Diane Trout [Wed, 14 Sep 2016 23:59:12 +0000 (16:59 -0700)]
Adapt response.content for RDF and xhtml validator
Irritatingly one wants bytes and one wants unicode under python3.
Diane Trout [Wed, 14 Sep 2016 23:06:05 +0000 (16:06 -0700)]
elpy+flake8 suggested some formatting improvements
Diane Trout [Wed, 14 Sep 2016 23:03:09 +0000 (16:03 -0700)]
Delete temp objects to avoid constraint error
Django 1.10 with Postgres 9.? was throwing an error because the
samples_htsuser id that was assigned to an affiliation didn't exist in
the database.
The simplest solution I found was to delete the objects from the ORM,
I don't think they were ever actually created in the db so I'm not sure
how the constraint check was happening.
Diane Trout [Wed, 14 Sep 2016 21:40:33 +0000 (14:40 -0700)]
Move to render and use simple context dictionaries
render_to_response is likely to be deprecated at some point
Diane Trout [Mon, 25 Jul 2016 23:38:31 +0000 (16:38 -0700)]
The DCC has complained about me making a few common typos, so I added some checks for those cases
Diane Trout [Mon, 25 Jul 2016 23:38:07 +0000 (16:38 -0700)]
some date cells contain two dates, which is treated as a string
Diane Trout [Fri, 24 Jun 2016 23:26:05 +0000 (16:26 -0700)]
Remove references to migrations on topic branches
Diane Trout [Thu, 2 Jun 2016 20:47:39 +0000 (13:47 -0700)]
Try providing new django apps-style configuration
Not sure if I actually needed to do this.
Diane Trout [Thu, 2 Jun 2016 20:46:47 +0000 (13:46 -0700)]
The sort order of lanes changed breaking my test
Diane Trout [Thu, 2 Jun 2016 20:45:38 +0000 (13:45 -0700)]
Define filters variable again
There's a conditional that still used it, however we still need to
actually implement the todo functionality with newer django.
Diane Trout [Thu, 2 Jun 2016 20:44:27 +0000 (13:44 -0700)]
Save new object before attaching to a collection
Django tests were throwing warning about the newfile object not being
saved when I added it to the datafile_set collection.
Diane Trout [Thu, 2 Jun 2016 20:43:28 +0000 (13:43 -0700)]
Update custom user model for django 1.9ish.
They implemented some nicer ways of overriding the user model
Diane Trout [Thu, 2 Jun 2016 20:21:24 +0000 (13:21 -0700)]
Remove null=True from a few fields
django check pointed out that null=True is confusing with blank or
ManyToMany fields.
Diane Trout [Thu, 2 Jun 2016 20:20:11 +0000 (13:20 -0700)]
Update multiplex_id max length to 255
we had a very heavily mutiplexed library
Diane Trout [Thu, 2 Jun 2016 00:10:01 +0000 (17:10 -0700)]
Query_set was renamed to queryset
and I forgot to update the access in this template.
Good thing my test case caught it, because there
was no other error.
Diane Trout [Thu, 2 Jun 2016 00:08:07 +0000 (17:08 -0700)]
Match what generate_sample_results_tree creates
The turtle rules I was using for scanning a submission directory
didn't match what I was creating, which was generating some
warning messages.
Fix this cut down on logger warning messages being generated
during test runs.
Diane Trout [Thu, 2 Jun 2016 00:05:52 +0000 (17:05 -0700)]
Use find_statements instead of SPARQL for a query
The SPARQL query ended up with an unbound variable which
generated a warning, I redid the query with just a model.find_statements
which doesn't generate a warning
(My test output was getting cluttered with too many logger warnings)
Diane Trout [Thu, 2 Jun 2016 00:04:40 +0000 (17:04 -0700)]
Admin url includes /change/ at the end
so my tests that were looking at
/admin/experiments/flowcel/{flowcell id}/
needed to change to
/admin/experiments/flowcel/{flowcell id}/change/
this of course means we now require django 1.9 for tests.
Diane Trout [Thu, 2 Jun 2016 00:03:26 +0000 (17:03 -0700)]
Remove unused variables
Diane Trout [Wed, 1 Jun 2016 23:58:59 +0000 (16:58 -0700)]
give LaneOptions object access to the admin site
Somewhere the changelist I was inheriting from needed a method from the
admin site. (empty_value_display)
Diane Trout [Wed, 1 Jun 2016 23:57:43 +0000 (16:57 -0700)]
white-space fix
Diane Trout [Wed, 1 Jun 2016 23:56:13 +0000 (16:56 -0700)]
Use render instead of render_to_response
Somtimes I needed to use context_instance=RequestContext(request)
in my templates, and that parameter was depreacted for
render_to_response.
It seemed easier to just universally switch to the newer render() call
which directly takes the request object.
Diane Trout [Wed, 1 Jun 2016 23:53:55 +0000 (16:53 -0700)]
Use named url pattern instead of package name
Diane Trout [Wed, 1 Jun 2016 23:52:32 +0000 (16:52 -0700)]
Replace permalink decorator with url reverse
Diane Trout [Wed, 1 Jun 2016 23:38:28 +0000 (16:38 -0700)]
Use reverse with named url patterns
instead of with the full package name
Diane Trout [Wed, 1 Jun 2016 23:33:24 +0000 (16:33 -0700)]
Name all of the view that we need to reverse
Django 1.9 wants to remove reversing by package name,
as far as I can tell the simplest way to then reverse a
name to find the view is to name the url pattern.
The next few commits should take advantage of the names.
Diane Trout [Tue, 24 May 2016 22:45:15 +0000 (15:45 -0700)]
Add migrations to the small apps.
Django 1.9 dropped the old way of creating the database so we needed to
update
Diane Trout [Tue, 24 May 2016 22:43:21 +0000 (15:43 -0700)]
Update template configuration for Django 1.9
Diane Trout [Tue, 24 May 2016 22:37:14 +0000 (15:37 -0700)]
Django 1.9? replaced request.REQUEST with .GET
update our code so we access the new variable name
Diane Trout [Wed, 1 Jun 2016 23:32:03 +0000 (16:32 -0700)]
Remove unused imports
Remove unused imports
Diane Trout [Wed, 1 Jun 2016 23:29:46 +0000 (16:29 -0700)]
Collapse multiple imports from the same module
Diane Trout [Wed, 1 Jun 2016 23:26:52 +0000 (16:26 -0700)]
Replace import * with explicit list of imports
Diane Trout [Tue, 12 Apr 2016 22:46:36 +0000 (15:46 -0700)]
Switch to GenericIPAddressField
Django 1.9 added support for ipv6 addresses and changed from
IPAddressField to GenericIPAddressField
Diane Trout [Fri, 8 Apr 2016 00:03:31 +0000 (17:03 -0700)]
Refactor out code to submit a single file from a loop.
I had some files to upload that weren't part of a
library result set... and that seemed like the easiest
way to reuse my code.
Diane Trout [Fri, 8 Apr 2016 00:01:46 +0000 (17:01 -0700)]
Django 1.9 deprecated string based url names and django.conf.url.patterns
I think those changes should be backwards, and they usually
shorten the url() lines so seemed reasonable to apply.
Diane Trout [Thu, 7 Apr 2016 19:47:31 +0000 (12:47 -0700)]
whitespace change
Diane Trout [Thu, 7 Apr 2016 19:47:20 +0000 (12:47 -0700)]
remove unused imports
Diane Trout [Fri, 24 Jun 2016 22:27:52 +0000 (15:27 -0700)]
Unicode munging for python3
Not sure if I'm breaking python2 though
Diane Trout [Tue, 21 Jun 2016 21:30:50 +0000 (14:30 -0700)]
Implement writing to compressed files for qseq2fastq
Along the way refactor some of the code I had in
desplit_fastq to make it easier to share the open compressed
streams logic
Diane Trout [Wed, 20 Apr 2016 22:48:54 +0000 (15:48 -0700)]
Extract part of get_json into get_response
For some experiments I wanted the ability to grab
the raw requests response, previously it was hidden
by just directly returning response.json()
Diane Trout [Mon, 11 Apr 2016 22:48:33 +0000 (15:48 -0700)]
Initial implementation of importencoded
This version reads from a json dump file and dumps it
into postgresql using sqlalchemy.
Considering the rest of htsworkflow uses django it might
be better to switch to using django's ORM and also to take advantage
of requests.
Diane Trout [Sat, 12 Mar 2016 01:05:23 +0000 (17:05 -0800)]
Increase size of Library.multiplex_id field
Diane Trout [Thu, 3 Dec 2015 22:48:39 +0000 (14:48 -0800)]
report run_type
Diane Trout [Thu, 3 Dec 2015 22:26:36 +0000 (14:26 -0800)]
report if a flowcell was single or paired ended as a file property
Diane Trout [Thu, 3 Dec 2015 19:28:31 +0000 (11:28 -0800)]
remove unused imports and variables
Diane Trout [Mon, 30 Nov 2015 21:48:30 +0000 (13:48 -0800)]
make a more informative log message
Diane Trout [Mon, 30 Nov 2015 21:47:33 +0000 (13:47 -0800)]
Read the first sequence out of the fastq to find the read_length
For some reason we had a flowcell where the sequencer thought
there were 66 cycles but the file only had 50.
Diane Trout [Mon, 30 Nov 2015 20:16:59 +0000 (12:16 -0800)]
refactor encode3 spreadsheet based object creation to be a bit easier to read
Diane Trout [Mon, 30 Nov 2015 20:16:17 +0000 (12:16 -0800)]
remove wsgiref requirement
Diane Trout [Wed, 11 Nov 2015 21:24:27 +0000 (13:24 -0800)]
argparse is in versions of python we care about
Diane Trout [Tue, 27 Oct 2015 18:20:13 +0000 (11:20 -0700)]
use decorator syntax for registering admin urls
Diane Trout [Tue, 27 Oct 2015 18:18:38 +0000 (11:18 -0700)]
update dotted path for python3
Diane Trout [Tue, 27 Oct 2015 18:18:17 +0000 (11:18 -0700)]
update url to new standard url
Diane Trout [Tue, 27 Oct 2015 18:18:03 +0000 (11:18 -0700)]
Update schema tests for upstreams release 33
Diane Trout [Tue, 27 Oct 2015 18:16:20 +0000 (11:16 -0700)]
make exception dotted name python3 compliant
Diane Trout [Tue, 20 Oct 2015 23:50:44 +0000 (16:50 -0700)]
this works better with python 3...
Diane Trout [Tue, 20 Oct 2015 23:50:14 +0000 (16:50 -0700)]
apparently json.dump can write to a stream
Diane Trout [Tue, 20 Oct 2015 23:49:54 +0000 (16:49 -0700)]
Add mode to connect to the DCC and make sure the files with a .upload file are actually present at the DCC
Diane Trout [Tue, 20 Oct 2015 23:19:55 +0000 (16:19 -0700)]
fix import path for HTTPError exception
Diane Trout [Tue, 20 Oct 2015 23:19:39 +0000 (16:19 -0700)]
fix typo, use print_function
Diane Trout [Tue, 20 Oct 2015 23:18:49 +0000 (16:18 -0700)]
add knowledge about file links
Diane Trout [Tue, 20 Oct 2015 23:18:37 +0000 (16:18 -0700)]
updates to deal with encoded 33 path changes
Diane Trout [Tue, 20 Oct 2015 23:17:47 +0000 (16:17 -0700)]
Merge branch 'django1.7' of mus.cacr.caltech.edu:htsworkflow into django1.7
Diane Trout [Tue, 20 Oct 2015 23:17:14 +0000 (16:17 -0700)]
move run_aws_cp command out of class to make it easier to use from other scripts
Diane Trout [Thu, 24 Sep 2015 18:49:18 +0000 (11:49 -0700)]
Return read_length for file properties
Diane Trout [Wed, 23 Sep 2015 21:57:32 +0000 (14:57 -0700)]
Use a re.split so we can accept both ', ' and ',' between list items.
Diane Trout [Tue, 8 Sep 2015 23:38:12 +0000 (16:38 -0700)]
indicate we want text not bytes
Diane Trout [Tue, 8 Sep 2015 23:37:48 +0000 (16:37 -0700)]
covert to using python3 config.get fallback=
Diane Trout [Tue, 8 Sep 2015 23:37:03 +0000 (16:37 -0700)]
convert from optparse to argparse
Diane Trout [Tue, 8 Sep 2015 23:36:25 +0000 (16:36 -0700)]
add some documentation -- shocking I know
Diane Trout [Mon, 20 Jul 2015 18:37:23 +0000 (11:37 -0700)]
python3 byte vs str compatibility for constructing document data urls
Diane Trout [Mon, 20 Jul 2015 18:35:58 +0000 (11:35 -0700)]
script to help remigrate from old sqlite database to new server
Diane Trout [Mon, 20 Jul 2015 18:35:18 +0000 (11:35 -0700)]
configuration file largely only useful for emacs elpy users
Diane Trout [Mon, 20 Jul 2015 18:34:25 +0000 (11:34 -0700)]
sort load_accession to make it easier to find things
Diane Trout [Thu, 28 May 2015 18:27:38 +0000 (11:27 -0700)]
remove unused imports
Diane Trout [Tue, 26 May 2015 23:58:49 +0000 (16:58 -0700)]
rename datarun to sequencing run, and propogate the change all over the place
Diane Trout [Tue, 26 May 2015 23:57:54 +0000 (16:57 -0700)]
set a created datetime in the factory, since I removed the default from the model
Diane Trout [Thu, 21 May 2015 23:13:27 +0000 (16:13 -0700)]
remove unused import
Diane Trout [Thu, 21 May 2015 23:13:15 +0000 (16:13 -0700)]
load in our encode3 accession numbers seperately from the migration system
Diane Trout [Thu, 21 May 2015 23:12:46 +0000 (16:12 -0700)]
add a few common accession agencies to the standard dataset
Diane Trout [Thu, 21 May 2015 23:11:29 +0000 (16:11 -0700)]
Add AccessionAgency and LibraryAccession
For all your library accessioning needs.
Diane Trout [Wed, 20 May 2015 21:56:47 +0000 (14:56 -0700)]
localize all the RDF imports and use skipUnless to avoid tests when we don't have redland installed
Diane Trout [Wed, 20 May 2015 21:32:19 +0000 (14:32 -0700)]
remove commented out code
Diane Trout [Wed, 20 May 2015 21:31:22 +0000 (14:31 -0700)]
import specific names instead of import factory
Diane Trout [Wed, 20 May 2015 21:28:55 +0000 (14:28 -0700)]
remove some unused imports
Diane Trout [Wed, 20 May 2015 21:24:03 +0000 (14:24 -0700)]
remove commented out code
Diane Trout [Tue, 12 May 2015 23:56:21 +0000 (16:56 -0700)]
remove unused imports
Diane Trout [Tue, 12 May 2015 23:55:32 +0000 (16:55 -0700)]
flake8 whitespace cleanup
Diane Trout [Tue, 12 May 2015 23:45:20 +0000 (16:45 -0700)]
remove unused imports
Diane Trout [Tue, 12 May 2015 23:40:58 +0000 (16:40 -0700)]
flake8 whitespace cleanup
Diane Trout [Tue, 12 May 2015 21:35:42 +0000 (14:35 -0700)]
flake8 whitespace cleanup
Diane Trout [Tue, 12 May 2015 19:18:47 +0000 (12:18 -0700)]
move comments out of experiments_flowcell flowcell id and into lane status
Diane Trout [Tue, 12 May 2015 19:17:03 +0000 (12:17 -0700)]
remove unused import
Diane Trout [Tue, 12 May 2015 19:16:31 +0000 (12:16 -0700)]
flake8 whitespace cleanup
Diane Trout [Tue, 12 May 2015 18:52:00 +0000 (11:52 -0700)]
flake8 whitespace change
Diane Trout [Tue, 12 May 2015 18:40:53 +0000 (11:40 -0700)]
recreate samples initial migration as strings instead of bytestrings
Diane Trout [Tue, 12 May 2015 18:39:47 +0000 (11:39 -0700)]
recreate initial migration as strings instead of bytestrings
Diane Trout [Tue, 12 May 2015 18:38:12 +0000 (11:38 -0700)]
move experiment templates into the experiments app
Diane Trout [Tue, 5 May 2015 23:31:13 +0000 (16:31 -0700)]
change the default for the DJANGO_SETTINGS_MODULE to be a little more flexible
Diane Trout [Tue, 5 May 2015 23:29:40 +0000 (16:29 -0700)]
simplify library report