| Age | Commit message (Expand) | Author |
|---|
| 2023-05-26 | Sanitize a generif entry from GN•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Add genotype dump•••* 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>
| Munyoki Kilyungi |
| 2023-05-26 | Fix broken utf-8 chars when dumping an investigator's names•••* 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>
| Munyoki Kilyungi |
| 2023-05-26 | Remove an investigator's email/phone from dump for privacy reasons•••* examples/dump-dataset-metadata.scm (dump-investigators) <foaf:phone,
foad:mbox>: Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Update a dataset's subject identifier to be a gn url•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Annotate createtime field correctly with xsd:date•••* examples/dump-phenotype.scm (dump-publishfreeze): Use xsd:date to
annotate PublishFreeze's CreateTime field.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Replace broken char-sets with an empty string•••* dump/strings.scm (sanitize-rdf-string): Add extra elements---broken
chars---to replace with "".
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Replace dump.scm with separete dumps for several tables•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Re-organize dumping macros and associated functions•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Update how info-page-files are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Update how publications are dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Dump phenotypes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Delete dump-published-phenotypes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | When a field is null during annotation, return an empty string•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Always use "~a" to output like "display"•••Replacing "~s" with "~a" will print utf-8 characters correctly.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Return an empty string if args passed to ontology is empty•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Replace chars not allowed in RDF•••* dump.scm (sanitize-rdf-string): New function
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Dump molecular traits, also referred to as Probesets•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Update how inbred-set in dumped•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Fix how a symbol is displayed in the final RDF•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Update how Species are dumped•••* 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>
| Munyoki Kilyungi |
| 2023-04-05 | Delete "operation" from fields•••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>
| Munyoki Kilyungi |
| 2023-04-05 | Simplify pattern matching when checking for a node•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Wrap the password in quotes•••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>
| Munyoki Kilyungi |
| 2023-04-05 | Update GeneRIF prefix•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add species data to generif entries•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Dump genewiki symbol•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Annotate gn:geneWikiEntry as a class and add a comment•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Dump species, symbols and indicate generif type when a geneid = 0•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Separate NCBI and GN wikientries in dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add dublin-core and uniprot prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Avoid prefixing 'pubmed: to an empty string•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Delete generif file dump•••* dump.scm (decode-html-entities, import-generif): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Refactor dump-generif-basic/dump-generif to dump-gn-genewiki-entries•••* dump.scm (dump-generif, dump-generif-basic): Refactor to ...
(dump-gn-genewiki-entries): ... this.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Use match syntax to print object correctly during dump•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Redefine how genewiki is dumped•••* dump.scm (dump-generif, dump-generif-basic): Replace with ...
(dump-gn-genewiki-entries): ... this.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Split substring int a list of substrings delimited by substring•••* dump.scm (string-split-substring): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add new special form for representing blank nodes•••* dump.scm (blank-node): New macro.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Allow running raw queries in field form•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Make dumping metadata about a given table optional defaulting to #f•••* 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>
| Munyoki Kilyungi |
| 2023-04-05 | Add "xsd:" and "owl:" prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Annotate fields with a custom scheme such as "^^xsd:datetime"•••* 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>
| Munyoki Kilyungi |
| 2023-04-05 | Dump GeneRIF wikidata•••* dump.scm (dump-generif-basic): Annotate createTime field with xsd.
* dump.scm (dump-generif): New dump.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add a method to transform epoch time to a human readable format•••* dump/utils.scm: Import srfi-19. Export time-unix->string.
(time-unix->string): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add pubmed, taxon and generif prefixes•••Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Create a method to define ontologies as symbols•••* dump/triples.scm: Export ontology.
(ontology): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-04-05 | Add ability to have operations such as GROUP_CONCAT in SELECT clause•••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>
| Munyoki Kilyungi |
| 2023-03-24 | Instructions for running in a container and added dependencies | Pjotr Prins |
| 2023-03-08 | Dump GeneWiki metadata•••* dump.scm (dump-generif): New data dump.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-03-06 | Dump relevant metadata about phenotypes•••* dump.scm (dump-publishfreeze, dump-published-phenotypes): New dumps.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
