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authorPjotr Prins2023-08-11 10:37:05 +0200
committerPjotr Prins2023-08-11 10:37:05 +0200
commit566537f47eff45f17e0da9c28ca965f600b6b9a9 (patch)
tree5a9297e917befabdf3dff7d22d131c461d59e1b1
parent4720feda6419ab3ceb6332ceb37ee214a0274e54 (diff)
downloadgn-guile-566537f47eff45f17e0da9c28ca965f600b6b9a9.tar.gz
Get expanded species1
-rwxr-xr-xweb/webserver.scm64
1 files changed, 40 insertions, 24 deletions
diff --git a/web/webserver.scm b/web/webserver.scm
index 771bebd..7690159 100755
--- a/web/webserver.scm
+++ b/web/webserver.scm
@@ -144,35 +144,50 @@
("up" . ,(mk-meta "species"))
))
+(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 "name"))])
+ (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-species)
"Here we add information related to each species"
(map (lambda (rec)
- (let ([wd-id (url-parse-id (assoc-ref rec "22-rdf-syntax-ns#isDefinedBy"))]
- [short-name (normalize-id (assoc-ref rec "name"))])
- (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 `("shortname" . ,shortname) - problematic
- (cons `("description" . ,(strip-lang descr))
- rec)))))))))))
- )
- )))
+ (expand-species rec)
) (get-species)
))
+(define (get-expanded-species1 short-name)
+ "Here we add information related to one taxonomy species"
+ (call/cc (lambda (return)
+ (for-each (lambda (rec)
+ (if (string=? (assoc-ref rec "shortName") short-name)
+ (return (expand-species rec))))
+ (get-species))
+ (return #f)
+)))
+
(define (get-species-api-str)
(scm->json-string #("https://genenetwork.org/api/v2/mouse/"
"https://genenetwork.org/api/v2/rat/")))
@@ -260,7 +275,8 @@
(let ([names (get-species-shortnames (get-expanded-species))])
(match (string->list id)
[(name ... #\. #\m #\e #\t #\a #\. #\j #\s #\o #\n) (render-json (get-expanded-taxon-meta (list->string name)))]
- [rest (render-json "WIP")])))
+ [(name ... #\. #\j #\s #\o #\n) (render-json (get-expanded-species1 (list->string name)))]
+ [rest (render-json "NOP")])))
(_ (not-found (request-uri request)))
))