genenetwork2/etc, branch lmdb-code/refactoringGeneNetwork (2nd generation)
http://git.genenetwork.org/genenetwork2/atom?h=lmdb-code%2Frefactoring2022-12-29T00:13:31+00:00Implement "login" via OAuth22022-12-29T00:13:31+00:00Frederick Muriuki Muriithi2022-12-28T02:57:13+00:00urn:sha1:bc709d1aaf1d4ce752394be9d575414de0c66307Query genenetwork3 API for search.2022-10-28T09:25:56+00:00Arun Isaac2022-10-28T09:25:56+00:00urn:sha1:fcf257bff816703433d10b942f959dbb78f6c5e3
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.
Add xapian database connection utilities.2022-09-26T08:09:45+00:00Arun Isaac2022-09-01T10:21:43+00:00urn:sha1:66a6593daf4580f3056c96ccfc658b556ea619fc
* etc/default_settings.py (XAPIAN_DB_PATH): New variable.
* wqflask/wqflask/database.py: Import xapian.
(xapian_database, xapian_writable_database): New functions.
Use `urllib.parse.urljoin` for urls2022-09-09T01:43:05+00:00Frederick Muriuki Muriithi2022-09-09T01:43:05+00:00urn:sha1:9dd474141c968dd9b22bbb11f3b2af80b31aa530
Use the `urllib.parse.urljoin` function to join urls rather than
string concatenation for uniformity.
Make GN_SERVER_URL the genenetwork3 API endpoint.2022-09-08T17:29:49+00:00Arun Isaac2022-09-08T17:10:35+00:00urn:sha1:203d073c9c28b2aa26c78718160136dab6dd8470
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.
Setup default GN_PROXY setting2022-08-16T03:42:10+00:00Frederick Muriuki Muriithi2022-08-16T03:42:10+00:00urn:sha1:62ec9231724fef6d94038d8f76bbda33ca0a209fetc: Close VERSION file after opening.2022-02-17T17:23:09+00:00Arun Isaac2022-02-17T12:55:55+00:00urn:sha1:25a817bfa97fcb6d202397252e55bba088ead32d
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.
Add "GN2_PROXY" as a configurable option2021-10-25T11:00:14+00:00BonfaceKilz2021-10-20T09:28:44+00:00urn:sha1:cc3ae4707d2418712d13261d4bf9d5a509169c7eAdd default setting for REDIS_URL2021-10-25T11:00:14+00:00BonfaceKilz2021-10-12T11:19:03+00:00urn:sha1:2f26b77c7be370dad03e9b8e2ce7f6040ccce528Remove hard-coded URL; use configured URL2021-09-25T02:22:23+00:00Frederick Muriuki Muriithi2021-09-25T02:22:23+00:00urn:sha1:62f26b901e49effb0105e517093fd873815c470c
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.