test: add new workflow repo fixture

.gitignore

@@ -17,14 +17,16 @@ instance
 **/__pycache__
 **/.npm
 *.pyc
-./certs
+/certs
 **/node_modules
 backups
-data
-lifemonitor/static/dist
-lifemonitor/static/src/node_modules
-docker-compose.yml
+#data
+/lifemonitor/static/dist
+/lifemonitor/static/src/node_modules
+/docker-compose.yml
 .*docker-compose.yml
-utils/certs/data
-tests/config/data/crates/*.zip
-tests/config/registries/seek/data
+/utils/certs/data
+/tests/config/registries/seek/data
+/tests/config/data/ro-crate*.zip
+/tests/config/data/crates/
+/interaction_experiments/_OLD_TEST_METADATA/data

settings.conf

@@ -73,7 +73,7 @@ MAIL_USE_SSL=True
 MAIL_DEFAULT_SENDER=''
 
 # Storage path of workflow RO-Crates
-# DATA_WORKFLOWS = "./data"
+DATA_WORKFLOWS = "/var/data/lm"
 
 # Cache settings
 CACHE_REDIS_DB=0

tests/config/data/make-test-rocrates.py

@@ -37,7 +37,7 @@
 logger.debug("RO-CRATES SOURCE PATH: %s", crates_source_path)
 
 crates_target_path = os.path.join(current_path, "crates")
-logger.debug("RO-CRATES SOURCE PATH: %s", crates_target_path)
+logger.debug("RO-CRATES TARGET PATH: %s", crates_target_path)
 
 # List of RO-Crates to be created.
 # New RO-crates are created by copying a path under crates_source_path to a path under crates_target_path.

tests/conftest.py

@@ -26,6 +26,7 @@
 import re
 import shutil
 import string
+import tempfile
 import uuid
 from collections.abc import Iterable
 from pathlib import Path
@@ -71,16 +72,21 @@
 os.environ.pop("FLASK_APP_CONFIG_FILE", None)
 
 
-@pytest.fixture
-def current_path():
-    return os.path.dirname(os.path.abspath(__file__))
-
-
 @pytest.fixture
 def headers():
     return helpers.get_headers()
 
 
+@pytest.fixture(scope='session')
+def test_repo_collection_path() -> Path:
+    return Path(__file__).parent / 'config' / 'data' / 'repos'
+
+
+@pytest.fixture(scope='session')
+def test_crate_collection_path() -> Path:
+    return Path(__file__).parent / 'config' / 'data' / 'crates'
+
+
 @pytest.fixture
 def lm() -> LifeMonitor:
     return LifeMonitor.get_instance()
@@ -490,3 +496,26 @@ def repository() -> Generator[LocalWorkflowRepository, None, None]:
         yield repo
     finally:
         repo.cleanup()
+
+
+@pytest.fixture
+def github_repository() -> GithubWorkflowRepository:
+    repo = GithubWorkflowRepository('iwc-workflows/gromacs-mmgbsa', ref="HEAD")
+    logger.debug("Github workflow repository: %r", repo)
+    return repo
+
+@pytest.fixture
+def simple_local_wf_repo(test_repo_collection_path: Path) -> Generator[LocalGitWorkflowRepository, None, None]:
+    """
+    On-disk git repository with a dummy Galaxy workflow.  Should follow best practices.
+    """
+    source_repo_path = test_repo_collection_path / 'test-galaxy-wf-repo'
+
+    # make a temporary copy of the source repository so that tests can freely
+    # modify it.
+    with tempfile.TemporaryDirectory(prefix=f"tmp-{source_repo_path.name}") as tmpdir:
+        tmp_repo_path = shutil.copytree(source_repo_path,
+                                        Path(tmpdir) / source_repo_path.name,
+                                        symlinks=True)
+        repo = LocalGitWorkflowRepository(str(tmp_repo_path))
+        yield repo

tests/unit/issues/test_rocrate_metadata.py

@@ -27,41 +27,34 @@
 logger = logging.getLogger(__name__)
 
 
-@pytest.fixture
-def repository() -> GithubWorkflowRepository:
-    repo = GithubWorkflowRepository('iwc-workflows/gromacs-mmgbsa', ref="HEAD")
-    logger.debug("Github workflow repository: %r", repo)
-    return repo
-
-
 @pytest.fixture
 def issue() -> MissingROCrateFile:
     return MissingROCrateFile()
 
 
-def test_check_true(repository: GithubWorkflowRepository, issue: MissingROCrateFile):
-    logger.debug("Workflow RO-Crate: %r", repository)
+def test_check_true(github_repository: GithubWorkflowRepository, issue: MissingROCrateFile):
+    logger.debug("Workflow RO-Crate: %r", github_repository)
 
     # detect workflow metadata
-    metadata = repository.metadata
+    metadata = github_repository.metadata
     logger.debug("Detected workflow metadata: %r", metadata)
     assert metadata, "Workflow metadata not found"
 
     # test if issue doesn't apply to the current repo
-    result = issue.check(repository)
+    result = issue.check(github_repository)
     assert result is False, "Workflow RO-Crate should have the workflow file"
 
 
-def test_check_false(repository: GithubWorkflowRepository, issue: MissingROCrateFile):
-    logger.debug("Workflow RO-Crate: %r", repository)
+def test_check_false(github_repository: GithubWorkflowRepository, issue: MissingROCrateFile):
+    logger.debug("Workflow RO-Crate: %r", github_repository)
 
     # detect workflow file
-    metadata = repository.metadata
+    metadata = github_repository.metadata
     logger.debug("Detected workflow file: %r", metadata)
     assert metadata, "Workflow file not found"
 
     # set reference to local copy of the remote repo
-    local = repository.local_repo
+    local = github_repository.local_repo
 
     # temporary remove workflow metadata from the local repo
     local.remove_file(metadata.repository_file)