Create a new probesetfreeze dump

This way, the probeset dump will become smaller.

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

2 files changed, 92 insertions, 39 deletions

diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
index a71f708..8e809a5 100755
--- a/examples/dump-probeset.scm
+++ b/examples/dump-probeset.scm
@@ -20,14 +20,6 @@
   (list-ref (command-line) 2))
 
 
-(define-dump dump-gene-chip
-  (tables (GeneChip))
-  (schema-triples
-   (gn:name rdfs:range rdfs:Literal))
-  (triples (string->identifier "platform" (field GeneChip Name))
-    (set rdf:type 'gn:platform)
-    (set gn:name (field GeneChip GeneChipName))))
-
 (define-dump dump-probeset
   (tables (ProbeSet
            (left-join ProbeSetXRef "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id")
@@ -144,35 +136,6 @@
     (set gn:secondaryNames (field ProbeSet SecondaryNames))
     (set gn:peptideSequence (field ProbeSet PeptideSequence))))
 
-;; Molecular Traits are also referred to as ProbeSets
-(define-dump dump-probesetfreeze
-  (tables (ProbeSetFreeze
-           (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
-           (left-join ProbeFreeze "USING (ProbeFreezeId)")
-           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
-           (left-join InbredSet "ON ProbeFreeze.InbredSetId=InbredSet.Id")
-           (left-join Tissue "USING (TissueId)"))
-          "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
-  (schema-triples
-   (gn:avgMethod rdfs:range rdfs:Literal)
-   (gn:dataScale rdfs:range rdfs:Literal))
-  (triples
-      (ontology 'probeset:
-                (regexp-substitute/global #f "[^A-Za-z0-9:]"
-                                          (field ProbeSetFreeze Name)
-                                          'pre "_" 'post))
-    (set rdf:type 'gn:probesetDataset)
-    (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
-    (set gn:fullName (field ProbeSetFreeze FullName))
-    (set gn:shortName (field ProbeSetFreeze ShortName))
-    (set dct:created (annotate-field
-                      (field ProbeSetFreeze CreateTime)
-                      '^^xsd:datetime))
-    (set gn:dataScale (field ProbeSetFreeze DataScale))
-    (set gn:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
-    (set gn:datasetOfInbredSet
-         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
-
 
 
 (call-with-target-database
@@ -203,7 +166,5 @@
        (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
        (prefix "probeset:" "<http://genenetwork.org/probeset/>")
        (newline)
-       (dump-gene-chip db)
-       (dump-probesetfreeze db)
        (dump-probeset db))
      #:encoding "utf8")))
diff --git a/examples/dump-probesetfreeze.scm b/examples/dump-probesetfreeze.scm
new file mode 100755
index 0000000..b238851
--- /dev/null
+++ b/examples/dump-probesetfreeze.scm
@@ -0,0 +1,92 @@
+#! /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-gene-chip
+  (tables (GeneChip))
+  (schema-triples
+   (gn:name rdfs:range rdfs:Literal))
+  (triples (string->identifier "platform" (field GeneChip Name))
+    (set rdf:type 'gn:platform)
+    (set gn:name (field GeneChip GeneChipName))))
+
+;; Molecular Traits are also referred to as ProbeSets
+(define-dump dump-probesetfreeze
+  (tables (ProbeSetFreeze
+           (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
+           (left-join ProbeFreeze "USING (ProbeFreezeId)")
+           (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
+           (left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
+           (left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
+          "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
+  (schema-triples
+   (gn:avgMethod rdfs:range rdfs:Literal)
+   (gn:dataScale rdfs:range rdfs:Literal))
+  (triples
+      (ontology 'probeset:
+                (regexp-substitute/global #f "[^A-Za-z0-9:]"
+                                          (field ProbeSetFreeze Name)
+                                          'pre "_" 'post))
+    (set rdf:type 'gn:probesetDataset)
+    (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
+    (set gn:fullName (field ProbeSetFreeze FullName))
+    (set gn:shortName (field ProbeSetFreeze ShortName))
+    (set dct:created (annotate-field
+                      (field ProbeSetFreeze CreateTime)
+                      '^^xsd:datetime))
+    (set gn:dataScale (field ProbeSetFreeze DataScale))
+    (set gn:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
+    (set gn:datasetOfInbredSet
+         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
+
+
+
+(call-with-target-database
+ %connection-settings
+ (lambda (db)
+   (with-output-to-file (string-append %dump-directory "dump-probesetfreeze.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#>")
+       (prefix "probeset:" "<http://genenetwork.org/probeset/>")
+       (newline)
+       (dump-gene-chip db)
+       (dump-probesetfreeze db))
+     #:encoding "utf8")))