Merge pull request #210 from ResearchObject/optional_gen_cwl

Make Galaxy to CWL workflow conversion optional

Author: simleo

.github/workflows/python-package.yml

@@ -24,19 +24,35 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
+    - name: Install
       run: |
         python -m pip install --upgrade pip
+        pip install -e .
         pip install flake8 pytest
-        pip install -r requirements.txt
     - name: Lint with flake8
       run: |
         flake8 -v .
     - name: Test
       run: |
         pytest -v test
+  check-ga2cwl:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - name: Install
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[ga2cwl]
+        pip install pytest
+    - name: Test
+      run: |
+        pytest -v test

requirements.txt

@@ -1,6 +1,5 @@
 requests
 arcp==0.2.1
-galaxy2cwl
 jinja2
 python-dateutil
 click

rocrate/model/computationalworkflow.py

@@ -24,7 +24,6 @@
 import os
 import tempfile
 from contextlib import redirect_stdout
-from galaxy2cwl import get_cwl_interface
 
 from .file import File
 
@@ -76,6 +75,10 @@ class Workflow(ComputationalWorkflow):
 
 
 def galaxy_to_abstract_cwl(workflow_path, delete=True):
+    try:
+        from galaxy2cwl import get_cwl_interface
+    except ImportError:
+        raise RuntimeError("conversion to cwl not available: package was not installed with the 'ga2cwl' option")
     with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix=".cwl") as f:
         with redirect_stdout(f):
             get_cwl_interface.main(['1', str(workflow_path)])

setup.py

@@ -82,6 +82,9 @@
                   f'{__version__}.tar.gz'),
     keywords="researchobject ro-crate ro metadata jsonld",
     install_requires=[required],
+    extras_require={
+        'ga2cwl': ['galaxy2cwl'],
+    },
     classifiers=[
         'Operating System :: OS Independent',
         'Development Status :: 3 - Alpha',

test/test_workflow_ro_crate.py

@@ -21,10 +21,17 @@
 import pytest
 
 from rocrate.rocrate import ROCrate, make_workflow_rocrate
+try:
+    import galaxy2cwl  # noqa: F401
+except ImportError:
+    CAN_CONVERT_TO_CWL = False
+else:
+    CAN_CONVERT_TO_CWL = True
 
 WF_CRATE = "https://w3id.org/workflowhub/workflow-ro-crate"
 
 
+@pytest.mark.skipif(not CAN_CONVERT_TO_CWL, reason="cwl gen not enabled")
 def test_galaxy_wf_crate(test_data_dir, tmpdir, helpers):
     wf_id = 'test_galaxy_wf.ga'
     wf_path = test_data_dir / wf_id
@@ -87,6 +94,7 @@ def test_cwl_wf_crate(test_data_dir, tmpdir, helpers):
         assert f1.read() == f2.read()
 
 
+@pytest.mark.skipif(not CAN_CONVERT_TO_CWL, reason="cwl gen not enabled")
 def test_create_wf_include(test_data_dir, tmpdir, helpers):
     wf_id = 'test_galaxy_wf.ga'
     wf_path = test_data_dir / wf_id