Replace dump.scm with separete dumps for several tables

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

1 files changed, 141 insertions, 0 deletions

diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
new file mode 100755
index 0000000..ed4113c
--- /dev/null
+++ b/examples/dump-species-metadata.scm
@@ -0,0 +1,141 @@
+#! /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))
+
+
+
+(define-dump dump-species
+  (tables (Species))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:displayName rdfs:range rdfs:Literal)
+   (gn:binomialName rdfs:range rdfs:Literal)
+   (gn:family rdfs:range rdfs:Literal))
+  (triples (string->identifier "species" (field Species FullName))
+    (set rdf:type 'gn:species)
+    (set gn:name (field Species SpeciesName))
+    (set gn:displayName (field Species MenuName))
+    (set gn:binomialName (field Species FullName))
+    (set gn:family (field Species Family))
+    (set up:organism (ontology 'taxon: (field Species TaxonomyId)))))
+
+(define-dump dump-strain
+  (tables (Strain
+           (join Species "ON Strain.SpeciesId = Species.SpeciesId")))
+  (schema-triples
+   (gn:strainOfSpecies rdfs:domain gn:strain)
+   (gn:strainOfSpecies rdfs:range gn:species)
+   (gn:name rdfs:range rdfs:Literal)
+   (gn:alias rdfs:range rdfs:Literal)
+   (gn:symbol rdfs:range rdfs:Literal))
+  (triples (string->identifier
+            "strain"
+            (regexp-substitute/global
+             #f "[^A-Za-z0-9:]"
+             (field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName))
+             'pre "_" 'post))
+    (set rdf:type 'gn:strain)
+    (set gn:strainOfSpecies
+         (string->identifier "species" (field Species FullName)))
+    ;; Name, and maybe a second name
+    (set gn:name (sanitize-rdf-string (field Strain Name)))
+    (set gn:name (sanitize-rdf-string (field Strain Name2)))
+    (set gn:alias (sanitize-rdf-string (field Strain Alias)))
+    (set gn:symbol (field Strain Symbol))))
+
+(define-dump dump-mapping-method
+  (tables (MappingMethod))
+  (triples (string->identifier "mappingMethod" (field MappingMethod Name))
+    (set rdf:type 'gn:mappingMethod)))
+
+(define-dump dump-inbred-set
+  (tables (InbredSet
+           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
+           (left-join MappingMethod
+                       "ON InbredSet.MappingMethodId=MappingMethod.Id")))
+  (schema-triples
+   (gn:fullName rdfs:range rdfs:Literal)
+   (gn:geneticType rdfs:range rdfs:Literal)
+   (gn:inbredSetCode rdfs:range rdfs:Literal)
+   (gn:inbredFamily rdfs:range rdfs:Literal)
+   (gn:inbredSetOfSpecies rdfs:range gn:species)
+   (gn:inbredSetType rdfs:range rdfs:Literal)
+   (gn:phenotype rdfs:range gn:inbredSetType)
+   (gn:genotype rdfs:range gn:inbredSetType)
+   (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod))
+  (triples (string->identifier "inbredSet" (field InbredSet Name))
+    (set rdf:type 'gn:inbredSet)
+    (set gn:binomialName (field InbredSet FullName))
+    (set gn:geneticType (field InbredSet GeneticType))
+    (set gn:inbredFamily (field InbredSet Family))
+    (set gn:inbredSetOfMappingMethod (field MappingMethod Name))
+    (set gn:inbredSetCode (field InbredSet InbredSetCode))
+    (set gn:inbredSetOfSpecies
+         (string->identifier "species" (field Species FullName BinomialName)))
+    (set gn:genotype
+         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
+    (set gn:phenotype
+         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))
+
+(define-dump dump-avg-method
+  ;; The Name and Normalization fields seem to be the same. Dump only
+  ;; the Name field.
+  (tables (AvgMethod))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal))
+  (triples (string->identifier "avgmethod" (field AvgMethod Name))
+    (set rdf:type 'gn:avgMethod)
+    (set gn:name (field AvgMethod Name))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-species-metadata.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-species db)
+       (dump-strain db)
+       (dump-mapping-method db)
+       (dump-inbred-set db)
+       (dump-avg-method db))
+     #:encoding "utf8")))