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2023-07-30Add table-dump? option to dump-configuration recordMunyoki Kilyungi
* 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>
2023-07-30Optionally self-document while dumpingMunyoki Kilyungi
2023-07-30Add a configuration record-type for for the define macroMunyoki Kilyungi
* dump/special-forms.scm: Import (srfi srfi-9 gnu). (<dump-configuration>): New record-type. (define-dump): Use the above record-type.
2023-07-30Remap identifiersPjotr Prins
2023-07-30README: updatePjotr Prins
2023-07-30Remap identifiersPjotr Prins
2023-07-29README fixesPjotr Prins
2023-07-29Updated species listPjotr Prins
2023-07-21Update wikidata metadataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Add dct: prefix to genotype dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Update phenotype dumpMunyoki Kilyungi
2023-07-21Make define-dump take extra args as keyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump prefixes correctly when auto-generating docsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump probesetfreeze metadata using new metadataMunyoki Kilyungi
2023-07-21Dump probeset-metadata using the new syntaxMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump genotypes with the new syntaxMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Use "gn:" and "gn-term:" when dumping phenotypesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Replace "publication:" with "pubmed:"Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Use "gn:" and "gn-terms" prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Make 'inputs' and 'outputs' fields listsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Remove unnecessary prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Use a min of 4 should the schema triples be manyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Only document a triple if it existsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Rename 'gn-id' prefix to 'gn'Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Replace :gn with :gn-id and :gn-termMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump phenotypes with documentation.Munyoki Kilyungi
2023-07-21Make the default ontology "gn-id:"Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump probeset metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Update tissue dump to use gn-term/gn-idMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Replace gn with gn-term and gn-id where suitableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Use size of the results set to come up with sparql exampleMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Replace gn:species with gn-speciesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Update dump-species to have lists for inputs and outputMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Add "gn:species:" prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Convert symbol to a string when show-casing triples in docMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Capitalize species identifierMunyoki Kilyungi
Replace gn:species_mus_musculus with gn:species:Mus_musculus.
2023-07-21Add string-capitalize-firstMunyoki Kilyungi
* dump/strings.scm: Export string-capitalize-first (string-capitalize-first): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Make string->identifier take optional keyword argsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Make dump-data? default to #f when dumping dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Rewrite dump-with-documentation to be order-agnosticMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump dataset metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump publication metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump tissue metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Dump species metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Conditionally dump documentationMunyoki Kilyungi
2023-07-21Make prefix function have an optional ttl?Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Revert "Pass port as an optional argument"Munyoki Kilyungi
This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643.
2023-07-21Add missing srfi-26 importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Create a new procedure for shadowing a file portMunyoki Kilyungi
* dump/documentation.scm (dump): Export call-with-documentation. (call-with-documentation): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Rename auto-documentation-port -> pathMunyoki Kilyungi
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>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-19 16:45:44 +0000