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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.
2018-04-13Check 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
2018-04-09Merge pull request #313 from pjotrp/testing-rm-TableToolszsloan
Remove TableTools.js
2018-04-07Dear @zsloan,Pjotr Prins
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" />
2018-04-06Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-04-06Mapping figure output now gives more accurate informationzsloan
Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
2018-04-06Merge pull request #311 from pjotrp/testing-rm-ValidationPluginzsloan
Testing rm validation plugin
2018-04-06Merge pull request #309 from pjotrp/testing-rm-bloatzsloan
Testing rm bloat
2018-04-06Removing use ValidationPlugin. See ↵Pjotr Prins
https://github.com/genenetwork/genenetwork2/issues/310
2018-04-06See #308.Pjotr Prins
Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
2018-04-05Removed cytoscape - it is in GuixPjotr Prins
2018-04-05Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Muriithi Frederick Muriuki
testing
2018-04-04Changed bar chart y axis range to avoid situation where all variation is ↵zsloan
clustered at the top or bottom
2018-04-04Merge pull request #303 from pjotrp/testingzsloan
Minor edits and document on ES
2018-04-04Authentication: comments addedPjotr Prins
2018-04-04ES: docPjotr Prins
2018-04-04Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2018-04-04Switched to plotly probability plotzsloan
Removed a variety of scripts that weren't being used on the trait page
2018-04-03Merge pull request #302 from pjotrp/testingzsloan
@acenteno added data upload scripts into main repo