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-rwxr-xr-xweb/webserver.scm163
1 files changed, 3 insertions, 160 deletions
diff --git a/web/webserver.scm b/web/webserver.scm
index 0f733d3..26b4a75 100755
--- a/web/webserver.scm
+++ b/web/webserver.scm
@@ -23,59 +23,15 @@
(web client)
(web request)
(web response)
- (web uri)
+; (web uri)
(fibers web server)
(gn cache memoize)
+ (web gn-uri)
(gn db sparql)
+ (gn data species)
(web sxml)
(web view doc))
-(define get-version
- "2.0")
-
-(define (base-url)
- "https://luna.genenetwork.org")
-
-(define (prefix)
- "Build the API URL including version"
- (string-append (base-url) "/api/v" get-version))
-
-(define (base-url)
- "http://localhost:8091")
-
-(define (prefix)
- "Build the API URL including version"
- (base-url))
-
-(define* (mk-url postfix #:optional (ext ""))
- "Add the path to the API URL"
- (string-append (prefix) "/" postfix ext))
-
-(define (mk-html path)
- "Create a pointer to HTML documentation"
- (string-append (base-url) "/" path ".html"))
-
-(define (mk-doc path)
- "Create a pointer to HTML documentation"
- (mk-html (string-append "doc/" path)))
-
-(define (mk-meta path)
- "Create a meta URL for the API path"
- (mk-url path ".meta.json"))
-
-(define (mk-data path)
- "Create a JSON URL for the API path"
- (mk-url path ".json"))
-
-(define (mk-term postfix)
- (mk-html (string-append "term" "/" postfix)))
-
-(define (mk-id postfix)
- (mk-html (string-append "id" "/" postfix)))
-
-(define (mk-predicate postfix)
- (mk-html (string-append "predicate" "/" postfix)))
-
(define info `(
("name" . "GeneNetwork REST API")
@@ -95,46 +51,10 @@
(,(mk-url "datasets")."Get a list of datasets")))))
-;; 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 (get-species)
- (receive (names res) (memo-sparql-species-meta)
- (let* ([table (get-rows names res)]
- [recs '()]
- [h (compile-species recs table)])
- (species-digest h))
- ))
; (define (wd-species-info wd)
; )
-(define (url-parse-id uri)
- (if uri
- (car (reverse (string-split uri #\057)))
- "unknown"
- ))
-
-(define (strip-lang s)
- "Strip quotes and language tag (@en) from RDF entries"
- (list->string (match (string->list s)
- [(#\"rest ... #\") rest]
- [(#\"rest ... #\" #\@ #\e #\n) rest]
- [rest rest]))
- )
-
-(define (normalize-id str)
- ;; (string-replace-substring (string-downcase str) " " "_")
- (string-replace-substring str " " "_")
- )
(define (get-expanded-taxon-meta id)
"Get information on a specific species, e.g. mouse"
@@ -145,83 +65,6 @@
("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)
- (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/")))
-
-(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)))))
;; ---- REST API web server handler