gn-transform-databases/transform/special-forms.scm, branch master
Data transformers for GeneNetwork (particularly to RDF)
http://git.genenetwork.org/gn-transform-databases/atom?h=master
2026-03-04T15:16:59+00:00
Revert "transform: add keyset pagination and streaming emit path"
2026-03-04T15:16:59+00:00
Munyoki Kilyungi
2026-03-04T15:16:59+00:00
urn:sha1:a5c1958d5b1abfaaa4ae2a2749ce7f8b0ed3055c
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>
transform: add keyset pagination and streaming emit path
2026-03-02T15:30:01+00:00
Munyoki Kilyungi
2026-03-02T15:19:27+00:00
urn:sha1:ba347362d64f9e634fad7f1aa8ab0a7753ff7a81
* 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>
path-without-extension: utility function.
2026-02-10T07:18:54+00:00
Munyoki Kilyungi
2026-02-10T07:18:54+00:00
urn:sha1:8ed23ab93ea5f82866dc8e97224c2aafbe54ed11
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Give "with-documentation" & "define-transformer" chunking ability.
2026-02-10T06:41:51+00:00
Munyoki Kilyungi
2026-02-10T06:41:51+00:00
urn:sha1:9dd449a2615fd18968c2dc84142f809241b498ad
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Fix bug with when terminating a short turtle pair.
2026-02-09T14:49:01+00:00
Munyoki Kilyungi
2026-02-09T14:48:39+00:00
urn:sha1:576ace2d3155411c42d483d0091efb3ca3386b17
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Don't create triple when string is blank.
2026-02-09T11:49:54+00:00
Munyoki Kilyungi
2026-02-09T11:49:54+00:00
urn:sha1:99d31d2be7bfc2e900db8fbd2c835ef7931360ba
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Use shorter triple-forms for ttl files where possible.
2026-02-09T08:00:43+00:00
Munyoki Kilyungi
2026-02-09T08:00:43+00:00
urn:sha1:0e3a7305f45d70bb4173b6cd1e8d543957b6899a
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Make documentation? and data? optional in special-forms.
2024-10-31T07:42:08+00:00
Munyoki Kilyungi
2024-10-31T07:42:08+00:00
urn:sha1:5c9676e401ac254d0b06c3e1f64a3c9527660094
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Delete blank-node construct
2023-08-23T15:02:19+00:00
Munyoki Kilyungi
2023-08-23T14:59:00+00:00
urn:sha1:824552578284b94d37cc5bfcf7f8f0b85ac29fe5
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Rename dump -> transform
2023-08-21T12:06:06+00:00
Munyoki Kilyungi
2023-08-21T12:03:20+00:00
urn:sha1:8e1e4cceab516afab46ccced63ca9edab663ca11
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>