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53 Commits
Author SHA1 Message Date
Nicola Soranzo 14259b11d9 Python3: finish first pass on whole codebase 2017-12-14 12:01:01 +00:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nuwan Goonasekera 52b26f45a2 Registered genomespace_importer as a tool needing Galaxy's python env 2017-08-19 00:38:08 +05:30
Nuwan Goonasekera 3e8bf3c4e7 Moved genomespace token to environment variable 2017-08-19 00:38:08 +05:30
Nuwan Goonasekera 46dc4a252c Fixed template formatting according to review comments 2017-08-19 00:38:08 +05:30
Nuwan Goonasekera b73e21b584 Formatting and linting fixes for GenomeSpace tool 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera 517fd23fc8 Fixed typo in exporter help text 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera 678d575a7a Improved recognition of compressed files 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera 46c04dcbd4 Fix incorrect reference when determining file type through file ext 2017-08-19 00:38:07 +05:30
Nuwan Goonasekera cb1b086324 Fixed pylint errors 2017-08-19 00:38:07 +05:30
slugger70 b04ccbe55b Fixed genomespace_importer.xml command block 2017-08-19 00:38:06 +05:30
Nuwan Goonasekera ad1b613445 Added support for pushing multiple files from GenomeSpace to Galaxy. 2017-08-19 00:38:06 +05:30
Nuwan Goonasekera e39901ef06 Moved back some code to wrapper and added back data type sniffing. 2017-08-19 00:38:06 +05:30
Nuwan Goonasekera 1342c2bd70 Integrated File Browsing and Workflow support for GenomeSpace 2017-08-19 00:38:06 +05:30
Nicola Soranzo a353b2e88f Fix E127 errors introduced by previous commit 
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
Dannon Baker c9ac723174 Revert genomespace tool changes related to FILENAME_VALID_CHARS 2016-08-11 11:01:20 -04:00
Dannon Baker f87b08efa0 Consolidate usage of 'valid_chars' in the application. 2016-08-05 13:57:40 -04:00
Nicola Soranzo 6ba6f798ec Fix more E203 flake8 errors 2016-05-17 23:53:16 +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 39da6c3278 Fix the remaining 2180 flake8 errors in tools/ . 2016-02-10 18:46:03 +00:00
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
Nicola Soranzo 69cda48690 Remove remaining references to galaxy.eggs . flake8 some files in tools/ . 2015-10-26 19:29:13 +00:00
Daniel Blankenberg a02e0f19c8 Set <options sanitize="False"> for genomespace_importer.xml 2015-10-21 11:33:45 -04:00
Daniel Blankenberg 54d4c266bd Have GenomeSpace tools report the GS tool name (for their internal metrics). Default is "Galaxy", but can be overridden by setting "GENOMESPACE_TOOLNAME" environment variable. 2015-09-10 14:45:40 -04:00
Dannon Baker 66ef2fc90e Merge over and resolve conflicts release->dev 2015-04-22 10:08:53 -04:00
Daniel Blankenberg 64fb5d15c1 Fix for GenomeSpace Exporter no longer allowing filenames to contain slashes. 2015-04-20 10:17:31 -04:00
Daniel Blankenberg 153bef1c52 Enable multi-part upload for the GenomeSpace export tool. Files greater than 5gb can once again be send to GenomeSpace from Galaxy. 
(cherry picked from commit 126ae073af)
 2015-04-16 09:48:42 -04:00
Daniel Blankenberg a25c5c025a Some basic Caching for the GenomeSpace Export Tool's list of available target directories, so we don't have to reload and download everything every time, especially now that we are calling the parameter's get options method 5 times (6 on reload) when a user loads the tool interface. For now, we'll use 30 seconds as the cache valid time length. 
(cherry picked from commit feb0a26f8d)
 2015-04-16 09:48:35 -04:00
Daniel Blankenberg 126ae073af Enable multi-part upload for the GenomeSpace export tool. Files greater than 5gb can once again be send to GenomeSpace from Galaxy. 2015-04-02 13:49:36 -04:00
Daniel Blankenberg feb0a26f8d Some basic Caching for the GenomeSpace Export Tool's list of available target directories, so we don't have to reload and download everything every time, especially now that we are calling the parameter's get options method 5 times (6 on reload) when a user loads the tool interface. For now, we'll use 30 seconds as the cache valid time length. 2015-03-17 13:08:06 -04:00
Daniel Blankenberg 4fdfc45156 Fixes for genomespace exporter recieving UnvalidatedValue objects. 2014-05-19 10:17:36 -04:00
Daniel Blankenberg 4d88ce03de Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool. 2014-04-09 17:24:56 -04:00
Daniel Blankenberg 745fa11661 Update GenomeSpace exporter directory listing to send the now working/required accept string. 2014-03-13 17:07:23 -04:00
Daniel Blankenberg 040fb029f8 Update GenomeSpace import tools to use current working directory instead of __new_file_path__ for extrafiles created using multiple outputs technique. Should resolve issue on our public servers where only the first selected file was being imported to the history. 2014-02-05 13:44:32 -05:00
Dannon Baker a40457ab09 Merge. 2014-01-10 07:40:02 -05:00
Dannon Baker 559ecb4ec8 Remove dependency on simplejson; convert everything over to using the json module in the python standard library. 2014-01-10 07:29:05 -05:00
Daniel Blankenberg 04cb164c1f Special case genomespace file browser import tool's handling of GenomeSpace format identifier 'http://www.genomespace.org/datamanager/dataformat/unknown' to cause datatype auto-dection via sniff with a fallback to using filename extention. 2014-01-09 10:54:58 -05:00
Daniel Blankenberg e25140647f Fix for GenomeSpace Export root directory listing. 2013-06-20 16:24:33 -04:00
Daniel Blankenberg 14cec88abc Update GenomeSpace tools to use __user__ as needed. 2013-05-03 16:02:40 -04:00
Daniel Blankenberg 167a334665 Display error to user when genomespace file browser tool is used with no imported datasets. 2013-05-02 15:46:06 -04:00
Daniel Blankenberg 508b5f3f36 Update GenomeSpace serverurl.properties file location. Should resolve network issues experienced with Jumbo Frames and the Broad. 2013-04-30 17:19:11 -04:00
Daniel Blankenberg 839a5744e5 When listing GenomeSpace directories in GenomeSpace export tool, if an API-discovered URL is invalid, skip gracefully. 2013-01-02 15:25:28 -05:00
Daniel Blankenberg 2c7f2c7106 Enhance GenomeSpace filebrowser importer to display a better history item name for additional primary datasets. 2012-10-24 12:33:34 -04:00
Daniel Blankenberg 43dafa165f Enhance GenomeSpace import tool to display a better history item name for additional primary datasets. 2012-10-24 12:33:34 -04:00
Daniel Blankenberg a986bcde0e Minor enhancements for GenomeSpace import naming of secondary files. 2012-10-19 15:26:51 -04:00
Daniel Blankenberg 14734e345a Update GenomeSpace exporter tool to use the newly introduced /personaldirectory as the root for auto-generated export paths. 2012-05-04 14:31:22 -04:00
Daniel Blankenberg 26e75b3e60 Allow GenomeSpace importer tool to sniff filetype when GSMetadata object is not available. 2012-05-03 12:25:06 -04:00