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2020-07-08Removed remaining unused references to the old qtlreaperzsloan
2020-07-06Fixed some of the logic with how traits are authenticated to avoid situation ↵zsloan
where a trait is authenticated twice
2020-06-24Temporary partial fix to issue of resources without info; need to add ↵zsloan
something that automatically inserts resources with default privileges
2020-06-20Fixed ports for proxy (though I need to add the port to global variables) ↵zsloan
and also simplified the check_owner_or_admin function a little
2020-06-20Added some admin functionality and fixed issue with temp traitszsloan
2020-06-17A user's id is now set as a parameter if it doesn't already existauthentication_testzsloan
2020-06-17Adding all the authentication stuffzsloan
2020-06-05Commiting other current group/resource management code, plus the new fileszsloan
2020-06-04Really should have split this into many more commits:zsloan
- Now use proxy to pull trait data and hide traits/results that the user doesn't have view permission for - Created a factory method for creating trait ob so it can return None when user doesn't have view permissions (this is why such a large number of files are changed) - Added metadata to permutation export - Added current group management code - Added fixed password verification e-mail code
2020-05-28Added lines calling proxy for publish datasets + added some resource redis ↵zsloan
queries and a missing import for the hmac functions
2020-05-12Merging Danny's changes and Bonface's changes to js importszsloan
2020-05-12Added change for F2s in r/qtl and fixed minor issue in save_user in redis_toolszsloan
2020-05-07Committing current progress on group manager + a minor fix in dataset.pyzsloan
2020-05-06Commiting a few minor changes plus returning rqtl_mapping.py to the same as ↵zsloan
on testing branch before merging Danny's changes and testing them
2020-05-06Replace CSS dependencies for datatablesBonfaceKilz
2020-04-26Merge master and testingmasterPjotr Prins
2020-04-24Replaced hard-coded instances of GN2 urls with ones pulled from settings filezsloan
2020-04-22Fixed a variety of issues related to users registering and logging inzsloan
GN2 should now work when Redis is empty
2020-04-16Many changes, including:zsloan
- Added permutation strata option for R/qtl - Made a variety of aesthetic changes to collections-related pages - Made a variety of aesthetic changes to the multi-trait tool options on the search result and correlation pages - Made some functional changes to collections that prevent duplicate traits and ensure new traits are at the top - The "Default Collection" is now always at the bottom of the collection list and renamed to "Your Default Collection"
2020-04-03Added option to select cofactors from collection for R/qtlzsloan
Fixed some issues with displaying the R/qtl results from the RData HET3-ITP dataa
2020-03-27Added integration for using RData files with R/qtl, plus some other changes ↵zsloan
to how it decides which mapping methods to display on the trait page
2020-03-10Fixed issue that caused some problems when verifying hmaczsloan
2020-03-09I think this should complete consolidating all the collections code.zsloan
2020-03-03Missed one more reference in helper_functionszsloan
2020-03-03was missing a couple files in last commitzsloan
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")
2018-09-05ELASTICSEARCH settings and fix runserver.py to run without gunicornPjotr Prins
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.
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