genenetwork2 - GeneNetwork (2nd generation)

Age	Commit message (Collapse)	Author
2022-11-25	mechanical-rob: Parser for GN1 results and some sample results	Frederick Muriuki Muriithi
	* 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.
2022-10-28	Refactor: run correlation computation externally	Frederick Muriuki Muriithi
	* 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.
2022-10-28	Add external process manager	Frederick Muriuki Muriithi
	* wqflask/jobs/__init__.py: New jobs module * wqflask/jobs/jobs.py: New jobs module * wqflask/scripts/run_external.py: new external process manager.
2022-10-28	Remove xapian indexing script.	Arun Isaac
	The xapian indexing script has been moved to genenetwork3. All further development will happen there. * wqflask/scripts/index.py: Delete file.
2022-09-29	Retrieve year as integer.	Arun Isaac
	* 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.
2022-09-29	Index prefixed fields and add values.	Arun Isaac
	* wqflask/scripts/index.py (main): Index fields with prefixes, and add values for range queries.
2022-09-29	Replace MonadicDictCursor with generator function.	Arun Isaac
	* 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.
2022-09-29	Open xapian database once, but SQL database once for each query.	Arun Isaac
	We reopen the SQL database once for each query because it times out if kept waiting. * wqflask/scripts/index.py (main): Open xapian database once, but SQL database once for each query.
2022-09-29	Abstract out writing documents into a xapian database.	Arun Isaac
	* wqflask/scripts/index.py (write_document): New function. (main): Use write_document.
2022-09-26	Add indexing script for global search.	Arun Isaac
	* wqflask/scripts/index.py: New file.
2022-09-08	Remove sql_alchemy initialisation when profiling correlations	Munyoki Kilyungi
	* wqflask/scripts/profile_corrs.py: Remove sqlalchemy, connect_db and shutdown_session. (__main__): Remove "g.db".
2022-09-08	Delete dead comment	Munyoki Kilyungi

2022-08-12	Add a profiling script	Frederick Muriuki Muriithi
	Add a script to enable profiling the code.