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2023-07-21Add 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
2023-07-21Make string->identifier take optional keyword args...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Make dump-data? default to #f when dumping data...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Rewrite dump-with-documentation to be order-agnostic...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Dump dataset metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Dump publication metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Dump tissue metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Dump species metadata with documentation...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Conditionally dump documentationMunyoki Kilyungi
2023-07-21Make prefix function have an optional ttl?...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Revert "Pass port as an optional argument"...This reverts commit 195ca590be5533935cf708d49fcb3736b3c78643. Munyoki Kilyungi
2023-07-21Add missing srfi-26 import...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Create 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
2023-07-21Rename 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
2023-07-21Move dump-configuration record type to (dump documentation)...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-07-21Construct example SQL query and expected resultsMunyoki Kilyungi
2023-07-21Pass port to scm->triples...* dump/triples.scm (scm->triples): Make define have an optional arg fn that defaults to "triple". Munyoki Kilyungi
2023-07-21Pass 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
2023-07-21Print 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
2023-07-21Add 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 annotations...* dump/schema-dump.scm (dump-schema-annotations): Replace call-with-genenetwork-database with call-with-target-database. Munyoki Kilyungi
2023-07-21Conditionally autogenerate schema triples during dumpMunyoki Kilyungi
2023-07-21Rename 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
2023-07-21Make dumping optional, defaulting to #t...There may be a case where one just wants to dump metadata about the s-exps only. Munyoki Kilyungi
2023-07-21Add 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
2023-07-21Optionally self-document while dumpingMunyoki Kilyungi
2023-07-21Add 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
2023-07-18Ignore 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 tests...* dump/special-forms.scm: Export map-alist. * tests.scm: Import strings, and special-forms. Munyoki Kilyungi
2023-06-19Chunk 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
2023-06-15Change the transaction log mode to 'autocommit' when deleting graph...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> Munyoki Kilyungi
2023-06-12Add a dataset's full name when dumping...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Use PublishFreeze Name as a fallback for InfoPageName...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Annotate a phenotype dataset with 'dataset:...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Replace "Unknown" in Publication fields with an empty string...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Annotate publications without a pmid with "unpublished"...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Use "publication:" as an identifier for publications...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Remove check for confidentiality/publicity during dataset dump...Should a dataset not be confidential/public, it's marked as private. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Add geoPlatfrom to dataset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Add missing Species join when dumping datasets...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Use the correct title for the a dataset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
2023-06-12Rename AboutProcessing alias to AboutDataProcessing...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com> Munyoki Kilyungi
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