Replace dump.scm with separete dumps for several tables

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

1 files changed, 131 insertions, 0 deletions

diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm
new file mode 100755
index 0000000..842e7e8
--- /dev/null
+++ b/examples/dump-phenotype.scm
@@ -0,0 +1,131 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (rnrs programs)
+             (rnrs io ports)
+             (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))
+
+
+
+;; Only dump publish freeze entries that were not dumped from the InfoFiles page
+(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 InfoFiles.InfoPageName IS NULL")
+  (schema-triples
+   (gn:datasetOfInbredSet rdfs:range gn:inbredSet)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:fullName rdfs:range rdfs:Literal)
+   (gn:shortName rdfs:range rdfs:Literal)
+   (gn:createTime rdfs:range rdfs:Literal))
+  (triples (string->identifier "dataset" (field PublishFreeze Name))
+    (set rdf:type 'gn:phenotypeDataset)
+    (set gn:name (field PublishFreeze Name))
+    (set gn:fullName (field PublishFreeze FullName))
+    (set gn:shortName (field PublishFreeze ShortName))
+    (set gn:createTime (field PublishFreeze CreateTime))
+    (set gn:datasetOfInbredSet
+         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+
+(define-dump dump-phenotypes
+  (tables (Phenotype
+           (left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
+           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
+           (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
+  (schema-triples
+   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset))
+  (triples (ontology 'phenotype:
+                     (regexp-substitute/global #f "[^A-Za-z0-9:]"
+                                               (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, ':')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
+                                               'pre "_" 'post))
+    (set rdf:type 'gn:phenotype)
+    (set gn:name (sanitize-rdf-string
+                  (field
+                   ("CAST(CONVERT(BINARY CONVERT(CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '-')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) USING latin1) USING utf8) AS VARCHAR(10000))"
+                    abbrev))))
+    ;; There is no row with an empty post-publication description so
+    ;; use this field as the main publication description
+    (set gn:publicationDescription
+         (sanitize-rdf-string
+          (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
+                  postPubDescr))))
+    (set gn:originalDescription (sanitize-rdf-string
+                                 (delete-substrings
+                                  (field Phenotype Original_description)
+                                  "Original post publication description: ")))
+    (set gn:prePublicationDescription
+         (sanitize-rdf-string
+          (field
+           ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
+            prePubDesc))))
+    (set gn:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
+    (set gn:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
+    (set gn:labCode (field Phenotype Lab_code))
+    (set gn:submitter (sanitize-rdf-string (field Phenotype Submitter)))
+    (set gn:owner (sanitize-rdf-string (field Phenotype Owner)))
+    (set gn:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
+                                 '^^xsd:double))
+    (set gn:locus (field PublishXRef Locus))
+    (set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float))
+    (set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
+    (set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
+    (set gn:phenotypeOfDataset (string->identifier "dataset" (field PublishFreeze Name)))
+    (set gn:phenotypeOfPublication
+         (let ((pmid (field
+                      ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
+                       pmid)))
+               (publication-id (field Publication Id)))
+           (if (string-null? pmid)
+               (string->identifier "publication"
+                                   (number->string publication-id))
+               (ontology 'pubmed: pmid))))))
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-phenotype.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-publishfreeze db)
+       (dump-phenotypes db))
+     #:encoding "utf8")))