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3 daysRevert "transform: add keyset pagination and streaming emit path"Munyoki Kilyungi
This reverts commit ba347362d64f9e634fad7f1aa8ab0a7753ff7a81. Causes and endless loop. See: https://ci.genenetwork.org/jobs/transform-genenetwork-database/99 Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
5 daystransform: add keyset pagination and streaming emit pathMunyoki Kilyungi
* transform/special-forms.scm (define-transformer): Add keyset arguments and cursor return path; add SQL helpers for keyset ordering/filtering; avoid po-alist allocation by streaming short turtle emission. (with-documentation): Add keyset pagination loop using per-input cursor state and configurable chunk key field. (emit-short-turtle): Emit triples in a single linear pass. * examples/probesets-experiment-metadata.scm: Enable keyset pagination and set composite chunk key fields for ProbeSetFreeze/ProbeSet join. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-16Make url char separator optional in "string->identifier".Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-16Add uuid function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-10path-without-extension: utility function.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-10Give "with-documentation" & "define-transformer" chunking ability.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Fix bug with when terminating a short turtle pair.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Don't create triple when string is blank.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Use shorter triple-forms for ttl files where possible.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Move blank-p to strings.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-28Move investigators transform to its own file.Munyoki Kilyungi
* examples/dataset-metadata.scm (investigators): Delete. (option-spec)[investigators]: Delete * transform/strings.scm (fix-email-id, investigator-attributes->id): Move these ... * examples/investigators.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-28Move fix-email-id/investigator-attributes->id to string.scmMunyoki Kilyungi
* examples/dataset-metadata.scm (fix-email-id, investigator-attributes->id): Move this ... * transform/strings.scm: here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-14Replace camelCase with snake_case.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Snake case variable.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Explicitly set the connection string to utf8.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Add extra string utility functions.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Strictly follow PN_LOCAL rules when constructing qnames.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Have an ID function as the default func for string->identifier.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Use "-" in qnames.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-01-13Move remap-species-identifiers to (transform triples).Munyoki Kilyungi
* examples/classification.scm (remap-species-identifiers): Move this... * transform/triples.scm: ... here. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-31Make documentation? and data? optional in special-forms.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-17Rename schema-dump.scm -> schema.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2024-10-16Delete uuid.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-12-20Fix srfi-26 import typo.Arun Isaac
2023-11-24Move remap-species-identifier to strings.scm.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-11-22Add 'lower-case-and-replace-spaces' functionMunyoki Kilyungi
* transform/strings.scm (lower-case-and-replace-spaces): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-30Add extra mappings for broken utf-8 characters to be replacedMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Set string->identifier to defaut to "" sep and string-capitalizeMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-28Treat strings wrapped in "()" as symbolsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Delete blank-node constructMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Add extra utility fn for removing duplicatesMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-23Add an extra module for generating unique idsMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-08-21Rename dump -> transformMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-03-07 07:38:02 +0000