Rename file

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

1 files changed, 150 insertions, 0 deletions

diff --git a/examples/strains.scm b/examples/strains.scm
new file mode 100755
index 0000000..89f2e27
--- /dev/null
+++ b/examples/strains.scm
@@ -0,0 +1,150 @@
+#! /usr/bin/env guile
+!#
+
+(use-modules (srfi srfi-1)
+             (srfi srfi-26)
+             (ice-9 getopt-long)
+             (ice-9 match)
+             (ice-9 regex)
+             (transform strings)
+             (transform sql)
+             (transform triples)
+             (transform special-forms))
+
+(define (remap-species-identifiers str)
+  "This procedure remaps identifiers to standard binominal. Obviously this should
+   be sorted by correcting the database!"
+  (match str
+    ["Fly (Drosophila melanogaster dm6)" "Drosophila melanogaster"]
+    ["Oryzias latipes (Japanese medaka)" "Oryzias latipes"]
+    ["Macaca mulatta" "Macaca nemestrina"]
+    ["Bat (Glossophaga soricina)" "Glossophaga soricina"]
+    [str str]))
+
+#!
+
+The ProbeData table contains StrainID.
+
+MariaDB [db_webqtl]> select * from ProbeData limit 2;
++--------+----------+---------+
+| Id     | StrainId | value   |
++--------+----------+---------+
+| 503636 |       42 | 11.6906 |
+| 503636 |       43 | 11.4205 |
++--------+----------+---------+
+
+Likewise
+
+MariaDB [db_webqtl]> select * from ProbeSetData wher limit 2;
++----+----------+-------+
+| Id | StrainId | value |
++----+----------+-------+
+|  1 |        1 | 5.742 |
+|  1 |        2 | 5.006 |
++----+----------+-------+
+
+To get at the strain use
+
+MariaDB [db_webqtl]> select * from Strain where Id=1 limit 15;
++----+--------+--------+-----------+--------+-------+
+| Id | Name   | Name2  | SpeciesId | Symbol | Alias |
++----+--------+--------+-----------+--------+-------+
+|  1 | B6D2F1 | B6D2F1 |         1 | NULL   | NULL  |
++----+--------+--------+-----------+--------+-------+
+
+A typical query may look like
+
+SELECT Strain.Name, Strain.Id FROM Strain, Species
+WHERE Strain.Name IN f{create_in_clause(self.samplelist)}
+AND Strain.SpeciesId=Species.Id
+AND Species.name = %s, (self.group.species,)
+
+At this point it is not very clear how Name, Name2, Symbol and Alias are used.
+
+!#
+
+(define-transformer strain
+  (tables (Strain
+           (left-join Species "ON Strain.SpeciesId = Species.SpeciesId")))
+  (schema-triples
+   (gnc:strain skos:broader gnc:species)
+   (gnt:belongsToSpecies rdfs:domain gnc:strain)
+   (gnt:belongsToSpecies skos:definition "This resource belongs to this species")
+   (gnt:belongsToSpecies a owl:ObjectProperty)
+   (gnt:belongsToSpecies skos:definition "This resource belongs to this species")
+   (gnt:alias rdfs:domain gnc:strain)
+   (gnt:alias a owl:ObjectProperty)
+   (gnt:symbol rdfs:domain gnc:strain)
+   (gnt:symbol a owl:ObjectProperty))
+  (triples (string->identifier
+            ""
+            (regexp-substitute/global
+             #f "[^A-Za-z0-9:]"
+             (field Strain Name)
+             'pre "_" 'post)
+            #:separator ""
+            #:proc string-capitalize-first)
+    (set rdf:type 'gnc:strain)
+    (set gnt:belongsToSpecies
+         (string->identifier "" (remap-species-identifiers (field Species Fullname))
+                             #:separator ""
+                             #:proc string-capitalize-first))
+    ;; Name, and maybe a second name
+    (set rdfs:label (sanitize-rdf-string (field Strain Name)))
+    (set rdfs:label (sanitize-rdf-string (field ("IF ((Strain.Name2 != Strain.Name), Strain.Name2, '')" Name2))))
+    (set gnt:alias (sanitize-rdf-string (field ("IF ((Strain.Alias != Strain.Name), Strain.Alias, '')" Alias))))
+    (set gnt:symbol (field ("IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '')" Symbol)))))
+
+(define-transformer mapping-method
+  (tables (MappingMethod))
+  (schema-triples
+   (gnc:mappingMethod a skos:Concept)
+   (gnc:mappingMethod skos:definition "Terms that decribe mapping/normalization methods used in GeneNetwork"))
+  (triples
+      (string->identifier "mappingMethod" (field MappingMethod Name))
+    (set rdf:type 'gnc:mappingMethod)
+    (set rdfs:label (field MappingMethod Name))))
+
+(define-transformer avg-method
+  ;; The Name and Normalization fields seem to be the same. Dump only
+  ;; the Name field.
+  (tables (AvgMethod))
+  (schema-triples
+   (gnc:avgMethod rdf:type owl:Class))
+  (triples (string->identifier "avgmethod" (field AvgMethod Name))
+    (set rdf:type 'gnc:avgMethod)
+    (set rdfs:label (field AvgMethod Normalization))))
+
+
+
+(let* ((option-spec
+        '((settings (single-char #\s) (value #t))
+          (output (single-char #\o) (value #t))
+          (documentation (single-char #\d) (value #t))))
+       (options (getopt-long (command-line) option-spec))
+       (settings (option-ref options 'settings #f))
+       (output (option-ref options 'output #f))
+       (documentation (option-ref options 'documentation #f))
+       (%connection-settings
+        (call-with-input-file settings
+          read)))
+
+  (with-documentation
+   (name "Species Metadata")
+   (connection %connection-settings)
+   (table-metadata? #f)
+   (prefixes
+    '(("gn:" "<http://genenetwork.org/id/>")
+      ("gnc:" "<http://genenetwork.org/category/>")
+      ("owl:" "<http://www.w3.org/2002/07/owl#>")
+      ("gnt:" "<http://genenetwork.org/term/>")
+      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
+      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
+      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
+      ("taxon:" "<http://purl.uniprot.org/taxonomy/>")))
+   (inputs
+    (list inbred-set species strain mapping-method avg-method))
+   (outputs
+    `(#:documentation ,documentation
+      #:rdf ,output))))
+