| Age | Commit message (Expand) | Author |
|---|---|---|
| 2023-07-21 | Replace :gn with :gn-id and :gn-term...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump phenotypes with documentation. | Munyoki Kilyungi |
| 2023-07-21 | Make the default ontology "gn-id:"...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump probeset metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Update tissue dump to use gn-term/gn-id...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Replace gn with gn-term and gn-id where suitable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Use size of the results set to come up with sparql example...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Replace gn:species with gn-species...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Update dump-species to have lists for inputs and output...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Add "gn:species:" prefix...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Convert symbol to a string when show-casing triples in doc...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Capitalize species identifier...Replace gn:species_mus_musculus with gn:species:Mus_musculus. | Munyoki Kilyungi |
| 2023-07-21 | Add string-capitalize-first...* dump/strings.scm: Export string-capitalize-first (string-capitalize-first): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Make string->identifier take optional keyword args...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Make dump-data? default to #f when dumping data...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Rewrite dump-with-documentation to be order-agnostic...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump dataset metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump publication metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump tissue metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Dump species metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Conditionally dump documentation | Munyoki Kilyungi |
| 2023-07-21 | Make prefix function have an optional ttl?...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Revert "Pass port as an optional argument"...This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643. | Munyoki Kilyungi |
| 2023-07-21 | Add missing srfi-26 import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Create a new procedure for shadowing a file port...* dump/documentation.scm (dump): Export call-with-documentation. (call-with-documentation): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Rename auto-documentation-port -> path...We don't need to pass around ports as part of a configuration when we can instead pass in a path that can be used to open a port. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Move dump-configuration record type to (dump documentation)...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Construct example SQL query and expected results | Munyoki Kilyungi |
| 2023-07-21 | Pass port to scm->triples...* dump/triples.scm (scm->triples): Make define have an optional arg fn that defaults to "triple". | Munyoki Kilyungi |
| 2023-07-21 | Pass port as an optional argument...* dump/triples.scm (triple): Add port as an optional argument. Defaults to #t. This enables us to use triple to print to other ports E.g in the case of dumping documentation to a different file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Print out triples with the from Table.Name or Table.Alias...* dump/special-forms.scm (field->datum): New function. (define-dump): Use the field->datum to convert triples into the form Table.Name or Table.Alias. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 2023-07-21 | Add table metadata to triple dump | Munyoki Kilyungi |
| 2023-07-21 | Add a section sub-heading for schema triples | Munyoki Kilyungi |
| 2023-07-21 | Wrap the dump title in quotes | Munyoki Kilyungi |
| 2023-07-21 | Replace #` with #'when fetching the name of the defined dump | Munyoki Kilyungi |
| 2023-07-21 | Use call-with-target-database when dumping schema annotations...* dump/schema-dump.scm (dump-schema-annotations): Replace call-with-genenetwork-database with call-with-target-database. | Munyoki Kilyungi |
| 2023-07-21 | Conditionally autogenerate schema triples during dump | Munyoki Kilyungi |
| 2023-07-21 | Rename dump-configuration slots...* dump/special-forms.scm: Export dump-configuration? Rename dump-configuration-table-metadata -> dump-configuration-triples?; dump-configuration-table-dump -> dump-configuration-table-metadata?; and dump-configuration-auto-document-path -> dump-configuration-auto-documentation-port (<dump-configuration>): Ditto renames. (dump-configuration): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> | Munyoki Kilyungi |
| 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 |
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index : gn-transform-databases | |
| Data transformers for GeneNetwork (particularly to RDF) |
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