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46 hoursRevert "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>
4 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>
4 daysexamples: Align ontology with BFO and normalize snake_case termsMunyoki Kilyungi
* examples/ontology.scm: Add BFO bridge classes and align GN classes under material/information entities. Define missing `gnt:'/`gnc:' terms used across transformers. Correct property kinds and domains/ranges for dataset, phenotype, genotype, probeset, and gene metadata. * examples/genelist.scm: Replace gnc:ResourceLink and gnc:PantherLink with snake_case terms. * examples/probesets-experiment-metadata.scm: Rename gnt:SE -> gnt:se. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-19Sanitize experiment data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-18Transform all wiki entries.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-18Add fan-out to probeset data points.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-18Only transform datasets with public > 0 and confidentiality < 1.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-16Add probesetXRef metadata.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-16Update generif metadata.Munyoki Kilyungi
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>
2026-02-14Add a checkpoint after every op.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-13Remove un-used namespace.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-12Remove duplicates in phenotype datasets.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-11Add guile-uuid to manifest.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-11Add probeset data.Munyoki Kilyungi
Trick: uri-encode problematic fields. 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 correct column name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Fix typo.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>
2026-02-09Add ".json" to lmdb end-point.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Fix ontology.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Delete (temporarily) probeset tx.Munyoki Kilyungi
This file is too big. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Update RIF transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Add RIF terms to ontology.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Add probesets transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-09Add probeset ontology.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-07Set phenotype name to datasetname+PublishXRef.Id.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-07Use correct table.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-07Use correct namespace for gnd.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-07Update gnd: prefix.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Remove extra ":" for gn-files in global namespace.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Add url-encoded "/" to gn-files to resolve.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Create namespace for geno-files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Link genotype files.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Add dna markers and snps.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Add marker count.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Clean up genotype transform.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-06Clean-up phenotype transform.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>
2026-02-05Update ontology.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-04Use correct name for documentation name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-04Add link to lmdb data.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-04Rename classification with-documentation name.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-04Display the locus as a string.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-03Update phenotypes.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2026-02-03Fix empty phenotypes trait page.Munyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-03-06 13:37:55 +0000