#! /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-transformer molecular-entities
  (tables (Tissue))
  (schema-triples
   (gnc:molecular_trait a owl:Class)
   (gnc:molecular_trait a skos:Concept)
   (gnc:molecular_trait rdfs:subClassOf obo:UBERON_0000479)
   (gnc:molecular_trait rdfs:label "Molecular Trait.   This describes a melecular trait of a given species.  We combine the species name and the tissue name in order to differentiate the traits across different inbredset groups."))
  (triples (string->identifier "tissue" (field Tissue Short_Name) #:separator "_")
    (set rdf:type 'gnc:molecular_trait)
    (set skos:prefLabel (field Tissue Name))
    (set skos:altLabel (field Tissue Short_Name))))

(define-transformer molecular-traits
  (tables (Species
           (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
           (inner-join ProbeFreeze "ON ProbeFreeze.InbredSetId = InbredSet.Id")
           (inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
           (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
          "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name")
  (schema-triples
   (gnt:has_molecular_trait rdf:type owl:ObjectProperty)
   (gnt:has_molecular_trait rdfs:domain gnc:set)
   (gnt:has_molecular_trait rdfs:range gnc:molecular_traits)
   (gnt:has_molecular_trait rdfs:label "has molecular trait"))
  (triples (string->identifier
            (format #f "trait_~a" (field Species Name))
            (field Tissue Short_Name)
            #:separator "_")
    (set rdf:type 'gnc:molecular_entity)
    (set gnt:has_strain
         (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
    (set gnt:has_species
         (string->identifier "" (remap-species-identifiers (field Species Fullname))))
    (multiset gnt:has_probeset_data
              (map (cut string->identifier "dataset" <> #:separator "_")
                   (string-split
                    (field ("GROUP_CONCAT(ProbeSetFreeze.Name SEPARATOR ',')"
                            dataset_name))
                    #\,)))
    (set gnt:has_molecular_trait
         (string->identifier "tissue"
                             (field Tissue Short_Name)
                             #:separator "_"))))

(define-transformer list-molecular-traits
  (tables (Species
           (inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
           (inner-join ProbeFreeze "ON ProbeFreeze.InbredSetId = InbredSet.Id")
           (inner-join ProbeSetFreeze "ON ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id")
           (inner-join Tissue "ON ProbeFreeze.TissueId = Tissue.Id"))
          "WHERE ProbeSetFreeze.public > 0 GROUP BY Species.Name, Tissue.Short_Name")
  (schema-triples
      (gnc:molecular_entity a owl:Class)
   (gnc:molecular_entity a skos:Concept)
   (gnc:molecular_entity rdfs:subClassOf obo:UBERON_0000479)
   (gnc:molecular_entity rdfs:label "This points this to resource which has molecular trait."))
  (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
    (set gnt:has_molecular_entity
         (string->identifier (format #f "trait_~a"
                                     (field Species Name))
                             (field Tissue Short_Name) #:separator "_"))))




(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 "Tissue Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("gn:" "<http://rdf.genenetwork.org/v1/id/>")
      ("obo:" "<http://purl.obolibrary.org/obo/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")))
   (inputs
    (list
     molecular-entities
     molecular-traits
     list-molecular-traits))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))