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2018-08-14Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
Added Phenogen track to mapping results Added comparison bar chart figure Simplified global search to not build trait/dataset objects, which speeds thing up considerably Fixed correlation matrix to correctly deal with 0 values Fixed issue where anonymous collections couldn't be created if none already existed
2018-08-10Added the command needed to start up elasticsearchzsloan
I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now.
2018-07-06Added square root transform optionszsloan
Figures now correctly rescale when transforms are applied Fixed height of probability plot Removed some text related to pylmm since it's currently not being used
2018-07-02Added option to transform/normalize trait sample values (log2 and qnorm) on ↵zsloan
trait page Got figures mostly working with transformed values, except for changing the y-axis range of one Fixed issue with the home page "Make Default" button position (as well as the drop-downs in general) Added timeout to Elasticsearch connection to fix related error
2018-06-08Added option to add traits to existing collection, which I had forgotten ↵zsloan
previously
2018-06-08User collections (now stored in ElasticSearch) are reimplemented now and ↵zsloan
should have their full functionality back (adding/removing collections, adding/removing traits, etc)
2018-05-25Fixed issue causing anonymous collections to not work on my branch and ↵zsloan
staging, though still not sure why it's working on production without that change Added script to convert the dryad format genotype files to BIMBAM removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
sample data into ElasticSearch Added option to replace trait page sample/strain values with normalized ones Began editing Lei's scatterplot code Changed elasticsearch_tools' get_elasticsearch_connection so that it can also be used for purposes other than user authentication (by adding a "for_user" parameter)
2018-05-01Merge /home/lei/gene into testingzsloan
2018-05-01Removed all code related to using GEMMA with PLINK input fileszsloan
2018-04-27Added marker filtering for data set groups with larger genotype fileszsloan
Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵zsloan
instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of ↵zsloan
set width Changed to using BIMBAM files to build Marker objects in dataset.py
2018-04-18Removed a little more code in webqtlDatabaseFunction.py and do_searchzsloan
2018-04-16Undoing changes to user_manager.py, because I think they may have caused ↵zsloan
some problem. Probably better to leave this file alone for the time being.
2018-04-16Resolved conflicts after pulling changeszsloan
2018-04-16Removed some unused code from collect.py and user_manager.pyzsloan
2018-04-16Removed file tracer.py that wasn't being usedzsloan
Removed some unused code from the other files listed
2018-04-16Removed a bunch of unused code from the following files:zsloan
marker_regression_gn1.py marker_regression.py do_search.py export_traits.py heatmap.py GeneUtil.py heatmap.html
2018-04-16Merge pull request #318 from pjotrp/testingzsloan
Testing
2018-04-16Merge branch 'testing' of https://github.com/fredmanglis/genenetwork2 into ↵Pjotr Prins
testing
2018-04-16Merge pull request #317 from pjotrp/testingzsloan
Testing
2018-04-16Remove statements that might be causing issuesMuriithi Frederick Muriuki
* I can't swear on this, but it seems the presence of these statements was causing elasticsearch to act weird.
2018-04-16login messages improvedPjotr Prins
2018-04-16Merge remote-tracking branch 'pjotrp/testing' into testingMuriithi Frederick Muriuki
2018-04-16Update mappings for Elasticsearch 6.2. Update loggerMuriithi Frederick Muriuki
* Update the indexes mappings to be compatible with the newer Elasticsearch 6.2.* series. Close the index before updating it, and reopen it after to help with the re-indexing of the data. * Update the error logger to include the exception that was thrown.
2018-04-16Docs on elasticsearch usePjotr Prins
2018-04-15Deactivate analysis of email_address fieldMuriithi Frederick Muriuki
* Prevent elasticsearch from analysing and tokenising the email_address field so as to avoid issue with getting back all email addresses with the same domain as the one being searched for.
2018-04-15Add tests for Forgot Password featureMuriithi Frederick Muriuki
* Add tests to ensure the "Forgot Password" feature works appropriately.
2018-04-15Use existing code. Delay after delete.Muriithi Frederick Muriuki
* Use existing code to get the elasticsearch connection. This should prevent tests from failing in case the way connections to elasticsearch are made change. * Delay a while after deleting to allow elasticsearch to re-index the data, thus preventing subtle bugs in the test.
2018-04-15Fix issue with indentationMuriithi Frederick Muriuki
* Ensure the return is at the correct indentation level so that it is executed correctly.
2018-04-13Last commit didn't conflict for some reason, hopefully this one shouldzsloan
2018-04-13Resolved conflicts for pulling from testing branchzsloan
2018-04-13Check email provided on forgot passwordMuriithi Frederick Muriuki
* Ensure that the user actually provides an email address when they try to use the forgot password feature.
2018-04-13Fix logging in testsMuriithi Frederick Muriuki
* Use the LOG_LEVEL provided by the application settings to enable easy control of logging when running tests. It helps avoid a lot of verbosity when running tests.
2018-04-13Use single entry-point for testsMuriithi Frederick Muriuki
* Remove the run-integration-tests.py, and use the test-website.py as the entry point for all tests. This simplifies running the tests for the site.
2018-04-13Merge remote-tracking branch 'pjotrp/testing' into testingMuriithi Frederick Muriuki
2018-04-12Merge pull request #315 from pjotrp/testingzsloan
README and docs
2018-04-12README and docsPjotr Prins
2018-04-11Added tissue correlation p value to correlation page results, since it was ↵zsloan
missing before Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
2018-04-11Merge remote-tracking branch 'pjotrp/testing' into testingMuriithi Frederick Muriuki
2018-04-10Most code in webqtlUtil.py has been removed. There is so little left that ↵zsloan
the remaining could should be migrated to the files that use them at some point. Some of this code was in the correlation code but not being used, so it wss removed from there as well.
2018-04-09Removed svg.py, which I know isn't used, and webqtlFormData, which I'm ↵zsloan
pretty sure also isn't used any more. Also removed some other unused code from the files listed
2018-04-09Fixed issue that caused and error for certain types of mapping due to ↵zsloan
variable not being initialized Removed a bunch of unused statistical functions from Plot.py and webqtlUtil.py. I figure that if we ever need them again, there's probably some third party library that includes them. Also removed unused file AJAX_table.py and other unused code from several other files
2018-04-09Removed unused code from get_select_dataset.py and get_group_samplelists.py ↵zsloan
scripts
2018-04-09Removed unused code from convert_geno_to_bimbam.py and corestats.pyzsloan
2018-04-09Removed the basicStatistics directory/contents because nothing there was ↵zsloan
being used except corestats, which I moved to utility Removed box plot code from Plot.py since we no longer use it either
2018-04-09Removed unused code from webqtlFormData.pyzsloan
2018-04-09Removed some unused code in webqtlConfig; some might need to be added back ↵zsloan
in later when other third party links are implemented on the trait/collection pages