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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>
2023-07-21Move dump-configuration record type to (dump documentation)Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-07-21Construct example SQL query and expected resultsMunyoki Kilyungi
2023-07-21Pass port to scm->triplesMunyoki Kilyungi
* dump/triples.scm (scm->triples): Make define have an optional arg fn that defaults to "triple".
2023-07-21Pass 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>
2023-07-21Print 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>
2023-07-21Add table metadata to triple dumpMunyoki Kilyungi
2023-07-21Add a section sub-heading for schema triplesMunyoki Kilyungi
2023-07-21Wrap the dump title in quotesMunyoki Kilyungi
2023-07-21Replace #` with #'when fetching the name of the defined dumpMunyoki Kilyungi
2023-07-21Use 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.
2023-07-21Conditionally autogenerate schema triples during dumpMunyoki Kilyungi
2023-07-21Rename 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>
2023-07-21Make dumping optional, defaulting to #tMunyoki Kilyungi
There may be a case where one just wants to dump metadata about the s-exps only.
2023-07-21Add 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>
2023-07-21Optionally self-document while dumpingMunyoki Kilyungi
2023-07-21Add 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>
2023-06-12Rename sql-alias of GN notes during dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add rdf defs for datasetOfSpeciesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add publicationTitle to dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Make geoSeries a link during dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Minor identation fixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Add organization to dataset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Use NCBI taxonomy browser instead of uniprotMunyoki Kilyungi
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>
2023-06-12Cast longtext fields to fix broket utf-8 charactersMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-06-12Remove dead commentsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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