diff options
Diffstat (limited to 'web/webserver.scm')
| -rw-r--r-- | web/webserver.scm | 157 |
1 files changed, 124 insertions, 33 deletions
diff --git a/web/webserver.scm b/web/webserver.scm index 6f40614..69f5098 100644 --- a/web/webserver.scm +++ b/web/webserver.scm @@ -1,4 +1,5 @@ (use-modules (json) + (config) (ice-9 match) (ice-9 format) (ice-9 iconv) @@ -7,6 +8,7 @@ (ice-9 exceptions) (srfi srfi-1) (srfi srfi-11) + (srfi srfi-13) (srfi srfi-19) (srfi srfi-26) (rnrs io ports) @@ -16,22 +18,24 @@ (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 config) (web view view) (web view doc) (web view markdown)) -(define +current-repo-path+ - (getenv "CURRENT_REPO_PATH")) - -(define +cgit-repo-path+ - (getenv "CGIT_REPO_PATH")) +(define (get-extension filename) + (let ((dot-pos (string-rindex filename #\.))) + (if dot-pos + (substring filename dot-pos) ""))) (define +info+ `(("name" . "GeneNetwork REST API") ("version" . ,get-version) @@ -56,6 +60,20 @@ 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)))) + (define (not-found2 request) (values (build-response #:code 404) (string-append "Resource X not found: " @@ -79,7 +97,7 @@ 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 '())) @@ -87,9 +105,9 @@ otherwise search for set/group data" (modified (and stat (make-time time-utc 0 (stat:mtime stat))))) - (list `((content-type ,(assoc-ref file-mime-types - (file-extension file-name))) - (last-modified ,(time-utc->date modified))) + (list `((content-type . ,(assoc-ref file-mime-types + (file-extension file-name))) + (last-modified . ,(time-utc->date modified))) (call-with-input-file file-name get-bytevector-all)))) @@ -100,9 +118,9 @@ otherwise search for set/group data" (modified (and stat (make-time time-utc 0 (stat:mtime stat))))) - (list `((content-type ,(assoc-ref file-mime-types - (file-extension path))) - (last-modified ,(time-utc->date modified))) + (list `((content-type . ,(assoc-ref file-mime-types + (file-extension path))) + (last-modified . ,(time-utc->date modified))) (call-with-input-file path get-bytevector-all)))) @@ -123,6 +141,11 @@ 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) @@ -154,7 +177,7 @@ otherwise search for set/group data" (cons (string->symbol (uri-decode key)) (uri-decode value)))) -(define (edit-file-handler repo request) +(define (edit-file-handler local-repo working-branch request) (catch 'file-error (lambda () (let* ((query (uri-query (request-uri request))) @@ -165,8 +188,12 @@ otherwise search for set/group data" (query-path (assoc-ref params 'file_path))) (if query-path - (build-json-response 200 - (fetch-file repo query-path)) + (begin + (git-invoke local-repo "fetch" "origin" working-branch) + (git-invoke local-repo "reset" "--hard" + (string-append "origin/" working-branch)) + (build-json-response 200 + (fetch-file local-repo query-path))) (throw 'file-error "Please provide a valid file path in the query")))) (lambda (key . args) @@ -175,6 +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)) @@ -185,7 +230,7 @@ otherwise search for set/group data" (format #f "The Key *** ~a *** is missing in your Json Data" target)))) -(define (commit-file-handler repo request body) +(define (commit-file-handler repo-checkout remote-url request body) (catch 'system-error (lambda () (let* ((post-data (decode-request-json body)) @@ -202,14 +247,14 @@ otherwise search for set/group data" (build-json-response 200 ((lambda () (let ((message - (commit-file +current-repo-path+ + (commit-file repo-checkout file-name content commit-message username email prev-commit))) - (git-invoke +current-repo-path+ "push" +cgit-repo-path+) + (git-invoke repo-checkout "push" remote-url) message)))))) (lambda (key . args) (let ((msg (car args))) @@ -217,20 +262,46 @@ otherwise search for set/group data" `(("error" . ,key) ("msg" . ,msg))))))) -(define (controller request body) +(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 config) (match-lambda (('GET) (render-json +info+)) (('GET "version") (render-json get-version)) (('GET "css" fn) - (render-static-file (string-append "css/" fn))) + (render-static-file (string-append (dirname (current-filename)) "/css/" fn))) (('GET "map" fn) - (render-static-file (string-append "css/" fn))) + (render-static-file (string-append (dirname (current-filename)) "/css/" fn))) (('GET "static" "images" fn) - (render-static-image (string-append "static/images/" fn))) + (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))) @@ -247,6 +318,8 @@ otherwise search for set/group data" (('GET "doc" path ... page) ;; serve documents from /doc/ (render-doc path page)) + (('GET "gene" "aliases" genename) + (render-json (get-gene-aliases genename))) (('GET "species.json") (render-json (get-species-data))) (('GET "species.meta.json") @@ -254,9 +327,13 @@ otherwise search for set/group data" (('GET "species") (render-json (get-species-meta))) (('GET "edit") - (edit-file-handler +current-repo-path+ request)) + (edit-file-handler (gn-guile-config-gn-docs-local-checkout config) + (gn-guile-config-gn-docs-working-branch config) + request)) (('POST "commit") - (commit-file-handler +current-repo-path+ request body)) + (commit-file-handler (gn-guile-config-gn-docs-local-checkout config) + (gn-guile-config-gn-docs-remote-url config) + request body)) (('GET id) (let ((names (get-species-shortnames (get-expanded-species)))) (match (string->list id) @@ -280,21 +357,31 @@ 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) (split-and-decode-uri-path (uri-path (request-uri request)))) -(define (handler request body) +(define (handler request body config) (format #t "~a ~a\n" (request-method request) (uri-path (request-uri request))) (apply values - ((controller request body) + ((controller request body config) (cons (request-method request) (request-path-components request))))) -(define (start-web-server address port) +(define (start-web-server address port config) (format (current-error-port) "GN REST API web server listening on http://~a:~a/~%" address port) ;; Wrap handler in another function to support live hacking via the @@ -302,14 +389,18 @@ otherwise search for set/group data" ;; REPL, the web server will still be using the old handler. The ;; 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)) + (run-server (cut handler <> <> config) + 'http + (list #:addr (inet-pton AF_INET address) + #:port port))) (define (main args) (write (string-append "Starting Guile REST API " get-version " server!")) (write args) (newline) - (let ((listen (inexact->exact (string->number (car (cdr args)))))) + (let* ((options (parse-cli-options args)) + (listen (option-ref options 'port))) + (when (option-ref options 'write) + (options-write options)) (display `("listening on" ,listen)) - (start-web-server "127.0.0.1" listen))) + (start-web-server "127.0.0.1" listen (cli-options->gn-guile-config options)))) |