Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0d68d4cf389f5864c6fc5676012c9301fe850daa https://github.com/galaxyproject/galaxy/commit/0d68d4cf389f5864c6fc567601... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/handler.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0136_add_copied_from_job_id_column.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/workflow/modules.py Log Message: ----------- WIP: skip job execution if equivalent job exists Commit: 34b99bd8aaa0a04df5d6b81a2a9abb92d8244abb https://github.com/galaxyproject/galaxy/commit/34b99bd8aaa0a04df5d6b81a2a... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/workflow/modules.py Log Message: ----------- Improve detection of equivalent jobs in workflows and collection-context Commit: cd32afe21e870898b7c8191628a2edcbee819527 https://github.com/galaxyproject/galaxy/commit/cd32afe21e870898b7c8191628... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Skip creation of JobWrapper for copied jobs, copy metrics and dependencies Commit: 7defcddd19dfcc259ef6c0d83a7375f2363dc3f3 https://github.com/galaxyproject/galaxy/commit/7defcddd19dfcc259ef6c0d83a... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Work around Exception("FileToolParameter cannot be persisted" Commit: e9a9b2a5c12921c4d9a80b02730f5bbe0f206598 https://github.com/galaxyproject/galaxy/commit/e9a9b2a5c12921c4d9a80b0273... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/workflow/modules.py Log Message: ----------- Also search jobs explicitly by version Commit: d3a93af1221b4bb747f7c6e1bf54b894ac8a389e https://github.com/galaxyproject/galaxy/commit/d3a93af1221b4bb747f7c6e1bf... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Cast tool_version to string and pre-filter jobs with wildcards Commit: fc92adc1cc7db1fd6d94cb09d5c30be0e892a6ee https://github.com/galaxyproject/galaxy/commit/fc92adc1cc7db1fd6d94cb09d5... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/workflow/modules.py M test/api/test_jobs.py M test/base/api.py M test/base/interactor.py Log Message: ----------- Take into account HDA name, metadata, element_identifier and datatype Commit: 009daeff81d60202ac6695304e40599dd1d4085c https://github.com/galaxyproject/galaxy/commit/009daeff81d60202ac6695304e... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M test/api/test_jobs.py Log Message: ----------- Fix the wildcard search Commit: e75daa1ddd6a5662bf9d837ecc867655c485a8cb https://github.com/galaxyproject/galaxy/commit/e75daa1ddd6a5662bf9d837ecc... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M test/api/test_jobs.py Log Message: ----------- Skip test that deletes the jobs input dataset This does not work at the moment, since we need to verify a jobs' input name, dataset and metadata, for which we don't have an explicit trail. The only trace is via the update_time (i.e if a input dataset hasn't been updated since the job was created we know these were the actual parameters in use during the execution of this job). Commit: 0df2e18058ecf66322f3a15d42d8735ace37a17b https://github.com/galaxyproject/galaxy/commit/0df2e18058ecf66322f3a15d42... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/base.py Log Message: ----------- Add mechanism for versioning database objects Commit: 409fa016b9651485d7648437b1f0b8766b4b0c90 https://github.com/galaxyproject/galaxy/commit/409fa016b9651485d7648437b1... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py Log Message: ----------- Add HistoryDatasetAssociationHistory to track mutations of HDAs Commit: c88d8826d0960af5067830f121d3a54622386aba https://github.com/galaxyproject/galaxy/commit/c88d8826d0960af5067830f121... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/mapping.py Log Message: ----------- Compare metadata through _metadata for HDAH objects HistoryDatasetsAssoicationHistory objects don't have the full blown metadata objects, instead we compare the raw JSON dumped into the database. Commit: be09b35ff2da39c97836fe5e61fc0fbefd45cb06 https://github.com/galaxyproject/galaxy/commit/be09b35ff2da39c97836fe5e61... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Avoid storing dbkey as list in metadata Commit: 91696783b185ca119499b836623a8954ce3a5d46 https://github.com/galaxyproject/galaxy/commit/91696783b185ca119499b83662... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_jobs.py Log Message: ----------- Uncomment test that relies on HDAHistory Commit: 255e3989b57dd90774d5219a97083cca92ed8678 https://github.com/galaxyproject/galaxy/commit/255e3989b57dd90774d5219a97... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: A lib/galaxy/model/migrate/versions/0137_add_hda_version.py A lib/galaxy/model/migrate/versions/0138_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0139_add_dataset_version_to_job_to_input_dataset_association_table.py Log Message: ----------- Add migration scripts Commit: 71da068e260ac6584ca9f4a77557a438e0c0f6fb https://github.com/galaxyproject/galaxy/commit/71da068e260ac6584ca9f4a775... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Require state to be OK in order to track version in database Commit: e6c374a05a9114c4004de0c54a0f70b6f0b27405 https://github.com/galaxyproject/galaxy/commit/e6c374a05a9114c4004de0c54a... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Fix JobToInputDatasetAssociation recording for tasks (dataset is None) Commit: 6c79785f6f87632d07aafa275e2d3877ddc5895c https://github.com/galaxyproject/galaxy/commit/6c79785f6f87632d07aafa275e... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Avoid recursion in chained sqlalchemy filter statements See https://stackoverflow.com/questions/41625847/maximum-recursion-depth-exce... for details. Commit: 40884fb94f41e6934483a4deee7d05b1e65c049c https://github.com/galaxyproject/galaxy/commit/40884fb94f41e6934483a4deee... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Reduce to single, non-chained query statement Commit: fac13deb6b979327664647f0e0f10828ae4adc15 https://github.com/galaxyproject/galaxy/commit/fac13deb6b979327664647f0e0... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Join for used data input ids This allows us to fetch all used job inputs with a single query as opposed to one query per input dataset. Commit: 70f0ec7930e256f0e93f91db07e03cea5e64f03c https://github.com/galaxyproject/galaxy/commit/70f0ec7930e256f0e93f91db07... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Fix search for tools without data inputs Commit: de75540182833732ddcd7e3a8981eb2c6beb80bb https://github.com/galaxyproject/galaxy/commit/de75540182833732ddcd7e3a89... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Skip second JobParameter filter if no input datasets have been used Commit: 732543ea3bbf49ef0a904d63b7fa61ae4efad0ea https://github.com/galaxyproject/galaxy/commit/732543ea3bbf49ef0a904d63b7... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/model/mapping.py Log Message: ----------- Move check for deleted output datasets to Job relationship properties Commit: 0e02cf3aac9636d97f6ce0086da048b909215617 https://github.com/galaxyproject/galaxy/commit/0e02cf3aac9636d97f6ce0086d... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Remove unused current_jobs_data_ids Commit: d53918eb2d6aad1865416432710b157d967badad https://github.com/galaxyproject/galaxy/commit/d53918eb2d6aad186541643271... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Use joinedload for job parameters which we iterate over Commit: 75ddb8ef62ca857f3a7f0707a6d7cd749ec32fa7 https://github.com/galaxyproject/galaxy/commit/75ddb8ef62ca857f3a7f0707a6... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Revert "Use joinedload for job parameters which we iterate over" This reverts commit a72dcca6ca3d27bf5ada4d98fde784408314e331. Commit: 528a05e00218ecba0c8180268f7f551cf09768e5 https://github.com/galaxyproject/galaxy/commit/528a05e00218ecba0c8180268f... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: A lib/galaxy/dependencies/dev-requirements.txt R lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/managers/jobs.py Log Message: ----------- Debug: add profiling to figure out why search is slow sometimes Commit: b5a4822edbf67eb02213a4f2a5ab762feef1a391 https://github.com/galaxyproject/galaxy/commit/b5a4822edbf67eb02213a4f2a5... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py Log Message: ----------- Optimize query Commit: 77b9610b59eaa294cfc0a5521e0db50b69caf07e https://github.com/galaxyproject/galaxy/commit/77b9610b59eaa294cfc0a5521e... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix passing correct completed job during threaded job submission Commit: c8a5ea2996a6af85d61e2db054c16a3826efa89b https://github.com/galaxyproject/galaxy/commit/c8a5ea2996a6af85d61e2db054... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: A lib/galaxy/dependencies/dev-requirements.txt R lib/galaxy/dependencies/dev-requirements.txt M lib/galaxy/tools/__init__.py Log Message: ----------- Fix bad rebase Commit: 3178cf13a1789ac18c238d7f180110dc9fabb0f3 https://github.com/galaxyproject/galaxy/commit/3178cf13a1789ac18c238d7f18... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/mapping.py Log Message: ----------- Fix import order Commit: fd0728abb9276c6e89b9e097cd10ce2d621ce8fa https://github.com/galaxyproject/galaxy/commit/fd0728abb9276c6e89b9e097cd... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: R lib/galaxy/model/migrate/versions/0136_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py R lib/galaxy/model/migrate/versions/0137_add_hda_version.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py R lib/galaxy/model/migrate/versions/0138_add_history_dataset_association_history_table.py R lib/galaxy/model/migrate/versions/0139_add_dataset_version_to_job_to_input_dataset_association_table.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py Log Message: ----------- Fix migrations Commit: f6413bfaa5e3d2d1a48355f79380cde0dec1be42 https://github.com/galaxyproject/galaxy/commit/f6413bfaa5e3d2d1a48355f793... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py Log Message: ----------- Linting fix (I201) Commit: 74dd664712909adf5857f34fc6c0b1fe8c866059 https://github.com/galaxyproject/galaxy/commit/74dd664712909adf5857f34fc6... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py Log Message: ----------- Make skipping job configurable Commit: 4b6e403622f1a50a7b31d5d1821c5e61032b111b https://github.com/galaxyproject/galaxy/commit/4b6e403622f1a50a7b31d5d182... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/tools/__init__.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_tools.py Log Message: ----------- Add use_cached_job param to tools and workflow API Also includes a simple test that runs cat1 three times, the second time with `use_cached_job=False` (the default), and the third time with `use_cached_job=True` and verifies that the second output is different from the third, and that the first and third output are identical. Commit: 0dcf9d7fd6504e449b7b222ab78f3b9e8a143043 https://github.com/galaxyproject/galaxy/commit/0dcf9d7fd6504e449b7b222ab7... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_tools.py Log Message: ----------- Refine cached job tool test to make less asumptions Commit: 1c4476a6af6f6042ef8daf7ca3c193bd58f8c96c https://github.com/galaxyproject/galaxy/commit/1c4476a6af6f6042ef8daf7ca3... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/managers/jobs.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/data/test_workflow_1.ga Log Message: ----------- Add a test for skipping jobs in workflow context This is using the simplest of workflows. I had to remove the chromInfo part from the workflow, because the path referenced would be changed dynamically and so the job search wouldn't recognize this as being equivalent. Commit: c6468f0677002dad4875b2b7cbeb67f018ef5be3 https://github.com/galaxyproject/galaxy/commit/c6468f0677002dad4875b2b7cb... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M lib/galaxy/workflow/run_request.py Log Message: ----------- Add conditional for use_cached_job to workflow run form Surprisingly the API endpoint that is used by the UI is a little different from the `create` endpoint the tests are testing, so this also adds a change in how the `use_cached_job` is passed along. Commit: 509b0ca7a1e6a5f53b76b2995551d7705d1376d1 https://github.com/galaxyproject/galaxy/commit/509b0ca7a1e6a5f53b76b29955... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js M lib/galaxy/webapps/galaxy/api/tools.py Log Message: ----------- Add the possibility to send reuse jobs via the tool form Commit: 9d38219d6531a4d956145a02d657c6c0ce22412e https://github.com/galaxyproject/galaxy/commit/9d38219d6531a4d956145a02d6... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M test/api/test_workflows.py Log Message: ----------- Pass use_cached_jobs on to subworkflow invoker Commit: 81c733d940eb716d48057446faf21c5f99065019 https://github.com/galaxyproject/galaxy/commit/81c733d940eb716d48057446fa... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Revert the dbkey metadata hack; the real fix is to copy the metadata correctly Commit: 78c37d32d9c0cdbb65b75960c820412185bd129f https://github.com/galaxyproject/galaxy/commit/78c37d32d9c0cdbb65b75960c8... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Assert that histories contains same dataset ids Commit: 43224af880f2a825d5fd2f655a3f9af11f04f689 https://github.com/galaxyproject/galaxy/commit/43224af880f2a825d5fd2f655a... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/model/migrate/versions/0138_add_hda_version.py M lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py Log Message: ----------- Fix migration comments Commit: c327594ed76fab4d235e547053ebc3ed5572b28a https://github.com/galaxyproject/galaxy/commit/c327594ed76fab4d235e547053... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Simplify use_cached_jobs workflow tests Commit: 81c3b8cc4d6439aa7d44b1d4cece284c0bb6b813 https://github.com/galaxyproject/galaxy/commit/81c3b8cc4d6439aa7d44b1d4ce... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M test/api/test_workflows.py Log Message: ----------- Include more information in assertion Commit: e973403ae58154de1c65f24dc822eff401e9febb https://github.com/galaxyproject/galaxy/commit/e973403ae58154de1c65f24dc8... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/api/users.py Log Message: ----------- Simplify retrieval of extra_user_preferences Commit: 3f3476495815e6fceaa555c5ca0bbb997515447d https://github.com/galaxyproject/galaxy/commit/3f3476495815e6fceaa555c5ca... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Only show use_cached_job options if user has activated this feature in the user preferences Commit: 58b8aa986bf3af32de71d6cf17f1f2c60adff17f https://github.com/galaxyproject/galaxy/commit/58b8aa986bf3af32de71d6cf17... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M config/user_preferences_extra_conf.yml.sample Log Message: ----------- Add template to user_preferences_extra_conf.yml.sample for activating job reuse feature Commit: 47c2f3c0d4e42c27c46ae7f7016900f60ea5c8eb https://github.com/galaxyproject/galaxy/commit/47c2f3c0d4e42c27c46ae7f701... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Don't assume extra_preferences exists Commit: 3d45cce423de3e4b323b54fb3fd22e354a52dad7 https://github.com/galaxyproject/galaxy/commit/3d45cce423de3e4b323b54fb3f... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Fix undefined variable Commit: 655af3026b154e02fb6b25f320b9828b64451deb https://github.com/galaxyproject/galaxy/commit/655af3026b154e02fb6b25f320... Author: mvdbeek <m.vandenbeek(a)gmail.com&gt; Date: 2017-12-31 (Sun, 31 Dec 2017) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js A static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js Log Message: ----------- Build client Commit: 32624dfeeeeffcc09b1afea55a4b537d9a15e00d https://github.com/galaxyproject/galaxy/commit/32624dfeeeeffcc09b1afea55a... Author: John Chilton <jmchilton(a)gmail.com&gt; Date: 2018-01-02 (Tue, 02 Jan 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M config/user_preferences_extra_conf.yml.sample M lib/galaxy/jobs/handler.py M lib/galaxy/managers/jobs.py M lib/galaxy/model/__init__.py M lib/galaxy/model/base.py M lib/galaxy/model/mapping.py A lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py A lib/galaxy/model/migrate/versions/0138_add_hda_version.py A lib/galaxy/model/migrate/versions/0139_add_history_dataset_association_history_table.py A lib/galaxy/model/migrate/versions/0140_add_dataset_version_to_job_to_input_dataset_association_table.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/webapps/galaxy/api/jobs.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/api/users.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/libs.bundled.js A static/scripts/libs/vue.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M test/api/test_jobs.py M test/api/test_tools.py M test/api/test_workflows.py M test/base/api.py M test/base/data/test_workflow_1.ga M test/base/interactor.py Log Message: ----------- Merge pull request #4690 from mvdbeek/skip_job_execution Skip job execution if equivalent job exists Compare: https://github.com/galaxyproject/galaxy/compare/8e93c2e070af...32624dfeeeef