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2018-10-01Missed something when previously resolving the merge conflictzsloan
2018-10-01Resolved conflictzsloan
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ju......- Cofactor color picker now works in Safari/Macs - Displays N for relevant samples in trait page sample table - Don't show bar chart when N>256 - Mapping loading page contents better centered - Anonymous collections timeout correctly listed as 30 days now - Minor allele frequency can actually be changed for GEMMA now (previously didn't work) - Fixed transcript position marker location for mapping results - Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password - Users can now map with submitted traits - Histogram width changes depending upon number of bins (need to improve this still) - Improved Q-q plot (previously called "probability plot") zsloan
2018-09-17Merge pull request #342 from pjotrp/gemma-20180915...Gemma optimized for productionzsloan
2018-09-15Run gemma without debug and checks in productionPjotr Prins
2018-09-15ES commentPjotr Prins
2018-09-15Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingPjotr Prins
2018-09-15Run gemma without debug and checks in productionPjotr Prins
2018-08-23Added "change user to elasticsearch"...Added "change user to elasticsearch" to the description of how to start elasticsearchzsloan
2018-08-15The issue with adding anonymous collections should be fixed nowzsloan
2018-08-15ES commentPjotr Prins
2018-08-14Fixed minor issue in user_manager.pyzsloan
2018-08-14Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotly...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 zsloan
2018-08-10Added the command needed to start up elasticsearch...I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now.zsloan
2018-07-06Added square root transform options...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 zsloan
2018-07-02Added option to transform/normalize trait sample values (log2 and qnorm) on t......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 zsloan
2018-06-08Added option to add traits to existing collection, which I had forgotten prev...zsloan
2018-06-08User collections (now stored in ElasticSearch) are reimplemented now and shou...zsloan
2018-05-25Fixed issue causing anonymous collections to not work on my branch and stagin......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 zsloan
2018-05-17Added script to quantile normalize a data set and enter its normalized sample......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) zsloan
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 files...Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups) zsloan
2018-04-23Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter in......Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py) zsloan
2018-04-19Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py zsloan
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 some...zsloan
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 used...Removed some unused code from the other files listed zsloan
2018-04-16Removed a bunch of unused code from the following files:...marker_regression_gn1.py marker_regression.py do_search.py export_traits.py heatmap.py GeneUtil.py heatmap.html zsloan
2018-04-16Merge pull request #318 from pjotrp/testing...Testingzsloan
2018-04-16Merge branch 'testing' of https://github.com/fredmanglis/genenetwork2 into te...Pjotr Prins
2018-04-16Merge pull request #317 from pjotrp/testing...Testingzsloan
2018-04-16Remove statements that might be causing issues...* I can't swear on this, but it seems the presence of these statements was causing elasticsearch to act weird. Muriithi Frederick Muriuki
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 logger...* 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. Muriithi Frederick Muriuki
2018-04-16Docs on elasticsearch usePjotr Prins
2018-04-15Deactivate analysis of email_address field...* 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. Muriithi Frederick Muriuki
2018-04-15Add tests for Forgot Password feature...* Add tests to ensure the "Forgot Password" feature works appropriately. Muriithi Frederick Muriuki
2018-04-15Use existing code. Delay after delete....* 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. Muriithi Frederick Muriuki
2018-04-15Fix issue with indentation...* Ensure the return is at the correct indentation level so that it is executed correctly. Muriithi Frederick Muriuki
2018-04-13Check email provided on forgot password...* Ensure that the user actually provides an email address when they try to use the forgot password feature. Muriithi Frederick Muriuki
2018-04-13Fix logging in tests...* 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. Muriithi Frederick Muriuki
2018-04-13Use single entry-point for tests...* 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. Muriithi Frederick Muriuki
2018-04-13Merge remote-tracking branch 'pjotrp/testing' into testingMuriithi Frederick Muriuki
2018-04-12Merge pull request #315 from pjotrp/testing...README and docszsloan
2018-04-12README and docsPjotr Prins
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