| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-27 | Fix Pair-Scan output paths | Frederick Muriuki Muriithi | |
| Related to 4940195460008192b6ca6269e1fb8c172ada4f17c | |||
| 2024-09-27 | Fix R/qtl output paths | zsloan | |
| The script now takes the --outdir parameter as the output directory, only using TMPDIR if nothing is passed "output" in the output directory was also changed to "gn3" to be consistent with recent changes to GN3's code | |||
| 2024-09-12 | Make sure dir exists before running R/qtl | Pjotr Prins | |
| 2024-09-12 | Getting Rqtl to run on fallback | Pjotr Prins | |
| 2024-07-23 | chore: add logging info | John Nduli | |
| 2024-07-23 | chore: mypy and pylint fixes | John Nduli | |
| 2024-07-23 | fix: resolve duplicate errors when updating data | John Nduli | |
| 2024-07-23 | refactor: clean query for insert | John Nduli | |
| 2024-07-23 | refactor: clean up insert query | John Nduli | |
| 2024-07-23 | refactor: reorganize update_rif script to be more pythonic | John Nduli | |
| 2024-07-23 | chore: fix pylint errors | John Nduli | |
| 2024-07-23 | refactor: rename addRIf to update_rif_table.py | John Nduli | |
| 2024-07-12 | Rename hash_rdf_graph -> md5hash_ttl_dir. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-12 | Use 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> | |||
| 2024-07-12 | fix: remove .py extension for addRif to prevent pylint checks | John Nduli | |
| 2024-07-12 | refactor: fix mypy and pylint errors | John Nduli | |
| 2024-07-12 | feat: copy addRif script from genenetwork1 | John Nduli | |
| original: https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/maintainance/addRif.py Included some changes to make it python3 compatible | |||
| 2024-07-08 | Pass output directory to R/qtl script instead of pulling it from the | zsloan | |
| environment Also fixes issue where the control marker keyword was wrong | |||
| 2024-07-03 | Return 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> | |||
| 2024-07-03 | Generate 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> | |||
| 2024-07-03 | Add 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> | |||
| 2024-07-03 | Refactor 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> | |||
| 2024-07-03 | Use correct cache for RIF/Wiki entries. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-07-03 | feat: drop intermediate folders when running parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: add support for parallel xapian compact | John Nduli | |
| 2024-07-03 | feat: index rif and wiki without positions | John Nduli | |
| 2024-07-03 | feat: drop common words when building rdf caches | John Nduli | |
| 2024-07-03 | feat: set 67 parallel processes to run in prod | John Nduli | |
| 2024-07-03 | fix: remove namespaces since child processes copy the rdf caches | John Nduli | |
| 2024-07-03 | fix: use correct prefix and index key; group wiki cache query | John Nduli | |
| 2024-07-03 | feat: add wikidata indexing | John Nduli | |
| 2024-07-03 | feat: add global wikicache | John Nduli | |
| 2024-07-03 | feat: add sparql query to get wikidata | John Nduli | |
| 2024-06-24 | Use dataset Name instead of FullName for indexing | zsloan | |
| The Name is generally used as the identifier, while the FullName can container spaces which can cause problems | |||
| 2024-06-18 | Revert "Set the file path for the logger." | Munyoki Kilyungi | |
| This reverts commit b21102bc4ad3678173e7c94d3e66333ec7c1d40a. | |||
| 2024-06-18 | refactor: drop global variables | John Nduli | |
| 2024-06-17 | Check 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> | |||
| 2024-06-17 | Fetch distinct comments. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-14 | fix: typehints in index-genenetwork script | John Nduli | |
| 2024-06-14 | fix: fix incorrect parameters in index_query function | John Nduli | |
| 2024-06-12 | Move the generated xapian files to the correct directory. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Set the file path for the logger. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Change the date format for the logger. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Log how long it takes to run the indexing script. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Check 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> | |||
| 2024-06-12 | Return 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> | |||
| 2024-06-12 | Explicitly pass sparql_uri to script. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
| 2024-06-12 | Rework 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. | |||
| 2024-06-12 | Add 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> | |||
| 2024-06-12 | Generate a SHA256 checksum for the generif graph. | Munyoki Kilyungi | |
| Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | |||
 |
index : genenetwork3 | |
| GeneNetwork3 REST API for data science and machine learning |
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