| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2023-10-06 | Provide default `CORRELATION_COMMAND` setting. Remove unused import. | Frederick Muriuki Muriithi | |
| 2023-08-10 | Set up defaults and check for mandatory settings | Frederick Muriuki Muriithi | |
| Use etc/default_settings.py to setup defaults for the application. Check for mandatory settings and notify users if any of the mandatory settings are not defined. | |||
| 2022-12-29 | Implement "login" via OAuth2 | Frederick Muriuki Muriithi | |
| 2022-10-28 | Query genenetwork3 API for search. | Arun Isaac | |
| genenetwork2 should be a thin wrapper web UI around the genenetwork3 API. Hence, this move. * etc/default_settings.py (XAPIAN_DB_PATH): Delete variable. * wqflask/wqflask/database.py: Remove xapian import. (xapian_database, xapian_writable_database): Delete functions. * wqflask/wqflask/gsearch.py: Do not import json, xapian, Nothing from pymonad.maybe, base, utility.authentication_tools and wqflask.database. Import MonadicDict from gn3.monads instead of utility.monads and GN3_LOCAL_URL from utility.tools. (GSearch.__init__): Query genenetwork3 search API instead of directly reading a Xapian index. | |||
| 2022-09-26 | Add xapian database connection utilities. | Arun Isaac | |
| * etc/default_settings.py (XAPIAN_DB_PATH): New variable. * wqflask/wqflask/database.py: Import xapian. (xapian_database, xapian_writable_database): New functions. | |||
| 2022-09-09 | Use `urllib.parse.urljoin` for urls | Frederick Muriuki Muriithi | |
| Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity. | |||
| 2022-09-08 | Make GN_SERVER_URL the genenetwork3 API endpoint. | Arun Isaac | |
| From now on, GN_SERVER_URL will be the genenetwork3 API endpoint. For example, GN_SERVER_URL=https://gn3.genenetwork.org/api * wqflask/wqflask/collect.py (view_collection), wqflask/wqflask/partial_correlations_views.py (partial_correlations, poll_partial_correlation_results), wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js (defaultStatusCodeFunctions): Do not append api to GN_SERVER_URL. * etc/default_settings.py (GN_SERVER_URL): Append /api. | |||
| 2022-08-16 | Setup default GN_PROXY setting | Frederick Muriuki Muriithi | |
| 2022-02-17 | etc: Close VERSION file after opening. | Arun Isaac | |
| Use a context manager so that the VERSION file is automatically closed on exiting the block. * etc/default_settings.py: Close VERSION file after opening. | |||
| 2021-10-25 | Add "GN2_PROXY" as a configurable option | BonfaceKilz | |
| 2021-10-25 | Add default setting for REDIS_URL | BonfaceKilz | |
| 2021-09-25 | Remove hard-coded URL; use configured URL | Frederick Muriuki Muriithi | |
| Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi * etc/default_settings.py: remove duplicate configuration variable * wqflask/wqflask/collect.py: use the configured url for the API server Use the configured URL rather that the hard-coded URL that was used for testing out the clustered heatmap generation. | |||
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz | |
| 2020-08-20 | Replace all references to python2.7 with python3.8 | BonfaceKilz | |
| Run: ``` find . -type f -print0 | xargs -0 sed -i \ "s|lib/python2.7/site-packages|lib/python3.8/site-packages|g" ``` | |||
| 2020-08-19 | Remove extra whitespace(or add it) from comma separated items | BonfaceKilz | |
| See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib> | |||
| 2020-04-28 | Merge with conflicts | Pjotr Prins | |
| 2020-04-28 | settings: force SERVER_PORT to align with environment variable | Pjotr Prins | |
| 2020-04-28 | Added a script for a default runner | Pjotr Prins | |
| 2020-04-26 | Merge master and testingmaster | Pjotr Prins | |
| 2020-04-26 | Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testing | zsloan | |
| 2020-04-26 | Updated default_settings to include default GN2 base url | zsloan | |
| 2020-04-26 | URL for finding services | Arthur Centeno | |
| 2019-09-24 | Fixed issue that caused logging in to stop working with new GUIX build | zsloan | |
| Removed some unused JS libraries | |||
| 2019-07-23 | Added 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 | |||
| 2019-02-13 | Removed pylmm references and related functions | Pjotr Prins | |
| 2018-09-05 | ELASTICSEARCH settings and fix runserver.py to run without gunicorn | Pjotr Prins | |
| 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 | |||
| 2018-04-02 | Version bump | Pjotr Prins | |
| Config files are store in https://github.com/genenetwork/gn-deploy-servers repo | |||
| 2018-03-30 | Fixes related to E-mail forgotten password | Pjotr Prins | |
| 2018-03-26 | Fixing authentication stuff so it uses parameters properly. Also no ↵ | Pjotr Prins | |
| PYTHONPATH needed as it is now in the Guix build. | |||
| 2018-01-29 | Gunicorn works | Pjotr Prins | |
| 2018-01-29 | Bumped version | Pjotr Prins | |
| 2017-12-20 | VERSION | Pjotr Prins | |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins | |
| 2017-09-04 | gemma-wrapper: find binary in profile | Pjotr Prins | |
| 2017-06-02 | settings: GENENETWORK_FILES | Pjotr Prins | |
| 2017-05-31 | JS module handling | Pjotr Prins | |
| 2017-05-21 | Merge from the diet branch. | Pjotr Prins | |
| * refactored ./bin/genenetwork2 and /etc/default_settings - better detection of Guix - removed unused parameters, such as GEMMA_RESULT_PATH and TEMP_TRAITS - removing some default settings, such as PYLMM_COMMAND - rename some settings, such as SQL_URI and LOG_SQL_ALCHEMY - added GUIX_JS_PATH for JS modules * Added documentation on installing binary GN2 * Updated Twitter board to latest version in Guix - it had broken * Updated many tools in the latest Guix profile | |||
| 2016-10-11 | Merge branch 'pjotr-gn2' into testing | Pjotr Prins | |
| 2016-10-09 | Add version information | Pjotr Prins | |
| 2016-10-07 | Add JS path to TWITTER_POST_FETCHER | Pjotr Prins | |
| 2016-10-06 | Logger: add more granular debug messages | Pjotr Prins | |
| 2016-09-26 | Settings: LOCAL_PRIVATE_FILES | Pjotr Prins | |
| 2016-09-25 | Logger: use output for assessing mapping parameters | Pjotr Prins | |
| 2016-09-25 | tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2 | Pjotr Prins | |
| 2016-06-24 | Default to no-GN_SERVER for now | Pjotr Prins | |
| 2016-06-24 | Log: and document SQL calls | Pjotr Prins | |
| 2016-06-23 | Settings: add GN_SERVER_URL | Pjotr Prins | |
| 2016-06-21 | Logger: switch for logging SQLALCHEMY | Pjotr Prins | |
| 2016-06-21 | Benchmarking: allow output select with LOG_BENCH | Pjotr Prins | |
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index : genenetwork2 | |
| GeneNetwork (2nd generation) |
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