Merge branch 'main' into helloDockerHostname-update-docker

.github/CONTRIBUTING.md

@@ -22,7 +22,7 @@ New unit test suggestions are tracked as GitHub issues. When creating a unit tes
 4. Ensure your proposed WDL runs locally via `miniwdl run` or `java -jar cromwell-86.jar run`
 5. If you are user of PROOF, please also make sure to test that the WDL unit test runs via PROOF.
     - If your WDL succeeds locally but fails in PROOF, please report the issue in the [proof-api repo](https://github.com/FredHutch/proof-api/issues).
-6. Add the WDL to a subdirectory by the same name, i.e. `coolUnitTest/coolUnitTest.wdl`
+6. Add the WDL to a subdirectory by the same name, i.e. `coolUnitTest/coolUnitTest.wdl`. If the WDL is expected to fail WOMtool the subdirectory AND the WDL file name must start with `badVal`. If the WDL is expected to fail both WOMtool and a Cromwell run, then the subdirectory AND the WDL file name must start with `badRun`.
 7. Make sure to include an `inputs.json` and `options.json` if required and make sure that any other. input files referenced in `inputs.json` are provided in the same directory.
 8. Add a README to the WDL's subdirectory describing the unit test's functionality and purpose.
 9. Commit and push your proposed changes to GitHub.

.github/workflows/api-tests.yml

@@ -24,7 +24,10 @@ jobs:
       - name: Set up Python
         run: uv python install 3.13
 
+      - name: Install dependencies
+        run: uv sync --all-extras
+
       - name: Run tests
         env:
           PROOF_API_TOKEN_DEV: ${{ secrets.PROOF_API_TOKEN_DEV }}
-        run: uv run pytest tests/cromwell-api/ --verbose
+        run: uv run pytest tests/cromwellapi/ --verbose

arrayOperations/README.md

@@ -87,7 +87,7 @@ miniwdl run arrayOperations.wdl \
   additional_strings='["foo", "bar"]' \
   nested_arrays='[["nested1", "nested2"], ["nested3", "nested4"]]' \
   numbers='[1, 2, 3, 4, 5]' \
-  input_files='["test1.txt", "test2.txt"]'
+  input_files='["data/test1.txt", "data/test2.txt"]'
 ```
 
 Example inputs.json:
@@ -101,9 +101,9 @@ Example inputs.json:
   ],
   "ArrayOperations.numbers": [1, 2, 3, 4, 5],
   "ArrayOperations.input_files": [
-    "test1.txt",
-    "test2.txt",
-    "test3.txt"
+    "data/test1.txt",
+    "data/test2.txt",
+    "data/test3.txt"
   ]
 }
 ```

arrayOperations/inputs.json

@@ -7,8 +7,8 @@
     ],
     "ArrayOperations.numbers": [1, 2, 3, 4, 5],
     "ArrayOperations.input_files": [
-        "arrayOperations/test1.txt",
-        "arrayOperations/test2.txt",
-        "arrayOperations/test3.txt"
+        "arrayOperations/data/test1.txt",
+        "arrayOperations/data/test2.txt",
+        "arrayOperations/data/test3.txt"
     ]
 }

badRunParseBatchFile/README.md

@@ -0,0 +1,15 @@
+# parseBatchFile WDL Workflow
+
+## Overview
+xxx
+
+## Workflow Components
+
+### Workflow: `parseBatchFile`
+xxx
+
+## Purpose
+To check Cromwell failures behavior
+
+## Version
+WDL 1.0

badRunParseBatchFile/badRunParseBatchFile.wdl

@@ -0,0 +1,46 @@
+version 1.0
+# This workflow takes a tab separated file where each row is a set of data to be used in each 
+# of the independent scattered task series that you have as your workflow process.  This file 
+# will, for example, have column names `sampleName`, `bamLocation`, and `bedlocation`.  This
+# allows you to know that regardless of the order of the columns in your batch file, the correct
+# inputs will be used for the tasks you define.  
+workflow parseBatchFile {
+  input {
+  File batchFile
+  }
+    Array[Object] batchInfo = read_objects(batchFile)
+  scatter (job in batchInfo){
+    String sampleName = job.sampleName
+    File bamFile = job.bamLocation
+    File bedFile = job.bedLocation
+
+    ## INSERT YOUR WORKFLOW TO RUN PER LINE IN YOUR BATCH FILE HERE!!!!
+    call test {
+        input: in1=sampleName, in2=bamFile, in3=bedFile
+    }
+
+  }  # End Scatter over the batch file
+# Outputs that will be retained when execution is complete
+  output {
+    Array[File] outputArray = test.item_out
+    }
+# End workflow
+}
+
+#### TASK DEFINITIONS
+# echo some text to stdout, treats files as strings just to echo them as a dummy example
+task test {
+  input {
+    String in1
+    String in2
+    String in3
+  }
+    command {
+    echo ~{in1}
+    echo ~{in2}
+    echo ~{in3}
+    }
+    output {
+        File item_out = stdout()
+    }
+}

badValMissingValue/README.md

@@ -0,0 +1,10 @@
+# badValMissingValue WDL Workflow
+
+## Overview
+A test workflow that demonstrates an invalid WDL.
+
+### Expected error
+
+```
+Cannot lookup value 'docker_image', it is never declared. Available values are: ['str']
+```

tests/cromwell-api/conftest.py → tests/cromwellapi/conftest.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import pytest
+
 from cromwell import CromwellApi
 from proof import ProofApi
 
@@ -13,7 +14,7 @@ def cromwell_api():
     return CromwellApi(url=cromwell_url)
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(scope="session")
 def submit_wdls(cromwell_api):
     """
     This fixture runs automatically before any tests.
@@ -25,7 +26,12 @@ def submit_wdls(cromwell_api):
 
     print(f"Submitting {len(wdl_paths)} wdls ...")
 
-    out = [cromwell_api.submit_workflow(wdl_path=path) for path in wdl_paths]
+    out = []
+    for path in wdl_paths:
+        opts_path = path.parent / "options.json"
+        opts_path = opts_path if opts_path.exists() else None
+        res = cromwell_api.submit_workflow(wdl_path=path, options=opts_path)
+        out.append(res)
 
     # Yield to let tests run
     yield out