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2023-07-30Make string->identifier take optional keyword argsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Make dump-data? default to #f when dumping dataMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Rewrite dump-with-documentation to be order-agnosticMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Dump dataset metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Dump publication metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Dump tissue metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Dump species metadata with documentationMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Conditionally dump documentationMunyoki Kilyungi
2023-07-30Make prefix function have an optional ttl?Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Revert "Pass port as an optional argument"Munyoki Kilyungi
This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643.
2023-07-30Add missing srfi-26 importMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Create 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>
2023-07-30Rename 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>
2023-07-30Move dump-configuration record type to (dump documentation)Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-30Construct example SQL query and expected resultsMunyoki Kilyungi
2023-07-30Pass port to scm->triplesMunyoki Kilyungi
* dump/triples.scm (scm->triples): Make define have an optional arg fn that defaults to "triple".
2023-07-30Pass port as an optional argumentMunyoki Kilyungi
* 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>
2023-07-30Print out triples with the from Table.Name or Table.AliasMunyoki Kilyungi
* 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>
2023-07-30Add table metadata to triple dumpMunyoki Kilyungi
2023-07-30Add a section sub-heading for schema triplesMunyoki Kilyungi
2023-07-30Wrap the dump title in quotesMunyoki Kilyungi
2023-07-30Replace #` with #'when fetching the name of the defined dumpMunyoki Kilyungi
2023-07-30Use call-with-target-database when dumping schema annotationsMunyoki Kilyungi
* dump/schema-dump.scm (dump-schema-annotations): Replace call-with-genenetwork-database with call-with-target-database.
2023-07-30Conditionally autogenerate schema triples during dumpMunyoki Kilyungi
2023-07-30Rename dump-configuration slotsMunyoki Kilyungi
* 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>
2023-07-30Make dumping optional, defaulting to #tMunyoki Kilyungi
There may be a case where one just wants to dump metadata about the s-exps only.
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.
2023-07-18Ignore emacs temporary backup filesFrederick Muriuki Muriithi
2023-06-28Updated species.ttlPjotr Prins
2023-06-28Add species mapping to wikidata to schemaPjotr Prins
2023-06-26Add "-m manifest.scm" flag to guix shell commandsMunyoki Kilyungi
2023-06-24Fix documentation errors that were leading to confusionFrederick Muriuki Muriithi
2023-06-24Add some missing dependenciesFrederick Muriuki Muriithi
2023-06-21Fix failing testsMunyoki Kilyungi
* dump/special-forms.scm: Export map-alist. * tests.scm: Import strings, and special-forms.
2023-06-19Chunk probeset dumpMunyoki Kilyungi
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>
2023-06-15Change the transaction log mode to 'autocommit' when deleting graphMunyoki Kilyungi
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>
2023-06-12Add a dataset's full name when dumpingMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Use PublishFreeze Name as a fallback for InfoPageNameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Annotate a phenotype dataset with 'dataset:Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Replace "Unknown" in Publication fields with an empty stringMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Annotate publications without a pmid with "unpublished"Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Use "publication:" as an identifier for publicationsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Remove check for confidentiality/publicity during dataset dumpMunyoki Kilyungi
Should a dataset not be confidential/public, it's marked as private. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add geoPlatfrom to dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add missing Species join when dumping datasetsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Use the correct title for the a datasetMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Rename AboutProcessing alias to AboutDataProcessingMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Replace citations to source from Datasets instead of InfoFilesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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