| Age | Commit message (Expand) | Author |
|---|
| 2023-07-30 | Dump species metadata with documentation•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-30 | Conditionally dump documentation | Munyoki Kilyungi |
| 2023-07-30 | Make prefix function have an optional ttl?•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-30 | Revert "Pass port as an optional argument"•••This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643.
| Munyoki Kilyungi |
| 2023-07-30 | Add missing srfi-26 import•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-30 | 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 |
| 2023-07-30 | 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 |
| 2023-07-30 | Move dump-configuration record type to (dump documentation)•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-30 | Construct example SQL query and expected results | Munyoki Kilyungi |
| 2023-07-30 | Pass port to scm->triples•••* dump/triples.scm (scm->triples): Make define have an optional arg fn
that defaults to "triple".
| Munyoki Kilyungi |
| 2023-07-30 | 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 |
| 2023-07-30 | 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 |
| 2023-07-30 | Add table metadata to triple dump | Munyoki Kilyungi |
| 2023-07-30 | Add a section sub-heading for schema triples | Munyoki Kilyungi |
| 2023-07-30 | Wrap the dump title in quotes | Munyoki Kilyungi |
| 2023-07-30 | Replace #` with #'when fetching the name of the defined dump | Munyoki Kilyungi |
| 2023-07-30 | 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 |
| 2023-07-30 | Conditionally autogenerate schema triples during dump | Munyoki Kilyungi |
| 2023-07-30 | 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 |
| 2023-07-30 | 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 |
| 2023-07-30 | 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 |
| 2023-07-30 | Optionally self-document while dumping | Munyoki Kilyungi |
| 2023-07-30 | 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 |
| 2023-07-30 | Remap identifiers | Pjotr Prins |
| 2023-07-30 | README: update | Pjotr Prins |
| 2023-07-30 | Remap identifiers | Pjotr Prins |
| 2023-07-29 | README fixes | Pjotr Prins |
| 2023-07-29 | Updated species list | Pjotr Prins |
| 2023-07-21 | Update wikidata metadata•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Add dct: prefix to genotype dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Update phenotype dump | Munyoki Kilyungi |
| 2023-07-21 | Make define-dump take extra args as key•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Dump prefixes correctly when auto-generating docs•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Dump probesetfreeze metadata using new metadata | Munyoki Kilyungi |
| 2023-07-21 | Dump probeset-metadata using the new syntax•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Dump genotypes with the new syntax•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Use "gn:" and "gn-term:" when dumping phenotypes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Replace "publication:" with "pubmed:"•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Use "gn:" and "gn-terms" prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Make 'inputs' and 'outputs' fields lists•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Remove unnecessary prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Use a min of 4 should the schema triples be many•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Only document a triple if it exists•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-07-21 | Rename 'gn-id' prefix to 'gn'•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 |
