diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/db/mysql.scm | 7 | ||||
| -rwxr-xr-x[-rw-r--r--] | gn/db/sparql.scm | 82 |
2 files changed, 40 insertions, 49 deletions
diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm index 623a726..8da7b60 100644 --- a/gn/db/mysql.scm +++ b/gn/db/mysql.scm @@ -37,9 +37,10 @@ ))) (define (call-with-db thunk) - (let [(db (db-open))] - (thunk db) - (dbi-close db))) + (let* [(db (db-open)) + (result (thunk db))] + (dbi-close db) + result)) (define (ensure db msg1) "Use DBI-style handle to report an error. On error the program will stop." diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm index bd7a306..fbcd2cc 100644..100755 --- a/gn/db/sparql.scm +++ b/gn/db/sparql.scm @@ -18,10 +18,11 @@ the case. #:use-module (json) #:use-module (srfi srfi-1) #:use-module (web client) + #:use-module (web http) #:use-module (web gn-uri) #:use-module (web request) + #:use-module (web response) #:use-module (web uri) - #:export (memo-sparql-species memo-sparql-species-meta sparql-species-meta @@ -37,9 +38,11 @@ the case. strip-lang make-table make-pairs - ) -) + sparql-http-get + sparql-by-term)) +(define virtuoso-endpoint + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/")) (define (strip-lang s) "Strip quotes and language tag (@en) from RDF entries" @@ -58,9 +61,9 @@ the case. (define (gn-sparql-prefix query) (string-append " -PREFIX gn: <http://genenetwork.org/id/> -PREFIX gnt: <http://genenetwork.org/term/> -PREFIX gnc: <http://genenetwork.org/category/> +PREFIX gn: <http://rdf.genenetwork.org/v1/id/> +PREFIX gnt: <http://rdf.genenetwork.org/v1/term/> +PREFIX gnc: <http://rdf.genenetwork.org/v1/category/> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " query)) @@ -108,46 +111,7 @@ Note this procedure works for GN, but does not yet work for wikidata" (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/id/Drosophila_melanogaster") -(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" - } - } ] - } -} -!# + (values (car lst) (cdr lst)))) (define (sparql-wd-species-info species) "Returns wikidata entry for species, e.g.: @@ -326,3 +290,29 @@ dump-species-metadata.ttl:gn:Axbxa gnt:belongsToSpecies gn:Mus_musculus . " gnid " ?key ?value . # FILTER ( !EXISTS{ " gnid " gnt:hasTissue ?value }) }"))) + + +(define* (sparql-http-get endpoint-url query #:optional (mime-type "text/microdata+html")) + (receive (response-status response-body) + (http-request + (format #f "~a?default-graph-uri=&query=~a&format=~a" + endpoint-url (uri-encode query) (uri-encode mime-type)) + #:method 'GET) + (values + (build-response + #:code (response-code response-status) + #:headers `((content-type . ,(parse-header 'content-type mime-type)))) + response-body))) + +(define (sparql-by-term prefix val) + (let ((url-alist '((gn . "<http://rdf.genenetwork.org/v1/id/>") + (gnc . "<http://rdf.genenetwork.org/v1/category/>") + (gnt . "<http://rdf.genenetwork.org/v1/term/>")))) + (format #f "PREFIX ~a: ~a + +CONSTRUCT { + ~a:~a ?p ?o . +} FROM <http://rdf.genenetwork.org/v1> +WHERE { + ~a:~a ?p ?o . +}" prefix (assoc-ref url-alist prefix) prefix val prefix val))) |