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6e185fa208c27564b4cd2db5e31f55bf58c6eb4e
Commit Graph
10665 Commits
Author SHA1 Message Date
Christian-B 6e185fa208 Allowed for capitailsed packgae name such as R 2015-11-23 17:05:46 +00:00
Greg Von Kuster a16cb06705 Fix for re-installing an uninstalled TS repository with a dependency 
where both the repository and the dependency were updated in the TS
after the repository was uninstalled.
 2015-11-22 16:50:39 -05:00
Martin Cech 2e510bd5e1 Merge pull request #1113 from jmchilton/format_source_collection 
Allow accessing collection elements in format_source.
 2015-11-21 23:38:39 -05:00
Martin Cech 7bb88b3f44 Merge pull request #1097 from jmchilton/cwl_refactoring 
Small Tool and Workflow Cleanups from CWL Work.
 2015-11-20 12:57:43 -05:00
Dannon Baker 05ed245353 Fix the bad merge :( 2015-11-19 20:48:16 -05:00
Dannon Baker f61ec1c3c0 Merge and rebuild client 2015-11-19 20:34:32 -05:00
Dannon Baker 0fdca7d40a A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). 2015-11-19 20:27:25 -05:00
Dannon Baker 96b17bd856 Merge pull request #1117 from jmchilton/input_hang 
Don't let $input hang cheetah evaluation...
 2015-11-19 17:18:57 -05:00
Eric Rasche 81f842743d Merge pull request #1131 from bgruening/IE_iobio 
Add BAM iobio visualisation as Interactive Environment
 2015-11-19 15:02:37 -06:00
Bjoern Gruening 5188b41790 make travis happy 2015-11-19 20:53:30 +01:00
Bjoern Gruening af36ca6d94 add BAM iobio visualisation as Interactive Environment 2015-11-19 18:58:43 +01:00
Nicola Soranzo d2bab13fa9 Merge pull request #1119 from jmchilton/maxseconds 
Revise and fix waiting for tool tests.
 2015-11-19 10:54:10 +00:00
John Chilton f770128915 Merge pull request #991 from erasche/fix-932 
Fixes #932
 2015-11-18 13:48:34 -05:00
John Chilton e4e44be27b Merge pull request #1004 from jj-umn/uniprotxml_datatype 
UniProtXML datatype
 2015-11-18 13:47:27 -05:00
John Chilton 7fef50f45f Merge pull request #881 from scholtalbers/role-page-fix 
Fix the issue where too many datasets are linked to a certain role
 2015-11-18 13:46:29 -05:00
John Chilton ee2b34c387 Merge pull request #950 from fescudie/dev 
Add BIOM v1 in default datatypes.
 2015-11-18 13:41:02 -05:00
John Chilton 05f3da308d Fix macro bug with empty CDATA being None instead of ''. 
Fixes galaxyproject/planemo#362 thanks for the report @erasche.

Test using the following command:

```
nosetests test/unit/tools/test_tool_loader.py
```
 2015-11-18 12:25:38 +00:00
John Chilton b25b8c3f24 Revise and fix waiting for tool tests. 
- maxseconds on test tag stopped being respected at some point, fix that.
- maxseconds on test tag stopped being parsed at some later point, fix that.
- Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT.
- Add test case to ensure there is no future regression of these behaviors.
 2015-11-18 11:22:40 +00:00
John Chilton 0ff8a21891 Add example tools demonstrating cheetah problem (unbound variable). 
Refine default override of input to raise an exception instead of just throwing in a dummy string.
 2015-11-18 10:40:57 +00:00
John Chilton 704144c169 Don't let $input hang cheetah evaluation... 
If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation.
 2015-11-18 10:20:23 +00:00
Nicola Soranzo c252987b4c Merge branch 'master' into dev 2015-11-18 10:15:22 +00:00
Nicola Soranzo 73f46f4e08 Merge branch 'release_15.07' into release_15.10 2015-11-18 10:06:53 +00:00
Martin Cech 729ed463aa Merge pull request #1108 from yhoogstrate/cram_datatype 
CRAM datatype definiton
 2015-11-17 16:27:22 -05:00
Dannon Baker 1063c175be Merge pull request #1114 from jmchilton/sync_more 
Give writing job script more time to flush and sync during verification.
 2015-11-17 15:36:52 -05:00
Dannon Baker e6d651be32 Merge pull request #1091 from natefoo/webob-string-to-none 
Fix bug with referer attribute type change in WebOb
 2015-11-17 15:17:29 -05:00
Nate Coraor d5fe49ec6f Incorporate @nsoranzo's suggestions 2015-11-17 12:50:20 -05:00
Nate Coraor d8152f3336 Merge branch 'release_15.10' into dev 2015-11-17 11:37:05 -05:00
John Chilton 7018753bc9 Give writing job script more time to flush and sync during verification. 
Still having occasional failures - https://jenkins.galaxyproject.org/job/docker-api/1172/testReport/junit/api.test_tools/ToolsTestCase/test_multirun_non_data_parameter/.
 2015-11-17 15:18:50 +00:00
John Chilton 0030f4c549 API test fix from @nsoranzo. 2015-11-17 15:13:49 +00:00
John Chilton 312746d169 Allow accessing collection elements in format_source. 
Can do it by numeric index or element name, e.g. input[0] or input["forward"]. Only works for 1-D collections.

Implements #699.

Run new and most relevant existing tests with the following commands:

```
nosetests test/unit/tools/test_actions.py
./run_tests.sh -framework -id output_format_collection
./run_tests.sh -framework -id output_format
```
 2015-11-17 14:13:14 +00:00
youri 3df95ae9a6 flake8 2015-11-16 23:09:44 +01:00
youri d40d384a86 CRAM format 2015-11-16 22:57:02 +01:00
Lance Parsons a610dc59a8 Better error when tool shed repo dir missing 
Check for a tool shed repository directory and throw exception if it's
missing. This avoids a cryptic NoneType error when searching for
tool_dependencies.xml file and directory was not found.
 2015-11-16 16:12:20 -05:00
Nicola Soranzo 040118aae3 Encode unicode string before passing to hashlib.sha1(). Fixes #673. 2015-11-16 19:58:56 +00:00
Martin Cech cfe45d8e0c Merge pull request #1095 from bgruening/ts_api_fail_if_installed 
Don't fail if a repository is already installed
 2015-11-15 22:31:14 -05:00
Björn Grüning 937f99b851 Fix API installation of tool_dependencies 
This should fix an installation issue with tool_dependencies via the API.
Tool dependency repositories to not have any tools specified and with this no metadata associated.

It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d4488437ffef9e5acf
So I think this should be part of 15.10.

Thanks to Greg for fixing this one.
 2015-11-15 22:28:18 -05:00
Martin Cech a26526b085 Merge pull request #1094 from bgruening/fix_api_ts_installation 
Fix api TS installation
 2015-11-15 22:27:13 -05:00
John Chilton 0b070f406c Add app property to workflow contents manager. 
Most other managers already have this.
 2015-11-15 20:33:13 +00:00
John Chilton 8189fb450b Add tool version to workflow extract. 2015-11-15 20:33:05 +00:00
John Chilton f629cbdb6a Refactor tool parsing, parse id first. 
Small refactoring cleans up downstream diff for dynamic tool branch.
 2015-11-15 20:32:56 +00:00
Björn Grüning 7e67368424 Don't fail if a repository is already installed 
If an repository is already installed `installed_tool_shed_repositories` is None and this does not work with map.
 2015-11-15 00:33:53 +01:00
Björn Grüning 1aecca7889 Fix API installation of tool_dependencies 
This should fix an installation issue with tool_dependencies via the API.
Tool dependency repositories to not have any tools specified and with this no metadata associated.

It was broken in https://github.com/galaxyproject/galaxy/commit/bb6a784f13ff3f91762244d4488437ffef9e5acf
So I think this should be part of 15.10.

Thanks to Greg for fixing this one.
 2015-11-14 23:56:19 +01:00
Dave B 75e7e4c2cf Fix 500 error when attempting to update installed repository. 2015-11-14 17:09:21 -05:00
Martin Cech 3ba139fe1b Merge pull request #1082 from davebx/hg_middleware 
Fix 500 error when attempting to update installed repository.
 2015-11-14 16:40:39 -05:00
Nate Coraor 638e36f51d Newer versions of WebOb set None in referer, older versions set an empty 
string. Handle cases where it is assumed to be a string.

I checked all other trans.request attributes to find other cases where
this might crop up and didn't find any.
 2015-11-14 01:46:20 -05:00
Dave B 87f35ea975 Use preexisting library to parse query string. 2015-11-13 14:37:44 -05:00
Dave B 321b64d8dc Ensure that invalid parameters don't break things. 2015-11-13 12:44:35 -05:00
Dave B 7c45bf13fa Fix 500 error when attempting to update installed repository. 2015-11-13 11:50:22 -05:00
Martin Cech 2dcb92aa0e Merge pull request #942 from davebx/docker 
Enable dockerized toolshed tests.
 2015-11-13 11:26:24 -05:00
Nate Coraor d824cca31f In interactive environments, the /import volume can now be made 
conditional. Also, fix a bug when using a proxy for the node proxy and
cookie_path is /
 2015-11-12 16:56:16 -05:00