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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.
2022-05-04Import guile-hashing in manifest.Arun Isaac
This is a follow-up from commit baa9b54f1eb232ed891beaf8a24c3d0d058fbd31 where this change was missed out. * manifest.scm: Import guile-hashing from (gnu packages guile-xyz).
2022-05-04Add script to load RDF into virtuoso.Arun Isaac
* load-rdf.scm: New file. * manifest.scm: Import virtuoso-ose from (gnu packages databases). Add virtuoso-ose to manifest.
2022-05-04Special case investigator ID for "Yohan Bossé".Arun Isaac
* dump.scm (investigator-attributes->id): Add special case for investigator "Yohan Bossé".
2022-04-15pre-inst-env: Rename prepend-path-env! to prepend-path-environment!.Arun Isaac
* pre-inst-env (prepend-path-env!): Rename to prepend-path-environment!. Adjust invocations of prepend-path-env!.
2022-03-10Ignore 0th command-line argument.Arun Isaac
* dump.scm (%connection-settings): Use 1th command-line argument. (%dump-directory): Use 2th command-line argument.
2022-03-10Accept connection parameters and dump directory as arguments.Arun Isaac
* dump.scm: Import (rnrs programs). (%connection-settings): New variable. (call-with-database): Use %connection-settings. (%database-name): Delete variable. (%dump-directory): Set from command-line arguments. (dump-data-table): Use %connection-settings instead of %database-name. * README.org (Using): Add command-line arguments to usage instructions.
2022-03-10Rename the delete verb of map-alist to remove.Arun Isaac
The delete verb of map-alist somehow interacts with the delete function from (srfi srfi-1), and I'm not able to figure out how. It is simpler to just rename the delete verb to remove. * dump/utils.scm: Do not rename the delete function from (srfi srfi-1). (map-alist): Rename the delete verb to remove. * tests.scm ("map-alist docstring example"): Update test.
2022-03-10Work around broken upstream guile-sparql package.Arun Isaac
* manifest.scm: Import guile-sparql with guix: prefix. (guile-sparql): New variable.
2022-03-10Remove guix: prefix from guile-libyaml.Arun Isaac
This reverses an accidental commit of work in progress code. * manifest.scm: Remove guix: prefix from guile-libyaml.
2022-03-10Use run64 to run tests.Arun Isaac
* manifest.scm: Import (guix build-system gnu) and (guix licenses). (run64): New variable. Add run64 to manifest. * Makefile (GUILE): Delete variable. (RUN64): New variable. (check): Use run64 instead of guile to run tests.
2022-03-10Add Makefile.Arun Isaac
* Makefile: New file.
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