Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: c99c7b4d842b844677673472b9aa2b13e4123aeb https://github.com/galaxyproject/galaxy/commit/c99c7b4d842b844677673472b9aa2... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- Fix type of some options in config_schema.yml
Also: - drop unused `nginx_x_archive_files_base` option, last use removed in commit fe5983aafca1fae0b60ed16838799b58f4aca11c - rebuild config samples and docs.
Commit: 80ac55b3ff132cf6e1778b99cb6ffb01bec9cfe8 https://github.com/galaxyproject/galaxy/commit/80ac55b3ff132cf6e1778b99cb6ff... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-21 (Wed, 21 Mar 2018)
Changed paths: M lib/galaxy/webapps/config_manage.py
Log Message: ----------- Don't quote ints in .ini to .yml config conversion
Commit: 1b13bfa48e1b3e805a46feec55a3c698ce1fa524 https://github.com/galaxyproject/galaxy/commit/1b13bfa48e1b3e805a46feec55a3c... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Log the pid of the first uWSGI process
So it is the same that gets written to file when using the `--pidfile` option of `uwsgi`.
Commit: 8fa8660b25dccf62a045597bee03441b5b68b71b https://github.com/galaxyproject/galaxy/commit/8fa8660b25dccf62a045597bee034... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/util/hash_util.py M scripts/grt/export.py M scripts/grt/grt.yml.sample
Log Message: ----------- Small improvements to scripts/grt/export.py for testing.
- Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this). - Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell.
Commit: 5f3f792f6f4ba67a2dd49e9c69b28567540c2c48 https://github.com/galaxyproject/galaxy/commit/5f3f792f6f4ba67a2dd49e9c69b28... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py M scripts/communication/communication_server.py M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py A test/integration/test_scripts.py
Log Message: ----------- Unification of Galaxy configuration parsing for scripts/*
Commit: 16d821e12e53655947a6859a221b19a8d05eb2c4 https://github.com/galaxyproject/galaxy/commit/16d821e12e53655947a6859a221b1... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/sync_reports_config.py M scripts/transfer.py
Log Message: ----------- Mark scripts/* that don't work with YAML configuraiton options as deprecated.
Commit: 1911a55390eb4c6f9c7beb69b8f364ff6b76a119 https://github.com/galaxyproject/galaxy/commit/1911a55390eb4c6f9c7beb69b8f36... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh
Log Message: ----------- Remove unused and unuseful scripts.
Commit: 49fed72eeab48cda9e962f2d1a678825f40842b2 https://github.com/galaxyproject/galaxy/commit/49fed72eeab48cda9e962f2d1a678... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh
Log Message: ----------- Drop data library whoosh/lucene scripts.
We don't set that config option in Galaxy anymore so these are broken anyway.
Commit: fea7953410a4145f45afbe1656735febcf390a92 https://github.com/galaxyproject/galaxy/commit/fea7953410a4145f45afbe1656735... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py
Log Message: ----------- Remove two scripts - dataset purging hasn't worked this way for a very long time.
Commit: b14928d97203d4d459c289c393589e4f4120e3e4 https://github.com/galaxyproject/galaxy/commit/b14928d97203d4d459c289c393589... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M test/integration/test_scripts.py
Log Message: ----------- Cleanup script integration tests.
Commit: 14e98becfe9c4d76677d9a9d0bc568c75f242bf2 https://github.com/galaxyproject/galaxy/commit/14e98becfe9c4d76677d9a9d0bc56... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/util/script.py
Log Message: ----------- Cleanup incorrect FIXME - spotted by @nsoranzo.
Commit: a177173672b86f4da8f83c3068dcb63f5f49cc40 https://github.com/galaxyproject/galaxy/commit/a177173672b86f4da8f83c3068dcb... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/util/script.py
Log Message: ----------- Fix missing ENV information in config parameter args.
Commit: 8fb6aa5860344cf80c18b8fef43b43b26856ec2a https://github.com/galaxyproject/galaxy/commit/8fb6aa5860344cf80c18b8fef43b4... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/util/script.py
Log Message: ----------- Bring in @nsoranzo's requested changes for config_file_from_args, etc.
Commit: bb90ae93d810cd829ef026a3d086d51c11ac5394 https://github.com/galaxyproject/galaxy/commit/bb90ae93d810cd829ef026a3d086d... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M scripts/grt/export.py M scripts/grt/upload.py M test/integration/test_scripts.py
Log Message: ----------- More grt fixes - spotted by @nsoranzo.
Commit: a1f0e1772ec5280a0523f2218008933f768e886e https://github.com/galaxyproject/galaxy/commit/a1f0e1772ec5280a0523f22180089... Author: John Chilton jmchilton@gmail.com Date: 2018-03-23 (Fri, 23 Mar 2018)
Changed paths: M lib/galaxy/util/script.py
Log Message: ----------- Redact help for --config-section option for @nsoranzo.
Kept the string in the file for in-code documentation but hiding it from users.
Commit: 04a901771b59d1fcf8070cd4c4de1f464e304e55 https://github.com/galaxyproject/galaxy/commit/04a901771b59d1fcf8070cd4c4de1... Author: John Chilton jmchilton@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message: ----------- [18.01] Fix SQL query for "workflows shared with me" as part of workflow index.
Before and after queries here:
https://gist.github.com/jmchilton/dc57bca60178341d9ce0f6cf6d4bd36f
You can see that before the joined load of the stored workflow wasn't being registered by SQLalchemy properly and so it was joining that table twice - once using the proper index and another time just walking the whole table. The filter and order by were being applied to the unconditional version - kind of like saying give me all the workflows and the right workflows and I will check all the workflows to see if this one is deleted instead of just the subset of workflows that are actually being shared with the target user.
Commit: ff0f0b611282fb0c4c5742c034f7cef0ec86f475 https://github.com/galaxyproject/galaxy/commit/ff0f0b611282fb0c4c5742c034f7c... Author: John Chilton jmchilton@gmail.com Date: 2018-03-26 (Mon, 26 Mar 2018)
Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py
Log Message: ----------- Fix model operations that produce datasets for 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03
Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB.
Includes test case that fails against 18.01.
Commit: 3876f12e7d3ce7ec73d14ae99f06edae01020412 https://github.com/galaxyproject/galaxy/commit/3876f12e7d3ce7ec73d14ae99f06e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths: M lib/galaxy/tools/actions/model_operations.py M test/api/test_tools.py
Log Message: ----------- Merge pull request #5784 from jmchilton/1801_fix_unzip
[18.01] Fix model operation tools that produce standalone datasets.
Commit: fbb47f6e03d0ca9190e3f665515ba45ac64e14ce https://github.com/galaxyproject/galaxy/commit/fbb47f6e03d0ca9190e3f665515ba... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths: M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/config_schema.yml
Log Message: ----------- Merge pull request #5745 from nsoranzo/release_18.01_fix_config
[18.01] Configuration fixes
Commit: 62d4582ef6913a4c681db2a08369a7757523de42 https://github.com/galaxyproject/galaxy/commit/62d4582ef6913a4c681db2a08369a... Author: John Chilton jmchilton@gmail.com Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths: M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/script.py
Log Message: ----------- Touch up script unification PR based on @natefoo comments.
Commit: d6be56256fcbee53509dc867d863819621ef1d08 https://github.com/galaxyproject/galaxy/commit/d6be56256fcbee53509dc867d8638... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-27 (Tue, 27 Mar 2018)
Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py
Log Message: ----------- Merge pull request #5782 from jmchilton/fix_1801
[18.01] Fix SQL query for "workflows shared with me" as part of workflow index.
Commit: 4d742c3b1316aa808201c5bf3faec2587c345590 https://github.com/galaxyproject/galaxy/commit/4d742c3b1316aa808201c5bf3faec... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M Makefile M client/README.md
Log Message: ----------- Clarify make targets, update client/README
Commit: b960260a3449a23dc35a0f126de41c37276d8cfd https://github.com/galaxyproject/galaxy/commit/b960260a3449a23dc35a0f126de41... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md
Log Message: ----------- Mention the client README specifically in CONTRIBUTING, to make it more obvious.
Commit: d61268cc6d58a5fbecc0399a7fe8087be45d4861 https://github.com/galaxyproject/galaxy/commit/d61268cc6d58a5fbecc0399a7fe80... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md
Log Message: ----------- Articles are important.
Commit: cbd7cb3cbcc93ef9abd651fff0760a91b5624127 https://github.com/galaxyproject/galaxy/commit/cbd7cb3cbcc93ef9abd651fff0760... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md
Log Message: ----------- Reflow text
Commit: 05584244a7a5fb8790c513d6e451ac629b2f2955 https://github.com/galaxyproject/galaxy/commit/05584244a7a5fb8790c513d6e451a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md
Log Message: ----------- Drop old bitbucket/galaxy/galaxy-dist reference.
Commit: c6ae97edaef3a146955731aefe510887f4c8b6d0 https://github.com/galaxyproject/galaxy/commit/c6ae97edaef3a146955731aefe510... Author: Nate Coraor nate@bx.psu.edu Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M lib/galaxy/web/stack/__init__.py
Log Message: ----------- Merge pull request #5774 from nsoranzo/release_18.01_fix_pid
[18.01] Log the pid of the first uWSGI process
Commit: 96d9d0e5a236eb3fc7cf6f6612d82915fa5790e8 https://github.com/galaxyproject/galaxy/commit/96d9d0e5a236eb3fc7cf6f6612d82... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Better re-use of `tool` attribute
Commit: 4f870490f2d289b2921c422ff66e92ee5decb352 https://github.com/galaxyproject/galaxy/commit/4f870490f2d289b2921c422ff66e9... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M lib/galaxy/datatypes/registry.py
Log Message: ----------- Simplify get_datatype_by_extension() method
Commit: 334aea3adc975793d215f1622efc892718ecad75 https://github.com/galaxyproject/galaxy/commit/334aea3adc975793d215f1622efc8... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md
Log Message: ----------- Erase trello from Contributing.
Commit: 7d394d243b7d041ab357a0279e4920ab4a03fe7b https://github.com/galaxyproject/galaxy/commit/7d394d243b7d041ab357a0279e492... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md M client/README.md
Log Message: ----------- Proofreading - thanks @nsoranzo
Commit: d53cbe3538f186da903726ac1d00630e94cfe894 https://github.com/galaxyproject/galaxy/commit/d53cbe3538f186da903726ac1d006... Author: Martin Cech marten@bx.psu.edu Date: 2018-03-28 (Wed, 28 Mar 2018)
Changed paths: M CONTRIBUTING.md M Makefile M client/README.md
Log Message: ----------- Merge pull request #5800 from dannon/client_readme_clarifications
[18.01] Client related readme/makefile clarifications
Commit: 288d13b60681a3729fd38c09b41763b520239317 https://github.com/galaxyproject/galaxy/commit/288d13b60681a3729fd38c09b4176... Author: mvdbeek m.vandenbeek@gmail.com Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- Fix metadata setting for CRAM files
Should fix https://github.com/galaxyproject/galaxy/issues/5801.
Commit: 7e5a90cc1fd5de729e416dd249f92621f883cce8 https://github.com/galaxyproject/galaxy/commit/7e5a90cc1fd5de729e416dd249f92... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/tools/repositories.py
Log Message: ----------- Use app.datatypes_registry in ValidationContext.from_app()
Commit: d5baea1dfc1998bcba5a0083b6b94769455bc247 https://github.com/galaxyproject/galaxy/commit/d5baea1dfc1998bcba5a0083b6b94... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/tools/parameters/basic.py
Log Message: ----------- Handle an empty datatypes_registry
Also transform it to an object attribute for re-use.
Commit: 2c4bf95c3c5416f381cd8aea210f66ffef43498d https://github.com/galaxyproject/galaxy/commit/2c4bf95c3c5416f381cd8aea210f6... Author: John Chilton jmchilton@gmail.com Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py
Log Message: ----------- Merge pull request #5806 from nsoranzo/release_18.01_ValidationContext_fixes
[18.01] Use app.datatypes_registry in ValidationContext.from_app()
Commit: 241fadc98159f206b26938ba5626c1f24b1120c2 https://github.com/galaxyproject/galaxy/commit/241fadc98159f206b26938ba5626c... Author: John Chilton jmchilton@gmail.com Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/datatypes/binary.py
Log Message: ----------- Merge pull request #5805 from mvdbeek/fix_cram_metadata
[18.01] Fix metadata setting for CRAM files
Commit: 009921387dc3f2ea0731e82fe137c7b8d06f7e8a https://github.com/galaxyproject/galaxy/commit/009921387dc3f2ea0731e82fe137c... Author: Martin Cech marten@bx.psu.edu Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M lib/galaxy/config.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py A test/integration/test_scripts.py
Log Message: ----------- Merge pull request #5769 from jmchilton/unify_scripts
[18.01] Fix scripts/ for YAML/ENV configuration processing
Commit: c5095d1634a95ebc3ee3d1108984acbcd746a603 https://github.com/galaxyproject/galaxy/commit/c5095d1634a95ebc3ee3d1108984a... Author: Martin Cech marten@bx.psu.edu Date: 2018-03-29 (Thu, 29 Mar 2018)
Changed paths: M CONTRIBUTING.md M Makefile M client/README.md M config/galaxy.yml.sample M config/reports.yml.sample M config/tool_shed.yml.sample M doc/source/admin/galaxy_options.rst M doc/source/admin/reports_options.rst M lib/galaxy/config.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/registry.py M lib/galaxy/model/orm/scripts.py M lib/galaxy/tools/actions/model_operations.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/repositories.py M lib/galaxy/util/hash_util.py M lib/galaxy/util/script.py M lib/galaxy/web/stack/__init__.py M lib/galaxy/webapps/config_manage.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/config_schema.yml M scripts/cleanup_datasets/admin_cleanup_datasets.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/populate_uuid.py R scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py R scripts/cleanup_datasets/rename_purged_datasets.py M scripts/cleanup_datasets/update_dataset_size.py M scripts/cleanup_datasets/update_metadata.py M scripts/communication/communication_server.py R scripts/data_libraries/build_lucene_index.py R scripts/data_libraries/build_lucene_index.sh R scripts/data_libraries/build_whoosh_index.py R scripts/data_libraries/build_whoosh_index.sh M scripts/db_shell.py M scripts/galaxy-main M scripts/grt/export.py M scripts/grt/grt.yml.sample M scripts/grt/upload.py M scripts/helper.py M scripts/manage_db.py R scripts/others/incorrect_gops_jobs.py R scripts/others/incorrect_gops_jobs.sh R scripts/others/incorrect_gops_join_jobs.py R scripts/others/incorrect_gops_join_jobs.sh M scripts/runtime_stats.py M scripts/secret_decoder_ring.py M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/sync_reports_config.py M scripts/transfer.py M test/api/test_tools.py A test/integration/test_scripts.py
Log Message: ----------- Merge branch 'release_18.01' into usegalaxy
Compare: https://github.com/galaxyproject/galaxy/compare/5d0d66e7289d...c5095d1634a9
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