genenetwork2/wqflask/scripts, branch lmdb-code/refactoringGeneNetwork (2nd generation)
http://git.genenetwork.org/genenetwork2/atom?h=lmdb-code%2Frefactoring2023-01-24T09:08:07+00:00scripts: Provide help info for script.2023-01-24T09:08:07+00:00Frederick Muriuki Muriithi2023-01-24T09:08:07+00:00urn:sha1:72ba40a0f4174232937af111a11e7b91d9edc707scripts: add GN2 results parsing to parser script2022-12-05T09:17:59+00:00Frederick Muriuki Muriithi2022-12-05T09:17:59+00:00urn:sha1:47f032329f967440f44889ee856f1a8510fb773c
* wqflask/scripts/parse_corr_gn1_results_to_csv.py: Rename script
* wqflask/scripts/parse_corr_html_results_to_csv.py:
* Use argparse to parse CLI arguments
* Add parsing for GN2 results
jobs: Add debug UI2022-12-03T03:43:27+00:00Frederick Muriuki Muriithi2022-12-03T03:43:27+00:00urn:sha1:1a651da72faf987f7e3d0c7ba4c60cafe850c7a0
* wqflask/scripts/run_external.py: Save the actual return code
* wqflask/wqflask/__init__.py: Use new jobs blueprint
* wqflask/wqflask/api/jobs.py: Add new jobs debug route
* wqflask/wqflask/templates/jobs/debug.html: new template for when job
is found
* wqflask/wqflask/templates/jobs/no-such-job.html: new template for
when the job is not found
mechanical-rob: Parser for GN1 results and some sample results2022-11-25T10:38:12+00:00Frederick Muriuki Muriithi2022-11-25T10:29:06+00:00urn:sha1:e33a3a78d33f409ae20c8486d0bd2453f189e2b1
* test/requests/correlation_results_text_files/*results.csv: csv files
with sample results from GN1 for the trait `1435464_at` in dataset
`HC_M2_0606_P`.
* wqflask/scripts/parse_corr_gn1_results_to_csv.py: parser for results
from GN1 when saved to a html file.
Refactor: run correlation computation externally2022-10-28T12:58:01+00:00Frederick Muriuki Muriithi2022-10-28T08:51:50+00:00urn:sha1:0bb49f9873e958cd480f7c9fc20f3a8db6f62003
* wqflask/scripts/corr_compute.py: move correlation computation to
external script.
* wqflask/wqflask/templates/loading_corrs.html: Provide UI to display
while computation is still not complete.
* wqflask/wqflask/views.py: Dispatch correlation computation to
external script and display appropriate UI for each valid state of
the computation.
Add external process manager2022-10-28T12:55:30+00:00Frederick Muriuki Muriithi2022-10-24T11:14:17+00:00urn:sha1:560eb051e127fe4b8b93104200fe55512a72038f
* wqflask/jobs/__init__.py: New jobs module
* wqflask/jobs/jobs.py: New jobs module
* wqflask/scripts/run_external.py: new external process manager.
Remove xapian indexing script.2022-10-28T08:00:58+00:00Arun Isaac2022-10-28T08:00:58+00:00urn:sha1:38e7b62c2e94fe4ae1dbaa91349b7b36792685ac
The xapian indexing script has been moved to genenetwork3. All further
development will happen there.
* wqflask/scripts/index.py: Delete file.
Retrieve year as integer.2022-09-29T10:45:48+00:00Arun Isaac2022-09-29T10:35:11+00:00urn:sha1:ef17e6b57b267922ad0af2423e5d6d523458c8ed
* wqflask/scripts/index.py (main): Retrieve year as an integer from
the SQL database.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Convert year from
integer to string.
Index prefixed fields and add values.2022-09-29T10:45:47+00:00Arun Isaac2022-09-28T16:26:42+00:00urn:sha1:d47977406a8c86e9e3afbfeb6b1779b041f7f4f6
* wqflask/scripts/index.py (main): Index fields with prefixes, and add
values for range queries.
Replace MonadicDictCursor with generator function.2022-09-29T10:45:47+00:00Arun Isaac2022-09-28T13:09:54+00:00urn:sha1:b23c36a8c7b66296cf972ac7b3dedfe8d427690c
* wqflask/utility/monads.py (MonadicDictCursor): Delete class.
(sql_query_mdict): New function.
* wqflask/scripts/index.py: Import sql_query_mdict instead of
MonadicDictCursor.
(main): Use sql_query_mdict.