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| author | Munyoki Kilyungi | 2023-08-21 14:41:23 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-08-21 14:41:23 +0300 |
| commit | add95e737f61fdf3e8f244dd7ebedca963514bb7 (patch) | |
| tree | 667b16a1a9081b4fc445b4c6cf1c2caa76a4f1ab /examples/dump-phenotype.scm | |
| parent | e25db8edf8615f59d0682841fde8d43367ebfa53 (diff) | |
| download | gn-transform-databases-add95e737f61fdf3e8f244dd7ebedca963514bb7.tar.gz | |
Move dumps related to datasets to one place
* examples/dump-dataset-metadata.scm: Add dump-gene-chip,
dump-publishfreeze, dump-genofreeze, dump-probesetfreeze
* examples/dump-genotype.scm: Delete dump-genofreeze.
* examples/dump-phenotype.scm: Delete dump-publishfreeze.
* examples/dump-probesetfreeze.scm: Delete file
Diffstat (limited to 'examples/dump-phenotype.scm')
| -rwxr-xr-x | examples/dump-phenotype.scm | 29 |
1 files changed, 0 insertions, 29 deletions
diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm index f5a8c3c..6c52ebb 100755 --- a/examples/dump-phenotype.scm +++ b/examples/dump-phenotype.scm @@ -19,34 +19,6 @@ read)) - -;; These are phenotype datasets that don't have Infofile metadata -(define-dump dump-publishfreeze - (tables (PublishFreeze - (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name") - (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId")) - "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL") - (triples - (string->identifier - "" - (regexp-substitute/global #f "[^A-Za-z0-9:]" - (field PublishFreeze Name) - 'pre "_" 'post) - #:separator "" - #:proc string-capitalize-first) - (set rdf:type 'gnc:phenotypeDataset) - (set rdfs:label (field PublishFreeze Name)) - (set skos:prefLabel (field PublishFreeze FullName)) - (set skos:altLabel (field PublishFreeze ShortName)) - (set dct:created (annotate-field - (field PublishFreeze CreateTime) - '^^xsd:date)) - (set gnt:belongsToSet - (string->identifier - "inbredSet" (field InbredSet Name) - #:separator "" - #:proc string-capitalize-first)))) - (define-dump dump-phenotypes (tables (PublishXRef (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") @@ -147,7 +119,6 @@ ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>"))) (inputs (list - dump-publishfreeze dump-phenotypes)) (outputs '(#:documentation "./docs/dump-phenotype.md" |