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326 Commits
Author SHA1 Message Date
Nicola Soranzo 3d57c22b63 Fix I201 errors from flake8-import-order 
Also fix Python3 compatibility.
Remove unused method
galaxy.tools.parameters.sanitize.ToolParameterSanitizer.restore_param() .
 2016-11-23 18:31:04 +00:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Dannon Baker cb6e25278c Refactoring, because it was bugging me. 2016-10-13 10:25:18 -04:00
Dannon Baker bb44288968 Failthrough to using imghdr when PIL does not detect an image correctly. 
Some misc cleanup, avoiding use of system functions as variable names,
etc.
 2016-10-13 09:55:01 -04:00
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
John Chilton d06e2a672b XSD discovered tool problems. 2016-09-08 11:40:01 -04:00
Nicola Soranzo cc336f61c0 Make some files compatible with Python3 
Also enlarge the set of files tested with flake8 under Python3
 2016-06-03 19:24:46 +01:00
Nicola Soranzo 8a43b2b492 Python 3: use "as" instead of comma in except clause 2016-05-17 23:53:16 +01:00
Nicola Soranzo ed4132d9c0 Python3: Use open() instead of file() 2016-05-17 23:53:16 +01:00
Dannon Baker 97110e2655 Merge branch 'release_16.04' into dev 2016-04-20 11:54:22 -04:00
Dannon Baker 1e7edf0bd7 no parens 2016-04-14 16:59:25 -04:00
Dannon Baker 7bed69ba17 Specify Ensembl biomart server in descriptions. 2016-04-14 16:56:47 -04:00
John Chilton 997b53f3ae Implement option to prevent FTP uploads from being deleted on import. 
- Simply set `ftp_upload_purge` to `False` in galaxy.ini to enable this.
 - xref http://dev.list.galaxyproject.org/Data-removal-after-ftp-import-td4667111.html
 - slight xref http://dev.list.galaxyproject.org/Uploading-files-to-galaxy-from-a-folder-td4664614.html
 2016-04-14 11:34:21 -04:00
Martin Cech c49e7803fa fix biomart url 2016-04-13 11:12:15 -04:00
Nicola Soranzo 501a10c3f1 Do not import dumps and loads from galaxy.util.json . 2016-03-02 19:04:24 +00:00
Nicola Soranzo 39da6c3278 Fix the remaining 2180 flake8 errors in tools/ . 2016-02-10 18:46:03 +00:00
Martin Cech db1bb2f191 Merge pull request #1556 from jmchilton/datatype_imports 
Code design and legacy cleanup of datatypes and metadata.
 2016-02-09 12:44:59 -05:00
John Chilton 448aee9f00 Fix for multi-byte char problem in PR #1556... 
... caught by @nsoranzo of course.
 2016-02-08 13:48:43 +00:00
guerler 193c5293d9 Remove invalid validator from upload.xml 2016-01-26 14:49:35 -05:00
John Chilton 499357e508 Remove unneeded galaxy.model import in upload.py... 
... and document the ability to remove from other data sources.
 2016-01-21 14:31:42 +00:00
John Chilton 50e531aa59 Refactor galaxy.datatypes.checkers into galaxy.util.checkers. 
- Primary reason is because it is used all over the place in contexts that have nothing to do with Galaxy datatype classes or datatype registery or sniffing, most importantly by the code in the tool shed for determining if something is a tool or not.
 - This code has no dependencies on the datatypes module or any hard dependencies on things not in the Python standard library.
 2015-12-17 15:41:06 +00:00
John Chilton 83f57c56c1 Refactor is_multi_byte out of galaxy.util. 
It introduces a fairly esoteric dependency in galaxy.util for just a couple uses in Galaxy. Separating it out like this will allow reuse of the entire galaxy.util with only one external dependency (docutils, which planemo for instance already depends on).
 2015-12-16 21:36:16 +00:00
Mark Einon d6d8e5ef86 upload.py: Remove unused function parameter 2015-11-13 11:33:56 +00:00
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Daniel Blankenberg 092fc17ec0 Merge pull request #846 from jmchilton/ucsc_cleanup 
UCSC Tool Cleanup
 2015-10-05 17:05:56 -04:00
Martin Cech f90c49e270 Merge pull request #847 from jmchilton/citations_5 
Add more distribution tool citations.
 2015-10-05 17:01:18 -04:00
John Chilton a6f9e62c1a Add citations to ucsc browser tools. 2015-10-05 15:55:21 +01:00
John Chilton 1aebbc3f68 Remove likely broken UCSC proxy and associated tools. 
Unused for many, many years and likely no longer works.
 2015-10-05 15:55:21 +01:00
Eric Rasche f50702f962 Remove unused echo tool 2015-10-05 15:21:39 +01:00
John Chilton 88239abf5c Add more distribution tool citations. 
xref #361.
 2015-10-05 15:16:50 +01:00
Nicola Soranzo 34d9388456 Use os.pardir everywhere instead of '..' . 2015-07-14 16:20:29 +01:00
Nicola Soranzo 7830bc62e0 Another fix for 3c40f32fa2 . 2015-06-17 19:21:13 +01:00
Nicola Soranzo 3c40f32fa2 PEP-8 and pylint fixes. 2015-06-16 16:53:49 +01:00
John Chilton 884e824d72 Merge remote-tracking branch 'vavrusa/table-datatype' into dev. 
Conflicts:
	lib/galaxy/datatypes/tabular.py
 2015-06-03 10:52:42 -04:00
John Chilton 1a39b6aa79 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-20 15:48:25 -04:00
Daniel Blankenberg af6172d14d Update default dbkey for worm_modencode.xml and bump version. 
ce10 is UCSC for WS220
 2015-05-20 12:42:05 -04:00
Daniel Blankenberg 93c51fa259 Update default dbkey for fly_modencode.xml and bump version. 
dm3 is UCSC for release 5
 2015-05-20 12:39:59 -04:00
Martin Cech 182fbd1bc6 fix the data source tools for modendcode with proper URLs 2015-05-19 16:53:25 -04:00
Nicola Soranzo 22d4a1d8c3 dos2unix of tools/ directory. Some whitespace and PEP-8 fixes. 2015-05-15 12:40:52 +01:00
Marek Vavrusa bc8bdadca8 datatypes: extracted TabularData superclass from Tabular, CSV subclass 2015-04-30 17:20:32 +02:00
peterjc fce2184e5b Make tool version explicit (Job runner would assume 1.0.0) 2015-03-09 15:21:48 +00:00
Dannon Baker 04bd3c77c1 Merged in dan/galaxy-central-prs (pull request #643) 
Add ZebrafishMine Data Source Tool.
 2015-02-02 12:04:23 -05:00
Daniel Blankenberg 538c07cc49 Add ZebrafishMine Data Source Tool. 2015-01-21 14:56:08 -05:00
Bjoern Gruening 5b96f80b48 Add CompressedArchive as datatype and do not uncomress it during upload. 2015-01-12 22:36:20 +01:00
Daniel Blankenberg b022e92f5b Add gemini.sqlite datatype. 2015-01-09 14:48:56 -05:00
Nate Coraor e56943de8c Always access UCSC Main via HTTPS. 2014-09-22 11:31:56 -04:00
John Chilton 4a17892400 Always access EBI SRA via HTTPS. 
Thanks to Ilya for opening pull request to make it conditionally use HTTPS - https://bitbucket.org/galaxy/galaxy-central/pull-request/491/remove-http-from-ebi-url-which-is/diff - but this goes one step further and always uses HTTPS as suggested by Nate in the pull request comments.
 2014-09-22 11:23:02 -04:00
Dannon Baker 9d85ca9e23 Switch to_json_string/from_json_string in galaxy/tools. 2014-09-09 10:06:35 -04:00
Kyle Ellrott 9d67f9c599 Hiding UUID input for upload tool 2014-08-18 16:37:30 -07:00
Kyle Ellrott a2ac71eab9 Enabling UUID in file upload 2014-08-14 17:08:29 -07:00