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22 Commits
Author SHA1 Message Date
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 3d72267f44 sample tracking data transfer mechanism streamlined. 
- eliminated the transfer_datasets.ini config file
- eliminated the data transfer user
- now the admin user initiating the data transfer is used as the data transfer user.
- the admin user is provided the add_library_item permission before data transfer if they dont have it
- sample update & data transfer amqp messages now includes api_key
 2010-11-07 19:46:59 -05:00
Ramkrishna Chakrabarty 1da8827235 Added validation checks in the data transfer script for sample tracking 2010-10-29 15:24:30 -04:00
Ramkrishna Chakrabarty d5d27b67ad adding setup_rabbitmq.sh script. 
web api minor code fixes
 2010-10-27 12:36:56 -04:00
Ramkrishna Chakrabarty 6a9ab2813a sample_tracking: 
- added web api methods to update requests, samples using restful api
- removed the old ad-doc web api
- modified the data transfer code to use this api
- code cleanup
 2010-10-26 10:00:23 -04:00
Ramkrishna Chakrabarty c925dc1f2c lims: 
- added a new table 'sample_dataset' to store sample datasets & their info when they are transfered from the sequencer
- the datasets transfer page now uses a grid to facilitate bulk renaming
- bulk renaming possible to fix the problem with the way SOLiD generates datasets
- the remote file browser is now independent of a specific sample, the user may select any sample when transferring datasets from the sequencer
 2010-07-29 10:55:08 -04:00
Ramkrishna Chakrabarty 45cb09579f lims: requests/request_admin controller refactor 
A new controller called requests_common now handles all common tasks like create/edit/delete requests & samples. The requests controller has only the grid definition and requests_admin controller has the request_type code and the sequencer data transfer code.
Also fixed a form importer bug in forms.py
 2010-06-30 10:46:50 -04:00
Ramkrishna Chakrabarty df780b03c9 lims: 
- bug fix - the data transfer module now works for file/folder names with spaces in them
- UI cleanup
 2010-06-11 10:18:13 -04:00
Ramkrishna Chakrabarty 37e3e9c006 lims: 
- UI enhancements to the remote file browser, double click to open folder
- data transfer folder name includes date now
 2010-06-09 13:07:05 -04:00
Ramkrishna Chakrabarty 3d9c8baaad lims: 
dataset rename issue fixed
 2010-04-22 09:35:44 -04:00
Ramkrishna Chakrabarty 53151321b5 lims: fixed data transfer bugs 2010-04-21 16:42:09 -04:00
Ramkrishna Chakrabarty 378ada9cd7 lims: 
- data transfer now uses rabbitmq
- datasets can now be renamed before transfering from the sequencer
- data transfer code refactored
 2010-04-21 10:41:30 -04:00
Kanwei Li 0952b28502 Sync hashbangs 2010-04-01 20:36:31 -04:00
Ramkrishna Chakrabarty 14a2326260 lims: data transfer bug fix 2010-03-23 10:09:12 -04:00
Ramkrishna Chakrabarty 6b45a2c1f9 lims: 
- code cleanup
- cleanup tmp files after data transfer
 2010-02-24 10:42:36 -05:00
Ramkrishna Chakrabarty dd4757f20a lims: 
- added error msg when dataset transfer is started for samples with no library
- fixed typos
- now dataset transfer does not affect sample state
- request completion logic restored.
 2010-02-24 10:04:03 -05:00
Ramkrishna Chakrabarty 2da3981679 LIMS: using threads for data transfer. first pass 2010-02-12 16:59:57 -05:00
Ramkrishna Chakrabarty 1e3bcd5d7c LIMS data transfer: 
- Fixed some config variable issues
- Now for the time being, Galaxy can transfer one dataset at a time.
 2010-02-12 14:01:45 -05:00
Ramkrishna Chakrabarty 453092bf74 fixed the 0037_sample_library migration script to work with sqlite 2010-02-11 09:25:29 -05:00
Ramkrishna Chakrabarty ebe405446a LIMS: replaced os.system with subprocess to spawn the data transfer daemon process 2010-02-09 11:21:53 -05:00
Ramkrishna Chakrabarty 5747633a06 LIMS data acquisition: now the data transfer user logs out after the transfer is complete 2010-02-04 17:00:46 -05:00
Ramkrishna Chakrabarty cea3324bbb Sequencer data acquisition for LIMS 
- Add a data transfer script which fetches datasets from the sequencer
- transfer_datasets.ini for setting up the separate user to login to Galaxy programmatically to add datasets to the data libraries.
- Added a dataset transfer page which includes remote file browser to select files for transfer

Removed library & folder foreign keys from the request table and added them to the sample table. Also the sample table now has a dataset_files column to store the datatsets and the their transfer status.
Add an egg for pexpect which is used in the remote file browser.
The request_type table has a new column datatx_info which stores all the login info for the sequencer machine
 2010-02-04 11:01:45 -05:00