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2020-03-03Refactored all the anonymous (not logged-in) user stuff so that both ↵zsloan
logged-in and anonymous users share the same code
2020-02-12Fixed issue that broke some logins with the new redis user codezsloan
2020-01-23Forgot to commit new file containing Redis functionszsloan
2019-10-18Fixed issue with collections orderingzsloan
2019-10-08Fixed serious issue that caused output to be wrong for new reaper mappingzsloan
Haplotype analyst now works for GEMMA Increased margin a bit to fix minor issue with buttons getting cut off on certain Safari versions for bar chart
2019-09-24Fixed issue that caused GEMMA to not work with genotype files without cM, ↵zsloan
though this issue still needs to be dealt with to get the new qtlreaper working
2019-09-06Fix name of javascript-twitter-post-fetcherPjotr Prins
2019-07-23Added change to automatically update datasets list using rest api instead of ↵zsloan
json file Removed option to edit certain html pages, like news, policies, etc
2019-06-07Global search and correlation results can handle null expression nowzsloan
2019-06-05Fixed issue that caused interval mapping to not work because the python ↵zsloan
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)
2019-05-24Replaced qtlreaper Dataset object with python objectzsloan
2019-05-06Removed some unused imports of htmlgenzsloan
Fixed a bug that sometimes occurred in search results Changed order of items on index page
2019-03-18- Added PCA traits to correlation matrix. You can't change their names yet ↵zsloan
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
2019-02-22Fixed some appearance issues with several tableszsloan
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
2019-02-18Updated installation instructions and SERVER_PORT for single flask serverPjotr Prins
2019-02-13Removed pylmm references and related functionsPjotr Prins
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
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")
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
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
2018-07-02Added option to transform/normalize trait sample values (log2 and qnorm) on ↵zsloan
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
2018-05-17Added script to quantile normalize a data set and enter its normalized ↵zsloan
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)
2018-04-16Resolved conflicts after pulling changeszsloan
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.
2018-04-16Merge 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.
2018-04-11Merge 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 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
2018-04-06See #308.Pjotr Prins
Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
2018-04-05Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Muriithi Frederick Muriuki
testing
2018-04-04ES: docPjotr Prins
2018-03-31Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵Muriithi Frederick Muriuki
testing * Fix conflicts
2018-03-29Type checking in its own filePjotr Prins
2018-03-26Skip automatic use of EXPLAIN_TEMPLATE_LOADING.Pjotr Prins
2018-03-26Refactor startup config for gunicorn and werkzeugPjotr Prins
2018-03-26FixPjotr Prins
2018-03-26Authentication: some mods around defaultsPjotr Prins
2018-03-26- Disabled PYTHONPATH injection - fix Guix instead, see ↵Pjotr Prins
https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-03-26Update module to make it more testableMuriithi Frederick Muriuki
* Update functions to make them more testable. * Update code using updated functions.
2018-03-26Check elasticsearch at point of useMuriithi Frederick Muriuki
* 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.
2018-03-26Add check for elasticsearchMuriithi Frederick Muriuki
* Add some extra checks to ensure that elasticsearch is running before presenting the UI to the user.
2018-03-26Refactor common items to more generic methods.Muriithi Frederick Muriuki
* Refactor code that can be used in more than one place to a more generic method/function that's called by other methods
2018-03-26Add SMTP configuration variablesMuriithi Frederick Muriuki
* Add configuration variables to enable the system connect to the configured SMTP server to send out emails.
2018-03-26Fail safely if elasticsearch is down or unconfiguredMuriithi Frederick Muriuki
* 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.
2018-03-26Set to None if no value providedMuriithi Frederick Muriuki
* 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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