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2023-12-29Namespace all modules under gn2.Arun Isaac
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
2023-10-06Provide default `CORRELATION_COMMAND` setting. Remove unused import.Frederick Muriuki Muriithi
2023-01-24scripts: Provide help info for script.Frederick Muriuki Muriithi
2022-12-05scripts: add GN2 results parsing to parser scriptFrederick Muriuki Muriithi
* 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
2022-12-03jobs: Add debug UIFrederick Muriuki Muriithi
* 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
2022-11-25mechanical-rob: Parser for GN1 results and some sample resultsFrederick 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.
2022-10-28Refactor: run correlation computation externallyFrederick 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.
2022-10-28Add external process managerFrederick 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.
2022-10-28Remove 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.
2022-09-29Retrieve 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.
2022-09-29Index prefixed fields and add values.Arun Isaac
* wqflask/scripts/index.py (main): Index fields with prefixes, and add values for range queries.
2022-09-29Replace 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.
2022-09-29Open 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.
2022-09-29Abstract out writing documents into a xapian database.Arun Isaac
* wqflask/scripts/index.py (write_document): New function. (main): Use write_document.
2022-09-26Add indexing script for global search.Arun Isaac
* wqflask/scripts/index.py: New file.
2022-09-08Remove sql_alchemy initialisation when profiling correlationsMunyoki Kilyungi
* wqflask/scripts/profile_corrs.py: Remove sqlalchemy, connect_db and shutdown_session. (__main__): Remove "g.db".
2022-09-08Delete dead commentMunyoki Kilyungi
2022-08-12Add a profiling scriptFrederick Muriuki Muriithi
Add a script to enable profiling the code.
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