diff options
| author | Munyoki Kilyungi | 2026-02-06 05:54:42 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2026-02-06 05:54:42 +0300 |
| commit | 9c43d6dea557d11ed936950cd190172883a34595 (patch) | |
| tree | b8c9a212d2c7f94caaabfba141bba26408e1b8aa /examples/genotype-datasets.scm | |
| parent | de0a0805415f3b1b2381345d4efd402f1e1249e2 (diff) | |
| download | gn-transform-databases-9c43d6dea557d11ed936950cd190172883a34595.tar.gz | |
Clean up genotype transform.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/genotype-datasets.scm')
| -rwxr-xr-x | examples/genotype-datasets.scm | 32 |
1 files changed, 19 insertions, 13 deletions
diff --git a/examples/genotype-datasets.scm b/examples/genotype-datasets.scm index 6f3a1cb..ba31088 100755 --- a/examples/genotype-datasets.scm +++ b/examples/genotype-datasets.scm @@ -15,22 +15,26 @@ (define-transformer gn:set->gn:dataset - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") + (tables (Species + (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id") (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")) - "WHERE GenoFreeze.public > 0 GROUP BY Datasets.DatasetId") + "WHERE GenoFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, GenoFreeze.ShortName") (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") - (set gnt:has_genotype_data (string->identifier "dataset" (field GenoFreeze Name) #:separator "_")))) + (multiset gnt:has_genotype_data + (map (cut string->identifier "dataset" <> #:separator "_") + (string-split + (field ("GROUP_CONCAT(GenoFreeze.Name SEPARATOR ',')" + dataset_name)) + #\,))))) -(define-transformer gn:dataset->gn:set - (tables (Datasets - (inner-join InfoFiles "ON InfoFiles.DatasetId = Datasets.DatasetId") - (inner-join InbredSet "ON InbredSet.Id = InfoFiles.InbredSetId") - (inner-join GenoFreeze "ON GenoFreeze.InbredSetId = InbredSet.Id")) - "WHERE GenoFreeze.public > 0 GROUP BY Datasets.DatasetId") +(define-transformer gn:dataset->metadata + (tables (GenoFreeze + (inner-join InbredSet "ON InbredSet.Id = GenoFreeze.InbredSetId") + (inner-join Species "ON InbredSet.SpeciesId = Species.Id")) + "WHERE GenoFreeze.public > 0 AND Species.Name != 'monkey'") (triples (string->identifier "dataset" (field GenoFreeze Name) #:separator "_") - (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")))) + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) + (set dct:created (annotate-field (field GenoFreeze CreateTime) '^^xsd:datetime)))) (let* ((option-spec @@ -61,7 +65,9 @@ ("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>") ("xsd:" "<http://www.w3.org/2001/XMLSchema#>"))) (inputs - (list gn:set->gn:dataset gn:dataset->gn:set)) + (list + gn:set->gn:dataset + gn:dataset->metadata)) (outputs `(#:documentation ,documentation #:rdf ,output)))) |