| Age | Commit message (Collapse) | Author |
|---|
|
|
|
There is not much use having a separate version file. Besides, not
having a separate file saves us all the trouble of dealing with the
path to that file.
|
|
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
|
|
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.
|
|
|
|
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.
|
|
* etc/default_settings.py (XAPIAN_DB_PATH): New variable.
* wqflask/wqflask/database.py: Import xapian.
(xapian_database, xapian_writable_database): New functions.
|
|
Use the `urllib.parse.urljoin` function to join urls rather than
string concatenation for uniformity.
|
|
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.
|
|
|
|
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.
|
|
|
|
|
|
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.
|
|
|
|
Run:
```
find . -type f -print0 | xargs -0 sed -i \
"s|lib/python2.7/site-packages|lib/python3.8/site-packages|g"
```
|
|
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Removed some unused JS libraries
|
|
json file
Removed option to edit certain html pages, like news, policies, etc
|
|
|
|
|
|
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
|
|
Config files are store in https://github.com/genenetwork/gn-deploy-servers repo
|
|
|
|
PYTHONPATH needed as
it is now in the Guix build.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* 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
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
