| Age | Commit message (Expand) | Author |
|---|
| 2020-04-22 | Fixed a variety of issues related to users registering and logging in...GN2 should now work when Redis is empty
| zsloan |
| 2020-04-16 | Many changes, including:...- 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"
| zsloan |
| 2020-04-03 | Added option to select cofactors from collection for R/qtl...Fixed some issues with displaying the R/qtl results from the RData HET3-ITP dataa
| zsloan |
| 2020-03-27 | Added integration for using RData files with R/qtl, plus some other changes t... | zsloan |
| 2020-03-10 | Fixed issue that caused some problems when verifying hmac | zsloan |
| 2020-03-09 | I think this should complete consolidating all the collections code. | zsloan |
| 2020-03-03 | Missed one more reference in helper_functions | zsloan |
| 2020-03-03 | was missing a couple files in last commit | zsloan |
| 2020-03-03 | Refactored all the anonymous (not logged-in) user stuff so that both logged-i... | zsloan |
| 2020-02-12 | Fixed issue that broke some logins with the new redis user code | zsloan |
| 2020-01-23 | Forgot to commit new file containing Redis functions | zsloan |
| 2019-10-18 | Fixed issue with collections ordering | zsloan |
| 2019-10-08 | Fixed serious issue that caused output to be wrong for new reaper mapping...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
| zsloan |
| 2019-09-24 | Fixed issue that caused GEMMA to not work with genotype files without cM, tho... | zsloan |
| 2019-09-06 | Fix name of javascript-twitter-post-fetcher | Pjotr Prins |
| 2019-07-23 | Added change to automatically update datasets list using rest api instead of ......Removed option to edit certain html pages, like news, policies, etc
| zsloan |
| 2019-06-07 | Global search and correlation results can handle null expression now | zsloan |
| 2019-06-05 | Fixed issue that caused interval mapping to not work because the python imple......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)
| zsloan |
| 2019-05-24 | Replaced qtlreaper Dataset object with python object | zsloan |
| 2019-05-06 | Removed some unused imports of htmlgen...Fixed a bug that sometimes occurred in search results
Changed order of items on index page
| zsloan |
| 2019-03-18 | - Added PCA traits to correlation matrix. You can't change their names yet or......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
| zsloan |
| 2019-02-22 | Fixed some appearance issues with several tables...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
| zsloan |
| 2019-02-18 | Updated installation instructions and SERVER_PORT for single flask server | Pjotr Prins |
| 2019-02-13 | Removed pylmm references and related functions | Pjotr Prins |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- 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")
| zsloan |
| 2018-08-14 | Added cofactors to correlation scatterplot and changed it to use Plotly...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
| zsloan |
| 2018-07-02 | Added option to transform/normalize trait sample values (log2 and qnorm) on t......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
| zsloan |
| 2018-05-17 | Added script to quantile normalize a data set and enter its normalized sample......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)
| zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-16 | Remove statements that might be causing issues...* I can't swear on this, but it seems the presence of these statements
was causing elasticsearch to act weird.
| Muriithi Frederick Muriuki |
| 2018-04-16 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki |
| 2018-04-16 | Update mappings for Elasticsearch 6.2. Update logger...* 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.
| Muriithi Frederick Muriuki |
| 2018-04-16 | Docs on elasticsearch use | Pjotr Prins |
| 2018-04-15 | Deactivate analysis of email_address field...* 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.
| Muriithi Frederick Muriuki |
| 2018-04-11 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki |
| 2018-04-10 | Most code in webqtlUtil.py has been removed. There is so little left that the......Some of this code was in the correlation code but not being used, so it wss removed from there as well.
| zsloan |
| 2018-04-09 | Removed svg.py, which I know isn't used, and webqtlFormData, which I'm pretty......Also removed some other unused code from the files listed
| zsloan |
| 2018-04-09 | Fixed issue that caused and error for certain types of mapping due to variabl......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
| zsloan |
| 2018-04-09 | Removed unused code from convert_geno_to_bimbam.py and corestats.py | zsloan |
| 2018-04-09 | Removed the basicStatistics directory/contents because nothing there was bein......Removed box plot code from Plot.py since we no longer use it either
| zsloan |
| 2018-04-06 | See #308....Cytoscape and related is now loaded from Guix. Use the latest GN2_PROFILE.
| Pjotr Prins |
| 2018-04-05 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te... | Muriithi Frederick Muriuki |
| 2018-04-04 | ES: doc | Pjotr Prins |
| 2018-03-31 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into te......* Fix conflicts
| Muriithi Frederick Muriuki |
| 2018-03-29 | Type checking in its own file | Pjotr Prins |
| 2018-03-26 | Skip automatic use of EXPLAIN_TEMPLATE_LOADING. | Pjotr Prins |
| 2018-03-26 | Refactor startup config for gunicorn and werkzeug | Pjotr Prins |
| 2018-03-26 | Fix | Pjotr Prins |
| 2018-03-26 | Authentication: some mods around defaults | Pjotr Prins |
| 2018-03-26 | - Disabled PYTHONPATH injection - fix Guix instead, see https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
| Pjotr Prins |
