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This reverts commit cc12fe06593f4957fb2b5b641ebe7e5cf43453b1.
Mistakenly included changes to tools.py that are only for the new guix build
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Increased width of permutation histogram
Increased a couple table widths that had crowded header text on certain browers (maybe just Safari)
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json file
Removed option to edit certain html pages, like news, policies, etc
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implementation of the reaper Dataset object doesn't include the addinterval method (so for those situations I still use reaper)
Fixed issue where the last chromosome wasn't displayed for mapping results (though still need to fix issue where points are drawn too far to the right when a specific range is viewed)
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Fixed a bug that sometimes occurred in search results
Changed order of items on index page
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or add them to a collection from the corr matrix page,
but you can click them and access them from the trait page. I'll add the option to access them from the corr matrix page as well,
but adding the option to change their names might be trickier since they're currently used as their Redis keys. I need some better
way of passing the Redis key around so it can be stored in collections, but this is tricky without changing the structure in ElasticSearch
- Fixed the way temp traits work so you can use them with various functions, like mapping, correlations, network graph, etc
- Fixed some appearance issue where the network graph options were too wide if a trait name was too long
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Fixed issue where cofactor selection screens were broken
Changed case attributes to be applied across groups, though need to discuss this with Rob since it shouldn't always be done this way
Added new inversion transformation
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just clicking their row in collection
- 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")
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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
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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
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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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* 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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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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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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Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
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testing
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testing
* Fix conflicts
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https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d
- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
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PYTHONPATH needed as
it is now in the Guix build.
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* Update functions to make them more testable.
* Update code using updated functions.
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* Instead of checking for the state of elasticsearch at startup, check
the state at the moment the user requests a feature that depends on
elasticsearch.
This reduces the chances that the user is dropped onto an exception
page when elasticsearch server goes down.
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* Add some extra checks to ensure that elasticsearch is running before
presenting the UI to the user.
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* Refactor code that can be used in more than one place to a more
generic method/function that's called by other methods
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* Add configuration variables to enable the system connect to the
configured SMTP server to send out emails.
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* If elasticsearch server is down, or the configuration variables are
not provided at startup or in a configuration file, then do not allow
the system to simply crash, but instead, inform the user that they
cannot use the services that depend on elasticsearch to be running.
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* Add a method to set the configuration variables to None if the
configuration values are not provided at startup or in the
configuration files.
The system already checks for these values, and if they are absent, it
simply fails to display the OAuth service as available for use to
login.
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* Have the authorisation URLs build up from the client id and client
secret values.
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* Elasticsearch need a short delay after adding document for it to index
the document for subsequent access.
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* Add configurations for elasticsearch and github.
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* On successful login via OAuth2, save the details of the user in
elasticsearch store, to avoid hitting the external provider for the
basic details.
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* Collect variables and functions for using the elasticsearch system in
a separate module.
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