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Galaxy Workflow Format 2 Descriptions

Project description


A simple wrapper around Galaxy’s galaxy-tool-test that runs tool tests for all the tools in a workflow.

Minimal Usage:

galaxy-workflow-tool-tests  -k <api_key> -u http://localhost:8080/ <encoded_workflow_id>

Program Help

$ galaxy-workflow-tool-tests --help
usage: galaxy-workflow-tool-tests [-h] [-u GALAXY_URL] [-k KEY] [-a ADMIN_KEY]
                                  [--force_path_paste] [-t TOOL_ID]
                                  [--tool-version TOOL_VERSION]
                                  [-i TEST_INDEX] [-o OUTPUT] [--append]
                                  [--skip-previously-executed | --skip-previously-successful]
                                  [-j OUTPUT_JSON] [--verbose]
                                  [-c CLIENT_TEST_CONFIG]
                                  [--suite-name SUITE_NAME]
                                  [--history-per-suite | --history-per-test-case]
                                  [--no-history-cleanup] [--publish-history]
                                  [--parallel-tests PARALLEL_TESTS]
                                  [--retries RETRIES] [--page-size PAGE_SIZE]
                                  [--page-number PAGE_NUMBER]
                                  [--download-attempts DOWNLOAD_ATTEMPTS]
                                  [--download-sleep DOWNLOAD_SLEEP]
                                  [--test-data TEST_DATA]

Script to quickly run a tool test against a running Galaxy instance.

positional arguments:
  WORKFLOW_ID           workflow id to scan for tools

optional arguments:
  -h, --help            show this help message and exit
  -u GALAXY_URL, --galaxy-url GALAXY_URL
                        Galaxy URL
  -k KEY, --key KEY     Galaxy User API Key
  -a ADMIN_KEY, --admin-key ADMIN_KEY
                        Galaxy Admin API Key
  --force_path_paste    This requires Galaxy-side config option
                        "allow_path_paste" enabled. Allows for fetching test
                        data locally. Only for admins.
  -t TOOL_ID, --tool-id TOOL_ID
                        Tool ID
  --tool-version TOOL_VERSION
                        Tool Version (if tool id supplied). Defaults to just
                        latest version, use * to test all versions
  -i TEST_INDEX, --test-index TEST_INDEX
                        Tool Test Index (starting at 0) - by default all tests
                        will run.
  -o OUTPUT, --output OUTPUT
                        directory to dump outputs to
  --append              Extend a test record json (created with --output-json)
                        with additional tests.
                        When used with --append, skip any test previously
                        When used with --append, skip any test previously
                        executed successfully.
  -j OUTPUT_JSON, --output-json OUTPUT_JSON
                        output metadata json
  --verbose             Verbose logging.
  -c CLIENT_TEST_CONFIG, --client-test-config CLIENT_TEST_CONFIG
                        Test config YAML to help with client testing
  --suite-name SUITE_NAME
                        Suite name for tool test output
                        Skip tests the Galaxy server believes use data tables
                        or loc files.
  --history-per-suite   Create new history per test suite (all tests in same
                        Create new history per test case.
  --no-history-cleanup  Perserve histories created for testing.
  --publish-history     Publish test history. Useful for CI testing.
  --parallel-tests PARALLEL_TESTS
                        Parallel tests.
  --retries RETRIES     Retry failed tests.
  --page-size PAGE_SIZE
                        If positive, use pagination and just run one 'page' to
                        tool tests.
  --page-number PAGE_NUMBER
                        If page size is used, run this 'page' of tests -
                        starts with 0.
  --download-attempts DOWNLOAD_ATTEMPTS
                        Galaxy may return a transient 500 status code for
                        download if test results are written but not yet
  --download-sleep DOWNLOAD_SLEEP
                        If download attempts is greater than 1, the amount to
                        sleep between download attempts.
  --test-data TEST_DATA
                        Add local test data path to search for missing test


0.0.2 (2020-12-16)

  • Fixes to project structure for PyPI.

0.0.1 (2020-12-16)

  • Initial testing release.

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