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2022-01-29Automate setting of the development GN3 repoFrederick Muriuki Muriithi
* When developing the GN2 code, there are times we need to use the latest code in GN3, and rather than manually editing the `bin/genenetwork` file every time we need that, this commit enables the use of an environment variable. In this case, launching the application with something like: $ env GN3_DEV_REPO_PATH="$HOME/genenetwork3" ...\ ./bin/genenetwork2 ./the_settings.py -gunicorn-dev will add the path to the development version to the PYTHONPATH. If the GN3_DEV_REPO_PATH variable is not set, then the PYTHONPATH is not altered, and would be as if there is no development version of GN3 in use.
2022-01-29Add "Partial Correlations" UI elements on collections pageFrederick Muriuki Muriithi
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add UI elements to trigger the partial correlations feature * Connect partial correlation view to the application * Point to correct application element for gunicorn
2022-01-28Update PYTHONPATHzsloan
The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).
2022-01-28Revert 'bin: Set shebang to sh instead of bash'zsloan
It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash): ./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpected
2022-01-28Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."Arun Isaac
This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
2022-01-28Revert "bin: Do not set environment variables set by guix shell."Arun Isaac
This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
2022-01-27Fix 'Bad substitution' issueFrederick Muriuki Muriithi
In posix shell, string indexing is undefined. This commit replaces the string indexing with a more portable implementation.
2022-01-06bin: Stop execution on error.Arun Isaac
* bin/genenetwork2: Pass -e flag to sh.
2022-01-06bin: Set shebang to sh instead of bash.Arun Isaac
/bin/sh is present on Guix System and other distros while /bin/bash is present only on other distros. * bin/genenetwork2: Set shebang to sh instead of bash.
2022-01-06bin: Do not set environment variables set by guix shell.Arun Isaac
The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
2022-01-06bin: Set GN2_PROFILE from GUIX_ENVIRONMENT.Arun Isaac
`guix shell' sets the profile path in an environment variable---GUIX_ENVIRONMENT. There is no need to pass it explicity as an input in GN2_PROFILE. * README.md: Remove all references to GN2_PROFILE. * bin/genenetwork2: Set GN2_PROFILE from GUIX_ENVIRONMENT. Do not check the value of GN2_PROFILE now that it is set automatically. Remove all references to GN2_PROFILE in example invocations.
2021-12-01Introduce GN3_PYTHONPATH environment variablePjotr Prins
2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-08-06gunicorn production settings: increase process refresh rate to clean up RAM. ↵Pjotr Prins
Also use the jitter switch.
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" ```
2020-07-25Updating docs and show how to include a local Python modulePjotr Prins
2020-05-12Remove eventletepysodePjotr Prins
2020-04-26Merge master and testingmasterPjotr Prins
2019-09-24Fixed issue that caused logging in to stop working with new GUIX buildzsloan
Removed some unused JS libraries
2019-02-13Removed pylmm references and related functionsPjotr Prins
2018-11-20Added option to select chromosome from trait page when mappingzsloan
Put transform/blocking tools into their own tab (still need to change formatting of tab's contents) Improved appearance of search result page table (still need to change a few other tables) Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool Basic Stats figures now load when the user clicks the tab, to improve initial page load time
2018-10-01- Can now remove cofactors from correlation scatterplot and select them by ↵zsloan
just clicking their row in collection - Cofactor color picker now works in Safari/Macs - Displays N for relevant samples in trait page sample table - Don't show bar chart when N>256 - Mapping loading page contents better centered - Anonymous collections timeout correctly listed as 30 days now - Minor allele frequency can actually be changed for GEMMA now (previously didn't work) - Fixed transcript position marker location for mapping results - Notifies user if their e-mail isn't associated with an account when they attempt to request forgotten password - Users can now map with submitted traits - Histogram width changes depending upon number of bins (need to improve this still) - Improved Q-q plot (previously called "probability plot")
2018-09-05Production updatesGN2
2018-04-16Docs on elasticsearch usePjotr Prins
2018-04-12README and docsPjotr Prins
2018-04-04ES: docPjotr Prins
2018-04-02Testing moved to PythonPjotr Prins
2018-03-26- Disabled PYTHONPATH injection - fix Guix instead, see ↵Pjotr Prins
https://github.com/pjotrp/genenetwork2/commit/63a5c8a42ad02e9126bb207465ff5eca98f6515d - Renamed WQFLASK_SETTINGS to GN2_SETTINGS
2018-03-26Requests addedPjotr 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.
2018-03-26Fix conflictPjotr Prins
2018-03-26Add elasticsearch module to the pathMuriithi Frederick Muriuki
* Add some code to set up the path for the python-elasticsearch module.
2018-02-11Added gunicorn pid so we can not run twicePjotr Prins
2018-02-11Using eventlet workerszsloan
2018-02-10Fix env variable $GEMMA_WRAPPER_COMMANDPjotr Prins
2018-02-10Fixing GEMMA LOCOPjotr Prins
2018-02-10Check for bimbam path and bail out if it is missingPjotr Prins
2018-01-31Startup: longer timeout for gunicorn-dev modePjotr Prins
2018-01-31Startup: added -cli optionPjotr Prins
2018-01-30gunicorn dev and prod modes addedPjotr Prins
2018-01-29Fixed gunicorn examplePjotr Prins
2018-01-29Gunicorn worksPjotr Prins
2018-01-29startup script: adapting for gunicornPjotr Prins
2018-01-29Added checks in startup script, removed r-auwerx pathPjotr Prins
2017-12-20Bring in some earlier work - mostly documentation and startup handlingPjotr Prins
2017-09-14./bin/genenetwork2: add GEM_PATH for gemma-wrapperPjotr 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 14:21:50 +0000