#! /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]))

(define-transformer 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 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 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 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 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))))