Age | Commit message (Collapse) | Author |
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* 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>
|
|
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>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (decode-html-entities, import-generif): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (dump-generif, dump-generif-basic): Refactor to ...
(dump-gn-genewiki-entries): ... this.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (dump-generif, dump-generif-basic): Replace with ...
(dump-gn-genewiki-entries): ... this.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (string-split-substring): New function.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (blank-node): New macro.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* 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>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* 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>
|
|
* dump.scm (dump-generif-basic): Annotate createTime field with xsd.
* dump.scm (dump-generif): New dump.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
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>
|
|
* dump.scm (dump-generif): New data dump.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (dump-publishfreeze, dump-published-phenotypes): New dumps.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (phenotype-id->id, dump-phenotype): Delete
(dump-publish-xref): Delete.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
* dump.scm (dump-inbred-set): Add mapping method and species as extra
metadata for inbredsets.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
|
|
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>
|
|
* dump.scm (dump-info-files): Set a dataset's name to InfoPageName.
|
|
* dump.scm: Add comment with URI to GeneRIF data.
|
|
* 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.
|
|
* dump.scm (string->identifier, string-blank?, triple, prefix): Move
to ...
* dump/triples.scm: ... new file.
* dump.scm: Import (dump triples).
|
|
* dump.scm (string-blank?): Move to ...
* dump/utils.scm (string-blank?): ... here.
|
|
* dump.scm (dump-investigators): Special case Yohan Bossé's last name.
|
|
The AvgMethod table no longer has duplicate "N/A" records.
* dump.scm (dump-avg-method): Do not deduplicate the AvgMethod table.
|
|
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>
|
|
* dump.scm (dump-publication): Delete vertical tab character in
abstracts.
|
|
* dump.scm (dump-groups): New dump.
(main): Call dump-groups.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
|
|
* dump.scm (dump-case-attributes): New dump.
(main): Call dump-case-attributes.
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
|
|
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>
|
|
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.
|
|
* dump.scm (investigator-attributes->id): Add special case for
investigator "Yohan Bossé".
|
|
* dump.scm (%connection-settings): Use 1th command-line argument.
(%dump-directory): Use 2th command-line argument.
|
|
* 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.
|
|
If these macro helper functions are not evaluated at macro expansion
time, the dependent macros will fail to compile.
* dump.scm (string->identifier, field->key, field->assoc-ref,
collect-fields, find-clause, remove-namespace, column-id, dump-id):
Eval at macro expansion time.
|
|
* dump.scm: Do not add to load path.
|
|
* dump.scm (define-dump): Add docstring.
|
|
* dump.scm (syntax-let): New macro.
(define-dump): Use syntax-let.
* .dir-locals.el (scheme-mode): Indent syntax-let correctly.
|
|
* dump.scm (define-dump): Automatically create domain triples for
predicates.
|
|
* dump.scm (remove-namespace, dump-id): New functions.
(define-dump): Dump metadata about the dump itself.
|