| Age | Commit message (Expand) | Author |
|---|
| 2022-10-28 | Query genenetwork3 API for search....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.
| Arun Isaac |
| 2022-09-26 | Add xapian database connection utilities....* etc/default_settings.py (XAPIAN_DB_PATH): New variable.
* wqflask/wqflask/database.py: Import xapian.
(xapian_database, xapian_writable_database): New functions.
| Arun Isaac |
| 2022-09-09 | Use `urllib.parse.urljoin` for urls...Use the `urllib.parse.urljoin` function to join urls rather than
string concatenation for uniformity.
| Frederick Muriuki Muriithi |
| 2022-09-08 | Make GN_SERVER_URL the genenetwork3 API endpoint....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.
| Arun Isaac |
| 2022-08-16 | Setup default GN_PROXY setting | Frederick Muriuki Muriithi |
| 2022-02-17 | etc: Close VERSION file after opening....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.
| Arun Isaac |
| 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...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.
| Frederick Muriuki Muriithi |
| 2021-04-30 | autopep8: Fix E301,E302,E303,E304,E305,E306 | BonfaceKilz |
| 2020-08-20 | Replace all references to python2.7 with python3.8...Run:
```
find . -type f -print0 | xargs -0 sed -i \
"s|lib/python2.7/site-packages|lib/python3.8/site-packages|g"
```
| BonfaceKilz |
| 2020-08-19 | Remove extra whitespace(or add it) from comma separated items...See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
| BonfaceKilz |
| 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...Removed some unused JS libraries
| zsloan |
| 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 |
| 2019-02-13 | 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...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 |
| 2018-04-02 | Version bump...Config files are store in https://github.com/genenetwork/gn-deploy-servers repo
| Pjotr Prins |
| 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 PYTHONPAT......it is now in the Guix build.
| Pjotr Prins |
| 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.... * 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
| Pjotr Prins |
| 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 |
| 2016-06-19 | gn_server: SQL handling | Pjotr Prins |
| 2016-06-19 | Remark added | Pjotr Prins |
| 2016-06-19 | Settings: reordering default_settings.py | Pjotr Prins |
