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Author SHA1 Message Date
Philipp Bayer
5d8431f4cb Adds test and testdata for new parsing for 23andme-exome-vcf 2014-09-15 16:48:34 +10:00
Philipp Bayer
b21e33fac7 Should fix many timeout errors in errbit 2014-09-14 15:03:31 +10:00
Philipp Bayer
451bb91a91 Merge branch 'master' of github.com:gedankenstuecke/snpr 2014-09-14 14:43:05 +10:00
Philipp Bayer
fec87dd0e0 Fixes another bug in DAS show with broken UserSNPs 2014-09-14 14:42:27 +10:00
Philipp Bayer
b0a27b742b Merge pull request #136 from tsujigiri/tweak_user_snp_insertion 
Remove genotype_id from temp table
 2014-09-10 17:21:09 +10:00
Helge Rausch
56136c2f25 Remove genotype_id from temp table 2014-09-10 08:51:41 +02:00
Philipp Bayer
e11782310f Adds rstrip to 23andme parsing, since the old parser did this too 2014-09-10 10:04:13 +10:00
Philipp Bayer
c3b3053d20 Merge pull request #135 from tsujigiri/tweak_user_snp_insertion 
Don't join temp table with user_snps
 2014-09-09 21:49:02 +10:00
Helge Rausch
9d1b8e2d1a Don't join temp table with user_snps 2014-09-09 13:19:52 +02:00
Philipp Bayer
6f52822725 Merge pull request #134 from tsujigiri/fastestest_import 
Use ActiveRecord to create Snps when parsing
 2014-09-05 06:52:46 +10:00
Helge Rausch
f5a19119f9 Use ActiveRecord to create Snps when parsing 
This way we keep Solr indexing them. Performance impact is low, as we
don't need to import many Snps anymore.
 2014-09-04 09:26:51 +02:00
Philipp Bayer
dd15c14af6 Turns off re-indexing in Solr when UserSNPs are added 2014-09-01 19:23:49 +10:00
Philipp Bayer
f608b9c16f Reintroduces proper schema.rb 2014-09-01 11:59:01 +10:00
Philipp Bayer
60e3d59f2b Turns off commit after every model save, instead turning over to autocommit every 10s or 1000 new objects 2014-09-01 11:27:47 +10:00
Philipp Bayer
171f53dcec git pushMerge branch 'master' of github.com:gedankenstuecke/snpr 2014-09-01 10:50:03 +10:00
Philipp Bayer
0c5a693777 Prevents Solr reindexing of user on login. Users can now log in even if Solr is off. See http://stackoverflow.com/questions/6040493/sunspot-index-only-when-searchable-fields-change 2014-09-01 10:49:50 +10:00
Philipp Bayer
d228526a99 Merge pull request #133 from tsujigiri/fastestest_import 
Send notification to the user after parsing
 2014-09-01 09:56:54 +10:00
Helge Rausch
302db3c5c3 Send notification to the user after parsing 2014-08-31 14:39:19 +02:00
Philipp Bayer
478580da47 Fixes bug in DAS view with dangling user-SNPs 2014-08-31 14:03:19 +10:00
Philipp Bayer
09bb3bb6f7 Merge pull request #132 from tsujigiri/fastestest_import 
Import genotypes using SQL COPY
 2014-08-31 12:18:03 +10:00
Helge Rausch
212fd4492a Remove require 'open3' 2014-08-30 15:19:14 +02:00
Helge Rausch
dbc04a7b6f Add IYG parsing 2014-08-30 15:12:06 +02:00
Helge Rausch
0e143e1fec Add ftdna parsing 2014-08-30 15:12:06 +02:00
Helge Rausch
ed55e1d900 Properly test genotype deletion 2014-08-30 15:12:06 +02:00
Helge Rausch
304a1ba57c Fix sanity check 2014-08-30 15:12:06 +02:00
Helge Rausch
91a4259620 Parse Ancestry genotypes 2014-08-30 15:12:06 +02:00
Helge Rausch
a78f5d9185 Add sanity checks 2014-08-30 15:12:06 +02:00
Helge Rausch
191c6c1496 Have a method for each filetype 2014-08-30 15:12:06 +02:00
Helge Rausch
143b399b88 Update Travis config 2014-08-30 15:12:06 +02:00
Helge Rausch
86b7b4afce Rewrite seeds in SQL to prevent Solr from indexing 2014-08-30 15:12:06 +02:00
Helge Rausch
23a00bb1bb Use schema.rb instead of migrations on Travis 2014-08-30 15:12:06 +02:00
Helge Rausch
da1bd29a5f Remove splitting of Genotype files from preparsing 2014-08-30 15:12:06 +02:00
Helge Rausch
c713f40f59 Include Snp creation in genotype parsing 2014-08-30 15:12:06 +02:00
Helge Rausch
c039918db4 Re-implement COPY approach in Ruby 2014-08-30 15:12:06 +02:00
Helge Rausch
e34aca1bd0 Add experimental genotype import bash script 2014-08-30 15:11:13 +02:00
Philipp Bayer
583ce874e8 Updates mediawiki gem. Fixes test by updating cassette. 2014-08-28 16:27:36 +10:00
Philipp Bayer
de22df8a71 String interpolation ahoy 2014-08-26 17:29:20 +10:00
Philipp Bayer
e391ee02b5 Merge pull request #131 from tsujigiri/remove_exceptional 
Remove exceptional
 2014-08-26 17:27:21 +10:00
Helge Rausch
2cda85d384 Remove exceptional 2014-08-26 09:18:48 +02:00
Philipp Bayer
f6d13e6649 Fixes PlosDetails worker. Honestly 2014-08-26 16:43:20 +10:00
Philipp Bayer
9e3107fc54 Refactors sleep part a bit, fixes one bug 2014-08-26 13:59:54 +10:00
Philipp Bayer
68b3caa76d And again >.< 2014-08-26 13:41:18 +10:00
Philipp Bayer
bd8ff1fd76 Stupid typo 2014-08-26 13:35:03 +10:00
Philipp Bayer
c27a1438ef Fixes a bug with Fitbit show for users with some missing data 2014-08-26 12:31:56 +10:00
Philipp Bayer
1e5af81825 Fixes bug in DAS-controller, still assumed that UserSNPs have user-ids 2014-08-26 11:52:38 +10:00
Philipp Bayer
0b6f591da0 JS notifier does not work on server, removing 2014-08-25 15:03:13 +10:00
Philipp Bayer
c163701a42 Turn off plos-details until 500 fixed 2014-08-25 14:53:16 +10:00
Philipp Bayer
954c470a69 Adds Javascript error notification to Airbrake/errbit 2014-08-25 14:36:32 +10:00
Philipp Bayer
4b10eb8944 Fixes test 2014-08-25 13:48:40 +10:00
Philipp Bayer
abaebf7021 Typo in config 2014-08-25 13:06:55 +10:00