| Age | Commit message (Expand) | Author |
|---|
| 2023-05-30 | Make a probeset's tissue multiset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-30 | Make a probeset's alias a multiset...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-30 | Move probeset metadata used for a given experiment to it's own dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Use a phenotype's abbreviation as it's name...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Make tissue a multi-set during the probeset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Remove some metadata from the probeset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Create a new probesetfreeze dump...This way, the probeset dump will become smaller.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Allow load-rdf script to read in data from a dir...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Return an empty string if a dataset doesn't have a name...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-05-26 | Remove unnecessary fields from probeset dump...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 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 |
