| Age | Commit message (Expand) | Author |
|---|
| 2022-02-17 | bin: Allow for not starting redis....redis needs to be started and managed as a separate service. We create
a flag NO_REDIS so that it can be so. If NO_REDIS is not defined, the
present behavior of starting redis remains. Thus current use cases are
not broken.
* bin/genenetwork2: Allow for not starting redis with the NO_REDIS
flag.
| Arun Isaac |
| 2022-02-07 | Double quote shell variables to prevent globbing and word splitting | Frederick Muriuki Muriithi |
| 2022-01-29 | Automate setting of the development GN3 repo...* 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.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Add "Partial Correlations" UI elements on collections page...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
| Frederick Muriuki Muriithi |
| 2022-01-28 | Update PYTHONPATH...The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production). | zsloan |
| 2022-01-28 | Revert 'bin: Set shebang to sh instead of bash'...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 | zsloan |
| 2022-01-28 | Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."...This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
| Arun Isaac |
| 2022-01-28 | Revert "bin: Do not set environment variables set by guix shell."...This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
| Arun Isaac |
| 2022-01-27 | Fix 'Bad substitution' issue...In posix shell, string indexing is undefined. This commit replaces the
string indexing with a more portable implementation.
| Frederick Muriuki Muriithi |
| 2022-01-06 | bin: Stop execution on error....* bin/genenetwork2: Pass -e flag to sh.
| Arun Isaac |
| 2022-01-06 | bin: Set shebang to sh instead of bash..../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.
| Arun Isaac |
| 2022-01-06 | bin: Do not set environment variables set by guix shell....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.
| Arun Isaac |
| 2022-01-06 | bin: Set GN2_PROFILE from GUIX_ENVIRONMENT....`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.
| Arun Isaac |
| 2021-12-01 | Introduce GN3_PYTHONPATH environment variable | Pjotr Prins |
| 2021-10-28 | Remove all elasticsearch references in gn2 | BonfaceKilz |
| 2021-08-06 | gunicorn production settings: increase process refresh rate to clean up RAM. ......the jitter switch.
| Pjotr Prins |
| 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 |
| 2020-07-25 | Updating docs and show how to include a local Python module | Pjotr Prins |
| 2020-05-12 | Remove eventletepysode | Pjotr Prins |
| 2020-04-26 | Merge master and testingmaster | Pjotr Prins |
| 2019-09-24 | Fixed issue that caused logging in to stop working with new GUIX build...Removed some unused JS libraries
| zsloan |
| 2019-02-13 | Removed pylmm references and related functions | Pjotr Prins |
| 2018-11-20 | Added option to select chromosome from trait page when mapping...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
| zsloan |
| 2018-10-01 | - Can now remove cofactors from correlation scatterplot and select them by ju......- 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")
| zsloan |
| 2018-09-05 | Production updates | GN2 |
| 2018-04-16 | Docs on elasticsearch use | Pjotr Prins |
| 2018-04-12 | README and docs | Pjotr Prins |
| 2018-04-04 | ES: doc | Pjotr Prins |
| 2018-04-02 | Testing moved to Python | Pjotr Prins |
| 2018-03-26 | - Disabled PYTHONPATH injection - fix Guix instead, see https://github.com/pj......- Renamed WQFLASK_SETTINGS to GN2_SETTINGS
| Pjotr Prins |
| 2018-03-26 | Requests added | 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 |
| 2018-03-26 | Fix conflict | Pjotr Prins |
| 2018-03-26 | Add elasticsearch module to the path...* Add some code to set up the path for the python-elasticsearch module.
| Muriithi Frederick Muriuki |
| 2018-02-11 | Added gunicorn pid so we can not run twice | Pjotr Prins |
| 2018-02-11 | Using eventlet workers | zsloan |
| 2018-02-10 | Fix env variable $GEMMA_WRAPPER_COMMAND | Pjotr Prins |
| 2018-02-10 | Fixing GEMMA LOCO | Pjotr Prins |
| 2018-02-10 | Check for bimbam path and bail out if it is missing | Pjotr Prins |
| 2018-01-31 | Startup: longer timeout for gunicorn-dev mode | Pjotr Prins |
| 2018-01-31 | Startup: added -cli option | Pjotr Prins |
| 2018-01-30 | gunicorn dev and prod modes added | Pjotr Prins |
| 2018-01-29 | Fixed gunicorn example | Pjotr Prins |
| 2018-01-29 | Gunicorn works | Pjotr Prins |
| 2018-01-29 | startup script: adapting for gunicorn | Pjotr Prins |
| 2018-01-29 | Added checks in startup script, removed r-auwerx path | Pjotr Prins |
| 2017-12-20 | Bring in some earlier work - mostly documentation and startup handling | Pjotr Prins |
| 2017-09-14 | ./bin/genenetwork2: add GEM_PATH for gemma-wrapper | Pjotr Prins |
| 2017-09-04 | gemma-wrapper: find binary in profile | Pjotr Prins |
| 2017-06-02 | settings: GENENETWORK_FILES | Pjotr Prins |
