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2023-05-26Return an empty string if a dataset doesn't have a nameMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Remove unnecessary fields from probeset dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Sanitize a generif entry from GNMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Add genotype dumpMunyoki Kilyungi
* examples/dump-genotype.scm: New dump for genotypes and their associated datasets(that were not dumped from the info-files table). Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Fix broken utf-8 chars when dumping an investigator's namesMunyoki Kilyungi
* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:name, foaf:givenName>: Binary convert fields first to latin1 then utf8. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Remove an investigator's email/phone from dump for privacy reasonsMunyoki Kilyungi
* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:phone, foad:mbox>: Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update a dataset's subject identifier to be a gn urlMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Annotate createtime field correctly with xsd:dateMunyoki Kilyungi
* examples/dump-phenotype.scm (dump-publishfreeze): Use xsd:date to annotate PublishFreeze's CreateTime field. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Replace broken char-sets with an empty stringMunyoki Kilyungi
* dump/strings.scm (sanitize-rdf-string): Add extra elements---broken chars---to replace with "". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Replace dump.scm with separete dumps for several tablesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Re-organize dumping macros and associated functionsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update how info-page-files are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update how publications are dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Dump phenotypesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Delete dump-published-phenotypesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26When a field is null during annotation, return an empty stringMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Always use "~a" to output like "display"Munyoki Kilyungi
Replacing "~s" with "~a" will print utf-8 characters correctly. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Return an empty string if args passed to ontology is emptyMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Replace chars not allowed in RDFMunyoki Kilyungi
* dump.scm (sanitize-rdf-string): New function Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Dump molecular traits, also referred to as ProbesetsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update how inbred-set in dumpedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Fix how a symbol is displayed in the final RDFMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-05-26Update how Species are dumpedMunyoki Kilyungi
* dump.scm (dump-species): Rename gn:menuName to gn:displayName. Add gn:family and up:organism triplets. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Delete "operation" from fieldsMunyoki Kilyungi
Nested raw queries: ((field (query alias)) alias) are now supported so an "operation is not needed". * dump.scm (field->key, field->assoc-ref): Delete ((field table column operation alias) alias)) Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Simplify pattern matching when checking for a nodeMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Wrap the password in quotesMunyoki Kilyungi
The password can contain special characters. As such, wrap it in quotes. * load-rdf.scm (delete-graph): Replace "~a" with "~s". Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Update GeneRIF prefixMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add species data to generif entriesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Dump genewiki symbolMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Annotate gn:geneWikiEntry as a class and add a commentMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Dump species, symbols and indicate generif type when a geneid = 0Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Separate NCBI and GN wikientries in dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add dublin-core and uniprot prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Avoid prefixing 'pubmed: to an empty stringMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Delete generif file dumpMunyoki Kilyungi
* dump.scm (decode-html-entities, import-generif): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Refactor dump-generif-basic/dump-generif to dump-gn-genewiki-entriesMunyoki Kilyungi
* dump.scm (dump-generif, dump-generif-basic): Refactor to ... (dump-gn-genewiki-entries): ... this. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Use match syntax to print object correctly during dumpMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Redefine how genewiki is dumpedMunyoki Kilyungi
* dump.scm (dump-generif, dump-generif-basic): Replace with ... (dump-gn-genewiki-entries): ... this. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Split substring int a list of substrings delimited by substringMunyoki Kilyungi
* dump.scm (string-split-substring): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add new special form for representing blank nodesMunyoki Kilyungi
* dump.scm (blank-node): New macro. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Allow running raw queries in field formMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Make dumping metadata about a given table optional defaulting to #fMunyoki Kilyungi
* dump.scm (define-dump): Add optional table-metadata? flag thats #f by default. If this flag is #t, dump metadata about the SQL table itself. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add "xsd:" and "owl:" prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Annotate fields with a custom scheme such as "^^xsd:datetime"Munyoki Kilyungi
* dump.scm (annotate-field): New function. * dump/triples.scm (triple): Print a string as they appear with DISPLAY should they contain "\"" thus enabling a triple that looks like: gn:species_mus_musculus gn:name "Mouse"^^xsd:string Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Dump GeneRIF wikidataMunyoki Kilyungi
* dump.scm (dump-generif-basic): Annotate createTime field with xsd. * dump.scm (dump-generif): New dump. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add a method to transform epoch time to a human readable formatMunyoki Kilyungi
* dump/utils.scm: Import srfi-19. Export time-unix->string. (time-unix->string): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add pubmed, taxon and generif prefixesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Create a method to define ontologies as symbolsMunyoki Kilyungi
* dump/triples.scm: Export ontology. (ontology): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-04-05Add ability to have operations such as GROUP_CONCAT in SELECT clauseMunyoki Kilyungi
This change enables having: "... GROUP_CONCAT(GeneRIF_BASIC.PubMedId) AS alias ..." as part of the query. * dump.scm (field->key, field->assoc-ref): Add new syntax-rule. * dump/sql.scm (select-query): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-24Instructions for running in a container and added dependenciesPjotr Prins
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