Remove "dump-" prefix

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

1 files changed, 0 insertions, 226 deletions

diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm
deleted file mode 100755
index b0ac6f8..0000000
--- a/examples/dump-species-metadata.scm
+++ /dev/null
@@ -1,226 +0,0 @@
-#! /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 (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]))
-
-(define-transformer dump-species
-  (tables (Species))
-  (schema-triples
-   (gnc:species a skos:Concept)
-   (gnc:species skos:description "This is a set of controlled terms that are used to describe a given species")
-   (gnc:species skos:broader gnc:family)
-   (gnt:binomialName a owl:ObjectProperty)
-   (gnt:binomialName rdfs:domain gnc:species)
-   (gnt:family a owl:ObjectProperty)
-   (gnt:family rdfs:domain gnc:species)
-   (gnt:family skos:definition "This resource belongs to this family")
-   (gnt:organism a owl:ObjectProperty)
-   (gnt:organism rdfs:domain gnc:species)
-   (gnt:shortName a owl:ObjectProperty)
-   (gnt:shortName rdfs:domain gnc:species))
-  (triples
-      (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                          #:separator ""
-                          #:proc string-capitalize-first)
-    (set rdf:type 'gnc:species)
-    (set skos:label (field Species SpeciesName))
-    (set skos:altLabel (field Species Name))
-    (set rdfs:label (field Species MenuName))
-    (set gnt:binomialName (field Species FullName))
-    (set gnt:family (field Species Family))
-    (set gnt:organism (ontology 'taxon: (field Species TaxonomyId)))))
-
-#!
-
-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 dump-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 dump-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 dump-inbred-set
-  (tables (InbredSet
-           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
-           (left-join MappingMethod
-                      "ON InbredSet.MappingMethodId=MappingMethod.Id")))
-  (schema-triples
-   (gnc:set skos:broader gnc:species)
-   (gnc:set skos:definition "A set of terms used to describe an set, which can be inbredSet, outbredSet etc etc.")
-   (gnt:geneticType a owl:ObjectProperty)
-   (gnt:geneticType rdfs:domain gnc:set)
-   (gnt:code a owl:ObjectProperty)
-   (gnt:code rdfs:domain gnc:set)
-   ;; Already defined as an owl prop in dump-species
-   (gnt:family rdfs:domain gnc:set)
-   (gnt:phenotype a owl:ObjectProperty)
-   (gnt:phenotype rdfs:domain gnc:set)
-   (gnt:genotype a owl:ObjectProperty)
-   (gnt:genotype rdfs:domain gnt:inbredSet)
-   (gnt:mappingMethod a owl:ObjectProperty)
-   (gnt:mappingMethod rdfs:domain gnc:set))
-  (triples (string->identifier
-            "set" (field InbredSet Name)
-            #:separator ""
-            #:proc string-capitalize-first)
-    (set rdf:type 'gnc:set)
-    (set rdfs:label (field InbredSet FullName))
-    (set skos:altLabel (field InbredSet Name))
-    (set gnt:geneticType (field InbredSet GeneticType))
-    (set gnt:family (field InbredSet Family))
-    (set gnt:mappingMethod (field MappingMethod Name))
-    (set gnt:code (field InbredSet InbredSetCode))
-    (set gnt:belongsToSpecies
-         (string->identifier "" (remap-species-identifiers (field Species Fullname))
-                             #:separator ""
-                             #:proc string-capitalize-first))
-    (set gnt:genotype
-         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
-    (set gnt:phenotype
-         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))
-    (multiset gnt:hasTissue
-              (map
-               (lambda (x)
-                 (string->identifier "tissue"
-                                     x))
-               (string-split-substring
-                (field ("(SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name)"
-                        molecularTrait))
-                "||")))))
-
-(define-transformer dump-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))))
-
-
-
-(dump-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
-   dump-inbred-set
-   dump-species
-   dump-strain
-   dump-mapping-method
-   dump-avg-method))
- (outputs
-  '(#:documentation "./docs/dump-species-metadata.md"
-    #:rdf "/export/data/genenetwork-virtuoso/dump-species-metadata.ttl")))