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2022-12-29Implement "login" via OAuth2Frederick Muriuki Muriithi
2022-10-28Query 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.
2022-09-26Add 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.
2022-09-09Use `urllib.parse.urljoin` for urlsFrederick Muriuki Muriithi
Use the `urllib.parse.urljoin` function to join urls rather than string concatenation for uniformity.
2022-09-08Make 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.
2022-08-16Setup default GN_PROXY settingFrederick Muriuki Muriithi
2022-02-17etc: 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.
2021-10-25Add "GN2_PROXY" as a configurable optionBonfaceKilz
2021-10-25Add default setting for REDIS_URLBonfaceKilz
2021-09-25Remove hard-coded URL; use configured URLFrederick 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.
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2020-08-20Replace all references to python2.7 with python3.8BonfaceKilz
Run: ``` find . -type f -print0 | xargs -0 sed -i \ "s|lib/python2.7/site-packages|lib/python3.8/site-packages|g" ```
2020-08-19Remove extra whitespace(or add it) from comma separated itemsBonfaceKilz
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
2020-04-28Merge with conflictsPjotr Prins
2020-04-28settings: force SERVER_PORT to align with environment variablePjotr Prins
2020-04-28Added a script for a default runnerPjotr Prins
2020-04-26Merge master and testingmasterPjotr Prins
2020-04-26Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-04-26Updated default_settings to include default GN2 base urlzsloan
2020-04-26URL for finding servicesArthur Centeno
2019-09-24Fixed issue that caused logging in to stop working with new GUIX buildzsloan
Removed some unused JS libraries
2019-07-23Added 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
2019-02-13Removed pylmm references and related functionsPjotr Prins
2018-09-05ELASTICSEARCH settings and fix runserver.py to run without gunicornPjotr Prins
2018-08-14Added cofactors to correlation scatterplot and changed it to use Plotlyzsloan
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
2018-04-02Version bumpPjotr Prins
Config files are store in https://github.com/genenetwork/gn-deploy-servers repo
2018-03-30Fixes related to E-mail forgotten passwordPjotr Prins
2018-03-26Fixing authentication stuff so it uses parameters properly. Also no ↵Pjotr Prins
PYTHONPATH needed as it is now in the Guix build.
2018-01-29Gunicorn worksPjotr Prins
2018-01-29Bumped versionPjotr Prins
2017-12-20VERSIONPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-09-04gemma-wrapper: find binary in profilePjotr Prins
2017-06-02settings: GENENETWORK_FILESPjotr Prins
2017-05-31JS module handlingPjotr Prins
2017-05-21Merge 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
2016-10-11Merge branch 'pjotr-gn2' into testingPjotr Prins
2016-10-09Add version informationPjotr Prins
2016-10-07Add JS path to TWITTER_POST_FETCHERPjotr Prins
2016-10-06Logger: add more granular debug messagesPjotr Prins
2016-09-26Settings: LOCAL_PRIVATE_FILESPjotr Prins
2016-09-25Logger: use output for assessing mapping parametersPjotr Prins
2016-09-25tools: export GENENETWORK_FILES and move cache into TMPDIR/gn2Pjotr Prins
2016-06-24Default to no-GN_SERVER for nowPjotr Prins
2016-06-24Log: and document SQL callsPjotr Prins
2016-06-23Settings: add GN_SERVER_URLPjotr Prins
2016-06-21Logger: switch for logging SQLALCHEMYPjotr Prins
2016-06-21Benchmarking: allow output select with LOG_BENCHPjotr Prins
2016-06-19gn_server: SQL handlingPjotr Prins
2016-06-19Remark addedPjotr Prins
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