diff options
| -rwxr-xr-x | dump.scm | 126 |
1 files changed, 68 insertions, 58 deletions
diff --git a/dump.scm b/dump.scm index 3fad0db..3701fbd 100755 --- a/dump.scm +++ b/dump.scm @@ -292,12 +292,21 @@ INNER JOIN InbredSet USING (InbredSetId)")) (define (fix-email-id email) (string-delete #\space email)) -(define (investigator-email->id email) - (string->identifier "investigator" (fix-email-id email))) +(define (investigator-attributes->id first-name last-name email) + ;; There is just one record corresponding to "Evan Williams" which + ;; does not have an email ID. To accommodate that record, we + ;; construct the investigator ID from not just the email ID, but + ;; also the first and the last names. It would be preferable to just + ;; find Evan Williams' email ID and insert it into the database. + (string->identifier "investigator" + (string-join (list first-name last-name (fix-email-id email)) + "_"))) (define (dump-investigators db) (sql-for-each (lambda (alist) - (let ((id (investigator-email->id (assoc-ref alist "Email")))) + (let ((id (investigator-attributes->id (assoc-ref alist "FirstName") + (assoc-ref alist "LastName") + (assoc-ref alist "Email")))) (triple id 'rdf:type 'foaf:Person) (scm->triples (cons (cons 'foaf:name (string-append @@ -320,10 +329,7 @@ INNER JOIN InbredSet USING (InbredSetId)")) db ;; There are a few duplicate entries. We group by ;; email to deduplicate. - ;; TODO: Find email ID for records with none. (This is - ;; just one record corresponding to "Evan Williams") "SELECT FirstName, LastName, Address, City, State, ZipCode, Phone, Email, Country, Url FROM Investigators -WHERE Email != '' GROUP BY Email")) (define avg-method-name->id @@ -363,57 +369,62 @@ GROUP BY Email")) (assoc-ref alist "GN_AccesionId"))))) (triple id 'rdf:type 'gn:dataset) (scm->triples - (filter-map (match-lambda - (('gn:gNAccesionId . accession-id) - (cons 'gn:accessionId - (string-append "GN" (number->string accession-id)))) - (('gn:datasetStatusName . status) - (cons 'gn:datasetStatus - (string-downcase status))) - (('gn:binomialName . binomial-name) - (cons 'gn:datasetOfSpecies - (binomial-name->species-id binomial-name))) - (('gn:inbredSetName . inbred-set-name) - (cons 'gn:datasetOfInbredSet - (inbred-set-name->id inbred-set-name))) - (('gn:shortName . short-name) - (cons 'gn:datasetOfTissue - (tissue-short-name->id short-name))) - (('gn:email . email) - (cons 'gn:datasetOfInvestigator - (investigator-email->id email))) - (('gn:avgMethodId . avg-method-id) - ;; If avg-method-id is 0, a - ;; non-existent method, assume - ;; N/A. - (and (zero? avg-method-id) - (cons 'gn:normalization - (avg-method-name->id "N/A")))) - (('gn:avgMethodName . avg-method-name) - (cons 'gn:normalization - (avg-method-name->id avg-method-name))) - (('gn:geneChip . name) - (cons 'gn:datasetOfPlatform - (gene-chip-name->id name))) - (('gn:summary . summary) - ;; TODO: Why are there unprintable - ;; characters in the summary? - (cons 'gn:summary - (delete-substrings summary "\x01" "\x03"))) - (('gn:aboutTissue . about-tissue) - ;; TODO: Why are there unprintable - ;; characters in the summary? - (cons 'gn:aboutTissue - (delete-substrings about-tissue "\x01" "\x03"))) - (('gn:geoSeries . geo-series) - (and (not (string-prefix-ci? "no geo series" geo-series)) - (cons 'gn:geoSeries geo-series))) - (x x)) - (process-metadata-alist alist)) + (cons (cons 'gn:datasetOfInvestigator + (investigator-attributes->id (assoc-ref alist "FirstName") + (assoc-ref alist "LastName") + (assoc-ref alist "Email"))) + (filter-map (match-lambda + (('gn:gNAccesionId . accession-id) + (cons 'gn:accessionId + (string-append "GN" (number->string accession-id)))) + (('gn:datasetStatusName . status) + (cons 'gn:datasetStatus + (string-downcase status))) + (('gn:binomialName . binomial-name) + (cons 'gn:datasetOfSpecies + (binomial-name->species-id binomial-name))) + (('gn:inbredSetName . inbred-set-name) + (cons 'gn:datasetOfInbredSet + (inbred-set-name->id inbred-set-name))) + (('gn:shortName . short-name) + (cons 'gn:datasetOfTissue + (tissue-short-name->id short-name))) + ;; Remove first name, last name and + ;; email. We are using it outside + ;; this filter-map. + (('gn:firstName . first-name) #f) + (('gn:lastName . last-name) #f) + (('gn:email . email) #f) + (('gn:avgMethodId . avg-method-id) + ;; If avg-method-id is 0, a + ;; non-existent method, assume + ;; N/A. + (and (zero? avg-method-id) + (cons 'gn:normalization + (avg-method-name->id "N/A")))) + (('gn:avgMethodName . avg-method-name) + (cons 'gn:normalization + (avg-method-name->id avg-method-name))) + (('gn:geneChip . name) + (cons 'gn:datasetOfPlatform + (gene-chip-name->id name))) + (('gn:summary . summary) + ;; TODO: Why are there unprintable + ;; characters in the summary? + (cons 'gn:summary + (delete-substrings summary "\x01" "\x03"))) + (('gn:aboutTissue . about-tissue) + ;; TODO: Why are there unprintable + ;; characters in the summary? + (cons 'gn:aboutTissue + (delete-substrings about-tissue "\x01" "\x03"))) + (('gn:geoSeries . geo-series) + (and (not (string-prefix-ci? "no geo series" geo-series)) + (cons 'gn:geoSeries geo-series))) + (x x)) + (process-metadata-alist alist))) id))) db - ;; TODO: Find email ID for records with none. (This is - ;; just one record corresponding to "Evan Williams") ;; TODO: Double check Platforms. It doesn't seem to ;; match up. "SELECT GN_AccesionId, InfoFileTitle AS Name, InfoFiles.Title, @@ -425,7 +436,7 @@ Datasets.Citation, Datasets.Acknowledgment, Species.FullName AS BinomialName, InbredSet.Name AS InbredSetName, Tissue.Short_Name, -Investigators.Email, +Investigators.FirstName, Investigators.LastName, Investigators.Email, AvgMethodId, AvgMethod.Name AS AvgMethodName, GeneChip.Name AS GeneChip FROM InfoFiles @@ -436,8 +447,7 @@ LEFT JOIN InbredSet USING (InbredSetId) LEFT JOIN Tissue USING (TissueId) LEFT JOIN Investigators USING (InvestigatorId) LEFT JOIN AvgMethod USING (AvgMethodId) -LEFT JOIN GeneChip USING (GeneChipId) -WHERE Investigators.Email != ''")) +LEFT JOIN GeneChip USING (GeneChipId)")) (define (dump-data-table db table-name data-field) (let ((dump-directory (string-append %dump-directory "/" table-name)) |