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(define-module (gn data species)
#:use-module (json)
#:use-module (ice-9 match)
#:use-module (ice-9 format)
#:use-module (ice-9 iconv)
#:use-module (ice-9 receive)
#:use-module (ice-9 string-fun)
#:use-module (gn db sparql)
#:use-module (gn data group)
#:use-module (web gn-uri)
#:export (
gnid-species
get-species-meta
get-species-data
get-species-shortnames
get-expanded-species
get-expanded-taxon-meta
get-expanded-taxon-data
))
(define (gnid-species short-name)
"Find the GN identifier from shortname, e.g. Mus_musculus"
(let ([rec (get-expanded-taxon-data short-name)])
(url-parse-id (assoc-ref rec "gnid"))
))
(define (get-species)
(receive (names res) (memo-sparql-species-meta)
(let* ([table (get-rows names res)]
[recs '()]
[h (compile-species recs table)])
(species-digest h))
))
;; result should be a vector of list of pair
(define (species-digest recs)
(map (lambda (r)
(let* ([k (car r)]
[v (cdr r)])
; with key use (cons k (map (lambda (i) (cons (car i) (car (cdr i)))) v))
(map (lambda (i) (cons (url-parse-id (car i)) (car (cdr i)))) v)
))
recs )
)
(define (expand-species rec)
(let ([wd-id (url-parse-id (assoc-ref rec "22-rdf-syntax-ns#isDefinedBy"))]
[short-name (normalize-id (assoc-ref rec "shortName"))])
(if (string=? wd-id "unknown")
rec
; wikidata query:
(receive (names row) (tsv->scm (memo-sparql-wd-species-info wd-id))
(match (pk (car row))
((taxonomy-name ncbi descr)
(let ([ncbi-id (strip-lang ncbi)]
[taxonomy-lnk (string-replace-substring (strip-lang taxonomy-name) " " "_")])
(cons `("id" . ,short-name)
(cons `("wikidata" . ,wd-id)
(cons `("taxonomy-id" . ,ncbi-id)
(cons `("ncbi-url" . ,(string-append "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" ncbi-id))
(cons `("uniprot-url" . ,(string-append "https://www.uniprot.org/taxonomy/" ncbi-id))
(cons `("wikidata-url" . ,(string-append "http://www.wikidata.org/entity/" wd-id))
(cons `("wikispecies-url" . ,(string-append "https://species.wikimedia.org/wiki/" taxonomy-lnk))
(cons `("taxonomy-name" . ,(strip-lang taxonomy-name))
(cons `("meta" . ,(mk-meta short-name))
(cons `("description" . ,(strip-lang descr))
rec))))))))))))
)
)))
)
(define (get-expanded-taxon-data short-name)
"Here we add information related to one taxonomy species"
(call/cc (lambda (return) ; use call/cc to be able to return early
(for-each (lambda (rec)
(if (string=? (assoc-ref rec "shortName") short-name)
(return (expand-species rec))))
(get-species))
(return #f)
)))
(define (get-expanded-species)
"Here we add information related to each species"
(map (lambda (rec)
(expand-species rec)
) (get-species)))
(define (get-species-api-str)
(scm->json-string #("https://genenetwork.org/api/v2/mouse/"
"https://genenetwork.org/api/v2/rat/")))
(define (get-species-shortnames recs)
(map (lambda r (assoc-ref (car r) "shortName")) recs))
(define (get-species-meta2 recs)
"Return a list of short names and expand them to URIs"
(map (lambda r
(let ([shortname (assoc-ref (car r) "shortName")])
(cons shortname (mk-meta shortname)))) recs)
)
(define (get-species-links recs)
"Return a list of short names and expand them to URIs"
(map (lambda r
(let ([shortname (assoc-ref (car r) "shortName")])
(cons shortname (mk-data shortname)))) recs)
)
(define (get-species-data)
(list->vector (get-expanded-species)))
(define (get-species-meta)
(let ([recs (get-expanded-species)])
`(("info" . "Get information on species by visiting the data link or one of the individual links")
("doc" . ,(mk-doc "species"))
("meta" . ,(mk-meta "species"))
("data" . ,(mk-data "species"))
("up" . ,(string-append (prefix) "/"))
("meta-links" . ,(get-species-meta2 recs))
("links" . ,(get-species-links recs)))))
(define (get-expanded-taxon-meta id)
"Get information on a specific species, e.g. mouse"
`(("info" . ,id)
("doc" . ,(mk-doc id))
("meta" . ,(mk-meta id))
("data" . ,(mk-data id))
("up" . ,(mk-meta "species"))
("meta-links" . ,(list->vector (get-group-links (gnid-species id)
(lambda (r) (mk-meta (url-parse-id r))))))
("links" . ,(list->vector (get-group-links (gnid-species id)
(lambda (r) (mk-data (url-parse-id r))))))
))
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