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Author SHA1 Message Date
Björn Grüning ea2bac8a12 yes, the name is tool not tools :( 2018-02-14 15:20:02 +01:00
John Chilton d5687bc418 PEP8 fixes. 2018-02-14 08:27:55 -05:00
Bjoern Gruening d7de19b072 fix toolbox filters 2018-02-13 23:28:24 +01:00
Martin Cech ed23cc652d Merge pull request #5514 from jmchilton/optimize_public_grids 
[18.01] Optimize public grid database interactions.
 2018-02-13 16:29:54 -05:00
Martin Cech fd1ac05cdf Merge pull request #5515 from jmchilton/optimize_workflow_list 
[18.01] Optimize database interaction for user workflow list.
 2018-02-13 15:15:04 -05:00
John Chilton 80a41f3274 Optimize public grid database interactions. 
For all four grid types (histories, viz, workflows, and pages), this computes rating average on the server and prefetches any annotations. This eliminates at least two extra queries for response element in the grid. See comment in the history controller for why I am fairly confident this is a good idea for annotations but tags are less obvious - these grids still go back to the postgres server multiple times per rendered item to render tags.

I'm confident we should either subqueryload, joinedload, or upgrade to sqlalchemy 2.2 and selectinload (http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalchemy.orm.selectinload) the tags as well - but I'm not sure which without being able to hack on a usegalaxy.org.

This also brings in less of the user model (only username instead of all of it) to reduce over-the-wire transmission of unneeded data from postgres to Galaxy.

For workflows we were LEFT OUTER JOIN-ing on the steps of the latest workflow - so we were bringing back a lot of extra rows for data that was completely unused. In light of this, it makes perfect sense to me why published workflows were the slowest of these and I suspect they will all be equally performant after this change (modulo the number of rows in the tables and the number of rows rendered).
 2018-02-13 14:29:29 -05:00
John Chilton e73731f552 Optimize database interaction for user workflow list. 
Don't LEFT OUTER JOIN workflow against its steps to produce step count - this causes a lot of duplicated workflow data and fetches step data not needed to just produce a step count.

Tweak pre-fetching for workflows shared with user also.
 2018-02-13 11:53:10 -05:00
John Chilton 321cd78ad8 Merge pull request #5512 from mvdbeek/fix_new_pysam 
[18.01] Make galaxy compatible with pysam 0.14
 2018-02-13 11:22:04 -05:00
mvdbeek 3b8a2f9edc Pin pysam to 0.14 2018-02-13 15:22:51 +01:00
mvdbeek 349b25b74a Minimize duplication of BAM set_meta code 2018-02-13 11:49:10 +01:00
Nate Coraor aefe0e1449 Merge pull request #5510 from martenson/ts-deny-codefile 
[18.01] do not allow codefiles for TS tool loading
 2018-02-12 16:46:11 -05:00
mvdbeek b87d57aac7 Make galaxy compatible with pysam 0.14 2018-02-12 22:03:49 +01:00
Martin Cech ba3b3d5c18 do not allow codefiles for TS tool loading 2018-02-12 14:06:50 -05:00
Björn Grüning c5568a7b1a Merge pull request #5467 from dannon/workflow_sharing_link_fixes 
[18.01] Workflow sharing link fixes
 2018-02-11 11:49:55 +01:00
Dannon Baker d91078024b Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone 
[18.01] Fix common_startup.sh for galaxy tarballs
 2018-02-08 13:20:46 -05:00
Dave B 3f50b45a4e Merge pull request #5445 from gregvonkuster/add-ideaspre 
[18.01] Add support for the ideaspre datatype
 2018-02-08 13:11:10 -05:00
Nicola Soranzo eba3fb4b35 Fix common_startup.sh for galaxy tarballs 
Do not assume git is installed and the `.git` directory is present.

Fix https://github.com/galaxyproject/galaxy/issues/5466
 2018-02-08 11:52:24 -05:00
Nate Coraor 977bbf1481 Install node and yarn in common_startup.sh using nodeenv and the venv's 
npm.
 2018-02-08 11:33:55 -05:00
Nate Coraor b463be78a5 Add nodeenv to dev requirements 2018-02-08 11:33:35 -05:00
John Chilton 64e4e8b572 Merge pull request #5482 from mvdbeek/bam_recursion_bug 
[18.01] Fix recursion bug in BamNative datatype
 2018-02-08 08:14:48 -05:00
John Chilton e9ed97f533 Merge pull request #5485 from scholtalbers/fix/#5484_rename_post_actions 
[18.01] Fix #5484
 2018-02-08 08:11:51 -05:00
Jelle Scholtalbers db069198af fix #5484 2018-02-08 10:42:31 +01:00
Marius van den Beek 8b0e3bd28f Fix recursion bug in BamNative datatype 
We introduced this in
https://github.com/galaxyproject/galaxy/pull/5180/ where we moved a lot
of code form the Bam class into the BamNative class.

Reported by @natefoo
 2018-02-07 23:00:44 +01:00
Dannon Baker 62540a9747 Merge pull request #5470 from natefoo/revert-5036 
[18.01] Revert #5036
 2018-02-07 14:49:06 -05:00
Nate Coraor 11ec4ee93d Revert "Try next dep. resolver if building env failed" 
This reverts commit e821d469e6.
 2018-02-07 13:16:18 -05:00
Nate Coraor 04e4da0d31 Revert "Avoid duplicate dependency installation" 
This reverts commit c0cf41a15c.
 2018-02-07 13:16:11 -05:00
Dannon Baker 9df2813524 Fix more workflow sharing broken links 2018-02-07 12:45:40 -05:00
Dannon Baker 7feef3dc0e Fix "Go back to workflows list" link on workflow sharing interface. 2018-02-07 12:45:40 -05:00
Nate Coraor c2abd3f813 Merge pull request #5395 from martenson/production-1801 
[18.01] Build production client
 2018-02-05 16:49:09 -05:00
Dannon Baker c3ada7f169 Merge pull request #5460 from jmchilton/fix_oom_parse 
[18.01] Fix tool stdio level parsing for OOM level.
 2018-02-05 15:04:30 -05:00
Martin Cech d537b2ac60 build client for release with maps 2018-02-05 14:28:03 -05:00
Dannon Baker f0a8243f7d Client-format post-merge 2018-02-05 13:06:29 -05:00
Dannon Baker 0704d63d0b Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01 2018-02-05 13:06:01 -05:00
John Chilton 2f020ef944 Fix tool stdio level parsing for OOM level. 
Backend was enhanced to allow this in #5196 and a new entry point to setting exit code for such exit conditions but the custom parsing wasn't updated to allow it. Thanks to @nsoranzo for the catch.
 2018-02-05 12:18:22 -05:00
Dannon Baker 2cb3af5d60 Merge pull request #5447 from natefoo/server-name-fix 
[18.01] Fix server_name when config is a dict
 2018-02-05 10:43:03 -05:00
Martin Cech b28fb7e4d7 change the history icon-btn selector to work with dropdowns 2018-02-04 20:10:36 -05:00
Dannon Baker 207f5faba0 Merge pull request #5449 from jmchilton/collection_mapping_fixes 
[18.01] Collection mapping fixes for regression in 18.01.
 2018-02-04 11:52:33 -05:00
John Chilton b2e8d891b7 Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable 
Fix setting job failure exception
 2018-02-03 15:01:17 -05:00
John Chilton 51e030f4f3 Bring in @mvdbeek's test cases from #5431. 2018-02-03 14:59:30 -05:00
John Chilton f99299f833 Pre-compute more collection state during mapping. 
Still dealing with fallout from 78babab645. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping.
 2018-02-03 14:59:30 -05:00
mvdbeek 7bbc46658a Fix setting job failure exception 
This can happen when the job's tool is unavailble and
outputs_to_working_directory is activated.
Fixes https://github.com/galaxyproject/galaxy/issues/5424.
 2018-02-03 18:09:57 +01:00
Martin Cech 1bd8c4fd26 Merge pull request #5455 from jmchilton/backport_flakey 
[18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests
 2018-02-03 11:45:16 -05:00
Nicola Soranzo 935b8c948c Add --skip_flakey_fails flag to CI script for API tests 
xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551
and following comments.
 2018-02-03 08:11:46 -05:00
Marius van den Beek 5aed347c30 Merge pull request #5418 from jmchilton/collection_pja 
[18.01] Implement more intuitive collection PJA
 2018-02-03 09:55:24 +01:00
Nate Coraor dac1ba5812 Fix failing integration tests for workflow handlers. 2018-02-02 15:40:22 -05:00
Martin Cech 3512096a14 remove unused classes and aria 2018-02-02 13:53:26 -05:00
Martin Cech 8019afb8b5 fix typo 2018-02-02 13:34:17 -05:00
Martin Cech 55b6d601a8 add empty href to links so the cursor is right 2018-02-02 13:32:56 -05:00
John Chilton 8e32e93d6d Implement more collection workflow post job actions. 
Implement hide, delete, add tag, and remove tag for output collections and mapped over collections.

Fixes https://github.com/galaxyproject/galaxy/issues/1680.
 2018-02-02 13:29:57 -05:00
greg 3fdd4edc5c Subclass IdeasPre from Html 2018-02-02 13:07:52 -05:00