diff options
Diffstat (limited to 'web')
| -rw-r--r-- | web/README.md | 1 | ||||
| -rw-r--r-- | web/view/brand/aging.scm | 7 | ||||
| -rw-r--r-- | web/view/brand/msk.scm | 2 | ||||
| -rw-r--r-- | web/view/doc.scm | 2 | ||||
| -rw-r--r-- | web/view/view.scm | 12 | ||||
| -rw-r--r-- | web/webserver.scm | 56 |
6 files changed, 68 insertions, 12 deletions
diff --git a/web/README.md b/web/README.md new file mode 100644 index 0000000..fc7e158 --- /dev/null +++ b/web/README.md @@ -0,0 +1 @@ +Run the webserver from one directory up. diff --git a/web/view/brand/aging.scm b/web/view/brand/aging.scm index 19db4d7..f1c48c9 100644 --- a/web/view/brand/aging.scm +++ b/web/view/brand/aging.scm @@ -45,15 +45,14 @@ )) ,@head) (body - ;; (header (p "TEST")) (main (@ (class "container")) (h1 ,title) (article - (img (@ (src "/static/images/ole-farmer.jpg") (alt "ol farmer by hohumhobo is licensed under CC BY 2.0") (width "400") (align "right"))) -,info) + ;; (img (@ (src "/static/images/ole-farmer.jpg") (alt "ol farmer by hohumhobo is licensed under CC BY 2.0") (width "400") (align "right"))) + ,info) (footer (hr) - (p "Copyright © 2005-2023 " + (p "Copyright © 2005-2025 " (a (@ (href "https://genenetwork.org/")) "GeneNetwork Webservices") " | GeneNetwork and this website runs fully on free software. See status and download the " (a (@ (href "https://ci.genenetwork.org/")) "source code") "."))) diff --git a/web/view/brand/msk.scm b/web/view/brand/msk.scm index 69c1253..4cbcec4 100644 --- a/web/view/brand/msk.scm +++ b/web/view/brand/msk.scm @@ -51,7 +51,7 @@ (p ,info) (footer (hr) - (p "Copyright © 2005-2023 " + (p "Copyright © 2005-2025 " (a (@ (href "https://genenetwork.org/")) "GeneNetwork Webservices") " | GeneNetwork and this website runs fully on free software. See status and download the " (a (@ (href "https://ci.genenetwork.org/")) "source code") "."))) diff --git a/web/view/doc.scm b/web/view/doc.scm index 71112eb..cec4400 100644 --- a/web/view/doc.scm +++ b/web/view/doc.scm @@ -44,7 +44,7 @@ ,(scm->json-string body #:pretty #t)) ; (p ,(parse-html "<b>some raw really <i>text</i> here</b>")) (footer - (p "Copyright © 2005—2023 by the GeneNetwork community with a touch of " (span (@ (class "lambda")) "λ") "!") + (p "Copyright © 2005—2025 by the GeneNetwork community with a touch of " (span (@ (class "lambda")) "λ") "!") (p "This is free software. Download the " (a (@ (href "https://ci.genenetwork.org/")) "source code") ".")) diff --git a/web/view/view.scm b/web/view/view.scm index 4300863..a7592ad 100644 --- a/web/view/view.scm +++ b/web/view/view.scm @@ -15,7 +15,7 @@ #:export (view-brand)) -(define (view-aging) +(define (view-aging-home) (aging-html #:info `( ,(markdown-github->sxml "genenetwork/gn-docs/general/brand/aging/home.md") @@ -45,7 +45,15 @@ data to benefit from the power of integrated datasets, please contact:") (define* (view-brand path) (match path - ("aging" (view-aging)) + ("aging/um-het3" (aging-html #:info + `(,(markdown-github->sxml "genenetwork/gn-docs/general/brand/aging/home.md")))) + ("aging/UM-HET3" (aging-html #:info + `(,(markdown-github->sxml "genenetwork/gn-docs/general/brand/aging/home.md")))) + ("aging/UMHET-3" (aging-html #:info + `(,(markdown-github->sxml "genenetwork/gn-docs/general/brand/aging/home.md")))) + ("aging/umhet-3" (aging-html #:info + `(,(markdown-github->sxml "genenetwork/gn-docs/general/brand/aging/home.md")))) + ("aging" (view-aging-home)) ("gnqa" (default-gn-template "genenetwork/gn-docs/general/brand/gnqa/gnqa.md" "GeneNetwork Question and Answer System")) diff --git a/web/webserver.scm b/web/webserver.scm index d2a8c8d..0c0bdd1 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) @@ -16,17 +17,24 @@ (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 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")) @@ -56,6 +64,20 @@ 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 +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 '())) @@ -123,6 +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) @@ -231,6 +258,24 @@ 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))) @@ -247,6 +292,8 @@ 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") @@ -303,8 +350,9 @@ 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!")) |