- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f93044: Make collection builder tests more robust against ...
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f93044d5836dee02e6984caa54b6e7b5b4a04fcb https://github.com/galaxyproject/galaxy/commit/f93044d5836dee02e6984caa54b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Make collection builder tests more robust against potential history panel glitches. Commit: d783ec5daf4637747d9d435be6cfa69f9062dd0f https://github.com/galaxyproject/galaxy/commit/d783ec5daf4637747d9d435be6cf… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-16 (Fri, 16 Mar 2018) Changed paths: M test/selenium_tests/test_collection_builders.py Log Message: ----------- Merge pull request #5705 from jmchilton/more_robust_collection_builder_test Make collection builder tests more robust against potential history panel glitches. Compare: https://github.com/galaxyproject/galaxy/compare/63f3b0c0041e...d783ec5daf46

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[galaxyproject/usegalaxy-playbook] 5a7643: Added new slide to slide rotation.
by GitHub 16 Mar '18

16 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5a7643266b41a39c8d94a60eb13786bce321ee47 https://github.com/galaxyproject/usegalaxy-playbook/commit/5a7643266b41a39c… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: A env/common/files/galaxy/static/welcome_img/gccbosc2018_ext.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Added new slide to slide rotation.

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[galaxyproject/galaxy] aadf82: Fix for merging of HDA & DCE models into one model...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aadf828d15a599b4b8e550ea912ad65c149ba561 https://github.com/galaxyproject/galaxy/commit/aadf828d15a599b4b8e550ea912a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Fix for merging of HDA & DCE models into one model in the client. I wish they weren't merged together like this but they are so try to to handle the IDs in a less buggy way. Should fix https://github.com/galaxyproject/galaxy/issues/3782 though I'm unsure. Commit: 63f3b0c0041e99ded69215062714f7293bb77302 https://github.com/galaxyproject/galaxy/commit/63f3b0c0041e99ded69215062714… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/dataset/dataset-model.js Log Message: ----------- Merge pull request #5703 from jmchilton/unwind_client_model_merge_issues_maybe_but_who_knows_how_are_the_tests Fix for merging of HDA & DCE models into one model in the client. Compare: https://github.com/galaxyproject/galaxy/compare/1df477b9218a...63f3b0c0041e

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[galaxyproject/usegalaxy-playbook] bf9461: Reenable GenomeSpace tools
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bf9461f8026ab5f758a85f5f9f75f36e55589e84 https://github.com/galaxyproject/usegalaxy-playbook/commit/bf9461f8026ab5f7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Reenable GenomeSpace tools Commit: b040873ac80688dd749c77e99b9f7ec8c24898bc https://github.com/galaxyproject/usegalaxy-playbook/commit/b040873ac80688dd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2f2df6a844b0...…

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[galaxyproject/galaxy] dd20f6: Don't let Selenium driver failures during debuggin...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dd20f640beedeeec10d091f4d5c6279b5b40132b https://github.com/galaxyproject/galaxy/commit/dd20f640beedeeec10d091f4d5c6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Don't let Selenium driver failures during debugging mask underlying errors. https://jenkins.galaxyproject.org/job/docker-selenium/1665/testReport/selen… Commit: 1df477b9218a94ad25ab5219c0bc3a972aba2ef9 https://github.com/galaxyproject/galaxy/commit/1df477b9218a94ad25ab5219c0bc… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/selenium_tests/framework.py Log Message: ----------- Merge pull request #5701 from jmchilton/screenshot_exception Don't let failure to save Selenium screenshot for debugging mask underlying errors. Compare: https://github.com/galaxyproject/galaxy/compare/8366d2b5fa32...1df477b9218a

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[galaxyproject/galaxy] 0ec022: Do not show composite datatypes for regular datase...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0ec0226e0c893bf9ea785350c749a284b07dae3d https://github.com/galaxyproject/galaxy/commit/0ec0226e0c893bf9ea785350c749… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Do not show composite datatypes for regular dataset upload in the dropdown shown on each row. Mirroring what is done already in `client/galaxy/scripts/mvc/upload/default/default-view.js` Commit: 8366d2b5fa32c5697306139426d85df86dac0782 https://github.com/galaxyproject/galaxy/commit/8366d2b5fa32c5697306139426d8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M client/galaxy/scripts/mvc/upload/default/default-row.js Log Message: ----------- Merge pull request #5700 from nsoranzo/dont_show_composite_datatypes Do not show composite datatypes for regular dataset upload Compare: https://github.com/galaxyproject/galaxy/compare/16751cd6ab9d...8366d2b5fa32

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[galaxyproject/galaxy] 39d7e2: Close file handles
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39d7e2e7397441fde631b25e4c1e7ec8e1ccc3a6 https://github.com/galaxyproject/galaxy/commit/39d7e2e7397441fde631b25e4c1e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/api/test_tools_upload.py Log Message: ----------- Close file handles Commit: 67330b2751f58e5c8f0a6ef8d1262c8207c9ea63 https://github.com/galaxyproject/galaxy/commit/67330b2751f58e5c8f0a6ef8d126… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Fix upload param to specify datatype Also use higher level `tools_post()` method of the dataset populator instead of `_post()`. Commit: b6944c5ad6c542054649e4bdb3df2c35a884fab3 https://github.com/galaxyproject/galaxy/commit/b6944c5ad6c542054649e4bdb3df… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Remove leftover log statements Commit: 6c3c076ef1d773c156ff6a4b318a4b183ae6ede7 https://github.com/galaxyproject/galaxy/commit/6c3c076ef1d773c156ff6a4b318a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Sort files and subdirectories when fetching an FTP directory Commit: 0944aee34910b3ecbb65168a45a8e06ca98b4fcc https://github.com/galaxyproject/galaxy/commit/0944aee34910b3ecbb65168a45a8… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M test/base/populators.py Log Message: ----------- Add velvet to the datatypes allowed for upload It was already allowed in `test/functional/tools/sample_datatypes_conf.xml` This will stop the skipping of tests requiring the `velvet` datatype, like `ToolsUploadTestCase.test_composite_datatype` in `test/api/test_tools_upload.py` . Commit: 5ae52b7f0616a43a08c5849d118adf152932e42b https://github.com/galaxyproject/galaxy/commit/5ae52b7f0616a43a08c5849d118a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Try to fix occasionally failing integration test See https://jenkins.galaxyproject.org/job/docker-integration/4293/testReport/ju… It seems `get_history_collection_details()` was called before the collection was completely populated. Also small fixes for a typo and class documentation found while researching the origin of the bug. Commit: 16751cd6ab9ddbc8f28b9bddab55b901c4c6576e https://github.com/galaxyproject/galaxy/commit/16751cd6ab9ddbc8f28b9bddab55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/tools.py M test/api/test_tools_upload.py M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Merge pull request #5691 from nsoranzo/test_fixes Various test fixes Compare: https://github.com/galaxyproject/galaxy/compare/0f3259c4b1f9...16751cd6ab9d

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[galaxyproject/galaxy] 059b04: Improve error logging for API-based testing.
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 059b0437f725732f97900366c3af48e6c19ed816 https://github.com/galaxyproject/galaxy/commit/059b0437f725732f97900366c3af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Improve error logging for API-based testing. ``` ====================================================================== FAIL: test_recover_mapping_in_subworkflow (api.test_workflows.WorkflowsApiTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/base/populators.py", line 64, in wrapped_method return method(api_test_case, *args, **kwargs) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 1467, in test_recover_mapping_in_subworkflow """, history_id=history_id, wait=True) File "/Users/john/workspace/galaxy/test/api/test_workflows.py", line 251, in _run_jobs self.workflow_populator.wait_for_workflow(workflow_id, invocation_id, history_id, assert_ok=assert_ok) File "/Users/john/workspace/galaxy/test/base/populators.py", line 445, in wait_for_workflow self.wait_for_invocation(workflow_id, invocation_id, timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 440, in wait_for_invocation return wait_on_state(lambda: self._get(url), desc="workflow invocation state", timeout=timeout) File "/Users/john/workspace/galaxy/test/base/populators.py", line 810, in wait_on_state raise TimeoutAssertionError("%s Current response containing state [%s]." % (e.message, response.json())) TimeoutAssertionError: Timed out after 60.25 seconds waiting on workflow invocation state. Current response containing state [{u'inputs': {u'0': {u'src': u'hda', u'id': u'adb5f5c93f827949', u'uuid': u'de3d999f-d993-447f-a7c4-0389a358034f'}}, u'update_time': u'2018-03-14T15:58:08.615444', u'uuid': u'7b0fc935-27a0-11e8-b255-784f435ea615', u'outputs': {}, u'history_id': u'adb5f5c93f827949', u'workflow_id': u'529fd61ab1c6cc36', u'output_collections': {}, u'state': u'ready', u'steps': [{u'workflow_step_label': u'outer_input', u'update_time': u'2018-03-14T15:58:05.629190', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'afafbeb3-c3d8-49c8-ae21-5add12558c90', u'order_index': 0, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb6e11b662890a90', u'id': u'adb5f5c93f827949'}, {u'workflow_step_label': u'first_cat', u'update_time': u'2018-03-14T15:58:06.015192', u'job_id': u'529fd61ab1c6cc36', u'state': u'scheduled', u'workflow_step_uuid': u'6a 5b3ac3-bacf-4e97-bcca-57ea8d8161dd', u'order_index': 1, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'cb227cec8ca83994', u'id': u'529fd61ab1c6cc36'}, {u'workflow_step_label': u'nested_workflow', u'update_time': u'2018-03-14T15:58:06.770332', u'job_id': None, u'state': u'scheduled', u'workflow_step_uuid': u'55640d5d-5e8d-490f-9d68-736f66b1b65a', u'order_index': 2, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'f3f73e481f432006', u'id': u'd9abeb98649a6a7e'}, {u'workflow_step_label': u'second_cat', u'update_time': u'2018-03-14T15:58:06.770643', u'job_id': None, u'state': u'new', u'workflow_step_uuid': u'67beb950-271c-46f4-aca0-42dbe59c6d57', u'order_index': 3, u'action': None, u'model_class': u'WorkflowInvocationStep', u'workflow_step_id': u'2234cb1fd1df4331', u'id': u'cb6e11b662890a90'}], u'model_class': u'WorkflowInvocation', u'id': u'adb5f5c93f827949'}]. -------------------- >> begin captured stdout << --------------------- Executing git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git fetch && git --work-tree test-data-cache/ad1daf4e1504da1acd42c088c6f49be6 --git-dir test-data-cache/ad1daf4e1504da1acd42c088c6f49be6/.git merge origin/master Problem in history with id adb5f5c93f827949 - summary of history's datasets and jobs below. -------------------------------------- | 1 - Test Dataset (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | uploaded txt file | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 2 - Concatenate datasets on data 1 (HID - NAME) | Dataset State: | ok | Dataset Blurb: | 65 lines | Dataset Info: | *Dataset info is empty.* | Peek: | <table cellspacing="0" cellpadding="3"><tr><td>chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 -</td></tr><tr><td>chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +</td></tr><tr><td>chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -</td></tr><tr><td>chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 +</td></tr><tr><td>chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 -</td></tr></table> | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- | 3 - Select random lines on data 2 (HID - NAME) | Dataset State: | running | Dataset Blurb: | queued | Dataset Info: | None | Peek: | None | Dataset Job Standard Output: | None | Dataset Job Standard Error: | None | -------------------------------------- | 4 - lines (HID - NAME) | Dataset Collection: {u'hid': 4, u'history_content_type': u'dataset_collection', u'populated_state_message': None, u'name': u'lines', u'populated': False, u'deleted': False, u'job_source_type': u'Job', u'history_id': u'adb5f5c93f827949', u'tags': [], u'element_count': None, u'job_source_id': u'f3f73e481f432006', u'visible': True, u'elements': [], u'collection_type': u'list', u'url': u'/api/histories/adb5f5c93f827949/contents/dataset_collections/adb5f5c93f827949', u'model_class': u'HistoryDatasetCollectionAssociation', u'type': u'collection', u'id': u'adb5f5c93f827949', u'populated_state': u'new'} | -------------------------------------- | Job d9abeb98649a6a7e | State: | running | Update Time: | 2018-03-14T15:58:09.483449 | Create Time: | 2018-03-14T15:58:06.139665 | -------------------------------------- | Job 529fd61ab1c6cc36 | State: | ok | Update Time: | 2018-03-14T15:58:08.633359 | Create Time: | 2018-03-14T15:58:05.706745 | -------------------------------------- | Job f3f73e481f432006 | State: | new | Update Time: | 2018-03-14T15:58:06.559809 | Create Time: | 2018-03-14T15:58:06.559799 | -------------------------------------- | Job adb5f5c93f827949 | State: | ok | Update Time: | 2018-03-14T15:58:04.602106 | Create Time: | 2018-03-14T15:58:00.368911 | -------------------------------------- ``` Commit: 0f3259c4b1f91b20965214d144b6705c802146ee https://github.com/galaxyproject/galaxy/commit/0f3259c4b1f91b20965214d144b6… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/base/populators.py Log Message: ----------- Merge pull request #5697 from jmchilton/api_test_logging Improve error logging for API-based testing. Compare: https://github.com/galaxyproject/galaxy/compare/2ace504daea6...0f3259c4b1f9

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[galaxyproject/galaxy] 070889: Better logging for a broad swath of workflow API t...
by GitHub 15 Mar '18

15 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 07088907d3c2ba58986e1025dc1fea6fc6ed0911 https://github.com/galaxyproject/galaxy/commit/07088907d3c2ba58986e1025dc1f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Better logging for a broad swath of workflow API tests. I did a few of these test conversions with 0ff639a29c6179e530c977b358cebf229c76139d but this covers many more the workflow API tests. The idea is to switch to this with statement and context manager that does a better job managing test histories including summarizing the history when problems occur (this summary will include job information after #5697). Commit: 2ace504daea607cc482d29d1bbdfefe53504d748 https://github.com/galaxyproject/galaxy/commit/2ace504daea607cc482d29d1bbdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-15 (Thu, 15 Mar 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Merge pull request #5699 from jmchilton/workflow_api_logging Better logging for a large number of workflow API tests. Compare: https://github.com/galaxyproject/galaxy/compare/1d9d39867c38...2ace504daea6

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[galaxyproject/galaxy] e806a3: Fix for running Yarn in Docker for tests that do n...
by GitHub 14 Mar '18

14 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e806a3d0e55cee2e72c59a87dba511583d2934a0 https://github.com/galaxyproject/galaxy/commit/e806a3d0e55cee2e72c59a87dba5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Fix for running Yarn in Docker for tests that do not need it. Commit: 1d9d39867c3842f9218a52eb15c9636342eeb4f1 https://github.com/galaxyproject/galaxy/commit/1d9d39867c3842f9218a52eb15c9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-14 (Wed, 14 Mar 2018) Changed paths: M run_tests.sh Log Message: ----------- Merge pull request #5690 from jmchilton/skip_client_build_docker Fix for running Yarn in Docker for tests that do not need it. Compare: https://github.com/galaxyproject/galaxy/compare/c6993caabff5...1d9d39867c38

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