Martin Cech
49560155dc
missing import
2014-09-02 15:46:24 -04:00
Carl Eberhard
a96e50b9a3
Test fixes for 5ce55f9; correct spaceghost.stderr to use system.stderr (thanks, John); correct api-workflow-tests (which I completely forgot *I* had made) and add test-data
2014-09-02 15:35:56 -04:00
Nate Coraor
824f66e080
Make it possible to load dynamic job runner rules from somewhere other than galaxy.jobs.rules.
2014-09-02 15:30:57 -04:00
Carl Eberhard
cabe8ed425
History API: remove set_as_current, api/histories/current, and POST api/histories with current == True (create new current history), replace with controllers/history/set_as_current, current_history_json, and create_new_current (respectively) - all returning json; add exceptions.DeprecatedMethod; pack scripts
2014-09-02 13:26:47 -04:00
Daniel Blankenberg
8ccf8287b4
Quote commandline arguments for extract genomic DNA tool.
2014-09-02 13:15:17 -04:00
Daniel Blankenberg
f20731c466
Fix for custom dbkeys when chrom count dataset has been deleted.
2014-09-02 12:50:37 -04:00
John Chilton
e7b0801f8d
Small improvements to JavaScript testing with run_tests.sh.
...
Add new -j|--casperjs option to run through the casperjs test suite. Ensure grunt is on path before attempting to run qunit tests. A more useful version of this changeset which automatically installed phantomjs, casperjs, grunt, and npm as needed and added the required tools to the tester's path (https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/0919fc9403933f88e458724b95b0d213117bbd0e ) proved unpopular because of implementation details - see conversation here https://bitbucket.org/galaxy/galaxy-central/pull-request/461/remove-deprecated-test-scripts-improved/diff .
2014-09-02 12:35:33 -04:00
John Chilton
8fb1a04b8e
Fixup comments and add README for test/casperjs directory.
2014-09-02 11:50:43 -04:00
John Chilton
b0c378bea4
Remove deprecated test running scripts.
...
- run_functional_tests.sh can be replaced with the backward compatible run_tests.sh.
- run_unit_tests.sh can be replaced with `run_tests.sh --unit` (or just -u)
- run_tool_shed_functional_tests.sh can be replaced with `./run_tests.sh -toolshed` (or just -t).
In each case run_tests.sh provides better documentation and superior argument parsing.
2014-09-02 11:50:43 -04:00
Martin Cech
f1ab7e05e8
next chunk of API managers - libs, folders, roles
2014-09-02 10:37:14 -04:00
Dannon Baker
fd53ed075d
Pack scripts.
2014-09-02 09:29:50 -04:00
John Chilton
e8b7272aa8
Merge latest stable changes.
2014-09-02 08:54:56 -04:00
Jeremy Goecks
0c75a102d0
HDA/LDDA models: synchronize them with 'data_type' and 'file_ext', properly fill data_type with Galaxy data types, and use file_ext in place of data_type throughput client code.
2014-08-29 17:17:44 -04:00
Dave Bouvier
db416f2a91
Correct path to original tool XML file in the event a temporary XML file had been generated.
2014-08-29 15:29:46 -04:00
Dave Bouvier
277d563e06
Merge with -central.
2014-08-29 15:22:08 -04:00
Dave Bouvier
ffbf0c3963
Find and add tool help images to the tarball. Delete any temporary files that were generated.
2014-08-29 15:21:30 -04:00
Nate Coraor
7a5fed6208
Update tag latest_2014.08.11 for changeset ea12550fbc34
2014-08-29 14:00:23 -04:00
Carl Eberhard
b8b1c4e36f
History contents: allow copying accessible datasets into this history
2014-08-29 10:43:51 -04:00
Dannon Baker
d3a50e2923
Merged in jmchilton/galaxy-central-fork-1/stable (pull request #479 )
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[STABLE] More collection-y workflow fixes.
2014-08-29 09:44:47 -04:00
Nate Coraor
d7b218b6ff
Update tag latest_2014.08.11 for changeset 0047ee06fef0
2014-08-29 09:00:25 -04:00
John Chilton
b78d059f4c
Pack scripts.
2014-08-29 00:31:59 -04:00
John Chilton
2641d8e552
Don't persist literal string '<DummyDataset...>' when updating tool state in workflow editor.
...
Doesn't seem to actually break the workflows because Galaxy tries to assign the value to the parameter afterward - fails and assigns it to None anyway and then connects up everything - but it does cause the workflow editor to pop-up an annoying warning about this value change.
2014-08-29 00:30:30 -04:00
John Chilton
d80d1b1a8f
Fix for at workflow editor glitch.
2014-08-29 00:30:30 -04:00
John Chilton
0aef022bb0
Merged in dannon/galaxy-central-prmaker/stable (pull request #478 )
...
[STABLE] Remove option for the (long since deprecated in favor of Data Managers) data_admin interface from admin
2014-08-29 00:27:45 -04:00
Dannon Baker
284edd5d62
Merge.
2014-08-28 17:21:42 -04:00
Dannon Baker
facac09e2e
Remove option for the (long since deprecated in favor of Data Managers) data_admin interface from admin
2014-08-28 17:21:03 -04:00
Dannon Baker
26d01cc464
Remove option for the (long since deprecated in favor of Data Managers) data_admin interface from admin
2014-08-28 17:21:03 -04:00
Carl Eberhard
8b1af7ece5
Fix to history: remove prev. loading indicator before showing another
2014-08-28 16:51:28 -04:00
Aysam Guerler
34e146b33d
ToolForm: Adds limits for repeat blocks and fixes
2014-08-28 16:35:59 -04:00
Dave Bouvier
e14fad2db7
Merge with -central tip.
2014-08-28 14:44:29 -04:00
Dave Bouvier
73113b826c
Add externally referenced files to the tool tarball. Code cleanup and error checking.
2014-08-28 14:43:55 -04:00
Aysam Guerler
5980c1e467
ToolForm: Enables hierarchical references and conversion of the tool form into a json/xml tree structure
2014-08-28 14:03:35 -04:00
Nate Coraor
7f927e54eb
Update tag latest_2014.08.11 for changeset a6cfe95047eb
2014-08-28 14:00:16 -04:00
Dave Bouvier
985f04a019
Merge tip.
2014-08-28 12:39:12 -04:00
Carl Eberhard
17a6595b5c
Fix: remove 'jquery.event.drag.js' from base_panels.mako; Paired collection creator: allow single/multiple pairs to be re-ordered by drag and drop
2014-08-28 12:19:16 -04:00
Nate Coraor
e24df033be
Merge stable.
2014-08-28 11:35:36 -04:00
Martin Cech
5f9a741889
library permissions API - check whether payload is present in the kwd and throw exception if it is not, also bugfix
2014-08-28 11:01:32 -04:00
Martin Cech
3446cda5b6
no need to expose the method through API anymore
2014-08-28 10:57:30 -04:00
Martin Cech
3c5d4734ee
allowing backward compatibility on setting library permissions API as per John's suggestion
2014-08-28 10:54:13 -04:00
Nicola Soranzo
09f1589ea4
Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
...
Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a
machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not
decompressed.
In fact, the sqlite3 command 'pragma schema_version' on any file returns
without error on this SQLite version.
2014-08-28 15:09:10 +02:00
Nicola Soranzo
df44527af2
Fix SQlite datatype sniffing for old sqlite3. Remove unused imports.
...
Bug fixed: when uploading a gzipped FASTQ file through upload1 tool on a
machine with SQLite 3.3.6, it was detected as 'sqlite' datatype and not
decompressed.
In fact, the sqlite3 command 'pragma schema_version' on any file returns
without error on this SQLite version.
2014-08-28 15:09:10 +02:00
Carl Eberhard
0690b2b9f7
Fix to df2a994: remove debuggging statements
2014-08-28 09:49:00 -04:00
Carl Eberhard
7017833f42
Vis registry: add two tests (has_attribute, not_eq); add see also for test types in visualization.dtd; correct applicability tests for trackster and circster using not_eq on datatype.track_type
2014-08-28 09:44:56 -04:00
Nate Coraor
bfb4688213
Update tag latest_2014.08.11 for changeset 109b170188e9
2014-08-28 09:00:13 -04:00
John Chilton
7543a567f2
Add workflow test demonstrating failure when multiple lists with different identifiers are using in workflows.
2014-08-27 16:32:26 -04:00
John Chilton
9b4ca59ff2
Remove workflow test that accidently depended on tool not in -central.
...
Opps.
2014-08-27 16:32:26 -04:00
John Chilton
401fad5e25
Add some more basic test tools for building simple workflows for testing.
2014-08-27 16:32:26 -04:00
John Chilton
565580a564
Update readme for functional test tools directory.
2014-08-27 16:32:26 -04:00
Dave Bouvier
cf419552da
Add feature to download a tarball containing tool XML, tool wrapper script, test inputs and outputs, and tool data table definitions + sample .loc file.
2014-08-27 14:55:43 -04:00
Carl Eberhard
fb5a6afa97
UI, Paired collection creator: fixes and refactoring, allow pairs to be selected
2014-08-27 14:47:54 -04:00
Martin Cech