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2024-07-23refactor: rename addRIf to update_rif_table.pyJohn Nduli
2024-07-12Rename hash_rdf_graph -> md5hash_ttl_dir.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-12Use correct ttl-dir path when generating checksums.Munyoki Kilyungi
* scripts/index-genenetwork (is_data_modified): Provide directory instead of specific ttl file. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-12fix: remove .py extension for addRif to prevent pylint checksJohn Nduli
2024-07-12refactor: fix mypy and pylint errorsJohn Nduli
2024-07-12feat: copy addRif script from genenetwork1John Nduli
original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py Included some changes to make it python3 compatible
2024-07-08Pass output directory to R/qtl script instead of pulling it from thezsloan
environment Also fixes issue where the control marker keyword was wrong
2024-07-05fix: return query error message from xapianJohn Nduli
2024-07-03Return a "-1" if the turtle directory does not exist.Munyoki Kilyungi
* scripts/index-genenetwork (hash_rdf_graph): Remove check for the turtle directory. (is_data_modified): Ditto. (create_xapian_index): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Generate a checksum for all the ttl files.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Rename to hash_rdf_graph. Generate a checksum of all the turtle files inside the ttl directory that's the basis for the GN virtuoso graph. (create_xapian_index): Rename hash_generif_graph -> hash_rdf_graph. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Add type-hints to hash_generif_graph.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Add proper type hints. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Refactor how the generif md5 sum is calculated and stored in XAPIAN.Munyoki Kilyungi
* scripts/index-genenetwork (hash_generif_graph): Build the generif checksum by directly building it from the file. (is_data_modified): Update how generif-checksums are verified. (create_xapian_index): Update how generif-checksums are stored in XAPIAN. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03Use correct cache for RIF/Wiki entries.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-07-03feat: drop intermediate folders when running parallel xapian compactJohn Nduli
2024-07-03feat: add support for parallel xapian compactJohn Nduli
2024-07-03feat: index rif and wiki without positionsJohn Nduli
2024-07-03feat: drop common words when building rdf cachesJohn Nduli
2024-07-03feat: set 67 parallel processes to run in prodJohn Nduli
2024-07-03fix: remove namespaces since child processes copy the rdf cachesJohn Nduli
2024-07-03fix: use correct prefix and index key; group wiki cache queryJohn Nduli
2024-07-03feat: add wikidata prefix to search apiJohn Nduli
2024-07-03feat: add wikidata indexingJohn Nduli
2024-07-03feat: add global wikicacheJohn Nduli
2024-07-03feat: add sparql query to get wikidataJohn Nduli
2024-06-26Increase max number of results to 50000 for Xapian searchzsloan
This change needs to be accompanied by a change in GN2! If it's lower than the GN2 MAX_SEARCH_RESULTS value, searches will throw an error.
2024-06-24Use dataset Name instead of FullName for indexingzsloan
The Name is generally used as the identifier, while the FullName can container spaces which can cause problems
2024-06-18Revert "Set the file path for the logger."Munyoki Kilyungi
This reverts commit b21102bc4ad3678173e7c94d3e66333ec7c1d40a.
2024-06-18refactor: drop global variablesJohn Nduli
2024-06-17Check table names in Xapian; if not, default to "-1".Munyoki Kilyungi
Without this check, there will always be an error when this script is run with the "is-data-modified" flag should there be no database in the XAPIAN_DIRECTORY. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-17Fetch distinct comments.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-14fix: typehints in index-genenetwork scriptJohn Nduli
2024-06-14fix: fix incorrect parameters in index_query functionJohn Nduli
2024-06-12Move the generated xapian files to the correct directory.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Set the file path for the logger.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Change the date format for the logger.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Log how long it takes to run the indexing script.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Check for a running process by viewing the build dir's contents.Munyoki Kilyungi
In the CI build, the actual build is run in the xapian_directory/build, which is seen as the xapian_directory in this script. The CI handles clean up WRT removing files related to the build process. * scripts/index-genenetwork (create_xapian_index): Create the xapian directory if it doesn't exist. If the xapian directory has files, exit. Create the temporary directory inside the xapian_directory. Remove "build_directory.rmdir()" Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Return 0 if data changes, else exit with 1.Munyoki Kilyungi
* scripts/index-genenetwork (is_data_modified): Replace click.echo with the respective sys.exit call. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Explicitly pass sparql_uri to script.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Rework how the indexes are built.Munyoki Kilyungi
Right now, the checks are done in Guix's build expression. This moves that work to the index-genenetwork script.
2024-06-12Add method to check the validity of the tables+RDF checksums.Munyoki Kilyungi
* scripts/index-genenetwork (verify_checksums): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12Generate a SHA256 checksum for the generif graph.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-12refactor: add db_utils global logger that will be the defaultJohn Nduli
2024-06-12fix: use current_app's logger to log db errorsJohn Nduli
2024-06-12fix: log errors when an exception occurs due to db_utilsJohn Nduli
2024-06-01Use global cache to store generif metadata.Munyoki Kilyungi
This global caches has 3,528 entries and there's no expectation for it to grow significantly. Since child processes inherit the parent’s memory, we can pass the global cache to them, reducing fetch times from 0.001s to 0.00001s, significantly boosting performance when indexing the entire database and enriching results with RDF metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-06-01Add geneRIF to gene index.Munyoki Kilyungi
* scripts/index-genenetwork: Import Template, lru_cache, SPARQLWrapper, JSON (get_rif_metadata): New function. (index_rif_comments): New function. (index_genes): Add rif comments to probeset index. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-20Delete search endpoints for datasets/publications.Munyoki Kilyungi
* gn3/api/metadata.py: Delete "query_and_frame" import. (search_datasets): Delete. (search_publications): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-05-20Remove unused variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 00:50:37 +0000