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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
2023-03-08Dump GeneWiki metadataMunyoki Kilyungi
* dump.scm (dump-generif): New data dump. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-06Dump relevant metadata about phenotypesMunyoki Kilyungi
* dump.scm (dump-publishfreeze, dump-published-phenotypes): New dumps. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-06Delete phenotype and publish_xref metadataMunyoki Kilyungi
* dump.scm (phenotype-id->id, dump-phenotype): Delete (dump-publish-xref): Delete. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-06Add mapping method and species info to inbredsets.Munyoki Kilyungi
* dump.scm (dump-inbred-set): Add mapping method and species as extra metadata for inbredsets. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-15Read metadata from a json fileMunyoki Kilyungi
* json-dump.scm: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-15Remove dump-case-attributesMunyoki Kilyungi
This information is already stored in LMDB. * dump.scm (dump-case-attributes): Delete. (main)(<dump-case-attributes>): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2022-12-06Use InfoPageName as a dataset's name.Munyoki Kilyungi
* dump.scm (dump-info-files): Set a dataset's name to InfoPageName.
2022-11-25Provide a sample conn.scm.Arun Isaac
* README.md (Using)[Set up connection parameters]: Provide a sample conn.scm.
2022-11-25Document generif-data-file connection parameter.Arun Isaac
* README.md (Using)[Set up connection parameters]: Document generif-data-file.
2022-11-25Split up README into subsections.Arun Isaac
* README.md (Using): Split into subsections.
2022-11-04Add comment with URI to GeneRIF data.Arun Isaac
* dump.scm: Add comment with URI to GeneRIF data.
2022-11-04Unite importing GeneRIF with dumping SQL data.Arun Isaac
* README.md: Document generif-data-file parameter in connection settings. * dump.scm: Import (srfi srfi-171), (ice-9 regex) and (zlib). (decode-html-entities, import-generif): New functions. (main): Call import-generif. * import-generif.scm: Delete file.
2022-11-04Revert "Put isql commands on a single line."Arun Isaac
This reverts commit 5aecbcd3e59119533658b792c6dafa0c6efd9d5b. Despite putting commands on a single line, isql still echoes and leaks the password.
2022-10-31Put isql commands on a single line.Arun Isaac
We put isql commands on a single line in the hope that they will not be echoed thus leaking the password. * load-rdf.scm (delete-graph): Put isql commands on a single line.
2022-10-30Import GeneRIF data into RDF.Arun Isaac
* import-generif.scm: New file.
2022-10-30Move triple utilities to new module.Arun Isaac
* dump.scm (string->identifier, string-blank?, triple, prefix): Move to ... * dump/triples.scm: ... new file. * dump.scm: Import (dump triples).
2022-10-30Move string-blank? to (dump utils).Arun Isaac
* dump.scm (string-blank?): Move to ... * dump/utils.scm (string-blank?): ... here.
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