Init new project for GN on guile.

3 files changed, 473 insertions, 0 deletions

diff --git a/web/.guix-shell b/web/.guix-shell
new file mode 100644
index 0000000..2be81ce
--- /dev/null
+++ b/web/.guix-shell
@@ -0,0 +1,8 @@
+#!/bin/bash
+#
+#  run with options '-- ./webserver.scm 8091' e.g.
+#  . .guix-shell -- guile --listen=1970 -e main ./webserver.scm 8091
+
+echo "Note run: running web-server"
+
+guix shell guile guile-fibers guile-json guile-gnutls guile-readline guile-redis openssl nss-certs $*
diff --git a/web/static/README.md b/web/static/README.md
new file mode 100644
index 0000000..8cb1b8c
--- /dev/null
+++ b/web/static/README.md
@@ -0,0 +1,2 @@
+IMPORTANT: this is a REST server. Any static CSS and HTML should be handled in
+the GN2 code base(!)
diff --git a/web/webserver.scm b/web/webserver.scm
new file mode 100755
index 0000000..ce754d8
--- /dev/null
+++ b/web/webserver.scm
@@ -0,0 +1,463 @@
+#!/usr/bin/env guile \
+-e main -s
+!#
+;; Minimal web server can be started from command line. Current example routes:
+;;
+;;    localhost:8080/
+;;
+
+(use-modules
+ (json)
+ (ice-9 match)
+ (ice-9 format)
+ (ice-9 iconv)
+ (ice-9 receive)
+ (ice-9 string-fun)
+ ;; (ice-9 debugger)
+ ;; (ice-9 breakpoints)
+ ;; (ice-9 source)
+ (srfi srfi-1)
+ (srfi srfi-11) ; let-values
+ (srfi srfi-13) ; hash table for memoize
+ (srfi srfi-26)
+ (web http)
+ (web client)
+ (web request)
+ (web response)
+ (web uri)
+ (fibers web server))
+
+;; basically lifted from https://lispdreams.wordpress.com/2016/04/08/lisp-memoization-techniques/
+
+(define (memoize f)
+  "Simple memoize just uses alists at this point and does not expire"
+  (let ((result-table '()))
+    (lambda (. args)
+      (let ((cache-value (assoc args (pk result-table))))
+	(if (pk cache-value)
+	    (cdr cache-value)
+	    (let ((result (apply f args)))
+	      (set! result-table 
+                    (alist-cons args result result-table)) result))))))
+
+(define (memoize2 f)
+  "Simple memoize functions that returns values pair and uses alists at this point and does not expire"
+  (let ((result-table '()))
+    (lambda (. args)
+      (let ((c (assoc args (pk result-table))))
+	(if (pk c)
+	    (values (car (cdr c)) (car (cdr (cdr c))))
+	    (let-values (((r1 r2) (apply f args)))
+	      (set! result-table 
+                    (alist-cons args (list r1 r2) result-table)) (values r1 r2)))))))
+
+(define get-version
+  "2.0")
+
+(define (base-url)
+  "https://genenetwork.org")
+
+(define (gn-sparql-endpoint-url)
+  "https://sparql.genenetwork.org/sparql")
+
+(define (wd-sparql-endpoint-url)
+  "https://query.wikidata.org/sparql")
+
+(define (prefix)
+  "Build the API URL including version"
+  (string-append (base-url) "/api/" get-version))
+
+(define* (mk-url postfix #:optional (ext ""))
+  "Add the path to the API URL"
+  (string-append (prefix) "/" postfix ext))
+
+(define (mk-html path)
+  "Create a pointer to HTML documentation"
+  (string-append (base-url) "/" path ".html"))
+
+(define (mk-doc path)
+  "Create a pointer to HTML documentation"
+  (mk-html (string-append "doc/" path)))
+
+(define (mk-meta path)
+  "Create a meta URL for the API path"
+  (mk-url path ".meta.json"))
+
+(define (mk-rec path)
+  "Create a JSON URL for the API path"
+  (mk-url path ".json"))
+
+(define (mk-term postfix)
+  (mk-html (string-append "term" "/" postfix)))
+
+(define (mk-id postfix)
+  (mk-html (string-append "id" "/" postfix)))
+
+(define (mk-predicate postfix)
+  (mk-html (string-append "predicate" "/" postfix)))
+
+(define (wdt-taxon-name) "wdt:P225")
+
+(define info `(
+  ("name" . "GeneNetwork REST API")
+  ("version" . ,get-version)
+  ("comment" . "This is the official REST API for the GeneNetwork service hosted at https://genenetwork.org/")
+  ("license" . (("source code" . "AGPL")))
+  ("note" . "work in progress (WIP)")
+  ("prefix" . ,(prefix))
+  ("links". (("species" . ,(mk-meta "species"))))))
+
+(define info-meta `(		    
+   ("doc" . ,(mk-html "info"))
+   ("API" .
+    ((,(mk-url "species")."Get a list of all species")
+     (,(mk-url "mouse")."Get information on mouse")
+     (,(mk-url "datasets")."Get a list of datasets")))))
+
+
+(define (sparql-exec endpoint-url query)
+  "Execute raw SPARQL query returning response as a UTF8 string"
+  (bytevector->string (receive (response-status response-body)
+                          (http-request (string-append endpoint-url "?default-graph-uri=&query=" (uri-encode query) "&format=application%2Fsparql-results%2Bjson"))
+                         
+                         response-body) "UTF-8"))
+
+(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\"))
+"
+  ; 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)
+                          (http-get (pk (string-append endpoint-url "?query=" (uri-encode query))) #:headers '((Accept . "text/tab-separated-values")(user-agent . "curl/7.74.0")))
+                         response-body))
+
+(define (unpack field response)
+  "Helper to get nested JSON field from SPARQL response"
+  (cdr (assoc field response)))
+
+(define (sparql-names response)
+  "Helper to get the names part of a SPARQL query"
+  (unpack "vars" (unpack "head" response)))
+
+(define (sparql-results response)
+  "Helper to get the results part of a SPARQL query"
+  (unpack "bindings" (unpack "results" response)))
+
+(define (sparql-scm endpoint-url query)
+  "Return dual S-exp 'resultset' of varnames and results"
+  (let ((response (json-string->scm (sparql-exec endpoint-url query))))
+   (values (sparql-names response) (sparql-results response))))
+
+(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/species_drosophila_melanogaster") ;; note switch!
+(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"
+      }
+    } ]
+  }
+}
+!#
+
+(define (sparql-wd-species-info species)
+  "Returns wikidata entry for species, e.g.:
+
+   (sparql-wd-species-info \"Q158695\") generates something like
+
+SELECT DISTINCT * where {  wd:Q158695 wdt:P225 ?o . } limit 10
+
+"
+  (sparql-tsv (wd-sparql-endpoint-url) (string-append "
+SELECT DISTINCT ?taxon ?ncbi ?descr where {  
+    wd:" species " " (wdt-taxon-name) " ?taxon ;
+               wdt:P685 ?ncbi ;
+      schema:description ?descr .
+    ?species wdt:P685 ?ncbi .
+    FILTER (lang(?descr)='en')
+} limit 5
+
+")))
+
+(define memo-sparql-wd-species-info
+  (memoize sparql-wd-species-info))
+
+#!
+gn:Mus_musculus rdf:type gnc:species .
+gn:Mus_musculus gnt:name "Mouse" .
+gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
+gn:Mus_musculus gnt:binomialName "Mus musculus" .
+gn:Mus_musculus gnt:family "Vertebrates" .
+gn:Mus_musculus gnt:organism taxon:10090 .
+!#
+
+(define (sparql-species)
+  (sparql-scm (gn-sparql-endpoint-url) "
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT DISTINCT ?species WHERE {
+    ?species rdf:type gnc:species .
+}"))
+
+(define memo-sparql-species
+  (memoize2 sparql-species))
+
+(define (sparql-species-meta)
+  "Return values names recs"
+  (sparql-scm (gn-sparql-endpoint-url) "
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+
+SELECT ?species ?p ?o WHERE {
+   MINUS { ?species rdf:type ?o . }
+{
+  SELECT DISTINCT ?species ?p ?o WHERE {
+    ?species rdf:type gnc:species .
+    ?species ?p ?o .
+   }}}"))
+
+(define memo-sparql-species-meta
+  (memoize2 sparql-species-meta))
+
+
+(define (get-values names row)
+  "Get values by name from a resultset row"
+  (map (lambda (n) (unpack "value" (unpack n row))) (array->list names)))
+
+(define (get-rows names results)
+  "Format results as a list of values ordered by names"
+  (map (lambda (row) (get-values names row)) (array->list results)))
+  
+;; from the triples first harvest the species URIs, followed by creating records of information
+
+(define (compile-species recs rows)
+  "Compile a matrix of species triples into records"
+  (for-each (lambda (r)
+		(let* ([s (car r)]
+		       [v (cdr (cdr r))]
+		       [p (car (cdr r))]
+		       [nrec '()]
+		       [kv (assoc s recs)]) ; find record to fill based on subject
+		  (if (not kv)
+		      (set! nrec '())
+		      (set! nrec (cdr kv))
+		      )
+		  (set! nrec (assoc-set! nrec p v))
+		  (set! recs (assoc-set! recs s nrec))
+		  ))
+		rows)
+  recs)
+
+;; result should be a vector of list of pair
+(define (species-digest recs)
+  (map (lambda (r)
+	 (let* ([k (car r)]
+		[v (cdr r)])
+	   ; with key use (cons k (map (lambda (i) (cons (car i) (car (cdr i)))) v))
+	   (map (lambda (i) (cons (url-parse-id (car i)) (car (cdr i)))) v)
+	   ))
+	 recs  )
+  )
+
+(define (get-species)
+  (receive (names res) (memo-sparql-species-meta)
+    (let* ([table (get-rows names res)]
+           [recs '()]
+           [h (compile-species recs table)])
+      (species-digest h))
+    ))
+
+; (define (wd-species-info wd)
+;  )
+
+(define (url-parse-id uri)
+  (if uri
+      (car (reverse (string-split uri #\057)))
+      "unknown"
+      ))
+
+(define (strip-lang s)
+  "Strip quotes and language tag (@en) from RDF entries"
+  (list->string (match (string->list s)
+		  [(#\"rest ... #\") rest]
+		  [(#\"rest ... #\" #\@ #\e #\n) rest]
+		  [rest rest]))
+  )
+
+(define (normalize-id str)
+  ;; (string-replace-substring (string-downcase str) " " "_")
+  (string-replace-substring str " " "_")
+  )
+
+(define (get-expanded-taxon id)
+  "Get information on a specific species, e.g. mouse"
+  #f
+  )
+
+(define (get-expanded-species)
+  "Here we add information related to each species"
+  (map (lambda (rec)
+	 (let ([wd-id (url-parse-id (assoc-ref rec "22-rdf-syntax-ns#isDefinedBy"))]
+	       [short-name (normalize-id (assoc-ref rec "name"))])
+	   (if (string=? wd-id "unknown")
+	       rec
+	       ; wikidata query:
+	       (receive (names row) (tsv->scm (memo-sparql-wd-species-info wd-id))
+		 (match (pk (car row))
+		   ((taxonomy-name ncbi descr)
+		    (let ([ncbi-id (strip-lang ncbi)]
+			  [taxonomy-lnk (string-replace-substring (strip-lang taxonomy-name) " " "_")])
+		      (cons `("id" . ,short-name)
+		      (cons `("wikidata" . ,wd-id)
+		      (cons `("taxonomy-id" . ,ncbi-id)
+		      (cons `("ncbi-url" . ,(string-append "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=" ncbi-id))
+		      (cons `("uniprot-url" . ,(string-append "https://www.uniprot.org/taxonomy/" ncbi-id))
+		      (cons `("wikidata-url" . ,(string-append "http://www.wikidata.org/entity/" wd-id))
+		      (cons `("wikispecies-url" . ,(string-append "https://species.wikimedia.org/wiki/" taxonomy-lnk))
+		      (cons `("taxonomy-name" . ,(strip-lang taxonomy-name))
+		      ; (cons `("shortname" . ,shortname) - problematic
+		      (cons `("description" . ,(strip-lang descr))
+			    rec)))))))))))
+		      )
+	   )))
+	 ) (get-species)
+))
+
+(define (get-species-api-str)
+  (scm->json-string #("https://genenetwork.org/api/v2/mouse/"
+                      "https://genenetwork.org/api/v2/rat/")))
+
+(define (get-species-shortnames recs)
+  (map (lambda r (assoc-ref (car r) "shortName")) recs))
+
+(define (get-species-links recs)
+  "Return a list of short names and expand them to URIs"
+  (map (lambda r
+	 (let ([shortname (assoc-ref (car r) "shortName")])
+	   (cons shortname (mk-rec shortname)))) recs)
+  )
+
+(define (get-species-rec)
+  (list->vector (get-expanded-species)))
+
+(define (get-species-meta)
+  (let ([recs (get-expanded-species)])
+    `(("comment" . "Get information on species")
+      ("doc" . ,(mk-doc "species"))
+      ("meta" . ,(mk-meta "species"))
+      ("rec" . ,(mk-rec "species"))
+      ("links" . ,(get-species-links recs)))))
+
+;; ---- REST API web server handler
+
+(define (not-found2 request)
+  (values (build-response #:code 404)
+          (string-append "Resource X not found: "
+                         (uri->string (request-uri request)))))
+
+(define (not-found uri)
+  (list (build-response #:code 404)
+        (string-append "Resource not found: " (uri->string uri))))
+
+(define (render-json json)
+  (list '((content-type . (application/json)))
+        (lambda (port)
+          (scm->json json port))))
+
+(define (render-json-string2 json)
+  (list '((content-type . (text/plain)))
+	(lambda (port)
+	  ;; (display "ThthxST" port)
+	  (format port "~a" "foo")
+	  )))
+  
+(define (controller request body)
+  (match-lambda
+    (('GET)
+     (render-json info))
+    (('GET "version")
+     (render-json get-version))
+    (('GET "species.json")
+     (render-json (get-species-rec)))
+    (('GET "species.meta.json")
+     (render-json (get-species-meta)))
+    (('GET "species")
+     (render-json (get-species-meta)))
+    (('GET id)
+     (let ([names (get-species-shortnames (get-expanded-species))])
+       (match (string->list id)
+	 [(name ... #\. #\j #\s #\o #\n) (render-json (list->string name))]
+	 [rest (render-json "WIP")])))
+    (_ (not-found (request-uri request)))
+    ))
+
+(define (request-path-components request)
+  (split-and-decode-uri-path (uri-path (request-uri request))))
+
+(define (handler request body)
+  (format #t "~a ~a\n"
+          (request-method request)
+          (uri-path (request-uri request)))
+  (apply values
+         ((controller request body)
+          (cons (request-method request)
+                (request-path-components request)))))
+
+(define (start-web-server address port)
+  (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
+  ;; REPL. If handler is passed as is and is then redefined via the
+  ;; 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))
+
+(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))))))
+    (display `("listening on" ,listen))
+    ;; (write listen)
+    ;; (run-server hello-world-handler 'http `(#:port ,listen))))
+    (start-web-server  "127.0.0.1" listen)))