Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 92b48412c5cbb50c31b26e97912c073b7c0f29e2 https://github.com/galaxyproject/galaxy/commit/92b48412c5cbb50c31b26e97912c0... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Extend job search for HDCA input Commit: 1d37c7d458f156e391d969bf7630044a476b9856 https://github.com/galaxyproject/galaxy/commit/1d37c7d458f156e391d969bf76300... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Check JobParameter match Matching the JobParameters will prevent returning jobs where a job uses the same input datasets, but where the inputs are used in a different order (and hence the result may differ) Commit: 2b7a1631280e19468021931ca827b94567bca457 https://github.com/galaxyproject/galaxy/commit/2b7a1631280e19468021931ca827b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Add job_search tests for other collection types Commit: 7089de8142199e1b5dadaeef215ae015042f018b https://github.com/galaxyproject/galaxy/commit/7089de8142199e1b5dadaeef215ae... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Reduce job_search test copypaste Commit: 04754c4c4d8c4c287a54e13bc0263f1fdaeaf00c https://github.com/galaxyproject/galaxy/commit/04754c4c4d8c4c287a54e13bc0263... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Allow job_search to find job even if current HDCA was copied from another HDCA and make sure that jobs with same inputs matched to different job parameter inputs are not considered as a match Commit: 64cf60b502daea924fbb7b1106c0040976cdbdc1 https://github.com/galaxyproject/galaxy/commit/64cf60b502daea924fbb7b1106c00... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Test deleting input datasets and recovering jobs from search This revealed a wrong query filter (comparing JobToInputDatasetAssociation.dataset_id == HistoryDatasetAssociation.id, instead of JobToInputDatasetAssociation.dataset_id == HistoryDatasetAssociation.dataset_id). Commit: df91074a3f587e6bd3270e67c4d00ffc321518af https://github.com/galaxyproject/galaxy/commit/df91074a3f587e6bd3270e67c4d00... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Test deleting HDCAs and finding equivalent jobs Commit: 9e3ceaa7f3410127c7ee8c2c1c3854f4208d5afc https://github.com/galaxyproject/galaxy/commit/9e3ceaa7f3410127c7ee8c2c1c385... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-22 (Fri, 22 Sep 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Don't return jobs with deleted HDAs/HDCAs from job_search Commit: 07daa4d248ba5f42facb86a0e38370c54fb9e7b6 https://github.com/galaxyproject/galaxy/commit/07daa4d248ba5f42facb86a0e3837... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-23 (Sat, 23 Sep 2017) Changed paths: A lib/galaxy/jobs/search.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Move job_search out of API for re-use Commit: 054cdd146a84460db07f4725a5251036bb42278f https://github.com/galaxyproject/galaxy/commit/054cdd146a84460db07f4725a5251... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/jobs/search.py Log Message: ----------- When querying jobs for data input parameters drop all other parameters Commit: 19818cb380889e584741caf4a78462e0502f30c1 https://github.com/galaxyproject/galaxy/commit/19818cb380889e584741caf4a7846... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Fix loading of model.JobToInputDatasetCollectionAssociation If we don't load this relationship we do not properly record a job's input_dataset_collections in `DefaultToolAction._record_inputs`. Commit: 87439012602cd500346a1fe442292b2e7cbaaeab https://github.com/galaxyproject/galaxy/commit/87439012602cd500346a1fe442292... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/jobs/search.py Log Message: ----------- Filter jobs on input data using JobToInput*Association. This has the advantage that for complex parameters we don't need to decompose parameter names like `queries_0|input2` in order to compare JobParameters. Commit: 5fc360a0829ae6819dc96ad0228940cda59d4fa7 https://github.com/galaxyproject/galaxy/commit/5fc360a0829ae6819dc96ad022894... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: R lib/galaxy/jobs/search.py A lib/galaxy/managers/jobs.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Move JobSearch to galaxy.managers.jobs Commit: 0e287d38ca1b779c306eb8e0a4c9d3c8bc140882 https://github.com/galaxyproject/galaxy/commit/0e287d38ca1b779c306eb8e0a4c9d... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-24 (Sun, 24 Sep 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Return empty list if type is unknown Commit: 480ee7980251848d09e837faef1cd9873b2e2e33 https://github.com/galaxyproject/galaxy/commit/480ee7980251848d09e837faef1cd... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Skip recording JobToInputDatasetCollection relations if the item to record is not a HistoryDatasetCollectionAssociation. This fixes ``` Error executing tool: Attempting to flush an item of type <class \'galaxy.model.DatasetCollectionElement\'> as a member of collection "JobToInputDatasetCollectionAssociation.dataset_collection". Expected an object of type <class \'galaxy.model.HistoryDatasetCollectionAssociation\'> or a polymorphic subclass of this type.' ``` It isn't ideal, but before 19818cb we didn't record Collection-like elements at all. Commit: 8f5125194630def8530c0e3e30f1b9a4439bd0fb https://github.com/galaxyproject/galaxy/commit/8f5125194630def8530c0e3e30f1b... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-25 (Mon, 25 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/managers/jobs.py Log Message: ----------- Linting fixes and drop unnecessary internal parenthesis (thanks @nsoranzo!). Commit: 7d260d0b50a5858af533fe136105ce357b4ef490 https://github.com/galaxyproject/galaxy/commit/7d260d0b50a5858af533fe136105c... Author: mvdbeek <m.vandenbeek@gmail.com> Date: 2017-09-28 (Thu, 28 Sep 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/managers/jobs.py M lib/galaxy/tools/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py Log Message: ----------- Tighten job search result We now expand incoming tool parameters, so that we have a dictionary of all tool parameters (i.e specified/posted parameters and defaults). We start the search by quering the database for jobs using the same tool id for the same owner with the same input datasets, taking into account copied dataset(-collection)s. We then replace all dataset ids (HDA/LDA or HDCA) in the parameter dict with the input data used for the jobs queried in the first step. This allows us to check every parameter for a match with the job. Commit: 4b7bd98b306155562d9e35610bd8189b4c4e1172 https://github.com/galaxyproject/galaxy/commit/4b7bd98b306155562d9e35610bd81... Author: John Chilton <jmchilton@gmail.com> Date: 2017-09-29 (Fri, 29 Sep 2017) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt A lib/galaxy/managers/jobs.py M lib/galaxy/model/mapping.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/util/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M test/api/test_jobs.py Log Message: ----------- Merge pull request #4665 from mvdbeek/extend_job_search Extend job search for hdcas Compare: https://github.com/galaxyproject/galaxy/compare/95a5e8d6c867...4b7bd98b3061