March 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f6b2cc: add basic cgroup metric collection
by GitHub 09 Mar '18

09 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f6b2cc65b900e67300efb573f3b124d82836a80a https://github.com/galaxyproject/galaxy/commit/f6b2cc65b900e67300efb573f3b1… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- add basic cgroup metric collection Commit: 899ea47c9af999d9d8bf177eadbf4992193521f7 https://github.com/galaxyproject/galaxy/commit/899ea47c9af999d9d8bf177eadbf… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- fix cgroup metric collector when no cgroup is available Commit: 7c40725f3fd77f881bc1be167dde760d89eec421 https://github.com/galaxyproject/galaxy/commit/7c40725f3fd77f881bc1be167dde… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M config/job_metrics_conf.xml.sample Log Message: ----------- fix broken xml in job_metrics.xml Commit: 7bf04bc88d0015e022d45e5c2b755e55a9e49e66 https://github.com/galaxyproject/galaxy/commit/7bf04bc88d0015e022d45e5c2b75… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- only need to check if /proc/36642/cgroup exists, not if its executable... Commit: 47caac3f5ca61051e84414dbb63bdeab88a53b36 https://github.com/galaxyproject/galaxy/commit/47caac3f5ca61051e84414dbb63b… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2018-03-02 (Fri, 02 Mar 2018) Changed paths: M lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- actually..also need to explicitly check if cgget is available.. Commit: c5df43cd000a1891ca6911d1ca85ed646c5b21fa https://github.com/galaxyproject/galaxy/commit/c5df43cd000a1891ca6911d1ca85… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M config/job_metrics_conf.xml.sample A lib/galaxy/jobs/metrics/instrumenters/cgroup.py Log Message: ----------- Merge pull request #5610 from scholtalbers/feature/cgroup_metrics Add basic cgroup metric collection Compare: https://github.com/galaxyproject/galaxy/compare/21959113e7a0...c5df43cd000a

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[galaxyproject/galaxy] 2270f7: Consistent sniffing regardless of in_place.
by GitHub 09 Mar '18

09 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2270f728c421b81ea14f022beb96203f007180dd https://github.com/galaxyproject/galaxy/commit/2270f728c421b81ea14f022beb96… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: e72e02cc7a98f6c721dbd14a52f5f18f5de33d5f https://github.com/galaxyproject/galaxy/commit/e72e02cc7a98f6c721dbd14a52f5… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Merge pull request #5643 from jmchilton/sniff_fix [18.01] Consistent sniffing regardless of in_place. Compare: https://github.com/galaxyproject/galaxy/compare/fa3ec5f60b9a...e72e02cc7a98

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[galaxyproject/galaxy] ebac0f: Upload simplification - just base this check on li...
by GitHub 09 Mar '18

09 Mar '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ebac0fd9e576f5d1cac797d71d470aedb911ec7d https://github.com/galaxyproject/galaxy/commit/ebac0fd9e576f5d1cac797d71d47… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Upload simplification - just base this check on link_only. Commit: 94cc4dfef690edbe0163eadca55d6371ef1c9968 https://github.com/galaxyproject/galaxy/commit/94cc4dfef690edbe0163eadca55d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/util/compression_utils.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Refactor shed's CompressedFile abstraction into galaxy.util.compression_util. I need to use this from upload code. Commit: 306dded24862d27a3cd2ef6bb5380bd4a267de4e https://github.com/galaxyproject/galaxy/commit/306dded24862d27a3cd2ef6bb538… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/library_contents.py Log Message: ----------- Improved doc for library API. Commit: a45cbfeb8d7d7cc3df5e2561b422023986e805d0 https://github.com/galaxyproject/galaxy/commit/a45cbfeb8d7d7cc3df5e2561b422… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Stronger assertion about link_data_only option in upload.py. Commit: 1c6cc02415f03b999767d97b049acfd1f39388de https://github.com/galaxyproject/galaxy/commit/1c6cc02415f03b999767d97b049a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/base/integration_util.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Hierarchical upload API optimized for folders & collections. Allows describing hierarchical data in JSON or inferring structure from archives or directories. Datasets or archive sources can be specified via uploads, URLs, paths (if admin && allow_path_paste), library_import_dir/user_library_import_dir, and/or FTP imports. Unlike existing API endpoints, a mix of these on a per file basis is allowed and they work seemlessly between libraries and histories. Supported "archives" include gzip, zip, bagit directories, bagit achives (with fetching and validations of downloads). The existing upload API endpoint is quite rough to work with both in terms of adding parameters (e.g. the file type and dbkey hanlding in 4563 was difficult to implement, terribly hacky, and should seemingly have been trivial) and in terms of building requests (one needs to build a tool form - not describe sensible inputs in JSON). This API is built to be intelligable from an API standpoint instead of being constrained to the older style tool form. Additionally it built with hierarchical data in mind in a way that would not be easy at all enhancing the tool form components we don't even render. This implements 5159 though much simpler YAML descriptions of data libraries should be possible basically as the API descriptions. We can replace the data library script in Ephemeris https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/setup_data… with one that converts a simple YAML file into an API call and allows many new options for free. In future PRs I'll add filtering options to this and it will serve as the backend to 4733. Commit: ce2170a56ede27c9caa2a3c881fa5c582c25b196 https://github.com/galaxyproject/galaxy/commit/ce2170a56ede27c9caa2a3c881fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Test case for link_to_files during upload. Commit: b6f4bffbbb89d3f96f7a292eca38e631cd950a44 https://github.com/galaxyproject/galaxy/commit/b6f4bffbbb89d3f96f7a292eca38… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Do not allow workflows to run tools that are not workflow-compatible. In the case of data-fetch there is extra validation that is done so this is somewhat important. Commit: 347f1e123bb4956361384935c28714e0734ac916 https://github.com/galaxyproject/galaxy/commit/347f1e123bb4956361384935c287… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/actions/library.py M test/base/driver_util.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Don't purge library path pastes and such in upload.py during testing. Concerning that they sometimes will get deleted in production with default settings - see 5361. Commit: 3bf5990155faea13ceaa7e43b76d61cfb7ec3cd2 https://github.com/galaxyproject/galaxy/commit/3bf5990155faea13ceaa7e43b76d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/webapps/galaxy/api/_fetch_util.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Allow uploading individual HDAs via fetch API. Commit: 1720354d86c29bcc5f50664139cbf935ebc51e5b https://github.com/galaxyproject/galaxy/commit/1720354d86c29bcc5f50664139cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- More upload testing, some input is getting deleted that shouldn't. Commit: 5c5dbd2b6587dee35fef329b9536cc627f2bf6a4 https://github.com/galaxyproject/galaxy/commit/5c5dbd2b6587dee35fef329b9536… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/data_fetch.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py Log Message: ----------- Handle compressed datatypes appropriately in data fetch API. Commit: 54ee573952215214a15cf21f20c79b735a394342 https://github.com/galaxyproject/galaxy/commit/54ee573952215214a15cf21f20c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload.py Log Message: ----------- Simplify and reduce duplication of upload actions. Commit: 60f632bb242c0c73831dbe0af204218f59b38d77 https://github.com/galaxyproject/galaxy/commit/60f632bb242c0c73831dbe0af204… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py 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 test/integration/test_upload_configuration_options.py Log Message: ----------- Precreate certain outputs for upload 2.0 API. Trying to improve the user experience of this rule based uploader by placing HDAs and HDCAs in the history at the outset that the history panel can poll and that we can turn red if the upload fails. >From Marius' PR review: > I can see that a job launched in my logs, but it failed and there were no visual indications of this in the UI Not every HDA for instance can be created, for example if reading them from a zip file for instance that happens on the backend still. Likewise if HDCAs don't define a collection type up front they cannot be pre-created (if for instance that is inferred from a folder structure). Library things aren't precreated at all in this commit. There is room to pre-create more but I think this is an atomic commit as it is now and it will hopefully improve the user experience for the rule based uploader considerably. Commit: d783fc33091e2952c2775f13a3453517bcffb9bb https://github.com/galaxyproject/galaxy/commit/d783fc33091e2952c2775f13a345… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Avoid symlinks in upload FTP tests. Commit: 33141835c9700c2fd93fc10ce6e68c6a41026377 https://github.com/galaxyproject/galaxy/commit/33141835c9700c2fd93fc10ce6e6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/data_fetch.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Cleanup hierarchical upload commit based on PR comments from @bgruening. - Remove seemingly unneeded hack in upload_common. - Remove stray debug statement. - Add more comments in the output collection code related to different destination types. - Restructure if/else in data_fetch to avoid assertion with constant. Commit: ca28000f8b74738e50bb33aab67eb933a2df6f7a https://github.com/galaxyproject/galaxy/commit/ca28000f8b74738e50bb33aab67e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Fixes for pre-creating HDAs using data fetch API. Commit: 495d1258fd50780ea1dffd05eeef558161dc041d https://github.com/galaxyproject/galaxy/commit/495d1258fd50780ea1dffd05eeef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Consistent sniffing regardless of in_place. Previously sniffing would happen on the original file (before carriage returns and tabular spaces were converted) if in_place was false and on the converted file if it was true. Commit: d651348da663966c1c04585f557820af53c5f651 https://github.com/galaxyproject/galaxy/commit/d651348da663966c1c04585f5578… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/datatypes/sniff.py M lib/galaxy/tools/data_fetch.py A test-data/1.csv M test/api/test_tools_upload.py M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- More upload tests and fixes. Commit: bca2c3cf173604910cc06d53afa9e0acbb02df49 https://github.com/galaxyproject/galaxy/commit/bca2c3cf173604910cc06d53afa9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/data_fetch.py Log Message: ----------- Fix for data_fetch sniffing. Commit: 21959113e7a02d9846d5ab311a9d412cd8eba18e https://github.com/galaxyproject/galaxy/commit/21959113e7a02d9846d5ab311a9d… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-03-09 (Fri, 09 Mar 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/app.py M lib/galaxy/datatypes/sniff.py A lib/galaxy/datatypes/upload_util.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/__init__.py M lib/galaxy/managers/collections.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py A lib/galaxy/tools/data_fetch.py A lib/galaxy/tools/data_fetch.xml M lib/galaxy/tools/execute.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/special_tools.py M lib/galaxy/util/compression_utils.py A lib/galaxy/webapps/galaxy/api/_fetch_util.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py A scripts/api/fetch_to_library.py A scripts/api/fetch_to_library_example.yml A test-data/1.csv A test-data/example-bag.zip A test-data/testdir1.zip M test/api/test_dataset_collections.py M test/api/test_libraries.py M test/api/test_tools_upload.py M test/base/driver_util.py M test/base/integration_util.py M test/base/populators.py M test/functional/tools/sample_datatypes_conf.xml M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5220 from jmchilton/upload_2.0 Hierarchical upload API optimized for folders & collections. Compare: https://github.com/galaxyproject/galaxy/compare/300fffe73ee0...21959113e7a0

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[galaxyproject/galaxy] 70ac42: Disentangle 'view' handling in trackster track ini...
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 70ac429f22899684d80190e576b176dbef6be1d7 https://github.com/galaxyproject/galaxy/commit/70ac429f22899684d80190e576b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Disentangle 'view' handling in trackster track initialization. This is a step towards making Trackster work again. Commit: 4112bd51cc59a0a16845fcfeba2b9b8cb3c3925b https://github.com/galaxyproject/galaxy/commit/4112bd51cc59a0a16845fcfeba2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix undefined incomplete_features reference, use correct 'this.view' for tiledtrack Commit: 975e41a0372c85d1caf86c5fde5492e2fa3c4ec9 https://github.com/galaxyproject/galaxy/commit/975e41a0372c85d1caf86c5fde54… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Removal of self reference and unused import in visualization.js Commit: ac872cccf5465a3f3fce197870222168d5b1f550 https://github.com/galaxyproject/galaxy/commit/ac872cccf5465a3f3fce19787022… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Trackster painters overhaul, fixes. Commit: 9c54765e6fb6164816c16ed79628ad37f73a9192 https://github.com/galaxyproject/galaxy/commit/9c54765e6fb6164816c16ed79628… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/slotting.js Log Message: ----------- Scope and minor cleanup in slotting.js Commit: 00f4ffe166716d91fefb6078881d3d79e014c2bb https://github.com/galaxyproject/galaxy/commit/00f4ffe166716d91fefb6078881d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/filters.js Log Message: ----------- Fix undefined var in trackster/filters -- still exists one that I need to fix here, but that'll take some digging. Commit: 2c51bdd5d04f267b5282ee06ed2312e1b3a44d25 https://github.com/galaxyproject/galaxy/commit/2c51bdd5d04f267b5282ee06ed23… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Incremental fixes and work on trackster/tracks.js -- still not painting.... Commit: 4d7539dbeccc2a51bb36a21b8b34733e7345ae8a https://github.com/galaxyproject/galaxy/commit/4d7539dbeccc2a51bb36a21b8b34… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More trackster/tracks work. More variable scoping issues fixed, function definitions standardized. One callback issue resolved. Commit: 4a7487400aa45a558a87982888c7ce75a234efa1 https://github.com/galaxyproject/galaxy/commit/4a7487400aa45a558a87982888c7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Minor regex fix, drop a debug statement. Commit: 80c7f369148919c93132c08e19e993b290cc4a84 https://github.com/galaxyproject/galaxy/commit/80c7f369148919c93132c08e19e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Fix another regex; var scoping adjustments for trackster. Commit: 43d632d16c2edee3080baa5008269526fc671898 https://github.com/galaxyproject/galaxy/commit/43d632d16c2edee3080baa500826… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Painter fixes, trying to track down initialization bug w/ this.prefs. Commit: 391ac34d5f1bc479b168b6187bd91bc1b21230fe https://github.com/galaxyproject/galaxy/commit/391ac34d5f1bc479b168b6187bd9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- More cleanup in tracks.js, still trying to track down painter initialization bug. Commit: 5d180ba5191f6c427448f836f44c2b3ca15b5d82 https://github.com/galaxyproject/galaxy/commit/5d180ba5191f6c427448f836f44c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Rewrite painters using ES6 classes, for my sanity and future maintenance. Still won't paint, but it's easier to track through the hierarchy now. Commit: 33d17bcbe6b6a7dc85ed35849b7dce95ba04a8fe https://github.com/galaxyproject/galaxy/commit/33d17bcbe6b6a7dc85ed35849b7d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Slight reorg in painters, post-rewrite Commit: 3ac2cabce822ff71ba2fbbb23b1f71ec5428c1e2 https://github.com/galaxyproject/galaxy/commit/3ac2cabce822ff71ba2fbbb23b1f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Spello Commit: 76c8dae70138e113774c43b54c68babfe26b0ed9 https://github.com/galaxyproject/galaxy/commit/76c8dae70138e113774c43b54c68… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- TracksterUI class-ification, minor cleanup. Disentangling globals next. Commit: d7b2e4942fa2e940cce236d0b87c0b48e3c83508 https://github.com/galaxyproject/galaxy/commit/d7b2e4942fa2e940cce236d0b87c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Global var refactoring, removal of some unused stuff. Commit: 9bd112bd9169f6fb782cc9fdd86cbb46824df49a https://github.com/galaxyproject/galaxy/commit/9bd112bd9169f6fb782cc9fdd86c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-01-23 (Tue, 23 Jan 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Trackster refactoring; this pulls apart using a global view. There is a trackster ui, which holds the main view, and should be accessed through it when necessary. Commit: 0e6e468608fd85c3a8bdb41bf329523c821152b0 https://github.com/galaxyproject/galaxy/commit/0e6e468608fd85c3a8bdb41bf329… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Import fixes in main trackster.js Commit: 7c9c9775753d539527ff4d74a2108563fe06a945 https://github.com/galaxyproject/galaxy/commit/7c9c9775753d539527ff4d74a210… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-28 (Wed, 28 Feb 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Misc cleanup while trying to debug nonexistent paint vars. Commit: ec8c92604239bdb5b7e92717586bc305fbbf8db3 https://github.com/galaxyproject/galaxy/commit/ec8c92604239bdb5b7e92717586b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Refactoring in feature painter draw. Commit: f0df326e2cdb2c90fb78e0a18dbaadee3d62de17 https://github.com/galaxyproject/galaxy/commit/f0df326e2cdb2c90fb78e0a18dba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-05 (Mon, 05 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Use static getters for default painter preferences, fix 'defailt' ironic typo. Commit: 4bca4a056cdf766eec8108db4aaa43ddbfb57c0e https://github.com/galaxyproject/galaxy/commit/4bca4a056cdf766eec8108db4aaa… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster/painters.js Log Message: ----------- Config.js fixes; it was trying to import itself and not use it. Commit: f33eee105f02d189cc68914dd72ed0a77f05cfcd https://github.com/galaxyproject/galaxy/commit/f33eee105f02d189cc68914dd72e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-03-06 (Tue, 06 Mar 2018) Changed paths: M client/galaxy/scripts/viz/trackster/tracks.js Log Message: ----------- Fix config parameter default building in tracks.js; ideally this turns into classes when the multiple inheritance is fixed/refactored, and we can use simple static getter/setter methods. Commit: fa3ec5f60b9a4b6bed0ee771166c6e49c8fa02d0 https://github.com/galaxyproject/galaxy/commit/fa3ec5f60b9a4b6bed0ee771166c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M client/galaxy/scripts/utils/config.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/filters.js M client/galaxy/scripts/viz/trackster/painters.js M client/galaxy/scripts/viz/trackster/slotting.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js Log Message: ----------- Merge pull request #5261 from dannon/trackster_fixes [18.01] Trackster fixes. Compare: https://github.com/galaxyproject/galaxy/compare/1761d85e7299...fa3ec5f60b9a

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[galaxyproject/usegalaxy-playbook] 086ff2: Test: Serve viz plugin static content from subdire...
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 086ff26fd1ab03f9173829d4de683e410a5e1525 https://github.com/galaxyproject/usegalaxy-playbook/commit/086ff26fd1ab03f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M env/test/templates/nginx/galaxy_test.j2 Log Message: ----------- Test: Serve viz plugin static content from subdirectories as well as directories.

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[galaxyproject/galaxy] d60b80: Show error message if user tries purging datasets
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: d60b80a537ae4b9d580805014c99d74bb6598896 https://github.com/galaxyproject/galaxy/commit/d60b80a537ae4b9d580805014c99… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if user tries purging datasets without having an associated history. This can be seen by pasting http://<gx_instance>/history/purge_deleted_datasets into an anonymous browser session (be careful to not delete something important ;)). Traceback is: ``` AttributeError: 'NoneType' object has no attribute 'datasets' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 1108, in purge_deleted_datasets for hda in trans.history.datasets: ``` Commit: 1761d85e7299ddd34565794c43b0c761b44a0bc5 https://github.com/galaxyproject/galaxy/commit/1761d85e7299ddd34565794c43b0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5664 from mvdbeek/show_error_message_if_no_history_associated [18.01] Show error message if user tries purging datasets Compare: https://github.com/galaxyproject/galaxy/compare/a0fd6307562b...1761d85e7299

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[galaxyproject/galaxy] fe444a: Show error message if history structure can't be s...
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: fe444ab3ef6bf37761859e09a0baf3ec38e7c6c4 https://github.com/galaxyproject/galaxy/commit/fe444ab3ef6bf37761859e09a0ba… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Show error message if history structure can't be shown Fixes: ``` AttributeError: 'NoneType' object has no attribute 'id' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/history.py", line 494, in display_structured assert (history.user and (history.user.id == trans.user.id) or ``` Commit: a0fd6307562b38a7ef93291c6450cb92bd0eaf59 https://github.com/galaxyproject/galaxy/commit/a0fd6307562b38a7ef93291c6450… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #5665 from mvdbeek/show_error_msg_when_history_structure_cannot_be_shown [18.01] Show error message if history structure can't be shown Compare: https://github.com/galaxyproject/galaxy/compare/0a95f20f5ba7...a0fd6307562b

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[galaxyproject/galaxy] 706efd: Fix exception if email is not specified
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 706efdc186177c36871aa47059de64aa0112f1a0 https://github.com/galaxyproject/galaxy/commit/706efdc186177c36871aa47059de… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Fix exception if email is not specified We render a regular error a few lines lower. Commit: 17e1786521e458819f2cdb9821fd3e96c18bc3a7 https://github.com/galaxyproject/galaxy/commit/17e1786521e458819f2cdb9821fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Avoid exception if email is wrong Avoids: ``` AttributeError: 'NoneType' object has no attribute 'active' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/user.py", line 938, in activate if user.active is True: ``` Commit: 0a95f20f5ba7e41282a29afb21a41290033cfed8 https://github.com/galaxyproject/galaxy/commit/0a95f20f5ba7e41282a29afb21a4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/user.py Log Message: ----------- Merge pull request #5663 from mvdbeek/user_activation_fix [18.01] Fix exception if email is not specified or email is wrong Compare: https://github.com/galaxyproject/galaxy/compare/3ce1273d7cc4...0a95f20f5ba7

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[galaxyproject/galaxy] cdae68: Fix exception if user preference value undefined
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: cdae68907bdacc4f290f561bff89f3b4525a7b4d https://github.com/galaxyproject/galaxy/commit/cdae68907bdacc4f290f561bff89… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Fix exception if user preference value undefined Fixes the following traceback on main: ``` AttributeError: 'NoneType' object has no attribute 'strip' File "galaxy/web/framework/middleware/sentry.py", line 43, in __call__ iterable = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/middleware/statsd.py", line 35, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 136, in __call__ return self.handle_request(environ, start_response) File "galaxy/web/framework/base.py", line 215, in handle_request body = method(trans, **kwargs) File "galaxy/webapps/galaxy/controllers/root.py", line 110, in index config.update(self._get_extended_config(trans)) File "galaxy/webapps/galaxy/controllers/root.py", line 57, in _get_extended_config 'toolbox' : app.toolbox.to_dict(trans, in_panel=False), File "galaxy/tools/toolbox/base.py", line 963, in to_dict filter_method = self._build_filter_method(trans) File "galaxy/tools/toolbox/base.py", line 1004, in _build_filter_method filters = self._filter_factory.build_filters(trans) File "galaxy/tools/toolbox/filters/__init__.py", line 37, in build_filters if value.strip(): ``` Commit: 3ce1273d7cc447d9088f9c056649d16c188d509d https://github.com/galaxyproject/galaxy/commit/3ce1273d7cc447d9088f9c056649… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/galaxy/tools/toolbox/filters/__init__.py Log Message: ----------- Merge pull request #5662 from mvdbeek/fix_build_filters [18.01] Fix exception if user preference value undefined Compare: https://github.com/galaxyproject/galaxy/compare/206182ea8f1a...3ce1273d7cc4

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[galaxyproject/galaxy] 2846fa: Use target file path when adding missing indexes
by GitHub 08 Mar '18

08 Mar '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 2846fa0aa1e92e770e01af15008ed76b93b41b52 https://github.com/galaxyproject/galaxy/commit/2846fa0aa1e92e770e01af15008e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-03-07 (Wed, 07 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Use target file path when adding missing indexes Previously we would load a TS tool during installation and ask if any of its tool datat tables are missing loc files. If thats the case we copy the sample file and call `handle_found_index_file` for the particular missing *.loc path of this data table. This does not work if the data table already existed (e.g for built-in data tables), but was missing the *.loc file, since we would atempt to load that path. Instead we do now load the path to the loc file that we just copied. Should fix https://github.com/galaxyproject/galaxy/issues/5648. Commit: 206182ea8f1ae437f4a5016fc49f74d5bf68f378 https://github.com/galaxyproject/galaxy/commit/206182ea8f1ae437f4a5016fc49f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-03-08 (Thu, 08 Mar 2018) Changed paths: M lib/tool_shed/util/tool_util.py Log Message: ----------- Merge pull request #5650 from mvdbeek/missing_index_file_fixes [18.01] Use sample file path when adding missing indexes Compare: https://github.com/galaxyproject/galaxy/compare/b601bcc429b4...206182ea8f1a

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