galaxy-workflow-tool-tests
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]
[--with-reference-data]
[--skip-with-reference-data]
[--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]
WORKFLOW_ID
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.
--skip-previously-executed
When used with --append, skip any test previously
executed.
--skip-previously-successful
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
--with-reference-data
--skip-with-reference-data
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
history).
--history-per-test-case
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
accessible.
--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
data
History
0.0.2 (2020-12-16)
Fixes to project structure for PyPI.
0.0.1 (2020-12-16)
Initial testing release.
Metadata
Release files for galaxy-workflow-tool-tests 0.0.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| galaxy-workflow-tool-tests-0.0.2.tar.gz | 9.2 kB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| galaxy_workflow_tool_tests-0.0.2-py3.6.egg | Legacy Egg format | - | - | Details |
| galaxy_workflow_tool_tests-0.0.2-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details |
Total release size: 23.8 kB
Release files / galaxy-workflow-tool-tests-0.0.2.tar.gz
| Download URL | galaxy-workflow-tool-tests-0.0.2.tar.gz |
|---|---|
| Size | 9.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Release files / galaxy_workflow_tool_tests-0.0.2-py3.6.egg
| Download URL | galaxy_workflow_tool_tests-0.0.2-py3.6.egg |
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| Size | 5.9 kB |
| Tags | Egg |
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Release files / galaxy_workflow_tool_tests-0.0.2-py2.py3-none-any.whl
| Download URL | galaxy_workflow_tool_tests-0.0.2-py2.py3-none-any.whl |
|---|---|
| Size | 8.8 kB |
| Tags | Python 2 Python 3 |
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SHA-256 checksum How to use checksums |
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