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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)
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Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
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instead of -lmm 1 (Wald test)
Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
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set width
Changed to using BIMBAM files to build Marker objects in dataset.py
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some problem. Probably better to leave this file alone for the time being.
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Removed some unused code from the other files listed
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marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
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Testing
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testing
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Testing
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* I can't swear on this, but it seems the presence of these statements
was causing elasticsearch to act weird.
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* 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.
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* 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.
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* Add tests to ensure the "Forgot Password" feature works appropriately.
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* 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.
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* Ensure the return is at the correct indentation level so that it is
executed correctly.
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* Ensure that the user actually provides an email address when they try
to use the forgot password feature.
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* 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.
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* 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.
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README and docs
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missing before
Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
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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.
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pretty sure also isn't used any more.
Also removed some other unused code from the files listed
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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
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scripts
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being used except corestats, which I moved to utility
Removed box plot code from Plot.py since we no longer use it either
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in later when other third party links are implemented on the trait/collection pages
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Remove TableTools.js
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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" />
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Committing partway through removing a bunch of unused code/files just in case something necessary gets removed
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Testing rm validation plugin
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Testing rm bloat
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https://github.com/genenetwork/genenetwork2/issues/310
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Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
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testing
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