| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2018-09-05 | Production updates | GN2 | |
| 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 | |
| 2018-08-14 | 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 | |
| 2018-04-10 | Most 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. | |||
| 2018-04-09 | Removed 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 | |||
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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