| Age | Commit message (Expand) | Author |
|---|---|---|
| 2023-07-21 | Make dumping optional, defaulting to #t...There may be a case where one just wants to dump metadata about the s-exps only. | Munyoki Kilyungi |
| 2023-07-21 | Add table-dump? option to dump-configuration record...* dump/special-forms.scm: Export dump-configuration-table-dump?. (<dump-configuration>): Add dump-configuration-table-dump. (dump-configuration): Make table-dump? default to #t. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Optionally self-document while dumping | Munyoki Kilyungi |
| 2023-07-21 | Add a configuration record-type for for the define macro...* dump/special-forms.scm: Import (srfi srfi-9 gnu). (<dump-configuration>): New record-type. (define-dump): Use the above record-type. | Munyoki Kilyungi |
| 2023-07-18 | Ignore emacs temporary backup files | Frederick Muriuki Muriithi |
| 2023-06-28 | Updated species.ttl | Pjotr Prins |
| 2023-06-28 | Add species mapping to wikidata to schema | Pjotr Prins |
| 2023-06-26 | Add "-m manifest.scm" flag to guix shell commands | Munyoki Kilyungi |
| 2023-06-24 | Fix documentation errors that were leading to confusion | Frederick Muriuki Muriithi |
| 2023-06-24 | Add some missing dependencies | Frederick Muriuki Muriithi |
| 2023-06-21 | Fix failing tests...* dump/special-forms.scm: Export map-alist. * tests.scm: Import strings, and special-forms. | Munyoki Kilyungi |
| 2023-06-19 | Chunk probeset dump...The probeset table has many columns, with about 5Million rows. As such, the dump can be huge. One problem with the dump is that rapper fails with an out-of-memory error. This commit chunks the data to make linting and uploading data more manageable. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-15 | Change the transaction log mode to 'autocommit' when deleting graph...During typical server operations, deleting one or more graphs containing a large number of triples can consume available memory to the point where the operation cannot be completed, and thus the graph can't be deleted. Such large graphs can be cleared by changing the transaction log mode to autocommit. Read the following for more: https://vos.openlinksw.com/owiki/wiki/VOS/VirtTipsAndTricksGuideDeleteLargeGraphs Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add a dataset's full name when dumping...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Use PublishFreeze Name as a fallback for InfoPageName...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Annotate a phenotype dataset with 'dataset:...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Replace "Unknown" in Publication fields with an empty string...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Annotate publications without a pmid with "unpublished"...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Use "publication:" as an identifier for publications...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Remove check for confidentiality/publicity during dataset dump...Should a dataset not be confidential/public, it's marked as private. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add geoPlatfrom to dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add missing Species join when dumping datasets...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Use the correct title for the a dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Rename AboutProcessing alias to AboutDataProcessing...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Replace citations to source from Datasets instead of InfoFiles...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Rename sql-alias of GN notes during dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add rdf defs for datasetOfSpecies...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add publicationTitle to dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Make geoSeries a link during dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Minor identation fix...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Add organization to dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Use NCBI taxonomy browser instead of uniprot...NCBI presents data in a user friendly way from the taxid. To get the same data from uniprot, you need a unique identify which requires an extra query to retrieve. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Cast longtext fields to fix broket utf-8 characters...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Remove dead comments...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Remove "^[Nn]one$" from some fields from the InfoFiles table...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Default to InfoFiles with the Dataset being a fallback for citations...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-06-12 | Make ((g/ph)enotype/probeset)Dataset subset of Dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Dump OMIM as a normal string without any annotation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Fix broken utf-8 strings in abstract field...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Add probeset as an extra prefix...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Delete unused prefixes...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Replace species with inbredSet metadata when dumping info-files...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Only dump public data...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Allow upleading all files in a directory to virtuoso...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Replace PUT with a POST when uploading data in virtuoso...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Sanitize a probeset's description...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Update the probeset's identifier(object)...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Make a probeset's tissue multiset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Make a probeset's alias a multiset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-05-30 | Move probeset metadata used for a given experiment to it's own dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
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| Data transformers for GeneNetwork (particularly to RDF) |
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