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-rwxr-xr-xweb/webserver.scm179
1 files changed, 2 insertions, 177 deletions
diff --git a/web/webserver.scm b/web/webserver.scm
index 910024f..657d82e 100755
--- a/web/webserver.scm
+++ b/web/webserver.scm
@@ -18,7 +18,6 @@
;; (ice-9 source)
(srfi srfi-1)
(srfi srfi-11) ; let-values
- (srfi srfi-13) ; hash table for memoize
(srfi srfi-26)
(web http)
(web client)
@@ -26,7 +25,8 @@
(web response)
(web uri)
(fibers web server)
- (gn cache memoize))
+ (gn cache memoize)
+ (gn db sparql))
(define get-version
"2.0")
@@ -34,11 +34,6 @@
(define (base-url)
"https://genenetwork.org")
-(define (gn-sparql-endpoint-url)
- "https://sparql.genenetwork.org/sparql")
-
-(define (wd-sparql-endpoint-url)
- "https://query.wikidata.org/sparql")
(define (prefix)
"Build the API URL including version"
@@ -73,7 +68,6 @@
(define (mk-predicate postfix)
(mk-html (string-append "predicate" "/" postfix)))
-(define (wdt-taxon-name) "wdt:P225")
(define info `(
("name" . "GeneNetwork REST API")
@@ -92,175 +86,6 @@
(,(mk-url "datasets")."Get a list of datasets")))))
-(define (sparql-exec endpoint-url query)
- "Execute raw SPARQL query returning response as a UTF8 string"
- (bytevector->string (receive (response-status response-body)
- (http-request (string-append endpoint-url "?default-graph-uri=&query=" (uri-encode query) "&format=application%2Fsparql-results%2Bjson"))
-
- response-body) "UTF-8"))
-
-(define (sparql-tsv endpoint-url query)
- "Execute raw SPARQL query returning response as a UTF8 string, e.g.
-(tsv->scm (sparql-tsv (wd-sparql-endpoint-url) \"wd:Q158695\"))
-"
- ; GET /sparql?query=SELECT%20DISTINCT%20%2A%20where%20%7B%0A%20%20wd%3AQ158695%20wdt%3AP225%20%3Fo%20.%0A%7D%20limit%205 HTTP/2
- (receive (response-status response-body)
- (http-get (pk (string-append endpoint-url "?query=" (uri-encode query))) #:headers '((Accept . "text/tab-separated-values")(user-agent . "curl/7.74.0")))
- response-body))
-
-(define (unpack field response)
- "Helper to get nested JSON field from SPARQL response"
- (cdr (assoc field response)))
-
-(define (sparql-names response)
- "Helper to get the names part of a SPARQL query"
- (unpack "vars" (unpack "head" response)))
-
-(define (sparql-results response)
- "Helper to get the results part of a SPARQL query"
- (unpack "bindings" (unpack "results" response)))
-
-(define (sparql-scm endpoint-url query)
- "Return dual S-exp 'resultset' of varnames and results"
- (let ((response (json-string->scm (sparql-exec endpoint-url query))))
- (values (sparql-names response) (sparql-results response))))
-
-(define (tsv->scm text)
- "Split a TSV string into a list of fields. Returns list of names header) and rows"
- (let ([lst (map (lambda (f) (string-split f #\tab) ) (delete "" (string-split text #\newline)))])
- (values (car lst) (cdr lst))
- ))
-
-#!
-(define-values (names res) (sparql-species-meta))
-(define table (get-rows names res))
-(define recs '())
-(define h (compile-species recs table))
-(assoc "http://genenetwork.org/species_drosophila_melanogaster" h)
-(assoc-ref h "http://genenetwork.org/species_drosophila_melanogaster") ;; note switch!
-(define d (car h))
-(assoc-ref (list d) "http://genenetwork.org/species_drosophila_melanogaster")
-
-(scm->json #(1 (("2" . 3))))
-;; [1,{"2":3}]
-(scm->json #("http://genenetwork.org/species_drosophila_melanogaster" (("http://genenetwork.org/menuName" . "Drosophila") ("http://genenetwork.org/binomialName" . "Drosophila melanogaster") )))
-;; ["http://genenetwork.org/species_drosophila_melanogaster",{"http://genenetwork.org/menuName":"Drosophila","http://genenetwork.org/binomialName":"Drosophila melanogaster"}]
-l
-;; (("http://genenetwork.org/menuName" "Drosophila") ("http://genenetwork.org/name" "Drosophila") ("http://genenetwork.org/binomialName" "Drosophila melanogaster"))
-(scm->json (map (lambda (i) (cons (car i) (car (cdr i)))) l))
-;; {"http://genenetwork.org/menuName":"Drosophila","http://genenetwork.org/name":"Drosophila","http://genenetwork.org/binomialName":"Drosophila melanogaster"}
-
-
-curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="SELECT DISTINCT * where {
- wd:Q158695 wdt:P225 ?o .
-} limit 5"
-{
- "head" : {
- "vars" : [ "o" ]
- },
- "results" : {
- "bindings" : [ {
- "o" : {
- "type" : "literal",
- "value" : "Arabidopsis thaliana"
- }
- } ]
- }
-}
-!#
-
-(define (sparql-wd-species-info species)
- "Returns wikidata entry for species, e.g.:
-
- (sparql-wd-species-info \"Q158695\") generates something like
-
-SELECT DISTINCT * where { wd:Q158695 wdt:P225 ?o . } limit 10
-
-"
- (sparql-tsv (wd-sparql-endpoint-url) (string-append "
-SELECT DISTINCT ?taxon ?ncbi ?descr where {
- wd:" species " " (wdt-taxon-name) " ?taxon ;
- wdt:P685 ?ncbi ;
- schema:description ?descr .
- ?species wdt:P685 ?ncbi .
- FILTER (lang(?descr)='en')
-} limit 5
-
-")))
-
-(define memo-sparql-wd-species-info
- (memoize sparql-wd-species-info))
-
-#!
-gn:Mus_musculus rdf:type gnc:species .
-gn:Mus_musculus gnt:name "Mouse" .
-gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
-gn:Mus_musculus gnt:binomialName "Mus musculus" .
-gn:Mus_musculus gnt:family "Vertebrates" .
-gn:Mus_musculus gnt:organism taxon:10090 .
-!#
-
-(define (sparql-species)
- (sparql-scm (gn-sparql-endpoint-url) "
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-
-SELECT DISTINCT ?species WHERE {
- ?species rdf:type gnc:species .
-}"))
-
-(define memo-sparql-species
- (memoize2 sparql-species))
-
-(define (sparql-species-meta)
- "Return values names recs"
- (sparql-scm (gn-sparql-endpoint-url) "
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <http://genenetwork.org/term/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-
-SELECT ?species ?p ?o WHERE {
- MINUS { ?species rdf:type ?o . }
-{
- SELECT DISTINCT ?species ?p ?o WHERE {
- ?species rdf:type gnc:species .
- ?species ?p ?o .
- }}}"))
-
-(define memo-sparql-species-meta
- (memoize2 sparql-species-meta))
-
-
-(define (get-values names row)
- "Get values by name from a resultset row"
- (map (lambda (n) (unpack "value" (unpack n row))) (array->list names)))
-
-(define (get-rows names results)
- "Format results as a list of values ordered by names"
- (map (lambda (row) (get-values names row)) (array->list results)))
-
-;; from the triples first harvest the species URIs, followed by creating records of information
-
-(define (compile-species recs rows)
- "Compile a matrix of species triples into records"
- (for-each (lambda (r)
- (let* ([s (car r)]
- [v (cdr (cdr r))]
- [p (car (cdr r))]
- [nrec '()]
- [kv (assoc s recs)]) ; find record to fill based on subject
- (if (not kv)
- (set! nrec '())
- (set! nrec (cdr kv))
- )
- (set! nrec (assoc-set! nrec p v))
- (set! recs (assoc-set! recs s nrec))
- ))
- rows)
- recs)
-
;; result should be a vector of list of pair
(define (species-digest recs)
(map (lambda (r)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-19 18:45:16 +0000