From 681372e916e48a74c2ee436c7898b8c2b5b299cf Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 8 Sep 2022 18:26:18 +0100 Subject: [PATCH 1/7] Add directory for ``area/database`` label --- .github/labeler.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/labeler.yml b/.github/labeler.yml index 64fca73235c..946e996ab1c 100644 --- a/.github/labeler.yml +++ b/.github/labeler.yml @@ -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 From e7d4790b80c6770cb02e852eb015abdcc593016c Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 8 Sep 2022 18:27:10 +0100 Subject: [PATCH 2/7] Ignore Planemo tool test output files --- .gitignore | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitignore b/.gitignore index ce4ad4211eb..321dab6ab4a 100644 --- a/.gitignore +++ b/.gitignore @@ -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 From 4dd4a6ab661a39a94272211eebd59a3f3118e84f Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 8 Sep 2022 18:28:56 +0100 Subject: [PATCH 3/7] Add my current work email address to ``CONTRIBUTORS.md`` --- CONTRIBUTORS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index c5363982eb5..e38b9ea764f 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -142,7 +142,7 @@ The following individuals have contributed code to Galaxy: * Sourav Singh * Clare Sloggett * Eteri Sokhoyan @Sokhoyan -* Nicola Soranzo +* Nicola Soranzo * Nick Stoler * Roy Storey * Hanfei Sun From ac6ffb28d16cb5e453e2c68975748a4ecd39e509 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Thu, 8 Sep 2022 18:32:01 +0100 Subject: [PATCH 4/7] Fix typos --- client/src/components/Workflow/WorkflowList.vue | 4 ++-- lib/galaxy/webapps/galaxy/api/workflows.py | 4 ++-- tools/expression_tools/pick_value.xml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/client/src/components/Workflow/WorkflowList.vue b/client/src/components/Workflow/WorkflowList.vue index 17d0be88862..c7918396772 100644 --- a/client/src/components/Workflow/WorkflowList.vue +++ b/client/src/components/Workflow/WorkflowList.vue @@ -96,9 +96,9 @@ returned. So name:'RNAseq' would show only workflows named exactly
tag
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.
is:published
-
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.
+
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.
is:shared
-
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.
+
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.
`; diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 2f919c8e45d..d194b71fd30 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -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, diff --git a/tools/expression_tools/pick_value.xml b/tools/expression_tools/pick_value.xml index 0440b2c12af..427fe94c771 100644 --- a/tools/expression_tools/pick_value.xml +++ b/tools/expression_tools/pick_value.xml @@ -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 From 08bcea53702bbebd85e2c26eb819168981a5cdf0 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 9 Sep 2022 11:47:14 +0100 Subject: [PATCH 5/7] Fix Makefile rule and update ``run_tests_help.txt`` --- doc/Makefile | 4 ++-- doc/source/dev/run_tests_help.txt | 13 ++++++++----- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/doc/Makefile b/doc/Makefile index fc986bd6376..9fd91e5c683 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -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 > $@ diff --git a/doc/source/dev/run_tests_help.txt b/doc/source/dev/run_tests_help.txt index 176f140e89b..fad1437fe2c 100644 --- a/doc/source/dev/run_tests_help.txt +++ b/doc/source/dev/run_tests_help.txt @@ -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 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 From 404da60afa39606afc788e762fb403456fe62924 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 9 Sep 2022 14:44:04 +0100 Subject: [PATCH 6/7] Fix Tool Shed link --- doc/source/admin/tool_panel.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/admin/tool_panel.rst b/doc/source/admin/tool_panel.rst index 92825461de3..e92ac3c60fc 100644 --- a/doc/source/admin/tool_panel.rst +++ b/doc/source/admin/tool_panel.rst @@ -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 `__, 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 ~~~~~~~~~~~~~~ From dda6feb3916d12304e849e4f3601d57e692479e6 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 9 Sep 2022 16:25:21 +0100 Subject: [PATCH 7/7] Remove redundant license info from package READMEs The license is already specified in `setup.cfg` , which is the canonical place. This will simplify the transition to the MIT license. --- packages/app/README.rst | 1 - packages/auth/README.rst | 1 - packages/config/README.rst | 1 - packages/data/README.rst | 1 - packages/files/README.rst | 1 - packages/job_execution/README.rst | 1 - packages/job_metrics/README.rst | 1 - packages/navigation/README.rst | 1 - packages/objectstore/README.rst | 1 - packages/selenium/README.rst | 1 - packages/test_api/README.rst | 1 - packages/test_base/README.rst | 1 - packages/test_driver/README.rst | 1 - packages/test_selenium/README.rst | 1 - packages/tool_util/README.rst | 1 - packages/tours/README.rst | 1 - packages/util/README.rst | 1 - packages/web_framework/README.rst | 1 - packages/web_stack/README.rst | 1 - packages/webapps/README.rst | 1 - 20 files changed, 20 deletions(-) diff --git a/packages/app/README.rst b/packages/app/README.rst index 898b0262617..b42731a0cd7 100644 --- a/packages/app/README.rst +++ b/packages/app/README.rst @@ -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/ diff --git a/packages/auth/README.rst b/packages/auth/README.rst index 13915272fcb..6046010d376 100644 --- a/packages/auth/README.rst +++ b/packages/auth/README.rst @@ -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/ diff --git a/packages/config/README.rst b/packages/config/README.rst index fde16673c89..eccca94fbeb 100644 --- a/packages/config/README.rst +++ b/packages/config/README.rst @@ -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/ diff --git a/packages/data/README.rst b/packages/data/README.rst index daf960bc982..0e1df46037d 100644 --- a/packages/data/README.rst +++ b/packages/data/README.rst @@ -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/ diff --git a/packages/files/README.rst b/packages/files/README.rst index e4c454e8f07..d89e08aae79 100644 --- a/packages/files/README.rst +++ b/packages/files/README.rst @@ -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/ diff --git a/packages/job_execution/README.rst b/packages/job_execution/README.rst index 8ec9c6f91cf..7eabea401d8 100644 --- a/packages/job_execution/README.rst +++ b/packages/job_execution/README.rst @@ -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/ diff --git a/packages/job_metrics/README.rst b/packages/job_metrics/README.rst index f584e6b993d..81c98553f2e 100644 --- a/packages/job_metrics/README.rst +++ b/packages/job_metrics/README.rst @@ -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/ diff --git a/packages/navigation/README.rst b/packages/navigation/README.rst index f85be59e7e8..97fe36c3d1c 100644 --- a/packages/navigation/README.rst +++ b/packages/navigation/README.rst @@ -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/ diff --git a/packages/objectstore/README.rst b/packages/objectstore/README.rst index ceaa2466eaf..5df23e59898 100644 --- a/packages/objectstore/README.rst +++ b/packages/objectstore/README.rst @@ -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/ diff --git a/packages/selenium/README.rst b/packages/selenium/README.rst index b66238cd3b1..adfd385762c 100644 --- a/packages/selenium/README.rst +++ b/packages/selenium/README.rst @@ -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/ diff --git a/packages/test_api/README.rst b/packages/test_api/README.rst index 6b19adae56c..f1eac734d91 100644 --- a/packages/test_api/README.rst +++ b/packages/test_api/README.rst @@ -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/ diff --git a/packages/test_base/README.rst b/packages/test_base/README.rst index feb0c31fd03..3f5aa6e728d 100644 --- a/packages/test_base/README.rst +++ b/packages/test_base/README.rst @@ -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/ diff --git a/packages/test_driver/README.rst b/packages/test_driver/README.rst index 6a9177b983c..43f356b46ac 100644 --- a/packages/test_driver/README.rst +++ b/packages/test_driver/README.rst @@ -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/ diff --git a/packages/test_selenium/README.rst b/packages/test_selenium/README.rst index 36fa941e20e..8fac8a9a6c4 100644 --- a/packages/test_selenium/README.rst +++ b/packages/test_selenium/README.rst @@ -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/ diff --git a/packages/tool_util/README.rst b/packages/tool_util/README.rst index 5b0345140f3..c0587da36fc 100644 --- a/packages/tool_util/README.rst +++ b/packages/tool_util/README.rst @@ -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/ diff --git a/packages/tours/README.rst b/packages/tours/README.rst index 21d1c841ae8..759805f1f02 100644 --- a/packages/tours/README.rst +++ b/packages/tours/README.rst @@ -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/ diff --git a/packages/util/README.rst b/packages/util/README.rst index 378cb991e37..a9cb97eba39 100644 --- a/packages/util/README.rst +++ b/packages/util/README.rst @@ -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/ diff --git a/packages/web_framework/README.rst b/packages/web_framework/README.rst index 2f71d34d375..59796fc86cf 100644 --- a/packages/web_framework/README.rst +++ b/packages/web_framework/README.rst @@ -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/ diff --git a/packages/web_stack/README.rst b/packages/web_stack/README.rst index a0a63b19d2d..638cdd66940 100644 --- a/packages/web_stack/README.rst +++ b/packages/web_stack/README.rst @@ -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/ diff --git a/packages/webapps/README.rst b/packages/webapps/README.rst index 43024db40ba..b1156681ae2 100644 --- a/packages/webapps/README.rst +++ b/packages/webapps/README.rst @@ -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/