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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 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
2018-04-11Added tissue correlation p value to correlation page results, since it was mi......Removed a bunch of unused coded from all correlation-related files and the ctl analysis code zsloan
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 the......Some of this code was in the correlation code but not being used, so it wss removed from there as well. zsloan
2018-04-09Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty......Also removed some other unused code from the files listed zsloan
2018-04-09Fixed issue that caused and error for certain types of mapping due to variabl......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 zsloan
2018-04-09Removed unused code from get_select_dataset.py and get_group_samplelists.py s...zsloan
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 bein......Removed box plot code from Plot.py since we no longer use it either zsloan
2018-04-09Removed unused code from webqtlFormData.pyzsloan
2018-04-09Removed some unused code in webqtlConfig; some might need to be added back in...zsloan
2018-04-09Merge pull request #313 from pjotrp/testing-rm-TableTools...Remove TableTools.jszsloan
2018-04-07Dear @zsloan,...This patch removes TableTools. I don't think we use it. I have compared the look and feel of below pages and I see no difference. If that is correct we can simply ditch it by merging this PR. Note that if we are using such functionality this package is considered obsolete by the authors. According to https://datatables.net/extensions/tabletools/: This extension has now been retired and has been replaced by the Buttons and Select extensions. The documentation is retained for legacy reference only. New projects should use Buttons and Select in preference to TableTools. Moving Tabletools CSS --- a/wqflask/wqflask/static/packages/TableTools/media/css/TableTools.css +++ b/wqflask/wqflask/static/packages/TableTools/media/css/TableTools.css @@ -319,3 +319,8 @@ div.DTTT_collection a.DTTT_button { line-height: 20px; } +.no-sort::after { display: none!important; } +.no-sort { pointer-events: none!important; + cursor: default!important; +} + wqflask/wqflask/templates/correlation_matrix.html: <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> wqflask/wqflask/templates/collections/list.html: <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> wqflask/wqflask/templates/search_error.html: <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> wqflask/wqflask/templates/corr_scatterplot.html: <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> wqflask/wqflask/templates/pair_scan_results.html: <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" /> Pjotr Prins
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