more WIP

ncbi-api-test/index.js

@@ -1,18 +1,45 @@
-searchQuery = "science[journal]+AND+breast+cancer+AND+2008[pdat]";
+let searchQuery = "science[journal]+AND+breast+cancer+AND+2008[pdat]";
+let url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
 
-function testSearch(query) {
+
-    fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=${query}`)
+function testSearchPubmed(query) {
+    fetch(`${url}/esearch.fcgi?db=pubmed&term=${query}`)
     .then((res) => {
-        console.log(`Status: ${res.status}`);
+        res.blob().then(val => {
-        let reader = res.body.getReader();
+            val.text().then(val => {
-        // while (!reader.closed) {
+                let xmlParser = (new DOMParser()).parseFromString(val, "text/xml");
-        reader.read().then(out => {
+                let els = xmlParser.getElementsByTagName("Id");
-            // console.log(out)
+                let ids = [];
-            var decoder = new TextDecoder('utf8');
+                for (let i = 0; i < els.length; i++) {
-            console.log(decoder.decode(out.value));
+                    ids.push(els[i].innerHTML);
+                }
+                console.log(ids);
+                return ids;
+            })
+        })
+    });
+}
+
+function testSearchGene(query) {
+    fetch(`${url}/esearch.fcgi?db=gene&term=${query}`)
+    .then((res) => {
+        res.blob().then(val => {
+            val.text().then(val => {
+                console.log(val);
+            })
+        })
+    });
+}
+
+function testLookupGeneById(ids) {
+    fetch(`${url}/esummary.fcgi?db=gene&id=${String(ids)}`)
+    .then(res => {
+        res.blob().then(val => {
+            val.text().then(val => {
+                console.log(val)
+            })
         })
-        // }
     })
 }
 
-testSearch(searchQuery);
+testLookupGeneById(7157);

reagent-test/package.json

@@ -1,5 +1,7 @@
 {
   "scripts": {
+    "build": "shadow-cljs compile app",
+    "dev": "shadow-cljs watch app",
     "test": "shadow-cljs compile tests",
     "repl": "shadow-cljs node-repl"
   },

reagent-test/shadow-cljs.edn

@@ -1,7 +1,9 @@
 {:source-paths ["src"]
  :dependencies [[binaryage/devtools "1.0.6"]
                 [nrepl "1.0.0"]
-                [reagent "1.1.1"]]
+                [reagent "1.1.1"]
+                [cljs-http "0.1.46"]]
+
  :builds       {:app {:target     :browser
                       :output-dir "public/js"
                       :asset-path "/js"
@@ -13,6 +15,7 @@
                         :output-dir "tests-out/output"
                         :modules    {:app {:entries [reagent-test.core-test
                                                      reagent-test.ncbi-test]}}
-                        :autorun    true}}
+                        :autorun    true
+                        :devtools {:ignore-warnings true}}}
 
  :dev-http     {3000 {:root "public"}}}

reagent-test/src/reagent_test/core.cljs

@@ -1,21 +1,14 @@
 (ns reagent-test.core
-  (:require
+  (:require [cljs.core.async :refer [<! go]]
-   [reagent.core :as r]
+            [reagent-test.ncbi :refer [ncbi-search]]
-   [reagent.dom :as d]
+            [reagent.dom :as d]))
-   [reagent-test.ncbi :refer [ncbi-search]]))
 
 ;; -------------------------
 ;; Component data (custom)
 
-(def action-btns [{:text "file"
+(def action-btns [{:text "tools" :action #(js/console.log "hi")}
-                   :items [{:text "new" :action #(dorun (js/console.log "test")
+                  {:text "search" :action #((go (let [res (<! (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]"))]
-                                                        (js/console.log "hi"))}
+                                                  (js/console.log res))))}
-                           {:text "new" :action #(js/alert "hi")}
-                           {:text "quit" :action #()}]}
-                  {:text "edit"
-                   :items [{:text "hi" :action #(js/console.log "test2")}
-                           {:text "bye" :action #(js/console.log "bye")}]}
-                  {:text "view" :action #(js/console.log "test3")}
                   {:text "help" :action #(js/console.log "test4")}])
 
 ;; -------------------------

reagent-test/src/reagent_test/ncbi.cljs

@@ -1,16 +1,33 @@
 (ns reagent-test.ncbi
-  (:require [clojure.core.async :refer [take!]]
+  (:require [cljs.core.async :refer [<! go]]
+            [cljs-http.client :as http]
             [goog.string :as gstring]
-            [goog.string.format]))
+            [goog.string.format]
+            [goog.dom.xml :refer [loadXml]]))
 
-(defn ncbi-search
+(def base-url "https://eutils.ncbi.nlm.nih.gov/entrez/eutils")
-  "Send search query to NCBI database.
+
+(defn ncbi-db-search
+  "Send search query to NCBI database, and get back a list of ID strings.
    [More info](https://www.ncbi.nlm.nih.gov/books/NBK25500/#_chapter1_Searching_a_Database_)
 
    Example Query: `science[journal]+AND+breast+cancer+AND+2008[pdat]`"
-  [query]
+  [db-id query]
-  (let [res (->> query
+  (go (let [res (<! (http/get (gstring/format
-                 (gstring/format "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%s")
+                               "%s/esearch.fcgi?db=%s&term=%s"
-                 js/fetch
+                               base-url db-id query)))
-                 take!)]
+            xml-doc (loadXml res)]
-    (js/console.log res)))
+        (. xml-doc getElementByTagName "Id"))))
+
+(defn ncbi-db-get-summary
+  "Get summary by ID.
+   [More info](https://www.ncbi.nlm.nih.gov/books/NBK25500/#_chapter1_Downloading_Document_Summaries_)"
+  [db-id id]
+  (go (let [res (<! (http/get (gstring/format
+                              "%s/esummary.fcgi?db=%s&id=%s"
+                               base-url db-id id)))
+            xml-doc (loadXml res)]
+        (js/console.log "hi"))))
+
+(defn ncbi-search-gene [query] (ncbi-db-search "gene" query))
+(defn ncbi-id-gene [query] (ncbi-db-search "gene" query))

reagent-test/src/reagent_test/ncbi_test.cljs

@@ -1,10 +1,21 @@
 (ns reagent-test.ncbi-test
-  (:require [cljs.test :refer [deftest is async?]]
+  (:require [cljs.pprint :refer [pprint]]
-            [clojure.core.async :refer [<! go]]
+            [cljs.test :refer [deftest]]
+            [cljs.core.async :refer [<! go]]
             [reagent-test.ncbi :refer [ncbi-search]]))
 
-(deftest a-test
+;; (deftest test-ncbi-search-pubmed
-  (dorun
+;;   (go (let [res (<! (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]"))
-  (go
+;;             status (:status res)
-    (let [res (<! (ncbi-search "science[journal]+AND+breast+cancer+AND+2008[pdat]"))]
+;;             buf (:buf res)]
-      (js/console.log res)))))
+;;         (assert (not (nil? res)))
+;;         (assert (not (nil? buf)))
+;;         (assert (= status 200))
+;;         (pprint res)
+;;         (pprint "hi"))))
+
+(deftest test-ncbi-search-pubmed
+  (let [res (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]")]
+        (assert (not (nil? res)))
+        (pprint res)
+        (pprint "hi")))