Skip tests relying on quay.io, the Tool Sheds, Dockstore and usegalaxy.eu when they are down

tests/test_cmd_autoupdate.py

@@ -12,6 +12,8 @@
     CliTestCase,
     mark,
     skip_if_environ,
+    skip_if_testtoolshed_down,
+    skip_if_toolshed_down,
 )
 
 
@@ -91,6 +93,7 @@ def test_autoupdate_no_update_needed(self):
             assert f"No updates required or made to {xmlfile}." in result.output
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_toolshed_down
     def test_autoupdate_multiple_workflows(self):
         """Test autoupdate command for a workflow is needed."""
         with (
@@ -126,6 +129,7 @@ def test_autoupdate_multiple_workflows(self):
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     @mark.tests_galaxy_branch
+    @skip_if_toolshed_down
     def test_autoupdate_gxformat2_workflow(self):
         with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:
             wf_file = os.path.join(f, "diff-refactor-test.gxwf.yml")
@@ -144,6 +148,8 @@ def test_autoupdate_gxformat2_workflow(self):
             assert wf["release"] == "0.1.1"
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_toolshed_down
+    @skip_if_testtoolshed_down
     def test_autoupdate_workflow_from_multiple_tool_sheds(self):
         with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:
             wf_file = os.path.join(f, "wf_autoupdate_test_multiple_repos.ga")
@@ -161,6 +167,7 @@ def test_autoupdate_workflow_from_multiple_tool_sheds(self):
             assert wf["steps"]["0"]["inputs"][0]["description"] == ""
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_toolshed_down
     def test_autoupdate_workflow_unexisting_version(self):
         """Test autoupdate command for a workflow where the version of the tool is not in the toolshed."""
         with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:
@@ -172,6 +179,7 @@ def test_autoupdate_workflow_unexisting_version(self):
             # In future versions it could be great that it gives the last valid version.
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_toolshed_down
     def test_autoupdate_workflow_unexisting_tool(self):
         """Test autoupdate command for a workflow where the tool is not in the toolshed."""
         with self._isolate_with_test_data("wf_repos/autoupdate_tests") as f:

tests/test_cmd_serve.py

@@ -20,6 +20,7 @@
     run_verbosely,
     safe_rmtree,
     skip_if_environ,
+    skip_if_quay_down,
     skip_unless_environ,
     skip_unless_executable,
     target_galaxy_branch,
@@ -156,6 +157,7 @@ def test_serve_daemon(self):
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     @skip_unless_executable("docker")
     @mark.tests_galaxy_branch
+    @skip_if_quay_down
     def test_serve_interactivetool(self):
         self._serve_artifact = os.path.join(TEST_TOOLS_DIR, "interactivetool_simple.xml")
         extra_args = [

tests/test_cmd_test.py

@@ -20,6 +20,8 @@
     PROJECT_TEMPLATES_DIR,
     run_verbosely,
     skip_if_environ,
+    skip_if_quay_down,
+    skip_if_toolshed_down,
     skip_unless_module,
     TEST_DATA_DIR,
     TEST_TOOLS_DIR,
@@ -95,6 +97,7 @@ def test_data_manager(self):
                 assert json.load(fh)["summary"]["num_tests"] == 1
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_quay_down
     def test_data_manager_docker_mount(self):
         """Test testing a data manager that needs (ro) access to the test-data folder."""
         with self._isolate(), NamedTemporaryFile(prefix="data_manager_test_json") as json_out:
@@ -281,6 +284,8 @@ def test_workflow_test_collection_inputs(self):
             #    raise
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_quay_down
+    @skip_if_toolshed_down
     def test_workflow_test_repository_installation_gxformat2(self):
         """Test testing a workflow with collection inputs Galaxy."""
         with self._isolate():

tests/test_cmd_training_generate_from_wf.py

@@ -7,6 +7,7 @@
     CliTestCase,
     mark,
     skip_if_environ,
+    skip_if_usegalaxy_eu_down,
     TEST_DATA_DIR,
 )
 
@@ -64,6 +65,7 @@ def test_training_generate_from_wf_command_local_wf(self):
             shutil.rmtree("topics")
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_usegalaxy_eu_down
     def test_training_generate_from_wf_command_remote_wf(self):
         """Test training_generate_from_wf command with workflow on running instance."""
         with self._isolate():

tests/test_cmd_training_init.py

@@ -6,6 +6,7 @@
     CliTestCase,
     mark,
     skip_if_environ,
+    skip_if_usegalaxy_eu_down,
     skip_if_zenodo_down,
     TEST_DATA_DIR,
 )
@@ -114,6 +115,7 @@ def test_training_init_command_tutorial_local_wf(self):
             self._check_exit_code(training_init_command, exit_code=0)
 
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
+    @skip_if_usegalaxy_eu_down
     def test_training_init_command_tutorial_remote_wf(self):
         """Test training_init command to create new tutorial with workflow on running instance."""
         with self._isolate():

tests/test_cmd_workflow_lint.py

@@ -5,6 +5,7 @@
 
 from .test_utils import (
     CliTestCase,
+    skip_if_toolshed_down,
     TEST_DATA_DIR,
 )
 
@@ -215,6 +216,7 @@ def test_json_value_out(self):
         lint_cmd = ["workflow_lint", workflow_path, "--fail_level", "error"]
         self._check_exit_code(lint_cmd, exit_code=0)
 
+    @skip_if_toolshed_down
     def test_tool_id_linting_wrong_version(self):
         workflow_path = "/".join(
             (TEST_DATA_DIR, "wf_repos", "autoupdate_tests", "workflow_with_unexisting_version_of_tool.ga")
@@ -226,12 +228,14 @@ def test_tool_id_linting_wrong_version(self):
             in result.output
         )
 
+    @skip_if_toolshed_down
     def test_tool_id_linting_wrong_tool(self):
         workflow_path = "/".join((TEST_DATA_DIR, "wf_repos", "autoupdate_tests", "workflow_with_unexisting_tool.ga"))
         lint_cmd = ["workflow_lint", workflow_path]
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
         assert "ERROR: The ToolShed returned an error when searching" in result.output
 
+    @skip_if_toolshed_down
     def test_tool_id_linting_mismatched_changeset(self):
         # tp_easyjoin_tool/1.1.0 is a valid tool version, but the pinned
         # changeset_revision (288462ec2630) only provides version 1.0.0.
@@ -245,13 +249,15 @@ def test_tool_id_linting_mismatched_changeset(self):
             "is not provided by the pinned changeset_revision 288462ec2630" in result.output
         )
 
+    @skip_if_toolshed_down
     def test_tool_id_linting_matching_changeset(self):
         # tp_easyjoin_tool/1.1.0 is provided by changeset_revision 20344ce0c811.
         workflow_path = "/".join((TEST_DATA_DIR, "wf_repos", "autoupdate_tests", "workflow_with_matching_changeset.ga"))
         lint_cmd = ["workflow_lint", "--skip", "best_practices", workflow_path]
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
         assert "All tool ids appear to be valid." in result.output
 
+    @skip_if_toolshed_down
     def test_tool_id_linting_without_tool_shed_repository(self):
         # A tool step without a tool_shed_repository has nothing to validate the
         # tool_id/version against, so the check is skipped even for an otherwise
@@ -264,6 +270,7 @@ def test_tool_id_linting_without_tool_shed_repository(self):
         assert "not in the toolshed" not in result.output
         assert "All tool ids appear to be valid." in result.output
 
+    @skip_if_toolshed_down
     def test_tool_version_linting_mismatch(self):
         # tool_id encodes version 1.1.0 but the step's tool_version is 1.0.0.
         workflow_path = "/".join(
@@ -276,6 +283,7 @@ def test_tool_version_linting_mismatch(self):
             "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.0" in result.output
         )
 
+    @skip_if_toolshed_down
     def test_tool_version_linting_match(self):
         # tool_id and tool_version agree in this fixture.
         workflow_path = "/".join((TEST_DATA_DIR, "wf_repos", "autoupdate_tests", "workflow_with_matching_changeset.ga"))

tests/test_github_create_release.py

@@ -2,6 +2,7 @@
 import uuid
 
 import pytest
+from galaxy.util.unittest_utils import skip_if_github_down
 
 from planemo import git
 from planemo.github_util import (
@@ -97,6 +98,7 @@ def test_add_dir_contents_to_repo_dry_run():
         )
 
 
+@skip_if_github_down
 def test_git_ls_remote():
     ctx = create_test_context()
     tags_and_commits = git.ls_remote(ctx, "https://github.com/galaxyproject/galaxy")

tests/test_lint.py

@@ -1,6 +1,8 @@
 import glob
 import os
 
+from galaxy.util.unittest_utils import skip_if_github_down
+
 from .test_utils import (
     CliTestCase,
     PROJECT_TEMPLATES_DIR,
@@ -25,6 +27,7 @@ def test_ok_urls(self):
         self._check_exit_code(lint_cmd)
 
     @skip_if_environ("PLANEMO_SKIP_SLOW_TESTS")
+    @skip_if_github_down
     def test_ok_http(self):
         lint_cmd = [
             "lint",

tests/test_run.py

@@ -13,6 +13,7 @@
     CWL_DRAFT3_DIR,
     mark,
     PROJECT_TEMPLATES_DIR,
+    skip_if_dockstore_down,
     skip_if_environ,
     target_galaxy_branch,
     TEST_DATA_DIR,
@@ -276,6 +277,7 @@ def test_run_export_invocation(self):
     )
     @skip_if_environ("PLANEMO_SKIP_GALAXY_TESTS")
     @mark.tests_galaxy_branch
+    @skip_if_dockstore_down
     def test_run_trs_id(self):
         """Test importing and running a workflow using a TRS ID from GitHub."""
         with self._isolate() as f:

tests/test_utils.py

@@ -62,6 +62,13 @@
 NON_ZERO_EXIT_CODE = object()
 ZENODO_TEST_RECORD_API_URL = "https://zenodo.org/api/records/1321885"
 skip_if_zenodo_down = skip_if_site_down(ZENODO_TEST_RECORD_API_URL)
+# galaxy-util already exports skip_if_github_down/skip_if_workflowhub_down; define the
+# rest here until the pinned galaxy-util catches up with galaxyproject/galaxy#23685.
+skip_if_dockstore_down = skip_if_site_down("https://dockstore.org/")
+skip_if_quay_down = skip_if_site_down("https://quay.io/")
+skip_if_toolshed_down = skip_if_site_down("https://toolshed.g2.bx.psu.edu/")
+skip_if_testtoolshed_down = skip_if_site_down("https://testtoolshed.g2.bx.psu.edu/")
+skip_if_usegalaxy_eu_down = skip_if_site_down("https://usegalaxy.eu/")
 CWLTOOL_CACHE_ENV_PROP = "PLANEMO_CWLTOOL_CACHE_DIRECTORY"