diff options
Diffstat (limited to 'gn/db')
| -rw-r--r-- | gn/db/mysql.scm | 9 | ||||
| -rw-r--r-- | gn/db/sources/wikidata.scm | 65 | ||||
| -rw-r--r-- | gn/db/sparql.scm | 60 |
3 files changed, 123 insertions, 11 deletions
diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm index ccd414a..223b5fd 100644 --- a/gn/db/mysql.scm +++ b/gn/db/mysql.scm @@ -32,22 +32,23 @@ ;; (display "===> OPENING DB") ;; (newline) (let [(db (dbi-open "mysql" "webqtlout:webqtlout:db_webqtl:tcp:127.0.0.1:3306"))] - (ensure db) + (ensure db "Can't open connection") db ))) (define (call-with-db thunk) (thunk (db-open))) -(define (ensure db) +(define (ensure db msg1) "Use DBI-style handle to report an error. On error the program will stop." (match (dbi-get_status db) ((stat . msg) (if (= stat 0) #t (begin - (display msg) + (display "SQL Connection ERROR! ") + (display (string-append msg1 " - " msg) (newline) - (assert stat)))))) + (assert #f))))))) (define (has-result? db) "Return #t or #f if result is valid" diff --git a/gn/db/sources/wikidata.scm b/gn/db/sources/wikidata.scm new file mode 100644 index 0000000..954ce93 --- /dev/null +++ b/gn/db/sources/wikidata.scm @@ -0,0 +1,65 @@ +#! + +Wikidata queries, initially lifted over from the gn3 gene-alias code (that was written in Racket). + +Note you can take a SPARQL query and push it into https://query.wikidata.org/. E.g. generate a query and +copy paste into the query service: + +scheme@(guile-user) [3]> (display (wikidata-query-geneids "Shh")) +``` +SELECT DISTINCT ?wikidata_id + WHERE { + ?wikidata_id wdt:P31 wd:Q7187; + wdt:P703 ?species . + VALUES (?species) { (wd:Q15978631 ) ( wd:Q83310 ) ( wd:Q184224 ) } . + ?wikidata_id rdfs:label "Shh"@en . + } +``` + +It is possible to run queries through curl with + +``` +curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query=" + SELECT DISTINCT ?alias + WHERE { + wd:Q24420953 rdfs:label ?name ; + skos:altLabel ?alias . + FILTER(LANG(?name) = \"en\" && LANG(?alias) = \"en\"). + }" +``` +!# + +(define-module (gn db sources wikidata) + #:export (wikidata-query-geneids + wikidata-query-gene-aliases + ) +) + +(define ps-encoded-by "ps:P702") +(define wdt-instance-of "wdt:P31") +(define wdt-in-taxon "wdt:P703") +(define wd-human "wd:Q15978631") +(define wd-mouse "wd:Q83310") +(define wd-rat "wd:Q184224") +(define wd-gene "wd:Q7187") +(define wd-shh-rat "wd:Q24420953") + +(define (wikidata-query-geneids gene_name) + "SPARQL query to get the wikidata identifiers pointing to genes of listed species, e.g. 'Shh'" + (string-append + "SELECT DISTINCT ?wikidata_id + WHERE { + ?wikidata_id " wdt-instance-of " " wd-gene "; + " wdt-in-taxon " ?species . + VALUES (?species) { (" wd-human " ) ( " wd-mouse" ) ( " wd-rat" ) } . + ?wikidata_id rdfs:label \"" gene_name "\"@en .}")) + +(define (wikidata-query-gene-aliases wikidata_id) + "SPARQL query to get a list of gene aliases based on a wikidata identifier, e.g. for Q24420953. This +version supports the expanded id only, so <http://www.wikidata.org/entity/Q24420953> including the <,>." + (string-append + "SELECT DISTINCT ?stripped_alias + WHERE { " wikidata_id " rdfs:label ?name ; + skos:altLabel ?alias . + BIND (STR(?alias) AS ?stripped_alias) . + FILTER(LANG(?name) = \"en\" && LANG(?alias) = \"en\").}")) diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm index b7d94f3..bd7a306 100644 --- a/gn/db/sparql.scm +++ b/gn/db/sparql.scm @@ -2,23 +2,25 @@ Module for handling SPARQL primitives. -Note that GN queries should go into gn/data - this is currently not +Note that GN queries should go into gn/db/sources - this is currently not the case. !# (define-module (gn db sparql) - #:use-module (json) - #:use-module (ice-9 match) + #:use-module (gn cache memoize) + #:use-module (gn db sources wikidata) #:use-module (ice-9 format) #:use-module (ice-9 iconv) + #:use-module (ice-9 match) #:use-module (ice-9 receive) #:use-module (ice-9 string-fun) + #:use-module (json) + #:use-module (srfi srfi-1) #:use-module (web client) + #:use-module (web gn-uri) #:use-module (web request) #:use-module (web uri) - #:use-module (gn cache memoize) - #:use-module (web gn-uri) #:export (memo-sparql-species memo-sparql-species-meta @@ -26,6 +28,8 @@ the case. sparql-groups-meta sparql-group-info memo-sparql-wd-species-info + memo-sparql-wd-gene-aliases + memo-sparql-wd-geneids compile-species compile-groups-meta get-rows @@ -72,7 +76,9 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> (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\")) +(tsv->scm (sparql-tsv (wd-sparql-endpoint-url) \"wd:Q158695\")). + +Note this procedure works for wikidata, but not for gn! " ; 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) @@ -92,7 +98,9 @@ PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> (unpack "bindings" (unpack "results" response))) (define (sparql-scm endpoint-url query) - "Return dual S-exp 'resultset' of varnames and results" + "Return dual S-exp 'resultset' of varnames and results. + +Note this procedure works for GN, but does not yet work for wikidata" (let ((response (json-string->scm (sparql-exec endpoint-url (gn-sparql-prefix query))))) (values (sparql-names response) (sparql-results response)))) @@ -160,9 +168,47 @@ SELECT DISTINCT ?taxon ?ncbi ?descr where { "))) +(define (flatten lst) + (cond ((null? lst) '()) + ((pair? lst) (append (flatten (car lst)) (flatten (cdr lst)))) + (else (list lst)))) + +(define (remove-quotes s) + (substring s 1 (- (string-length s) 1))) + (define memo-sparql-wd-species-info (memoize sparql-wd-species-info)) +(define (sparql-wd-geneids gene-name) + "Return a list of expanded wikidata ids, e.g. +(\"<http://www.wikidata.org/entity/Q14860079>\" \"<http://www.wikidata.org/entity/Q24420953>\")" + (receive (type values) + (tsv->scm (sparql-tsv (wd-sparql-endpoint-url) (wikidata-query-geneids gene-name))) + (map (lambda (item) (car item)) values) ;; flatten list + )) + +(define memo-sparql-wd-geneids + (memoize sparql-wd-geneids)) + +(define (sparql-wd-gene-aliases geneids) + "Returns a flattened and dedpulicated list of geneids with +(sparql-wd-gene-aliases '(\"Q14860079\" \"Q24420953\")) +" + (let* ([aliases + (map (lambda (geneid) + (receive (type values) + (tsv->scm (sparql-tsv (wd-sparql-endpoint-url) (wikidata-query-gene-aliases (pk geneid)))) + (map (lambda (item) (car item)) values) ;; flatten list)) + ) + ) geneids)] + [rm-quotes-aliases (map (lambda (s) (remove-quotes s)) (flatten aliases))] + ) + (delete-duplicates rm-quotes-aliases))) + +(define memo-sparql-wd-gene-aliases + (memoize sparql-wd-gene-aliases)) + + #! gn:Mus_musculus rdf:type gnc:species . gn:Mus_musculus gnt:name "Mouse" . |