Merge pull request #26 from DNAstack/develop

v0.1.5

README.md

@@ -86,7 +86,7 @@ jobs:
         with:
           submodules: true
       - name: wdl-ci
-        uses: dnastack/wdl-ci@0.1.4
+        uses: dnastack/wdl-ci@v0.1.5
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -114,7 +114,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/wdl-ci@0.1.4
+        uses: dnastack/wdl-ci@v0.1.5
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -144,7 +144,7 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
           ref: ${{ github.event.pull_request.head.ref }}
       - name: wdl-ci
-        uses: dnastack/wdl-ci@0.1.4
+        uses: dnastack/wdl-ci@v0.1.5
         with:
           wallet-url: ${{ secrets.WALLET_URL }}
           wallet-client-id: ${{ secrets.WALLET_CLIENT_ID }}
@@ -337,18 +337,12 @@ Test params can be used to avoid repeating paths and values for test inputs and
 }
 ```
 
-
-# Custom workflow linters
-
-Custom linters may be added to [src/wdlci/linters/custom_linters.py](src/wdlci/linters/custom_linters.py).
-
-
 # WDL-based tests
 
 Tests are defined in the [src/wdlci/wdl_tests](src/wdlci/wdl_tests) directory.
 
 - Tests are written in WDL
-- Test files must be named `${test_name}.wdl`
+- Test files must be named `<test_name>.wdl`
 - In the test WDL file, before the task declaration, add a short description of what the purpose of this test is and what input type is expected, e.g.:
 
 ```wdl
@@ -358,17 +352,21 @@ version 1.0
 # Input type: String
 
 task compare_string {
+  input {
+    String current_run_output
+    String validated_output
+  }
   ...
 ```
 
-- Each test file should contain a single test task, named `${test_name}`
+- Each test file should contain a single test task, named `<test_name>`
 - Tests must specify two inputs:
-  - `${input_type} current_run_output`
-  - `${input_type} validated_output`
+  - `<input_type> current_run_output`
+  - `<input_type> validated_output`
 - The `current_run_output` and `validated_output` will be passed to the test task automatically; it is up to the test writer to implement the desired comparison
 
 
-Tests can be selected and applied to input sets by including the `${test_name}` as part of the `workflows.${workflow}.tasks.${task}.tests.[],test_tasks` array. For example, to run the `compare` test, which compares various output types, the `test_tasks` section should be set to `["compare"]`. Additional test tasks may be added for the same input set by adding test names to the `test_tasks` array for that set of inputs.
+Tests can be selected and applied to task outputs by including the `<test_name>` as part of the `test_tasks` array in [the output tests block](#output_tests). For example, to run the `compare_string` test, the `test_tasks` section for the output to be tested should be set to `["compare_string"]`.
 
 ## Array comparison
 

action.yml

@@ -50,19 +50,19 @@ 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:latest
+      uses: docker://dnastack/wdl-ci:v0.1.5
       with:
         args: lint
     - name: detect-changes
-      uses: docker://dnastack/wdl-ci:latest
+      uses: docker://dnastack/wdl-ci:v0.1.5
       with:
         args: detect-changes
     - name: submit
-      uses: docker://dnastack/wdl-ci:latest
+      uses: docker://dnastack/wdl-ci:v0.1.5
       with:
         args: submit
     - name: monitor
-      uses: docker://dnastack/wdl-ci:latest
+      uses: docker://dnastack/wdl-ci:v0.1.5
       with:
         args: monitor --update-digests
       # If a test fails, still update task digests for any tests that succeeded
@@ -76,6 +76,6 @@ runs:
         default_author: github_actions
     - name: cleanup
       if: always()
-      uses: docker://dnastack/wdl-ci:latest
+      uses: docker://dnastack/wdl-ci:v0.1.5
       with:
         args: cleanup

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "wdl-testing-cli"
 description = "DNAstack WDL testing CLI"
-version = "0.1.4"
+version = "v0.1.5"
 authors = [
     { name = "DNAstack", email = "[email protected]" }
 ]

src/wdlci/cli/monitor.py

@@ -118,6 +118,7 @@ def monitor_handler(kwargs):
                     f"run with id '{workflow_run.wes_run_id}' failed execution with a state of {workflow_run.wes_state}"
                 )
                 task_status[workflow_path][task]["succeeded"] = False
+                task_status[workflow_path][task]["workflow_run"] = workflow_run
             elif (
                 workflow_run.status == SubmissionStateWorkflowRun.STATUS_FINISH_SUCCESS
                 and workflow_run.validation_status
@@ -128,12 +129,14 @@ def monitor_handler(kwargs):
                     f"run with id '{workflow_run.wes_run_id}' failed output validation. message: {workflow_run.validation_message}"
                 )
                 task_status[workflow_path][task]["succeeded"] = False
+                task_status[workflow_path][task]["workflow_run"] = workflow_run
             else:
                 fail_n += 1
                 print(
                     f"run with id '{workflow_run.wes_run_id}' failed with an unspecified error"
                 )
                 task_status[workflow_path][task]["succeeded"] = False
+                task_status[workflow_path][task]["workflow_run"] = workflow_run
 
         submission_state_encoded = jsonpickle.encode(submission_state)
         open(SUBMISSION_JSON, "w").write(submission_state_encoded)
@@ -160,6 +163,9 @@ def monitor_handler(kwargs):
                             print(
                                 f"At least one test failed for [{workflow_path} - {task_name}]."
                             )
+                            ewes_client.get_failed_task_logs(
+                                tasks[task_name]["workflow_run"]
+                            )
 
         if config_updated:
             config.write()

src/wdlci/workbench/ewes_client.py

@@ -29,7 +29,9 @@ def submit_workflow_run(self, workflow_run):
 
         headers = {"Authorization": "Bearer " + self.ewes_auth.access_token}
 
-        output_test_task_params = {k: workflow_run._outputs[k]['value'] for k in workflow_run._outputs.keys()}
+        output_test_task_params = {
+            k: workflow_run._outputs[k]["value"] for k in workflow_run._outputs.keys()
+        }
 
         form_data = {
             "workflow_url": f"{env.workbench_workflow_service_url}/{env.workbench_namespace}/workflows/{workflow_run._workflow_id}/versions/v1_0_0/descriptor",
@@ -71,5 +73,37 @@ def poll_workflow_run_status_and_update(self, workflow_run):
             elif wes_state in set(["COMPLETE"]):
                 workflow_run.finish_success()
 
+    def _print_stderr(self, stderr_url, headers, task_name):
+        terminal_format_bold = "\033[1m"
+        terminal_format_end = "\033[0m"
+        print(
+            f"{terminal_format_bold}═════ stderr ═════════════════════════════════════════ [{task_name}]{terminal_format_end}"
+        )
+        print()
+        response = requests.get(stderr_url, headers=headers)
+        print(response.content.decode("ascii"))
+        print(
+            f"{terminal_format_bold}═══════════════════════════════════════════════════════{terminal_format_end}"
+        )
+        print()
+
+    def get_failed_task_logs(self, workflow_run):
+        env = Config.instance().env
+        base_url, namespace = env.workbench_ewes_url, env.workbench_namespace
+        url = (
+            f"{base_url}/{namespace}/ga4gh/wes/v1/runs/{workflow_run.wes_run_id}/tasks"
+        )
+        headers = {"Authorization": "Bearer " + self.ewes_auth.access_token}
+
+        response = requests.get(url, headers=headers)
+        if response.status_code == 200:
+            for task in response.json()["tasks"]:
+                if task["state"] == "EXECUTOR_ERROR":
+                    task_name = task["pretty_name"].split(".")[1]
+                    print(
+                        f"EXECUTOR_ERROR for [{workflow_run._workflow_key} - {task_name}]."
+                    )
+                    self._print_stderr(task["stderr"], headers, task_name)
+
     def __get_url(self):
         return Config.instance().workbench_ewes_url