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Merge pull request #14592 from nsoranzo/misc_fixes_202209

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Misc fixes 202209
This commit is contained in:
Nicola Soranzo
2022-09-09 21:34:38 +01:00
committed by GitHub
parent 2141078ae8 dda6feb391
commit e08deef224
29 changed files with 21 additions and 36 deletions
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.github/labeler.yml
+2
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@@ -9,6 +9,8 @@ area/auth:
- lib/galaxy/authnz/**/*
area/client:
- client/*
area/database:
- lib/galaxy/model/**/*
area/datatypes:
- lib/galaxy/datatypes/**/*
- lib/galaxy/config/sample/datatypes_conf.xml.sample
.gitignore
+2 -2
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@@ -58,8 +58,6 @@ universe_wsgi.ini
reports_wsgi.ini
reports.ini
tool_shed_wsgi.ini
# Config files.
datatypes_conf.xml
tool_conf.xml
external_service_types_conf.xml
@@ -123,6 +121,8 @@ htmlcov
run_unit_tests.html
test/unit/**.log
.tox
tool_test_output.html
tool_test_output.json
# Project files
*.kpf
CONTRIBUTORS.md
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@@ -142,7 +142,7 @@ The following individuals have contributed code to Galaxy:
* Sourav Singh <ssouravsingh12@gmail.com>
* Clare Sloggett <sloc@unimelb.edu.au>
* Eteri Sokhoyan @Sokhoyan
* Nicola Soranzo <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
* Nicola Soranzo <nicola.soranzo@earlham.ac.uk> <nicola.soranzo@tgac.ac.uk> <nsoranzo@tiscali.it> <soranzo@crs4.it>
* Nick Stoler <nick@nstoler.com>
* Roy Storey <kiwiroy@gmail.com>
* Hanfei Sun <ad9075@gmail.com>
client/src/components/Workflow/WorkflowList.vue
+2 -2
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@@ -96,9 +96,9 @@ returned. So <code>name:'RNAseq'</code> would show only workflows named exactly
<dt><code>tag</code></dt>
<dd>This filters only against the workflow tag. You may also just click on a tag in your list of workflows to filter on that tag using this directly.</dd>
<dt><code>is:published</code></dt>
<dd>This filters the workflows such that only published workflows are shown. You may also just click on the "published" icon of a worklfow in your list to filter on this directly.</dd>
<dd>This filters the workflows such that only published workflows are shown. You may also just click on the "published" icon of a workflow in your list to filter on this directly.</dd>
<dt><code>is:shared</code></dt>
<dd>This filters the workflows such that only workflows shared from another user directly with you are are shown. You may also just click on the "shared with me" icon of a worklfow in your list to filter on this directly.</dd>
<dd>This filters the workflows such that only workflows shared from another user directly with you are are shown. You may also just click on the "shared with me" icon of a workflow in your list to filter on this directly.</dd>
</dl>
</div>
`;
doc/Makefile
+2 -2
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@@ -42,8 +42,8 @@ help:
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
@echo " updaterst to update Sphinx RST files for lib/ to reflect code structure changes"
source/dev/run_tests_help.txt:
bash ../run_tests.sh --help >> source/dev/run_tests_help.txt
source/dev/run_tests_help.txt: ../run_tests.sh
bash ../run_tests.sh --help > source/dev/run_tests_help.txt
source/dev/schema.md: parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd ## Build Github-flavored Markdown from Galaxy Tool XSD (expects lxml in environment)
python parse_gx_xsd.py schema_template.md ../lib/galaxy/tool_util/xsd/galaxy.xsd > $@
doc/source/admin/tool_panel.rst
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@@ -13,7 +13,7 @@ In the past, the file named by your ``tool_config_file`` configuration setting i
Tool Shed tools
~~~~~~~~~~~~~~~
For purposes of the Galaxy [Tool Shed](/src/toolshed/index.md) the ``tool_config_file`` setting allows for a comma-separated list of files (e.g., ``tool_config_file = tool_conf.xml,shed_tool_conf.xml``,etc.). The additional shed-related tool panel configuration files (``shed_tool_conf.xml``, etc.) are automatically modified when you install or uninstall a Tool Shed repository (that contains tools) to your Galaxy.
For purposes of the Galaxy `Tool Shed <https://galaxyproject.org/toolshed/>`__, the ``tool_config_file`` setting allows for a comma-separated list of files (e.g., ``tool_config_file = tool_conf.xml,shed_tool_conf.xml``,etc.). The additional shed-related tool panel configuration files (``shed_tool_conf.xml``, etc.) are automatically modified when you install or uninstall a Tool Shed repository (that contains tools) to your Galaxy.
Migrated tools
~~~~~~~~~~~~~~
doc/source/dev/run_tests_help.txt
+8 -5
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@@ -3,6 +3,8 @@
'run_tests.sh -list' for listing all the tool ids
'run_tests.sh -api (test_path)' for running all the test scripts in the ./lib/galaxy_test/api directory, test_path
can be pytest selector
'run_tests.sh -cwl (test_path)' for running all the test scripts in the ./lib/galaxy_test/api/cwl directory, test_path
can be pytest selector
'run_tests.sh -integration (test_path)' for running all integration test scripts in the ./test/integration directory, test_path
can be pytest selector
'run_tests.sh -toolshed (test_path)' for running all the test scripts in the ./lib/tool_shed/test directory
@@ -51,7 +53,7 @@ as test_path. A few examples are shown below.
Run all API tests:
./run_tests.sh -api
The same test as above can be run using nosetests directly as follows:
The same test as above can be run using pytest directly as follows:
pytest lib/galaxy_test/api
However when using pytest directly output options defined in this
@@ -141,6 +143,10 @@ Extra options:
--verbose_errors Force some tests produce more verbose error reporting.
--no_cleanup Do not delete temp files for Python functional tests
(-toolshed, -framework, etc...)
--coverage Generate a test coverage report. This option currently
should work with every test that uses pytest, but the
results may not be reliable with selenium or other
frameworks that primarily test the client.
--debug On python test error or failure invoke a pdb shell for
interactive debugging of the test
--report_file Path of HTML report to produce (for Python Galaxy
@@ -150,10 +156,6 @@ Extra options:
functional tests).
--skip-venv Do not create .venv (passes this flag to
common_startup.sh)
--dockerize Run tests in a pre-configured Docker container (must be
first argument if present).
--db <type> For use with --dockerize, run tests using partially
migrated 'postgres', 'mysql', or 'sqlite' databases.
--external_url External URL to use for Galaxy testing (only certain
tests).
--external_master_key Master API key used to configure external tests.
@@ -238,6 +240,7 @@ TOOL_SHED_TEST_TMP_DIR Defaults to random /tmp directory - place for
tool shed test server files to be placed.
TOOL_SHED_TEST_OMIT_GALAXY Do not launch a Galaxy server for tool shed
testing.
GALAXY_TEST_DISABLE_ACCESS_LOG Do not log access messages
Unit Test Environment Variables
lib/galaxy/webapps/galaxy/api/workflows.py
+2 -2
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@@ -1663,7 +1663,7 @@ class FastAPIWorkflows:
@router.post(
"/api/invocations/{invocation_id}/prepare_store_download",
summary="Prepare a worklfow invocation export-style download.",
summary="Prepare a workflow invocation export-style download.",
)
def prepare_store_download(
self,
@@ -1679,7 +1679,7 @@ class FastAPIWorkflows:
@router.post(
"/api/invocations/{invocation_id}/write_store",
summary="Prepare a worklfow invocation export-style download and write to supplied URI.",
summary="Prepare a workflow invocation export-style download and write to supplied URI.",
)
def write_store(
self,
packages/app/README.rst
-1
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ application logic (backend).
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/auth/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ auth framework and default plugins.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/config/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ config module.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/data/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ models, datatype framework, and datatype implementations.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/files/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ file sources framework and default plugins.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/job_execution/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ job execution runtime module.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/job_metrics/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ job metrics framework and default plugins.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/navigation/README.rst
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@@ -11,7 +11,6 @@ The Galaxy_ client DOM navigation framework.
Navigation data that feeds tours generation, Jest testing, and Selenium testing.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/objectstore/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ object store framework and default implementations.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/selenium/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ selenium framework.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/test_api/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ API tests.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/test_base/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ testing base package.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/test_driver/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ test driver package.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/test_selenium/README.rst
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@@ -9,7 +9,6 @@ Overview
The Galaxy_ Selenium tests.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/tool_util/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ tool utilities.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy/tree/dev/packages/tool_util
.. _Galaxy: http://galaxyproject.org/
packages/tours/README.rst
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@@ -11,7 +11,6 @@ The Galaxy_ tours backend framework.
This package includes models, utilities for reading tours from disk, and
tour validation scripting.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/util/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ utilities module.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/web_framework/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ web framework.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/web_stack/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ web strack abstraction.
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
packages/webapps/README.rst
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@@ -8,7 +8,6 @@ Overview
The Galaxy_ web apps (Galaxy, Reports, Tool Shed).
* Free software: Academic Free License version 3.0
* Code: https://github.com/galaxyproject/galaxy
.. _Galaxy: http://galaxyproject.org/
tools/expression_tools/pick_value.xml
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@@ -166,7 +166,7 @@ are non-null.
inputs are non-null.
- "Pick first value (or fail)" will cause the tool execution to fail if none of the selections are
non-null. This can be important because it provides a clearer indication that something went
wrong and can prevent the further evaluation of a worklfow.
wrong and can prevent the further evaluation of a workflow.
- "Pick only value" is like "First value (or fail)" in that it will cause an error if none of the
inputs are non-null but it will go further to ensure that exactly one value is non-null. When
building conditonal paths through a workflow this can ensure that at most one path is