diff options
| -rwxr-xr-x | dump.scm | 52 |
1 files changed, 32 insertions, 20 deletions
@@ -638,13 +638,14 @@ must be remedied." (set rdf:type 'gn:platform) (set gn:name (field GeneChip GeneChipName)))) -;; TODO: Double check Platforms. It doesn't seem to match up. +;; Dumping Datasets from InfoFiles that don't exist in PublishFreeze and GenoFreeze (define-dump dump-info-files (tables (InfoFiles + (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name") + (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name") (left-join Datasets "USING (DatasetId)") (left-join DatasetStatus "USING (DatasetStatusId)") (left-join Species "USING (SpeciesId)") - (left-join InbredSet "USING (InbredSetId)") (left-join Tissue "USING (TissueId)") (left-join Investigators "USING (InvestigatorId)") (left-join AvgMethod "USING (AvgMethodId)") @@ -681,8 +682,22 @@ must be remedied." (gn:citation rdfs:range rdfs:Literal) (gn:acknowledgment rdfs:range rdfs:Literal)) (triples (string->identifier "dataset" - (number->string (field InfoFiles GN_AccesionId))) + (field InfoFiles InfoPageName)) (set rdf:type 'gn:dataset) + (set gn:name (field InfoFiles InfoPageName)) + (set dct:created + (let* ((genotype-create-time + (field ("IFNULL(GenoFreeze.CreateTime, '')" + createTimeGenoFreeze))) + (phenotype-create-time + (field ("IFNULL(PublishFreeze.CreateTime, '')" + createTimePublishFreeze))) + (create-time + (if (string-null? genotype-create-time) + phenotype-create-time genotype-create-time))) + (annotate-field + create-time + '^^xsd:datetime))) (set gn:datasetOfInvestigator (investigator-attributes->id (field Investigators FirstName) (field Investigators LastName) @@ -693,7 +708,6 @@ must be remedied." (field DatasetStatus DatasetStatusName))) (set gn:datasetOfSpecies (binomial-name->species-id (field Species FullName BinomialName))) - (set gn:datasetOfInbredSet (inbred-set-name->id (field InbredSet Name InbredSetName))) (set gn:datasetOfTissue (tissue-short-name->id (field Tissue Short_Name))) (set gn:normalization (avg-method-name->id @@ -702,29 +716,27 @@ must be remedied." "N/A" (field AvgMethod Name AvgMethodName)))) (set gn:datasetOfPlatform (gene-chip-name->id (field GeneChip Name GeneChip))) (set gn:summary - ;; TODO: Why are there unprintable characters? - (delete-substrings (field Datasets Summary) - "\x01" "\x03")) + (sanitize-rdf-string (field Datasets Summary))) (set gn:aboutTissue - ;; TODO: Why are there unprintable characters? - (delete-substrings (field Datasets AboutTissue) - "\x01" "\x03")) + (sanitize-rdf-string (field Datasets AboutTissue))) (set gn:geoSeries (and (not (string-prefix-ci? "no geo series" (field Datasets GeoSeries))) (field Datasets GeoSeries))) - (set gn:name (field InfoFiles InfoPageName)) (set gn:title (field InfoFiles Title)) - (set gn:specifics (field InfoFiles Specifics)) + (set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics))) (set gn:datasetGroup (field Datasets DatasetName DatasetGroup)) - (set gn:aboutCases (field Datasets AboutCases)) - (set gn:aboutPlatform (field Datasets AboutPlatform)) - (set gn:aboutDataProcessing (field Datasets AboutDataProcessing)) - (set gn:notes (field Datasets Notes)) - (set gn:experimentDesign (field Datasets ExperimentDesign)) - (set gn:contributors (field Datasets Contributors)) - (set gn:citation (field Datasets Citation)) - (set gn:acknowledgment (field Datasets Acknowledgment)))) + (set gn:aboutCases (sanitize-rdf-string (field Datasets AboutCases))) + (set gn:aboutPlatform (sanitize-rdf-string (field Datasets AboutPlatform))) + (set gn:aboutDataProcessing (sanitize-rdf-string + (field Datasets AboutDataProcessing))) + (set gn:notes (sanitize-rdf-string (field Datasets Notes))) + (set gn:experimentDesign (sanitize-rdf-string + (field Datasets ExperimentDesign))) + (set gn:contributors (sanitize-rdf-string (field Datasets Contributors))) + (set gn:citation (sanitize-rdf-string (field Datasets Citation))) + (set gn:acknowledgment (sanitize-rdf-string + (field Datasets Acknowledgment))))) ;; Dumping Phenotypes from PublishFreeze that are not present in the InfoFiles tables (define-dump dump-phenotypes |