Diane Trout [Mon, 14 Sep 2009 18:51:30 +0000 (18:51 +0000)]
Fix ticket:145 this patch includes the tar.bz2 extension in the scores pattern.
Also for good measure I check for tar.gz and .tgz. This'll
help avoid the problem of something else showing up in the directory
that matches the pattern scores*, like scores.tar.bz2.md5
Diane Trout [Fri, 11 Sep 2009 01:41:12 +0000 (01:41 +0000)]
Apparently I should've rendered the emails in plain text.
Also lorian wanted to include the cluster estimate in the email.
Diane Trout [Fri, 11 Sep 2009 00:44:01 +0000 (00:44 +0000)]
None is better than a baddly munged string for when we don't know the cluster/tile value
Diane Trout [Thu, 10 Sep 2009 23:54:33 +0000 (23:54 +0000)]
Don't crash if there are no lane result summary entries when rendering
output by not looking inside the empty dictionary.
Diane Trout [Thu, 10 Sep 2009 23:52:33 +0000 (23:52 +0000)]
Report if the Summary.htm file is missing the Lane Results Summary block.
Diane Trout [Thu, 10 Sep 2009 19:45:34 +0000 (19:45 +0000)]
Remove spurious pring debugging statements as they make mod_wsgi very sad
Brandon King [Thu, 3 Sep 2009 22:10:47 +0000 (22:10 +0000)]
wsgi print error fixed.
Diane Trout [Wed, 2 Sep 2009 23:03:04 +0000 (23:03 +0000)]
remove spurious debug print statement
Diane Trout [Tue, 1 Sep 2009 23:03:01 +0000 (23:03 +0000)]
Report who the site managers are for the BCC
also include the affiliations email as one of the entities being notified
about a library.
Brandon King [Tue, 25 Aug 2009 18:27:41 +0000 (18:27 +0000)]
Added control_lane column to Flowcell.
* updated upgrade_v0.2.6_to_v0.3.py script to update flowcell table.
Brandon King [Sat, 22 Aug 2009 00:28:26 +0000 (00:28 +0000)]
No printing allowed; fixed.
Diane Trout [Sat, 22 Aug 2009 00:09:37 +0000 (00:09 +0000)]
Now adding a user adds the key linking the htsuser object to the auth_user object.
(I overrode the user admin class and two supporting forms.)
Brandon King [Sat, 22 Aug 2009 00:08:55 +0000 (00:08 +0000)]
Implemented custom templates by inventory type using PrinterTemplate object.
* bcmagic app now has a Printer object which stores useable printers
* PrinterTemplate links Item Type, Printer, and Template together.
* Templates now stored in db in PrinterTemplate object.
Diane Trout [Thu, 20 Aug 2009 23:40:12 +0000 (23:40 +0000)]
Implement a send started email feature.
The UI is linked to from the admin page by overriding the django
admin change_form for experments/flowcell to include an new link
in the object-tools block.
The actual page is implemented as a custom view. Its designed to
render the emails to a preview page, and then, at the bottom
of the page there's a button to actually send the emails.
It'll re-load the page but with a small status message about
what happened with the email in question.
Additionally this requires that users be attached to affiliations
and that users have email addresses.
I forgot we were also going to extract an email address from the
affiliation as well, if it was set.
Diane Trout [Thu, 20 Aug 2009 23:31:33 +0000 (23:31 +0000)]
Reorder imports in model to make me happy.
(stdlib -> large dependencies -> app specific parts)
Brandon King [Thu, 20 Aug 2009 21:29:49 +0000 (21:29 +0000)]
Update user db when doing update.
Diane Trout [Wed, 19 Aug 2009 23:50:30 +0000 (23:50 +0000)]
Use hasattr instead of checking for django version number to check
for the new admin.site.urls (django 1.1 compatibility)
Brandon King [Wed, 19 Aug 2009 23:11:44 +0000 (23:11 +0000)]
Finished removing bcprinter module by moving what little code there
was to the bcmagic module. Removed app from settings. Fixed major bug
that I just created (and fixed) that caused only admin views to work.
Brandon King [Wed, 19 Aug 2009 23:04:31 +0000 (23:04 +0000)]
Moved bcprinter.util to bcmagic.util.
Brandon King [Wed, 19 Aug 2009 23:03:19 +0000 (23:03 +0000)]
Moved bcprinter/util.py to bcmagic/util.py
Brandon King [Wed, 19 Aug 2009 23:00:13 +0000 (23:00 +0000)]
Hard Drive Shell label made by Lorian; templatized by me.
Brandon King [Wed, 19 Aug 2009 22:58:28 +0000 (22:58 +0000)]
Admin compatibility for changes in Django >= 1.1.
Diane Trout [Wed, 19 Aug 2009 00:50:22 +0000 (00:50 +0000)]
Forgot to update one request to request.REQUEST variable lookup
Diane Trout [Wed, 19 Aug 2009 00:30:48 +0000 (00:30 +0000)]
Convert stanford/hudson alpha's updStatus to work with django 1.0.2's
WSGIRequest objects.
(Mostly this means accessing request.REQUEST instead of just request)
Also I changed the user restriction from 'rami' to is_superuser, as for
some reason the user variable attached to the request is an actual django
user.
Diane Trout [Tue, 18 Aug 2009 23:45:12 +0000 (23:45 +0000)]
Update hudson alpha's eland config file generator to work with the
lane table.
Diane Trout [Tue, 18 Aug 2009 23:44:19 +0000 (23:44 +0000)]
Update eland_config generator to work with the new seperate lane table
Diane Trout [Tue, 18 Aug 2009 22:42:01 +0000 (22:42 +0000)]
Update Rami's flowcell report to work with our new seperate lane table.
Diane Trout [Tue, 18 Aug 2009 22:41:26 +0000 (22:41 +0000)]
Add a custom (inherited) user object named HTSUser to the samples table.
This is so I can attach users (and their email addresses) to the
affiliation object.
Diane Trout [Tue, 18 Aug 2009 22:34:31 +0000 (22:34 +0000)]
Fix code where the python str() function had been overridden with a
string named str.
Brandon King [Fri, 14 Aug 2009 22:05:27 +0000 (22:05 +0000)]
Lorian's request for a thin comment field implemented.
Brandon King [Fri, 14 Aug 2009 21:22:06 +0000 (21:22 +0000)]
Lorian's requested filter by status; requires at least 2 status types.
Brandon King [Thu, 13 Aug 2009 23:04:35 +0000 (23:04 +0000)]
New way of accessing pM for a lane in _summary_stats
Brandon King [Thu, 13 Aug 2009 22:38:54 +0000 (22:38 +0000)]
Lane number fix for _summary_stats function and library_to_flowcells view
Brandon King [Thu, 13 Aug 2009 22:24:48 +0000 (22:24 +0000)]
New lane model patch for library_to_flowcells view.
Diane Trout [Wed, 12 Aug 2009 22:44:08 +0000 (22:44 +0000)]
Converted Brandon's scripts into a single python script that doesn't require
a previous version to run. It may however still require running syncdb.
It also improves on my first attempt of just using straight SQL to split the
flowcell into flowcell + lanes table in that now all the lanes for a single flowcell
are all next to each other.
Diane Trout [Wed, 12 Aug 2009 21:05:34 +0000 (21:05 +0000)]
Move Brandon's upgrade script in with all the other upgrade scripts.
Brandon King [Tue, 11 Aug 2009 19:54:46 +0000 (19:54 +0000)]
Making it more clear what the script does.
Brandon King [Tue, 11 Aug 2009 19:53:30 +0000 (19:53 +0000)]
Script for conversion of db; start of fixes brought on by changes to the db.
Brandon King [Mon, 10 Aug 2009 22:33:58 +0000 (22:33 +0000)]
print killing wsgi; minor fix.
Brandon King [Fri, 7 Aug 2009 22:43:06 +0000 (22:43 +0000)]
New Lane Table migration progress.
Brandon King [Thu, 6 Aug 2009 22:35:56 +0000 (22:35 +0000)]
Barcode Magic Initial Data
Brandon King [Tue, 4 Aug 2009 19:09:21 +0000 (19:09 +0000)]
Minor update.
Brandon King [Fri, 24 Jul 2009 22:22:03 +0000 (22:22 +0000)]
Lorian supplied quick fix for 32 char UUIDs.
Brandon King [Thu, 23 Jul 2009 21:30:54 +0000 (21:30 +0000)]
Lorian requested item search box
Diane Trout [Thu, 23 Jul 2009 20:01:32 +0000 (20:01 +0000)]
ReadPreps can also use the netcopy complete flags which causes problems
so I needed to force the "completion file" to be only checked in the root
of the runfolder.
Brandon King [Tue, 21 Jul 2009 22:53:42 +0000 (22:53 +0000)]
Moved from ext-3.0-rc2 to ext-3.0.0.
Diane Trout [Tue, 21 Jul 2009 22:23:21 +0000 (22:23 +0000)]
Allow specifying the we're finished sequencing file in the config file.
(Currently the default is netcopy_complete.txt, but that might not be a good
choice).
While I was in there I changed it to catch the current event, and set a
completed flag in the event instead of just directly sending the
sequencingFinished message.
I also put some effort into trying to only send startCopy messages for
things that look like runfolders, both by not sending a copy message
for the root of the watch directory and by checking to see if the
top level directory that contains the event looks kind of like a runfolder
name. (AKA "[0-9]{6}_" )
Brandon King [Mon, 20 Jul 2009 18:36:29 +0000 (18:36 +0000)]
Lorian requested save_as feature in admin interface.
Brandon King [Mon, 13 Jul 2009 23:37:10 +0000 (23:37 +0000)]
Prototype of bcmagic search plugin.
* Works for inventory item object.
Brandon King [Sat, 11 Jul 2009 00:03:01 +0000 (00:03 +0000)]
Adding ReagentLibrary & ReagentFlowcell tables in Inventory App.
Brandon King [Tue, 7 Jul 2009 00:23:31 +0000 (00:23 +0000)]
Attempted linking to archived hard drive.
Brandon King [Tue, 7 Jul 2009 00:20:56 +0000 (00:20 +0000)]
Attempted linking to archived hard drive.
Brandon King [Mon, 6 Jul 2009 23:46:14 +0000 (23:46 +0000)]
Update to item summary now displays Long Term Storage information if exists.
Brandon King [Mon, 6 Jul 2009 22:12:53 +0000 (22:12 +0000)]
Updated inventory to support display of inventory items based on uuid/barcode_id scans.
Brandon King [Thu, 2 Jul 2009 01:29:34 +0000 (01:29 +0000)]
Made Diane's suggest json problem fix for python 2.5/2.6 support... now using simplejson for <= python 2.5.
Brandon King [Thu, 2 Jul 2009 00:31:25 +0000 (00:31 +0000)]
Added a subtle but useful | to the toolbar
Brandon King [Thu, 2 Jul 2009 00:27:17 +0000 (00:27 +0000)]
Added a subtle but useful | to the toolbar
Brandon King [Thu, 2 Jul 2009 00:22:52 +0000 (00:22 +0000)]
NOTE: settings.py update:
Will need to include a section as follows to ini file:
[bcprinter]
printer1_host=<ip_address>
printer1_port=9100
printer2_host=<ip_address>
printer2_port=9100
Added a simple way to print out a label on inventory item summary
page. Needs major improvement on this page, but went for getting
labels printed to start with.
Brandon King [Wed, 1 Jul 2009 23:10:00 +0000 (23:10 +0000)]
Disabled menu selection when not logged in.
Brandon King [Wed, 1 Jul 2009 19:43:02 +0000 (19:43 +0000)]
Added start of inventory summary view and cleaned up inventory template location
Diane Trout [Wed, 1 Jul 2009 00:35:07 +0000 (00:35 +0000)]
Add LibraryType option, (this will probably require a dump/reload)
And you'll probably need to do it before updating to this version of the
database
Diane Trout [Wed, 1 Jul 2009 00:33:56 +0000 (00:33 +0000)]
Change the cluster station default to the current working cluster station.
Diane Trout [Tue, 30 Jun 2009 23:45:19 +0000 (23:45 +0000)]
Allow cellline and conditition to be blank [ticket:115] [ticket:105]
However this requires a dump and reload of the database to work.
This saves the data as a django 'fixture'
python manage.py dumpdata samples > /tmp/sampledata.json
python manage.py sqlreset samples | sqlite3 [path to db]
python manage.py loadddata /tmp/sampledata.json
Brandon King [Tue, 30 Jun 2009 22:43:48 +0000 (22:43 +0000)]
Auto resizing for grids based on collapsing and resizing of other components
Diane Trout [Tue, 30 Jun 2009 22:29:05 +0000 (22:29 +0000)]
Provide a dummy eland result lane class if there's nothing appropriate in the xml
files. Though this produces blank records in the library page, at least the
program doesn't crash.
Brandon King [Tue, 30 Jun 2009 20:03:16 +0000 (20:03 +0000)]
Behold the power of ExtJS grids! Muhahaha! =o)
Brandon King [Tue, 30 Jun 2009 19:06:56 +0000 (19:06 +0000)]
auto height test.
Brandon King [Tue, 30 Jun 2009 19:04:26 +0000 (19:04 +0000)]
two json modules... one for 2.5, one for 2.6... util that just works.
Brandon King [Tue, 30 Jun 2009 18:26:29 +0000 (18:26 +0000)]
Start of inventory app page.
Brandon King [Mon, 29 Jun 2009 21:38:44 +0000 (21:38 +0000)]
Activating bcmagic model & initial data.
Brandon King [Sat, 27 Jun 2009 01:59:13 +0000 (01:59 +0000)]
Pulling in barcode magic from sample tracker and starting to update it to use ExtJS
Brandon King [Fri, 26 Jun 2009 22:23:18 +0000 (22:23 +0000)]
Libraries Detail View integrated.
Brandon King [Fri, 26 Jun 2009 19:57:07 +0000 (19:57 +0000)]
Fixed dynamic east panel code
Brandon King [Fri, 26 Jun 2009 19:35:03 +0000 (19:35 +0000)]
CSS fix broke non-library index views; fix for fix.
Brandon King [Fri, 26 Jun 2009 19:31:47 +0000 (19:31 +0000)]
CSS fixes for library index
Brandon King [Fri, 26 Jun 2009 19:13:23 +0000 (19:13 +0000)]
Migrating the west panel menu to a 2nd toolbar menu.
Brandon King [Thu, 25 Jun 2009 18:32:15 +0000 (18:32 +0000)]
CSS fixes
Brandon King [Wed, 24 Jun 2009 22:55:55 +0000 (22:55 +0000)]
Made a dynamic way of adding div dynamically to the east panel.
* see app_base.html template for example.
Brandon King [Wed, 24 Jun 2009 21:51:59 +0000 (21:51 +0000)]
Sample Tracker EXTJS frontend merge part 1
Diane Trout [Tue, 23 Jun 2009 23:46:49 +0000 (23:46 +0000)]
The url validation code wasn't working on python2.4
the problem where rpc exception are being eaten by something is getting
really annoying.
Brandon King [Mon, 22 Jun 2009 23:18:30 +0000 (23:18 +0000)]
Schema update to inventory
Diane Trout [Sat, 20 Jun 2009 00:06:44 +0000 (00:06 +0000)]
Send the specific directory that needs to be copied in the startCopy message.
Also I changed it to send "urls" which need to match in both spoolwatcher
and copier. (as security feature it checks to make sure the rsync
directory it got over the network matches one of its internal list)
Diane Trout [Fri, 19 Jun 2009 22:49:16 +0000 (22:49 +0000)]
I started using ResultLane, so stop treating it like an abstract class.
I needed to initialize the ELAND class with something for the older
run xml files which don't have eland results initialized, So I initialized
some default values so the website wouldn't crash when accessing
these older files.
Diane Trout [Wed, 17 Jun 2009 19:36:00 +0000 (19:36 +0000)]
Add support for extracting data out of Illumina's new RTA runfolder.
I dropped extraction of matrix & phasing for the moment, no one was
looking for them, and I need to go back to one matrix per lane
for RTA Intensity directories. I'm also not sure where the phasing
information might be being stored.
Another weakness is if there is a firecrest directory the run scanning
wasn't finding the intensities directory.
Diane Trout [Wed, 17 Jun 2009 19:25:34 +0000 (19:25 +0000)]
Add a hack to add a frontend section if not present
This will allow the django test code to run on systems that aren't
setup to run the web site.
Diane Trout [Wed, 17 Jun 2009 19:24:29 +0000 (19:24 +0000)]
Loading really old run xml files caused the website to crash
with an attribute error.
frontend/samples/views.py line 220 had
eland_summary = run.gerald.eland_results.results[end][lane_id]
However really old run.xmls lacked any eland_results so
I added some code to add dummy entries if the Eland class
wasn't initialized.
Also this adds a bit of test code which at least tries to load
a couple run xml files.
Diane Trout [Wed, 17 Jun 2009 19:10:39 +0000 (19:10 +0000)]
Ignore *.py[co~] files to make svn status happier
Diane Trout [Wed, 17 Jun 2009 19:09:50 +0000 (19:09 +0000)]
Add stub uuid function to make this module import when running under python2.4
Diane Trout [Wed, 17 Jun 2009 19:07:23 +0000 (19:07 +0000)]
remove spurious debug print statements
Brandon King [Wed, 17 Jun 2009 18:58:12 +0000 (18:58 +0000)]
Arg... spelling!
Brandon King [Wed, 17 Jun 2009 18:57:31 +0000 (18:57 +0000)]
Once again, assumed I had a flowcell object when I actually had a dictionary!
Brandon King [Wed, 17 Jun 2009 18:39:42 +0000 (18:39 +0000)]
Apparently we might be receiving None, so this check should fix it.
Brandon King [Wed, 17 Jun 2009 18:14:47 +0000 (18:14 +0000)]
* Fixed urls for result_fc_cnm_eland_lane and summaryhtm_fc_cnm functions.
* Added listing of hard drives the results have been archived to on the "Raw Result Files" table.
Brandon King [Tue, 16 Jun 2009 22:54:43 +0000 (22:54 +0000)]
Updated Library view to show an icon if a record exists showing that the library has been archived.
Diane Trout [Tue, 16 Jun 2009 22:20:35 +0000 (22:20 +0000)]
The error being thrown by benderjab changed slightly.
Diane Trout [Tue, 16 Jun 2009 22:19:05 +0000 (22:19 +0000)]
Split rsync initialization out of run so we can test
it better. (needed to support the previous changes to test/test_copier.py
Diane Trout [Tue, 16 Jun 2009 21:55:27 +0000 (21:55 +0000)]
Fixed a couple of problems.
The name/description wasn't being updated.
there was a typo in the name of the outstream.
Diane Trout [Tue, 16 Jun 2009 21:36:59 +0000 (21:36 +0000)]
Update test copier code for the changes in the copier config file.
(Support for multiple source destinations)
Brandon King [Tue, 16 Jun 2009 19:46:02 +0000 (19:46 +0000)]
Icon added.
Removed unneed urllib module import (since we switched to urllib2).
Brandon King [Tue, 16 Jun 2009 18:58:13 +0000 (18:58 +0000)]
Managed to use a urllib python 2.6 feature... converting code to work in 2.5