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Author SHA1 Message Date
Nicola Soranzo 3cf84ea3da Merge branch 'release_18.01' into dev 2018-02-20 11:05:31 +00:00
Martin Cech 6a3ce34c09 Merge pull request #5443 from jmchilton/fix5117 
[18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection.
 2018-02-19 19:14:57 -05:00
Dannon Baker 49a8a317e8 Merge pull request #5567 from jmchilton/casperjs_remove 
Remove defunct casperjs tests.
 2018-02-19 17:58:20 -05:00
John Chilton af7b0ab1b6 Merge pull request #5556 from nsoranzo/release_18.01_fix_5486 
[18.01] Allow LDAP options not starting with OPT_
 2018-02-19 15:57:22 -05:00
John Chilton 0b516b67e9 Remove defunct casperjs tests. 
Tests not converted are tracked on #3853.
 2018-02-19 15:45:43 -05:00
Martin Cech 0c7dcc37c9 Merge pull request #5539 from jmchilton/per_request_sql_debugging 
Add middleware and instrumentation to allow per-request SQL debugging.
 2018-02-19 15:26:16 -05:00
Dannon Baker e7f7d5e29a Merge pull request #5558 from jmchilton/deletion_cleanup_1 
[18.01] Do not reload page when deleting collections.
 2018-02-19 12:35:34 -05:00
Martin Cech ca7cbaf2bf Merge pull request #5553 from nekrut/fasta_gz 
added fasta.gz
 2018-02-19 12:24:48 -05:00
Martin Cech 55a405f18a fix more fasta copypasta 2018-02-19 10:01:25 -05:00
Martin Cech 6359262b3c fix copypasta 2018-02-19 10:00:49 -05:00
nekrut 4390cd4142 fixed name of fastagz->fasta converter 2018-02-19 09:49:14 -05:00
John Chilton d964d594a5 [18.01] Do not reload page when deleting collections. 
Fixes #5499 reported by @mvdbeek (thanks for catching that).
 2018-02-19 08:57:51 -05:00
Nicola Soranzo 5e6a2572f8 Allow LDAP options not starting with OPT_ 
Fix https://github.com/galaxyproject/galaxy/issues/5486
 2018-02-19 11:15:05 +00:00
John Chilton b84da7a07a Allow per-request SQL debugging via URL parameter. 
This has been super helpful in debugging the SQL generated by Galaxy for recent PRs.

To use this simply enable the middleware, use your browser's network logger to find the URL of interest, copy the URL into the browser address bar and add ``?debug_sql=1`` to it. You will then see the sql in the logs only for that request and for every statement in that request.

Simply turning all logging on results in a deluge of logging I've never been able to grok and that is very hard to ping to particular request. Slow request logging is great but it doesn't make this kind of per-query full profile of the SQL generated as easy as this approach and isn't great at debugging performance problems when the result from a large number of small requests (you'd have to set a very low threshold to make sure you are logging every query and then it is no different from the full log).
 2018-02-18 13:37:19 -05:00
John Chilton a5bea5f885 Merge pull request #5448 from dannon/multidelete_fix_and_refactor 
History contents refactoring
 2018-02-18 13:30:34 -05:00
John Chilton f6ac13568f Don't fail rest of multi-action queue when attempting to purge a collection. 
Fixes https://github.com/galaxyproject/galaxy/issues/5117.
 2018-02-18 13:28:36 -05:00
nekrut 84e818577a removing stray whitespace 2018-02-16 15:55:35 -05:00
nekrut 0c2c9ba49e fixed flake8 errors 2018-02-16 15:03:42 -05:00
Nicola Soranzo 788934c3aa Merge branch 'release_18.01' into dev 
Conflicts:
	config/reports.yml.sample
	config/tool_shed.yml.sample
 2018-02-16 18:59:00 +00:00
nekrut 19eee525a1 added fasta.gz 2018-02-16 13:57:51 -05:00
Nicola Soranzo 0d029b39ac Merge branch 'release_17.09' into release_18.01 2018-02-16 18:48:56 +00:00
Nicola Soranzo 13e72e84c5 Merge pull request #5534 from natefoo/17.09-static-map-fix 
[17.09] Map static content by default for Reports and Tool Shed webapps
 2018-02-16 18:19:00 +00:00
Dannon Baker 5488cf29ea Merge pull request #5552 from davebx/18.01 
[18.01] Close tempfile handles.
 2018-02-16 10:22:12 -05:00
Dave B fa93d4e04b Close tempfile handles. 2018-02-16 09:41:27 -05:00
Nicola Soranzo c9c2e968da Merge pull request #5548 from bernt-matthias/topic/fix-obo-link 
fixed stale link
 2018-02-16 11:55:47 +00:00
Matthias Bernt d30811eea3 fixed stale link 2018-02-16 10:48:44 +00:00
Martin Cech f7b505e68d Merge branch 'release_18.01' into dev 2018-02-15 15:55:47 -05:00
Dannon Baker 6b0e20a7a9 Merge pull request #5526 from bgruening/user_filter 
[18.01] fix toolbox filters
 2018-02-15 15:26:15 -05:00
Dannon Baker a54681e8c6 Merge pull request #5334 from natefoo/doc-versioning 
Documentation version selection
 2018-02-15 14:38:16 -05:00
anup kumar a269a95cf0 Fix the bug 2018-02-15 14:25:36 -05:00
Martin Cech 92826fe5e7 Merge pull request #5531 from bgruening/bugfix_#5522 
Fix search overlay JS errors
 2018-02-15 14:24:41 -05:00
Nuwan Goonasekera 8c941ae35a Fix for: https://github.com/galaxyproject/galaxy/issues/5527 2018-02-15 13:28:48 -05:00
Martin Cech 298ef7ee19 Merge pull request #5528 from gvlproject/genomespace_18.01_bugfix 
Fix for GenomeSpace importer/exporter
 2018-02-15 13:27:17 -05:00
Martin Cech 78ee5f8451 Merge pull request #5450 from jmchilton/collection_mapping_cleanup 
Remove unused mapping code.
 2018-02-15 13:08:40 -05:00
Martin Cech 42c12c5188 Merge pull request #5533 from jmchilton/history_list_opts 
[18.01] Improve performance bugs and misleading summary info in history list.
 2018-02-15 13:06:55 -05:00
Nate Coraor 1ccd55a500 Merge pull request #5535 from jmchilton/pulsar_error_handling_1 
[18.01] Fix missing job stdout/stderr on Pulsar transfer failures.
 2018-02-15 12:18:19 -05:00
Dannon Baker 41a3196754 Merge pull request #5506 from davebx/close_temp_files 
Close tempfile handles.
 2018-02-15 11:10:38 -05:00
Dannon Baker a35d5a535e Merge pull request #5538 from jmchilton/rev_sqlalchemy 
Rev SQLAlchemy from 1.0.15 to 1.2.2.
 2018-02-15 10:59:36 -05:00
Martin Cech 755fb9fb21 style changes for history lists 
* include title for all state indicators
* shorten title
* change style of deleted indicator
* comment out unused less variables
 2018-02-15 10:35:19 -05:00
John Chilton 296af58c3d Merge pull request #5542 from martenson/optimize-nonadmin-nonanon-datalibs 
[18.01] optimize nonadmin and nonanon library list permission queries
 2018-02-15 10:13:30 -05:00
Martin Cech aed2b4a239 remove unused import 2018-02-15 10:07:52 -05:00
Martin Cech 7457ce426f optimize nonadmin and nonanon library list permission queries 
Before, the code would emit extra queries per each library to
find out whether the current user has permissions on it.
By pre-fetching all of them in one query and passing around as
 a dict object we should see a considerable speedup on Galaxies
with many libraries.
 2018-02-14 19:38:13 -05:00
John Chilton 99e1305c53 Rev SQLAlchemy from 1.0.15 to 1.2.2. 
It'd be nice to use [selectinload](http://docs.sqlalchemy.org/en/latest/orm/loading_relationships.html#sqlalchemy.orm.selectinload) when optimizing postgres calls.

xref https://github.com/galaxyproject/starforge/pull/191
 2018-02-14 15:17:23 -05:00
John Chilton 3de8593e19 Merge pull request #5540 from jmchilton/dev_merge_0 
Merge release_18.01 into dev.
 2018-02-14 15:16:07 -05:00
John Chilton 043fe35e95 Merge remote-tracking branch 'jmchilton/release_18.01' into dev_merge_0 2018-02-14 15:13:18 -05:00
Dannon Baker 0b137669d7 Merge pull request #5505 from guerler/revise_charts_ui 
Integration of charts into the generic visualization framework
 2018-02-14 14:06:15 -05:00
John Chilton 283ab0459f Improve performance bugs and misleading summary info in history list. 
Prefetch shared user information as counts instead of objects and do so in initial query to eliminate an extra 15 SQL queries per page and load less data related to sharing.

Replace columns that would cause HDA information to be joined into the query (history size and HDA state counts) with a spinner that will be fetched in subsequent queries on the client end. There can hundreds of thousands of datasets per history - this information shouldn't be summarized to get the initial page to render - it can be fetched one history at a time once the page is rendered.

This commit also adds a new column "Items" that corresponds to the next HID - and that I think is a good summary of the "history size" before the dataset state information is loaded and even gives additional information because that count includes collections. This also renders state information for deleted and hidden datasets that was previously missing and could cause confusion. That said I don't like the dataset summaries - I'd rather just have the item count and then job state summaries.
 2018-02-14 13:21:10 -05:00
Nicola Soranzo c20b68a5dd Merge pull request #5532 from mvdbeek/bam_native_converter_fix 
[18.01] Use profile="18.01" for BamNative converters
 2018-02-14 16:49:40 +00:00
John Chilton 7120739230 [18.01] Fix missing job stdout/stderr on Pulsar transfer failures. 
Shouldn't break backward compatiblity at all without it - but to get the outputs Pulsar requires an update (https://github.com/galaxyproject/pulsar/pull/159) as well.
 2018-02-14 11:30:03 -05:00
Nate Coraor 25952e81e7 Map static content by default for Reports and Tool Shed webapps. 2018-02-14 11:12:40 -05:00