diff options
Diffstat (limited to 'web/webserver.scm')
| -rw-r--r-- | web/webserver.scm | 90 |
1 files changed, 84 insertions, 6 deletions
diff --git a/web/webserver.scm b/web/webserver.scm index 880ab49..af27249 100644 --- a/web/webserver.scm +++ b/web/webserver.scm @@ -7,6 +7,7 @@ (ice-9 exceptions) (srfi srfi-1) (srfi srfi-11) + (srfi srfi-13) (srfi srfi-19) (srfi srfi-26) (rnrs io ports) @@ -16,21 +17,28 @@ (web request) (web response) (web uri) - (fibers web server) + (web server) (gn cache memoize) (web gn-uri) (gn db sparql) + (gn data dataset) (gn data species) (gn data group) + (gn runner gemma) (web sxml) (web view view) (web view doc) (web view markdown)) +(define (get-extension filename) + (let ((dot-pos (string-rindex filename #\.))) + (if dot-pos + (substring filename dot-pos) ""))) + (define +current-repo-path+ (getenv "CURRENT_REPO_PATH")) -(define +cgit-repo-path+ +(define +bare-repo-path+ (getenv "CGIT_REPO_PATH")) (define +info+ @@ -56,6 +64,16 @@ otherwise search for set/group data" (if taxoninfo taxoninfo (cdr (get-group-data id))))) +(define (get-bxd-publish) + "Return a list of published datasets by their record ID. We add the dataset ID and phenotype ID for quick reference" + (list->vector (get-bxd-publish-list))) + +(define* (get-bxd-publish-dataid-values dataid #:optional used-for-mapping?) + (get-bxd-publish-dataid-name-value-dict dataid used-for-mapping?)) + +(define* (get-bxd-publish-values dataid #:optional used-for-mapping?) + (get-bxd-publish-name-value-dict dataid used-for-mapping?)) + (define (get-gene-aliases genename) "Return a vector of aliases for genename." (list->vector (memo-sparql-wd-gene-aliases (memo-sparql-wd-geneids genename)))) @@ -83,7 +101,7 @@ otherwise search for set/group data" ("html" text/html))) (define (file-extension file-name) - (last (string-split file-name #\.))) + (last (string-split file-name #\.))) ;; FIXME: does not handle files with multiple dots (define* (render-static-image file-name #:key (extra-headers '())) @@ -127,6 +145,11 @@ otherwise search for set/group data" (lambda (port) (sxml->html (view-brand path) port)))) +(define (render-string str) + (list '((content-type application/txt)) + (lambda (port) + (put-string port str)))) + (define (render-json json) (list '((content-type application/json)) (lambda (port) @@ -179,6 +202,24 @@ otherwise search for set/group data" `(("error" . ,key) ("msg" . ,msg))))))) +(define (render-sparql request prefix val) + (let* ((mime (negotiate-mime request)) + (resp-mime (if (or (string-contains (symbol->string mime) "html") + (string-contains (symbol->string mime) "microdata")) + 'text/html + mime))) + (receive (sparql-header sparql-resp) + (sparql-http-get + (or (getenv "SPARQL-ENDPOINT") "http://localhost:8890/sparql/") + (sparql-by-term prefix val) + (symbol->string mime)) + (list `((content-type ,resp-mime)) + (lambda (port) + (let ((resp (if (string? sparql-resp) + sparql-resp + (utf8->string sparql-resp)))) + (put-string port resp))))))) + (define (invalid-data? data target) (if (string? (assoc-ref data target)) (if (string-null? (assoc-ref data target)) @@ -213,7 +254,7 @@ otherwise search for set/group data" username email prev-commit))) - (git-invoke +current-repo-path+ "push" +cgit-repo-path+) + (git-invoke +current-repo-path+ "push" +bare-repo-path+) message)))))) (lambda (key . args) (let ((msg (car args))) @@ -221,6 +262,14 @@ otherwise search for set/group data" `(("error" . ,key) ("msg" . ,msg))))))) +(define (negotiate-mime request) + (let* ((headers (request-headers request)) + (accept (caar (assoc-ref headers 'accept)))) + (if (or (eq? (string->symbol "*/*") accept) + (eq? (string->symbol "text/html") accept)) + 'application/x-nice-microdata + accept))) + (define (controller request body) (match-lambda (('GET) @@ -235,6 +284,24 @@ otherwise search for set/group data" (render-static-image (string-append (dirname (current-filename)) "/static/images/" fn))) (('GET "home" path) (render-brand path)) ; branding route for /home/aging, /home/msk etc + (('GET "home" "aging" path) + (render-brand (string-append "aging/" path))) ; branding route subs of /home/aging/... + (('GET "dataset" "bxd-publish" "list") + (render-json (get-bxd-publish))) + (('GET "dataset" "bxd-publish" "dataid" "values" page) + (match (get-extension page) + (".json" + (render-json (get-bxd-publish-dataid-values (basename page ".json")))) + (else (display "ERROR: unknown file extension")))) + (('GET "dataset" "bxd-publish" "values" page) + (match (get-extension page) + (".json" + (render-json (get-bxd-publish-values (basename page ".json")))) + ;; (".tsv" (render-string "TEST1\nTEST2")) + ;; (".gemma" (render-string (string-join (gemma-pheno-txt "BXD" (get-bxd-publish-values (basename page ".gemma"))) ""))) + (else (display "ERROR: unknown file extension")))) + (('GET "dataset" "bxd-publish" "mapping" "values" (string-append dataid ".json")) + (render-json (get-bxd-publish-values dataid #t))) (('GET "doc" "species.html") (render-doc "doc" "species.html" (get-species-meta))) @@ -286,6 +353,16 @@ otherwise search for set/group data" #\n) (render-json (get-id-data (list->string name)))) (rest (render-json "NOP"))))) + ;; RDF End-points + (('GET "v1" "id" id) + (render-sparql request 'gn id)) + + (('GET "v1" "category" category) + (render-sparql request 'gnc category)) + + (('GET "v1" "term" term) + (render-sparql request 'gnt term)) + (_ (not-found (request-uri request))))) (define (request-path-components request) @@ -309,8 +386,9 @@ otherwise search for set/group data" ;; only way to update the handler reference held by the web server ;; would be to restart the web server. (run-server (cut handler <> <>) - #:addr (inet-pton AF_INET address) - #:port port)) + 'http + (list #:addr (inet-pton AF_INET address) + #:port port))) (define (main args) (write (string-append "Starting Guile REST API " get-version " server!")) |