| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2018-09-05 | Production updates | GN2 | |
| 2018-08-23 | Added "change user to elasticsearch" | zsloan | |
| Added "change user to elasticsearch" to the description of how to start elasticsearch | |||
| 2018-08-15 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | zsloan | |
| production | |||
| 2018-08-15 | The issue with adding anonymous collections should be fixed now | zsloan | |
| 2018-08-15 | ES comment | Pjotr Prins | |
| 2018-08-14 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | zsloan | |
| production | |||
| 2018-08-14 | Fixed minor issue in user_manager.py | zsloan | |
| 2018-08-14 | Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into ↵ | zsloan | |
| production | |||
| 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 | zsloan | |
| 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 | |||
| 2018-08-10 | Added the command needed to start up elasticsearch | zsloan | |
| I added the command to start elasticsearch, since I've had to look it up/ask Pjotr about it a couple times now. | |||
| 2018-07-06 | Added square root transform options | zsloan | |
| 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 | |||
| 2018-07-02 | Added 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 | |||
| 2018-06-08 | Added option to add traits to existing collection, which I had forgotten ↵ | zsloan | |
| previously | |||
| 2018-06-08 | User collections (now stored in ElasticSearch) are reimplemented now and ↵ | zsloan | |
| should have their full functionality back (adding/removing collections, adding/removing traits, etc) | |||
| 2018-05-25 | Fixed issue causing anonymous collections to not work on my branch and ↵ | zsloan | |
| staging, though still not sure why it's working on production without that change 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 | |||
| 2018-05-17 | Added 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) | |||
| 2018-05-01 | 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 | zsloan | |
| Fixed issue where GEMMA + LOCO wasn't working with AIL (and probably some other groups) | |||
| 2018-04-23 | Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter ↵ | zsloan | |
| instead of -lmm 1 (Wald test) Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py) | |||
| 2018-04-19 | Changed width of top bar and a couple other html objects to 100% instead of ↵ | zsloan | |
| set width Changed to using BIMBAM files to build Marker objects in dataset.py | |||
| 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 ↵ | zsloan | |
| some problem. Probably better to leave this file alone for the time being. | |||
| 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 | zsloan | |
| Removed some unused code from the other files listed | |||
| 2018-04-16 | Removed a bunch of unused code from the following files: | zsloan | |
| marker_regression_gn1.py marker_regression.py do_search.py export_traits.py heatmap.py GeneUtil.py heatmap.html | |||
| 2018-04-16 | Merge pull request #318 from pjotrp/testing | zsloan | |
| Testing | |||
| 2018-04-16 | Merge branch 'testing' of https://github.com/fredmanglis/genenetwork2 into ↵ | Pjotr Prins | |
| testing | |||
| 2018-04-16 | Merge pull request #317 from pjotrp/testing | zsloan | |
| Testing | |||
| 2018-04-16 | Remove statements that might be causing issues | Muriithi Frederick Muriuki | |
| * I can't swear on this, but it seems the presence of these statements was causing elasticsearch to act weird. | |||
| 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 | Muriithi 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. | |||
| 2018-04-16 | Docs on elasticsearch use | Pjotr Prins | |
| 2018-04-15 | Deactivate analysis of email_address field | Muriithi 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. | |||
| 2018-04-15 | Add tests for Forgot Password feature | Muriithi Frederick Muriuki | |
| * Add tests to ensure the "Forgot Password" feature works appropriately. | |||
| 2018-04-15 | Use existing code. Delay after delete. | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-04-15 | Fix issue with indentation | Muriithi Frederick Muriuki | |
| * Ensure the return is at the correct indentation level so that it is executed correctly. | |||
| 2018-04-13 | Last commit didn't conflict for some reason, hopefully this one should | zsloan | |
| 2018-04-13 | Resolved conflicts for pulling from testing branch | zsloan | |
| 2018-04-13 | Check email provided on forgot password | Muriithi Frederick Muriuki | |
| * Ensure that the user actually provides an email address when they try to use the forgot password feature. | |||
| 2018-04-13 | Fix logging in tests | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-04-13 | Use single entry-point for tests | Muriithi Frederick Muriuki | |
| * 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. | |||
| 2018-04-13 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki | |
| 2018-04-12 | Merge pull request #315 from pjotrp/testing | zsloan | |
| README and docs | |||
| 2018-04-12 | README and docs | Pjotr Prins | |
| 2018-04-11 | Added tissue correlation p value to correlation page results, since it was ↵ | zsloan | |
| missing before Removed a bunch of unused coded from all correlation-related files and the ctl analysis code | |||
| 2018-04-11 | Merge remote-tracking branch 'pjotrp/testing' into testing | Muriithi Frederick Muriuki | |
 |
index : genenetwork2 | |
| GeneNetwork (2nd generation) |
| about summary refs log tree commit diff |