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1860 Commits
Author SHA1 Message Date
John Duddy c279ecd33b Upgrade of splitting code to do splitting in the tasks versus in the Galaxy process 2011-10-07 14:12:40 -07:00
John Duddy a2c0328241 Merge 2011-10-07 13:25:19 -07:00
Nate Coraor 8afb807a4d merge 2011-10-05 16:44:43 -04:00
Nate Coraor e7180eed8f New API scripts to do POST/PUT/DELETE without any guidance. Use like: 
./update.py key url param1=val param2=val
 2011-09-14 14:40:38 -04:00
Nate Coraor 9126df9685 Make it easier to run helper.py from outside the galaxy-dist root directory. 2011-09-08 12:09:10 -04:00
Nate Coraor d9126aa807 Clarify output messages of set_user_disk_usage.py 2011-09-07 15:07:05 -04:00
Nate Coraor eea0b7a81a Be more forgiving about running the disk accounting scripts from outside the galaxy-dist directory. 2011-09-07 09:05:52 -04:00
Nate Coraor df37c17b3c Typo in scramble.py. 2011-09-02 14:37:09 -04:00
Nate Coraor 4fe140d6d6 Missing import in library_contents.py 2011-08-29 14:42:04 -04:00
Nate Coraor 1f744be77d API enhancements: Rename the 'contents' controller to 'library_contents', move (some) sanity and security checks to galaxy.web.api.util, add some enhancements to the histories code and some sample scripts for histories. 2011-08-26 13:55:08 -04:00
Nate Coraor 3a1526ac8a Decrease user disk usage when files are removed from disk by the cleanup_datasets.py. 2011-08-22 16:19:49 -04:00
Nate Coraor 83163908e8 Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs. 2011-08-22 10:45:22 -04:00
Nate Coraor f7b2b1b0ab Bugfix for check_galaxy (monitor script) since dataset deletion moved to the dataset controller. 2011-08-04 11:01:22 -04:00
Nate Coraor 120b5f700c Bugfix for the offline egg packaging script. 2011-08-03 10:13:01 -04:00
Enis Afgan 2a3f9b4dea Merge 2011-08-01 17:36:28 -04:00
Enis Afgan 29253409ac Metadata is now being handled by the ObjectStore as well 2011-08-01 17:35:26 -04:00
Nate Coraor 0756941512 Move a number of dataset-related methods from the root controller to the dataset controller and encode their ids. Also add user disk usage accounting. 2011-07-26 13:30:07 -04:00
Dannon Baker d9bce945fd Case sensitivity note for login not found error. 2011-07-18 15:02:37 -04:00
Greg Von Kuster 581c3d9c67 Another patch from Assaf Gordon for the cleanup_datasets.py script. 
This patch adds messages for the "purge histories" step:
1. A message is printed when processing a new history (so that the user can tell to which history the following dataset/hda messages belong).
2. in "info_only" mode, a message is printed about each deleted history
3. in "info_only" mode, a message is printed for each HDA that is checked
4. The message for HDA is changed to include the associated dataset id.
 2011-07-14 15:58:06 -04:00
Greg Von Kuster 8eb0033904 Add patch from Assaf Gordon to the cleanup_datasets.py script. The changes are: 
1. If a dataset is skipped (because it's shared/cloned and was already process), no message is printed at all.
2. If a dataset can not be deleted because it is shared, and one instance is not marked as "deleted", a proper message is printed.
3. If a dataset has metadata files, the message is changed depending on "info_only" and "remove_from_disk" flags.
4. The final summary message is slightly changed.
 2011-07-13 09:39:02 -04:00
Greg Von Kuster 40d02d1e7b Add patch from Assaf Gordon to fix the cleanup_dataset.py script, correcting the behavior of setting the info_only flag to True when running delete_datasets.sh and purge_datasets.sh. 2011-07-06 09:52:28 -04:00
Ross Lazarus d53c3e984f Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository 
This is a backout of commit 5765
 2011-07-06 09:44:56 +10:00
Ross Lazarus 86b55bb0c0 branch merge 2011-07-05 12:40:43 +10:00
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