.workflows[test_key]._workflow_id
 

src/wdlci/utils/write_workflow.py

@@ -76,6 +76,7 @@ def _get_output_type(main_task_output_types, output_key):
 
 def write_workflow(
     workflow_name,
+    main_doc,
     main_task,
     output_tests,
     output_file,
@@ -86,6 +87,7 @@ def write_workflow(
     Write a workflow out to a file
     Args:
         workflow_name (str): Name of the test workflow being generated (workflow entrypoint)
+        main_doc (WDL.Tree.Document): Document from which the main task originated
         main_task (WDL.Tree.Task): Task to be tested
         output_tests ({output_name: {"value": output_value, "tasks": ["task0", "task1", "task2"]}}):
             Array of validated outputs and the test tasks to apply to them.
@@ -171,7 +173,7 @@ def write_workflow(
                 except:
                     subprocess.run(["miniwdl", "check", str(test_wdl)])
                     raise WdlTestCliExitException(f"Invalid test task [{test_wdl}]", 1)
-                test_tasks[test_task_key] = test_task_doc
+                test_tasks[test_task_key] = {"task": test_task_doc, "doc": test_doc}
 
                 f.write(
                     f"{scatter_indent}\tcall {test_task_doc.name} as {test_task_key} {{\n"
@@ -196,8 +198,8 @@ def write_workflow(
 
         ## Outputs
         f.write("\n\toutput {\n")
-        for test_task_key, test_task_doc in test_tasks.items():
-            for task_output in test_task_doc.outputs:
+        for test_task_key, task_info in test_tasks.items():
+            for task_output in task_info["task"].outputs:
                 f.write(
                     f"\t\t{task_output.type} {test_task_key}_{task_output.name} = {test_task_key}.{task_output.name}\n"
                 )
@@ -207,12 +209,14 @@ def write_workflow(
         f.write("}\n")
         f.write("\n")
 
-    _write_task(main_task, output_file)
+    _write_task(main_doc, main_task, output_file)
     tasks_written = list()
-    for test_task_doc in test_tasks.values():
-        if test_task_doc.name not in tasks_written:
-            _write_task(test_task_doc, output_file)
-            tasks_written.append(test_task_doc.name)
+    for task_info in test_tasks.values():
+        test_doc = task_info["doc"]
+        test_task = task_info["task"]
+        if test_task.name not in tasks_written:
+            _write_task(test_doc, test_task, output_file)
+            tasks_written.append(test_task.name)
 
     # Ensure the workflow is valid
     try:
@@ -223,44 +227,48 @@ def write_workflow(
         )
 
 
-def _write_task(doc_task, output_file):
+def _write_task(doc, task, output_file):
     """
     Write a task out to a file
     Args:
-        doc_task (WDL.Tree.Task): task to write
+        doc (WDL.Tree.Document): Document containing task to write
+        task (WDL.Tree.Task): task to write
         output_file (str): Path to file to write task to
     """
     with open(output_file, "a") as f:
-        f.write(f"task {doc_task.name} {{\n")
+        f.write(f"task {task.name} {{\n")
 
         ## Inputs
         f.write("\tinput " + "{\n")
-        for task_input in doc_task.inputs:
+        for task_input in task.inputs:
             f.write(f"\t\t{task_input}\n")
         f.write("\t}\n")
         f.write("\n")
 
         ## Post inputs
-        for post_input in doc_task.postinputs:
+        for post_input in task.postinputs:
             f.write(f"\t{post_input}\n")
         f.write("\n")
 
         ## Command
         f.write("\tcommand <<<\n")
-        f.write(f"\t\t{doc_task.command}\n")
+        task_cmd_start = task.command.pos.line
+        task_cmd_end = task.command.pos.end_line - 1
+        for line in doc.source_lines[task_cmd_start:task_cmd_end]:
+            f.write(f"{line}\n")
         f.write("\t>>>\n")
         f.write("\n")
 
         ## Outputs
         f.write("\toutput {\n")
-        for task_output in doc_task.outputs:
+        for task_output in task.outputs:
             f.write(f"\t\t{task_output}\n")
         f.write("\t}\n")
         f.write("\n")
 
         ## Runtime
         f.write("\truntime {\n")
-        for runtime_key, runtime_value in doc_task.runtime.items():
+        for runtime_key, runtime_value in task.runtime.items():
             f.write(f"\t\t{runtime_key}: {runtime_value}\n")
         f.write("\t}\n")