Replace dump.scm with separete dumps for several tables

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 220 insertions, 0 deletions

diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm
new file mode 100755
index 0000000..aa7a5f2
--- /dev/null
+++ b/examples/dump-dataset-metadata.scm
@@ -0,0 +1,220 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 match)
+             (ice-9 regex)
+             (dump strings)
+             (dump sql)
+             (dump triples)
+             (dump special-forms))
+
+
+
+(define %connection-settings
+  (call-with-input-file (list-ref (command-line) 1)
+    read))
+
+(define %dump-directory
+  (list-ref (command-line) 2))
+
+
+
+;; One email ID in the Investigators table has spaces in it. This
+;; function fixes that.
+(define (fix-email-id email)
+  (string-delete #\space 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
+                       ;; Add special case for Yohan Bossé whose name
+                       ;; has unprintable characters.
+                       ;; TODO: Fix Yohan Bossé's name in the database.
+                       (let ((last-name (if (string=? first-name "Yohan")
+                                            "Bosse"
+                                            last-name)))
+                         (list first-name last-name (fix-email-id email)))
+                       "_")))
+
+(define-dump dump-investigators
+  ;; There are a few duplicate entries. We group by email to
+  ;; deduplicate.
+  (tables (Investigators)
+          "GROUP BY Email")
+  (schema-triples
+   ;; TODO: Are ranges required for FOAF predicates? Can they not be
+   ;; obtained from the FOAF spec?
+   (foaf:name rdfs:range rdfs:Literal)
+   (foaf:givenName rdfs:range rdfs:Literal)
+   (foaf:familyName rdfs:range rdfs:Literal)
+   (foaf:phone rdfs:range rdfs:Literal)
+   (foaf:mbox rdfs:range rdfs:Literal)
+   (foaf:homepage rdfs:range rdfs:Literal)
+   (gn:address rdfs:range rdfs:Literal)
+   (gn:city rdfs:range rdfs:Literal)
+   (gn:state rdfs:range rdfs:Literal)
+   (gn:zipCode rdfs:range rdfs:Literal)
+   (gn:country rdfs:range rdfs:Literal))
+  (triples (investigator-attributes->id (field Investigators FirstName)
+                                        (field Investigators LastName)
+                                        (field Investigators Email))
+    (set rdf:type 'foaf:Person)
+    ;; Special case Yohan Bossé's name since the last name has
+    ;; unprintable characters.
+    (set foaf:name (string-append (field Investigators FirstName) " "
+                                  (if (string=? (field Investigators FirstName) "Yohan")
+                                      "Bossé"
+                                      (field Investigators LastName))))
+    (set foaf:givenName (field Investigators FirstName))
+    ;; Special case Yohan Bossé's name since the last name has
+    ;; unprintable characters.
+    (set foaf:familyName (if (string=? (field Investigators FirstName) "Yohan")
+                             "Bossé"
+                             (field Investigators LastName)))
+    (set foaf:phone (field Investigators Phone))
+    (set foaf:mbox (fix-email-id (field Investigators Email)))
+    (set foaf:homepage (field Investigators Url))
+    (set gn:address (field Investigators Address))
+    (set gn:city (field Investigators City))
+    (set gn:state (field Investigators State))
+    (set gn:zipCode (field Investigators ZipCode))
+    (set gn:country (field Investigators Country))))
+
+(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 ProbeSetFreeze "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+           (left-join Datasets "USING (DatasetId)")
+           (left-join DatasetStatus "USING (DatasetStatusId)")
+           (left-join Species "USING (SpeciesId)")
+           (left-join Tissue "USING (TissueId)")
+           (left-join Investigators "USING (InvestigatorId)")
+           (left-join AvgMethod "USING (AvgMethodId)")
+           (left-join GeneChip "USING (GeneChipId)"))
+          "WHERE GN_AccesionId IS NOT NULL")
+  (schema-triples
+   (gn:datasetOfInvestigator rdfs:domain gn:dataset)
+   (gn:datasetOfInvestigator rdfs:range foaf:Person)
+   (gn:datasetOfSpecies rdfs:domain gn:dataset)
+   (gn:datasetOfSpecies rdfs:range gn:species)
+   (gn:datasetOfInbredSet rdfs:domain gn:dataset)
+   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
+   (gn:datasetOfTissue rdfs:domain gn:dataset)
+   (gn:datasetOfTissue rdfs:range gn:tissue)
+   (gn:normalization rdfs:domain gn:dataset)
+   (gn:normalization rdfs:range gn:avgMethod)
+   (gn:datasetOfPlatform rdfs:domain gn:dataset)
+   (gn:datasetOfPlatform rdfs:range gn:geneChip)
+   (gn:accessionId rdfs:range rdfs:Literal)
+   (gn:datasetStatusName rdfs:range rdfs:Literal)
+   (gn:summary rdfs:range rdfs:Literal)
+   (gn:aboutTissue rdfs:range rdfs:Literal)
+   (gn:geoSeries rdfs:range rdfs:Literal)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:title rdfs:range rdfs:Literal)
+   (gn:specifics rdfs:range rdfs:Literal)
+   (gn:datasetGroup rdfs:range rdfs:Literal)
+   (gn:aboutCases rdfs:range rdfs:Literal)
+   (gn:aboutPlatform rdfs:range rdfs:Literal)
+   (gn:aboutDataProcessing rdfs:range rdfs:Literal)
+   (gn:notes rdfs:range rdfs:Literal)
+   (gn:experimentDesign rdfs:range rdfs:Literal)
+   (gn:contributors rdfs:range rdfs:Literal)
+   (gn:citation rdfs:range rdfs:Literal)
+   (gn:acknowledgment rdfs:range rdfs:Literal))
+  (triples (string->identifier "dataset"
+                               (field InfoFiles InfoPageName))
+    ;; Add GeneChipName and GeoPlatform:
+    ;; GeneChip.GeneChipName AS gene_chip_name
+    ;; GeneChip.GeoPlatform AS geo_platform
+    (set rdf:type (string->symbol
+                   (field ("IF(GenoFreeze.Id IS NOT NULL, 'gn:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gn:phenotypeDataset', 'gn:dataset'))"
+                           rdfType))))
+    (set gn:name (field InfoFiles InfoPageName))
+    (set dct:created
+         (field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))"
+                 createTimeGenoFreeze)))
+    (set gn:datasetOfInvestigator
+         (investigator-attributes->id (field Investigators FirstName)
+                                      (field Investigators LastName)
+                                      (field Investigators Email)))
+    (set gn:accessionId (string-append "GN" (number->string
+                                             (field InfoFiles GN_AccesionId))))
+    (set gn:datasetStatusName (string-downcase
+                               (field DatasetStatus DatasetStatusName)))
+    (set gn:datasetOfSpecies (string->identifier "species"
+                              (field Species FullName BinomialName)))
+    (set gn:datasetOfTissue (string->identifier "tissue"
+                                                (field Tissue Short_Name)))
+    (set gn:normalization
+         (string->identifier "avgmethod"
+          ;; If AvgMethodName is NULL, assume N/A.
+          (if (string-blank? (field AvgMethod Name AvgMethodName))
+              "N/A" (field AvgMethod Name AvgMethodName))))
+    (set gn:datasetOfPlatform
+         (string->identifier "platform"
+                             (field GeneChip Name GeneChip)))
+    (set gn:summary
+         (sanitize-rdf-string (field Datasets Summary)))
+    (set gn:aboutTissue
+         (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:title (field InfoFiles Title))
+    (set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics)))
+    (set gn:datasetGroup (field Datasets DatasetName DatasetGroup))
+    (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)))))
+
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-info-pages.ttl")
+     (lambda ()
+       (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
+       (prefix "dct:" "<http://purl.org/dc/terms/>")
+       (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>")
+       (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>")
+       (prefix "gn:" "<http://genenetwork.org/>")
+       (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>")
+       (prefix "homologene:" "<https://bio2rdf.org/homologene:>")
+       (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>")
+       (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>")
+       (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>")
+       (prefix "omim:" "<https://www.omim.org/entry/>")
+       (prefix "owl:" "<http://www.w3.org/2002/07/owl#>")
+       (prefix "phenotype:" "<http://genenetwork.org/phenotype/>")
+       (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
+       (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")
+       (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+       (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+       (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>")
+       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
+       (prefix "up:" "<http://purl.uniprot.org/core/>")
+       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
+       (newline)
+       (dump-info-files db)
+       (dump-investigators db))
+     #:encoding "utf8")))