add tests

tests/data/wf_repos/basic_wf_iwc_invalid_version/.dockstore.yml

@@ -0,0 +1,11 @@
+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Super-simple-workflow.ga
+  testParameterFiles:
+  - /Super-simple-workflow-tests.yml
+  authors:
+  - name: Lucille Delisle
+    orcid: 0000-0002-1964-4960

tests/data/wf_repos/basic_wf_iwc_invalid_version/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.1] 2024-06-17
+
+First release.

tests/data/wf_repos/basic_wf_iwc_invalid_version/README.md

@@ -0,0 +1,3 @@
+# Super simple workflow
+
+This is a super simple workflow which generates a file with x lines with 'hello'

tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow-tests.yml

@@ -0,0 +1,10 @@
+- doc: Test outline for Super-simple-workflow
+  job:
+    n_rows: 5
+  outputs:
+    outfile:
+      asserts:
+        has_n_lines:
+          n: 5
+        has_line:
+          line: "hello"

tests/data/wf_repos/basic_wf_iwc_invalid_version/Super-simple-workflow.ga

@@ -0,0 +1,95 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This workflow generates a file with x lines with 'hello'",
+    "comments": [],
+    "creator": [
+        {
+            "class": "Person",
+            "identifier": "https://orcid.org/0000-0002-1964-4960",
+            "name": "Lucille Delisle"
+        }
+    ],
+    "format-version": "0.1",
+    "license": "MIT",
+    "release": "0.2",
+    "name": "Super simple workflow",
+    "report": {
+        "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
+    },
+    "steps": {
+        "0": {
+            "annotation": "Number of rows to generate",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Number of rows to generate",
+                    "name": "n_rows"
+                }
+            ],
+            "label": "n_rows",
+            "name": "Input parameter",
+            "outputs": [],
+            "position": {
+                "left": 0,
+                "top": 0
+            },
+            "tool_id": null,
+            "tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
+            "tool_version": null,
+            "type": "parameter_input",
+            "uuid": "2ee42c13-83f5-4ac4-b35d-74294edf7dea",
+            "when": null
+        },
+        "1": {
+            "annotation": "this creates a file with a given number of lines",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "token_set_0|repeat_select|times": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "label": "create file",
+            "name": "Create text file",
+            "outputs": [
+                {
+                    "name": "outfile",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "left": 236,
+                "top": 11
+            },
+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1",
+            "tool_shed_repository": {
+                "changeset_revision": "fbf99087e067",
+                "name": "text_processing",
+                "owner": "bgruening",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"hello\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "9.3+galaxy1",
+            "type": "tool",
+            "uuid": "a86ff433-8dce-417c-baf0-bc106a93ee48",
+            "when": null,
+            "workflow_outputs": [
+                {
+                    "label": "outfile",
+                    "output_name": "outfile",
+                    "uuid": "34572088-8ad8-4661-81a2-6dfe2d83a0fe"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "72c87042-27a8-4bcc-92af-ca74704e6161",
+    "version": 3
+}

tests/test_cmd_workflow_lint.py

@@ -226,6 +226,44 @@ def test_workflow_linting_asserts(self):
         result = self._runner.invoke(self._cli.planemo, lint_cmd)
         assert "ERROR: Invalid assertion in tests: assert_has_line missing a required argument: 'line'" in result.output
 
+    def test_workflow_linting_iwc(self):
+        # Check the output of workflow_lint --iwc on a basic workflow with .dockstore
+        repo = _wf_repo("basic_format2_dockstore")
+        lint_cmd = ["workflow_lint", "--skip", "best_practices", "--iwc", repo]
+        result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+        errors = [
+            "The file README.md is missing but required.",
+            "The file CHANGELOG.md is missing but required.",
+            ".dockstore.yml workflow entry missing recommended key name",
+            "Workflow  have no 'authors' in the .dockstore.yml.",
+            "The workflow tests/data/wf_repos/basic_format2_dockstore/basic_format2.gxwf.yml has no release"
+        ]
+
+        for error in errors:
+            assert error in result.output
+
+        # Check that skipping the good steps makes it work        
+        lint_cmd = ["workflow_lint", "--iwc", "--skip", "best_practices,required_files,dockstore_best_practices,release", repo]
+        self._check_exit_code(lint_cmd, exit_code=0)
+
+        # Check the output of workflow_lint --iwc on a good workflow but with an issue with the release
+        repo = _wf_repo("basic_wf_iwc_invalid_version")
+        lint_cmd = ["workflow_lint", "--iwc", repo]
+        result = self._runner.invoke(self._cli.planemo, lint_cmd)
+
+        errors = [
+            "The release of workflow",
+            " does not match the version in the CHANGELOG."
+        ]
+
+        for error in errors:
+            assert error in result.output
+
+        # Check that skipping the good steps makes it work        
+        lint_cmd = ["workflow_lint", "--iwc", "--skip", "release", repo]
+        self._check_exit_code(lint_cmd, exit_code=0)
+
 
 def _wf_repo(rel_path):
     return os.path.join(TEST_DATA_DIR, "wf_repos", rel_path)