Merge pull request #53 from FredHutch/womtool-pythonize

Womtool and Cromwell test run pythonize

.github/workflows/cromwell-test-run.yml

@@ -42,15 +42,18 @@ jobs:
       - name: Pull Cromwell Jarfile
         run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/cromwell-86.jar
 
-      - name: Execute Test Run of WDL Workflows
-        run: |
-          cmd="java -jar cromwell-86.jar run ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl"
-          if [[ -f "${{ matrix.wdl }}/inputs.json" ]]; then
-            cmd="$cmd -i ${{ matrix.wdl }}/inputs.json"
-          fi
-          if [[ -f "${{ matrix.wdl }}/options.json" ]]; then
-            cmd="$cmd -o ${{ matrix.wdl }}/options.json"
-          fi
-          echo "Running command: $cmd"
-          eval "$cmd"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.16"
 
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Execute Test Run of WDL Workflows
+        env:
+          CROMWELL_PATH: cromwell-86.jar
+        run: uv run pytest tests/cromwelljava/test-run.py --wdl-path=${{ matrix.wdl }} --verbose -s

.github/workflows/womtools-validate.yml

@@ -29,27 +29,30 @@ jobs:
       matrix:
         wdl: ${{ fromJson(needs.generate-matrix.outputs.matrix) }}
     steps:
-      -
-        name: Checkout
+      - name: Checkout
         uses: actions/checkout@v4
 
-      -
-        name: Set Up Java
+      - name: Set Up Java
         uses: actions/setup-java@v4
         with:
           distribution: 'temurin'
           java-version: '21'
 
-      -
-        name: Pull WOMtool Jarfile
+      - name: Pull WOMtool Jarfile
         run: wget -q https://github.com/broadinstitute/cromwell/releases/download/86/womtool-86.jar
 
-      - 
-        name: Validate WDL Scripts
-        run: |
-          cmd="java -jar womtool-86.jar validate ${{ matrix.wdl }}/${{ matrix.wdl }}.wdl"
-          if [[ -f "${{ matrix.wdl }}/inputs.json" ]]; then
-            cmd="$cmd -i ${{ matrix.wdl }}/inputs.json"
-          fi
-          echo "Running command: $cmd"
-          eval "$cmd"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.16"
+
+      - name: Set up Python
+        run: uv python install 3.13
+
+      - name: Install dependencies
+        run: uv sync --all-extras
+
+      - name: Validate WDL Scripts
+        env:
+          WOMTOOL_PATH: womtool-86.jar
+        run: uv run pytest tests/cromwelljava/test-validate.py --wdl-path=${{ matrix.wdl }} --verbose -s

badFile/badFile.wdl

@@ -0,0 +1,19 @@
+version 1.0
+## This is a test workflow that fails against womtool.
+## From https://github.com/broadinstitute/cromwell
+
+#### WORKFLOW DEFINITION
+
+workflow oops {
+  call oopsie
+}
+
+#### TASK DEFINITIONS
+
+task oopsie {
+  input {
+    String str
+  }
+  command { echo ${str} }
+  runtime { docker: docker_image }
+}

pyproject.toml

@@ -7,5 +7,6 @@ requires-python = ">=3.13"
 dependencies = [
     "httpx>=0.28.1",
     "pytest>=8.3.4",
+    "sh>=2.1.0",
     "tenacity>=9.0.0",
 ]

tests/cromwelljava/conftest.py

@@ -0,0 +1,13 @@
+import pytest
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--wdl-path",
+        action="store",
+        default="default_value",
+        help="Path to a directory with a WDL file to test"
+    )
+
+@pytest.fixture
+def wdl_path(pytestconfig):
+    return pytestconfig.getoption("--wdl-path")

tests/cromwelljava/test-run.py

@@ -0,0 +1,11 @@
+from utils import CromwellJava
+
+cromwell = CromwellJava()
+
+
+def test_cromwell_run(wdl_path):
+    is_valid = cromwell.run(wdl_path)
+    if wdl_path.startswith("bad"):
+        assert not is_valid
+    else:
+        assert is_valid

tests/cromwelljava/test-validate.py

@@ -0,0 +1,11 @@
+from utils import Womtool
+
+wom = Womtool()
+
+
+def test_womtool_validate(wdl_path):
+    is_valid = wom.validate(wdl_path)
+    if wdl_path.startswith("bad"):
+        assert not is_valid
+    else:
+        assert is_valid

tests/cromwelljava/utils.py

@@ -0,0 +1,71 @@
+import os
+from pathlib import Path
+
+import sh
+
+
+class Womtool(object):
+    """Womtool class"""
+
+    def __init__(self):
+        self.womtool_path = os.getenv("WOMTOOL_PATH")
+        if not self.womtool_path:
+            raise Exception("failed setting WOMTOOL_PATH")
+        self.womtool = sh.Command("java").bake("-jar", self.womtool_path)
+
+    def has_inputs(self, wdl_path):
+        path = Path(f"{wdl_path}/inputs.json")
+        if path.exists():
+            self.womtool = self.womtool.bake(i=str(path))
+
+    def validate(self, wdl_path, show_cmd=False):
+        try:
+            self.womtool = self.womtool.bake(
+                "validate",
+                f"{wdl_path}/{wdl_path}.wdl",
+            )
+            self.has_inputs(wdl_path)
+            if show_cmd:
+                print(self.womtool)
+            self.womtool()
+        except sh.ErrorReturnCode as e:
+            print(f"Command {e.full_cmd} exited with {e.exit_code}")
+            return False
+
+        return True
+
+class CromwellJava(object):
+    """Cromwell Java class - run Cromwell Java jar"""
+
+    def __init__(self):
+        self.cromwell_path = os.getenv("CROMWELL_PATH")
+        if not self.cromwell_path:
+            raise Exception("failed setting CROMWELL_PATH")
+        self.cromwell = sh.Command("java").bake("-jar", self.cromwell_path)
+
+    def has_inputs(self, wdl_path):
+        path = Path(f"{wdl_path}/inputs.json")
+        if path.exists():
+            self.cromwell = self.cromwell.bake(i=str(path))
+
+    def has_options(self, wdl_path):
+        path = Path(f"{wdl_path}/options.json")
+        if path.exists():
+            self.cromwell = self.cromwell.bake(o=str(path))
+
+    def run(self, wdl_path, show_cmd=False):
+        try:
+            self.cromwell = self.cromwell.bake(
+                "run",
+                f"{wdl_path}/{wdl_path}.wdl",
+            )
+            self.has_inputs(wdl_path)
+            self.has_options(wdl_path)
+            if show_cmd:
+                print(self.cromwell)
+            self.cromwell()
+        except sh.ErrorReturnCode as e:
+            print(f"Command {e.full_cmd} exited with {e.exit_code}")
+            return False
+
+        return True