Nate Coraor
61f392c235
Disk space usage accounting: Users can see how much disk a history is consuming. Disk used is also a column on the history grid. Users can also forcibly purge a dataset from their history. Included is a script (scripts/set_dataset_sizes.py) which will set the value of the new total_size column on the dataset table (includes the contents of the extra_files_path and metadata files).
2011-06-14 12:43:42 -04:00
Nate Coraor
478470e8b0
Testing Python 2.7.
2011-06-08 23:50:07 -04:00
Nate Coraor
758e13ac28
Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).
2011-06-08 12:10:51 -04:00
Greg Von Kuster
cbd7fd8caa
Commit versions of tools from the last_gen tool shed in order of oldest -> newest in the next-gen tool shed. Fixes issue # 578.
2011-06-07 11:32:11 -04:00
Greg Von Kuster
5dde45d61b
Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!
2011-06-02 15:18:35 -04:00
Greg Von Kuster
212433fe2c
First pass of the next-gen Galaxy tool shed. See it demonsrated and discussed at the 2011 Gallaxy Community Conference in Lunteren on May 24,25,26.
2011-05-20 16:04:30 -04:00
Nate Coraor
467885c59d
Merge changes from the NBIC Galaxy Hackathon. Includes the addition of scripts which automatically generate the tool_conf.xml from tool configuration files. Tool configuration files also support optional syntax which specifies their placement in sections, as well as what tags the tool should be associated with. Also includes support for associating tags with tool IDs and filtering tools by tag in the tool menu.
2011-04-19 08:21:54 -04:00
Nate Coraor
f60a292e91
Scramble script for bx-python on Solaris (needs some C99 defines).
2011-04-18 16:40:43 -04:00
Nate Coraor
96ef29d991
Use Egg.fetch() instead of Egg.resolve() to get dependencies when dist-scrambling.
2011-04-18 14:04:06 -04:00
vdtoorn@hotmail.com
1c221447e9
introduction of toolboxposition elements
2011-04-14 15:09:00 +02:00
Ross Lazarus
ee6bd2cf46
Changes to allow all test outputs generated by twill to be saved to a folder pointed to by
...
an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving
2011-04-14 08:09:48 -04:00
Rob Hooft
db3fae4c2b
* Remove Todo's that have been done
2011-04-14 14:07:36 +02:00
Rob Hooft
f04e5682b4
* Restructured to use toolboxposition elements instead of section elements. Now
...
handles order and labels
2011-04-14 14:07:05 +02:00
Rob Hooft
e8c98020d6
* Special cased the "off" tag to leave a tool out of the toolbox.
2011-04-14 10:02:10 +02:00
Rob Hooft
0203246152
* Two Scripts:
...
* Extract "section" headers from the toolbox XML file, and put them into the tool XML;
prepare the tool XML for associating "tags" with the tool.
* Build a toolbox XML file based on augmented tool XML files with section identification.
2011-04-13 22:36:57 +02:00
Greg Von Kuster
9102fc3472
1. Add support for manual file transfer from external services to a Galaxy data library using scp. This is currently enabled via the enable_beta_job_managers flag. This should not currently be used because it hits the db significantly to determine if dererred jobs are queued for running. The plan is to use messaging for this, but that approach is not yet implemented. Rabbit mq is still being used to enable manual file transfer to Galaxy data libraries when the enable_beta_job_managers flag is not set.
...
2. Clean up the code that renders the jquery file browser plugin - things work much cleaner now. One remaining item is handing the issue where rsh / ssh keys are not set. Also clean up a lot of code related to manual file transfers in the requests_admin controller.
3. In addition to the new ManualDataTransferPlugin, add the Pacific Biosciences SMRTPortalPlugin that automatically transfers files produced by SMRT Portal to a Galaxy data library.
4. Add the external service type config for Pac Bio SMRT Portal version 1.1.0.
2011-04-13 13:52:05 -04:00
Kanwei Li
962f7d06ba
Fix some scramble problems
2011-04-12 22:08:09 -04:00
Nate Coraor
05ba81a93d
Update the check_galaxy script for the recent changes to the User controller
2011-03-24 14:33:05 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Daniel Blankenberg
1aa7034e17
Fix minor typo in 5233:b5f4df8c3956
2011-03-18 13:40:58 -04:00
Daniel Blankenberg
4ff307c613
Add a script that will check a maf_index.loc file for inconsistencies between listed information and content of MAF indexes and files.
2011-03-18 13:39:19 -04:00
Dannon Baker
082bd83a5c
Fix for example workflow api script failing when the requested library doesn't exist and an attempt is made to create it.
2011-03-15 15:39:35 -04:00
Dannon Baker
9655aa55f5
Set workflow scripts ugo+x, like the others in scripts/api.
2011-03-05 12:44:32 -05:00
Dannon Baker
159c25eb68
Example script that uses the API to watch a folder for inputs, upload (filepath upload) those to a data library, and then execute a specified workflow on them.
2011-03-05 12:28:16 -05:00
Dannon Baker
e62494e2b0
Initial commit of workflows API. Supports simple execution, multiple input datasets. Does not support runtime tool parameter modification.
2011-03-05 11:47:12 -05:00
Nate Coraor
154b8c61ce
Bugfix for the last commit when running functional tests with sqlite.
2011-02-28 09:52:17 -05:00
Nate Coraor
8e995a23be
Increase the SQLAlchemy SuquePool limits for functional tests.
2011-02-28 07:58:52 -05:00
Nate Coraor
92de52f6e0
Fixes for scrambling python-daemon and pysam.
2011-02-09 16:29:50 -05:00
Greg Von Kuster
b0b5df4e93
Add a purged column to the LibraryDataset table - a LibraryDataset is marked purged when all associated LibraryDatasetDatasetAssociations are marked deleted. Fix the cleanup_datasets.py script to more correclty handle the lifecycle of LibraryDatasets.
2011-02-09 15:42:09 -05:00
Greg Von Kuster
7058041133
Brad Chapman's patch for fixing an issue where the current user roles were not passed to a template.
2011-02-01 13:11:24 -05:00
Greg Von Kuster
e8e6753c47
Apply patch from Brad Chapman that fixes an issue when downloading a zip archive of library datasets. Also include some miscellansous imporvements and code cleanup related to changes made in change set 4964:82107691d26e.
2011-02-01 11:21:41 -05:00
Greg Von Kuster
5f9f45a068
Several data library improvements:
...
1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.
2. Add Brad Chapman's latest patch for fixing the lucene search implementation
3. Eliminate searches on dataset state for both whoosh and lucene searches
4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.
5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.
6. Add a "select all" checkbox to the browse_library.mako template.
7. Fixed library functional tests accordingly.
2011-01-31 16:41:03 -05:00
Greg Von Kuster
a34be28c89
Add support for searching components of library datasets using whoosh. This includes changes to the approach used to search using lucene.
2011-01-26 16:00:27 -05:00
Greg Von Kuster
a815321f83
Second of 2 patches from Brad Chapman for searching data libraries.
2011-01-24 13:52:55 -05:00
Greg Von Kuster
2a96a3af51
First of 2 pataches from Brad Chapman for indexing / searching data libraries.
2011-01-24 11:31:46 -05:00
Nate Coraor
0f9e7fc26d
Do away with the daemonized transfer manager and have the deferred job runner start off individual daemonized transfer workers. The workers update their own major states and can be queries for in-transfer progress via a socket, and an interface to that socket in app.transfer_manager. All socket communication is now JSON-RPC.
2011-01-19 10:06:44 -05:00
Ramkrishna Chakrabarty
d4f484e9ae
Moving sample state and dataset transfer status update api methods to the samples api controller.
2010-12-20 16:05:08 -05:00
Ramkrishna Chakrabarty
7858868650
First pass of the new sequencer_type & sequencer framework
...
- sequencer table now populated with the unique sequencer in the request_type table
- sequencer_type is introduced which defines a sequencer
- support for sequencer (create, delete, edit)
- added support for a simple sequencer for backward compatibility
- added support for Solid sequencer
- tweaked the request_type api methods. removed the sequencer login info.
2010-12-20 10:50:50 -05:00
Ramkrishna Chakrabarty
028137a54d
added 'name' attribute to the sample xml form
2010-12-13 17:30:51 -05:00
Ramkrishna Chakrabarty
b34ef29442
Adding a 'name' attribute in the field dict for form_definitions. In the 'form_values'
...
table, the 'content' column is now a JSON dict instead of a list. Made appropriate code changes.
2010-12-13 17:29:23 -05:00
Daniel Blankenberg
7b7453366f
Initial pass on API for forms, request_type, users and roles.
...
Additional effort is needed to abstract more previously existing functionality out of web controllers.
Add script that is able to create a sequencer configuration for the sample tracking system using API.
2010-12-02 16:04:34 -05:00
Nate Coraor
246ea04cc7
Add support for the new test/data repository and a fix for the bowtie tests.
2010-11-22 10:54:31 -05:00
Ramkrishna Chakrabarty
b8652ecc4e
- added the change data library sample operation functional test.
...
- renaming dataset now checks for incorrect filename characters
- fixed bugs
2010-11-17 11:33:54 -05:00
Ramkrishna Chakrabarty
dec7e64355
Restored the function to stop the edit samples form from getting submitted when return key is pressed. This is needed in this form as the barcode scanner (when in keyboard emulation mode) may send a return key appended to the scanned barcode string.
2010-11-15 15:38:44 -05:00
Anton Nekrutenko
fa410d3ddc
Tweaks to taxonomy tools
2010-11-15 15:04:59 -05:00
Nate Coraor
6cf36abfcc
(recommit): porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility
2010-11-10 10:26:43 -05:00
Nate Coraor
1e4fba1360
Backed out changeset 081ce300b688 (some files accidentally committed).
2010-11-10 10:26:07 -05:00
Anton Nekrutenko
7c4ca2927b
porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility
2010-11-10 10:17:12 -05:00
Kelly Vincent
a0a1f44c32
Added a sample loc file listing all fasta files and a script to generate the file given a base genome directory.
2010-11-08 00:43:02 -05:00
Ramkrishna Chakrabarty
7d8a5c650a
Improved error handling in api methods.
2010-11-07 22:18:22 -05:00
Nate Coraor