#! /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-species
  (tables (Species))
  (schema-triples
   (gn:name rdfs:range rdfs:Literal)
   (gn:displayName rdfs:range rdfs:Literal)
   (gn:binomialName rdfs:range rdfs:Literal)
   (gn:family rdfs:range rdfs:Literal))
  (triples (string->identifier "species" (field Species FullName))
    (set rdf:type 'gn:species)
    (set gn:name (field Species SpeciesName))
    (set gn:displayName (field Species MenuName))
    (set gn:binomialName (field Species FullName))
    (set gn:family (field Species Family))
    (set gn:organism (ontology 'ncbiTaxon: (field Species TaxonomyId)))))

(define-dump dump-strain
  (tables (Strain
           (join Species "ON Strain.SpeciesId = Species.SpeciesId")))
  (schema-triples
   (gn:strainOfSpecies rdfs:domain gn:strain)
   (gn:strainOfSpecies rdfs:range gn:species)
   (gn:name rdfs:range rdfs:Literal)
   (gn:alias rdfs:range rdfs:Literal)
   (gn:symbol rdfs:range rdfs:Literal))
  (triples (string->identifier
            "strain"
            (regexp-substitute/global
             #f "[^A-Za-z0-9:]"
             (field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName))
             'pre "_" 'post))
    (set rdf:type 'gn:strain)
    (set gn:strainOfSpecies
         (string->identifier "species" (field Species FullName)))
    ;; Name, and maybe a second name
    (set gn:name (sanitize-rdf-string (field Strain Name)))
    (set gn:name (sanitize-rdf-string (field Strain Name2)))
    (set gn:alias (sanitize-rdf-string (field Strain Alias)))
    (set gn:symbol (field Strain Symbol))))

(define-dump dump-mapping-method
  (tables (MappingMethod))
  (triples (string->identifier "mappingMethod" (field MappingMethod Name))
    (set rdf:type 'gn:mappingMethod)))

(define-dump dump-inbred-set
  (tables (InbredSet
           (left-join Species "ON InbredSet.SpeciesId=Species.Id")
           (left-join MappingMethod
                       "ON InbredSet.MappingMethodId=MappingMethod.Id")))
  (schema-triples
   (gn:fullName rdfs:range rdfs:Literal)
   (gn:geneticType rdfs:range rdfs:Literal)
   (gn:inbredSetCode rdfs:range rdfs:Literal)
   (gn:inbredFamily rdfs:range rdfs:Literal)
   (gn:inbredSetOfSpecies rdfs:range gn:species)
   (gn:inbredSetType rdfs:range rdfs:Literal)
   (gn:phenotype rdfs:range gn:inbredSetType)
   (gn:genotype rdfs:range gn:inbredSetType)
   (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod))
  (triples (string->identifier "inbredSet" (field InbredSet Name))
    (set rdf:type 'gn:inbredSet)
    (set gn:binomialName (field InbredSet FullName))
    (set gn:geneticType (field InbredSet GeneticType))
    (set gn:inbredFamily (field InbredSet Family))
    (set gn:inbredSetOfMappingMethod (field MappingMethod Name))
    (set gn:inbredSetCode (field InbredSet InbredSetCode))
    (set gn:inbredSetOfSpecies
         (string->identifier "species" (field Species FullName BinomialName)))
    (set gn:genotype
         (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP)))
    (set gn:phenotype
         (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP)))))

(define-dump dump-avg-method
  ;; The Name and Normalization fields seem to be the same. Dump only
  ;; the Name field.
  (tables (AvgMethod))
  (schema-triples
   (gn:name rdfs:range rdfs:Literal))
  (triples (string->identifier "avgmethod" (field AvgMethod Name))
    (set rdf:type 'gn:avgMethod)
    (set gn:name (field AvgMethod Name))))



(call-with-target-database
 %connection-settings
 (lambda (db)
   (with-output-to-file (string-append %dump-directory "dump-species-metadata.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 "ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>")
       (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>")
       (prefix "up:" "<http://purl.uniprot.org/core/>")
       (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>")
       (newline)
       (dump-species db)
       (dump-strain db)
       (dump-mapping-method db)
       (dump-inbred-set db)
       (dump-avg-method db))
     #:encoding "utf8")))