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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.
2022-10-30Special case Yohan Bossé's last name.Arun Isaac
* dump.scm (dump-investigators): Special case Yohan Bossé's last name.
2022-10-30Do not deduplicate the AvgMethod table.Arun Isaac
The AvgMethod table no longer has duplicate "N/A" records. * dump.scm (dump-avg-method): Do not deduplicate the AvgMethod table.
2022-10-21Authenticate when deleting graph from virtuoso.Arun Isaac
* load-rdf.scm (delete-graph): Accept password argument. (main): Call delete-graph with password.
2022-08-20Add gn:traitId and gn:publicationId.Munyoki Kilyungi
In GeneNetwork, a phenonytpe is currently identified by it's ID (primary key of the table from MariaDB). The only way to relate it to a publication is through a publication ID. This is important because there are some publications with a NULL value for "pubmed ID" and as such without the publication ID, some data is lost as there's no way to point to publication with a NULL "pubmed ID." * dump.scm (dump-publish-xref): Define gn:traitId and gn:publicationId. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-08-02Add new functions to read CSV files in a flexible way.Munyoki Kilyungi
We add new functions---parse-raw-table and parse-aggregate-table---to parse raw ungrouped data and grouped data respectively. * csv-dump.scm (assoc-set, parse-raw-table, parse-aggregate-table): New functions. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-06-24Try uploading twice into virtuoso.Arun Isaac
* load-rdf.scm (put-graph): Accept retry? argument, and retry if it is #t. (main): Call put-graph with a #t retry? argument.
2022-06-24Delete vertical tab character in publication abstracts.Arun Isaac
* dump.scm (dump-publication): Delete vertical tab character in abstracts.
2022-06-23Add gitignore.Arun Isaac
* .gitignore: New file.
2022-06-23Dump groups.BonfaceKilz
* dump.scm (dump-groups): New dump. (main): Call dump-groups. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-06-23Dump case-attributes.BonfaceKilz
* dump.scm (dump-case-attributes): New dump. (main): Call dump-case-attributes. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-06-23Remove "." if it occurs at the end of a turtle identifier.BonfaceKilz
A "." at the end of a turtle identifier---for example "gn:caseAttribute_ethn."---generates an error when trying to validate the generated RDF. * dump.scm (string->identifier): Remove trailing "." if it occurs in the identifier. Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2022-05-05Document source compilation.Arun Isaac
* README.md (Using): Document source compilation.
2022-05-05Makefile: Disable auto-compilation while compiling.Arun Isaac
* Makefile (%.go): Set GUILE_AUTO_COMPILE to 0.
2022-05-05Compile scheme sources.Arun Isaac
* Makefile (GUILD, top_level_module_dir, sources, objects): New variables. (all, %.go, clean): New targets. * pre-inst-env: Use built object files.
2022-05-05manifest: Add gnu-make.Arun Isaac
* manifest.scm: Import gnu-make from (gnu packages base). Add gnu-make to manifest.
2022-05-05Validate dumped RDF using rapper.Arun Isaac
* manifest.scm: Import raptor2 from (gnu packages rdf). Add raptor2 to manifest. * README.md (Using): Document validation using rapper.
2022-05-05README: Advertise continuous integration build artifacts.Arun Isaac
* README.md (Using): Advertise continuous integration build artifacts.
2022-05-05README: Document loading RDF and visualizing schema.Arun Isaac
* README.md (Using): Document loading RDF and visualizing schema.
2022-05-05Prefix SQL connection parameters with sql-.Arun Isaac
This differentiates it from virtuoso and SPARQL connection parameters. * dump.scm (call-with-genenetwork-database, dump-data-table): Prefix SQL connection parameters with sql-. * README.md (Using): Update documentation of SQL connection parameters.
2022-05-05README: Replace org mode with markdown.Arun Isaac
Markdown is a simpler format and easier to render to the web. In particular, this change is prompted by Gitea not handling image links correctly. * README.org: Replace with ... * README.md: ... this.
2022-05-05README: Link to genenetwork.org CI.Arun Isaac
* README.org: Link to genenetwork.org CI instead of systemreboot.net CI.
2022-05-05README: Add CI badges.Arun Isaac
* README.org: Add CI badges.
2022-05-04Read SPARQL connection settings from file.Arun Isaac
* visualize-schema.scm (%sparql-host, %sparql-port): New parameters. (sparql-query-records): Use %sparql-host and %sparql-port parameters. (main): Accept connection settings file as argument, read it, and parameterize %sparql-host and %sparql-port. Pass command-line arguments to main.
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