| Age | Commit message (Expand) | Author |
|---|
| 2018-09-17 | Merge pull request #342 from pjotrp/gemma-20180915...Gemma optimized for production | zsloan |
| 2018-09-15 | Run gemma without debug and checks in production | Pjotr Prins |
| 2018-09-15 | ES comment | Pjotr Prins |
| 2018-09-15 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | Pjotr Prins |
| 2018-09-15 | Run gemma without debug and checks in production | Pjotr Prins |
| 2018-08-23 | Added "change user to elasticsearch"...Added "change user to elasticsearch" to the description of how to start elasticsearch | zsloan |
| 2018-08-15 | The issue with adding anonymous collections should be fixed now | zsloan |
| 2018-08-15 | ES comment | Pjotr Prins |
| 2018-08-14 | Fixed minor issue in user_manager.py | zsloan |
| 2018-08-14 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | 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 |
| 2018-08-10 | Added the command needed to start up elasticsearch...I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now. | zsloan |
| 2018-07-06 | Added square root transform options...Figures now correctly rescale when transforms are applied
Fixed height of probability plot
Removed some text related to pylmm since it's currently not being used
| 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 |
| 2018-06-08 | Added option to add traits to existing collection, which I had forgotten prev... | zsloan |
| 2018-06-08 | User collections (now stored in ElasticSearch) are reimplemented now and shou... | zsloan |
| 2018-05-25 | Fixed issue causing anonymous collections to not work on my branch and stagin......Added script to convert the dryad format genotype files to BIMBAM
removed db_uri from parameters of parse_db_uri in gen_select_dataset.py, since it can now just pull it from settings as a global variable
| 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 |
| 2018-05-01 | Merge /home/lei/gene into testing | zsloan |
| 2018-05-01 | Removed all code related to using GEMMA with PLINK input files | zsloan |
| 2018-04-27 | Added marker filtering for data set groups with larger genotype files...Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups)
| zsloan |
| 2018-04-23 | Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter in......Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)
| zsloan |
| 2018-04-19 | Changed width of top bar and a couple other html objects to 100% instead of s......Changed to using BIMBAM files to build Marker objects in dataset.py
| zsloan |
| 2018-04-18 | Removed a little more code in webqtlDatabaseFunction.py and do_search | zsloan |
| 2018-04-16 | Undoing changes to user_manager.py, because I think they may have caused some... | zsloan |
| 2018-04-16 | Resolved conflicts after pulling changes | zsloan |
| 2018-04-16 | Removed some unused code from collect.py and user_manager.py | zsloan |
| 2018-04-16 | Removed file tracer.py that wasn't being used...Removed some unused code from the other files listed
| zsloan |
| 2018-04-16 | Removed a bunch of unused code from the following files:...marker_regression_gn1.py
marker_regression.py
do_search.py
export_traits.py
heatmap.py
GeneUtil.py
heatmap.html
| zsloan |
| 2018-04-16 | Merge pull request #318 from pjotrp/testing...Testing | zsloan |
| 2018-04-16 | Merge branch 'testing' of https://github.com/fredmanglis/genenetwork2 into te... | Pjotr Prins |
| 2018-04-16 | Merge pull request #317 from pjotrp/testing...Testing | 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 | login messages improved | Pjotr Prins |
| 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 |
| 2018-04-15 | Add tests for Forgot Password feature...* Add tests to ensure the "Forgot Password" feature works appropriately.
| Muriithi Frederick Muriuki |
| 2018-04-15 | Use existing code. Delay after delete....* 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.
| Muriithi Frederick Muriuki |
| 2018-04-15 | Fix issue with indentation...* Ensure the return is at the correct indentation level so that it is
executed correctly.
| Muriithi Frederick Muriuki |
| 2018-04-13 | Check email provided on forgot password...* Ensure that the user actually provides an email address when they try
to use the forgot password feature.
| Muriithi Frederick Muriuki |
| 2018-04-13 | Fix logging in tests...* 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.
| Muriithi Frederick Muriuki |
| 2018-04-13 | Use single entry-point for tests...* 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.
| Muriithi Frederick Muriuki |
| 2018-04-13 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki |
| 2018-04-12 | Merge pull request #315 from pjotrp/testing...README and docs | zsloan |
| 2018-04-12 | README and docs | Pjotr Prins |
| 2018-04-11 | Added tissue correlation p value to correlation page results, since it was mi......Removed a bunch of unused coded from all correlation-related files and the ctl analysis code
| zsloan |
| 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 |
