From ea2aea1fc85cb3253e6926f1dd9a2c4c0aa1cdbe Mon Sep 17 00:00:00 2001
From: turtlebasket <turtlebasket@gmail.com>
Date: Sat, 4 Feb 2023 17:17:48 -0800
Subject: [PATCH] more WIP

---
 ncbi-api-test/index.js                       | 51 +++++++++++++++-----
 reagent-test/package.json                    |  2 +
 reagent-test/shadow-cljs.edn                 |  7 ++-
 reagent-test/src/reagent_test/core.cljs      | 19 +++-----
 reagent-test/src/reagent_test/ncbi.cljs      | 37 ++++++++++----
 reagent-test/src/reagent_test/ncbi_test.cljs | 25 +++++++---
 6 files changed, 97 insertions(+), 44 deletions(-)

diff --git a/ncbi-api-test/index.js b/ncbi-api-test/index.js
index 6acc328..a1f4e93 100644
--- a/ncbi-api-test/index.js
+++ b/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: ${res.status}`);
-        let reader = res.body.getReader();
-        // while (!reader.closed) {
-        reader.read().then(out => {
-            // console.log(out)
-            var decoder = new TextDecoder('utf8');
-            console.log(decoder.decode(out.value));
+        res.blob().then(val => {
+            val.text().then(val => {
+                let xmlParser = (new DOMParser()).parseFromString(val, "text/xml");
+                let els = xmlParser.getElementsByTagName("Id");
+                let ids = [];
+                for (let i = 0; i < els.length; i++) {
+                    ids.push(els[i].innerHTML);
+                }
+                console.log(ids);
+                return ids;
+            })
+        })
+    });
+}
+
+function testSearchGene(query) {
+    fetch(`${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);
diff --git a/reagent-test/package.json b/reagent-test/package.json
index fc9f83e..101d8d9 100644
--- a/reagent-test/package.json
+++ b/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"
   },
diff --git a/reagent-test/shadow-cljs.edn b/reagent-test/shadow-cljs.edn
index 4351bc4..1de2f76 100644
--- a/reagent-test/shadow-cljs.edn
+++ b/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"}}}
diff --git a/reagent-test/src/reagent_test/core.cljs b/reagent-test/src/reagent_test/core.cljs
index a8696c2..b8d76ec 100644
--- a/reagent-test/src/reagent_test/core.cljs
+++ b/reagent-test/src/reagent_test/core.cljs
@@ -1,21 +1,14 @@
 (ns reagent-test.core
-  (:require
-   [reagent.core :as r]
-   [reagent.dom :as d]
-   [reagent-test.ncbi :refer [ncbi-search]]))
+  (:require [cljs.core.async :refer [<! go]]
+            [reagent-test.ncbi :refer [ncbi-search]]
+            [reagent.dom :as d]))
 
 ;; -------------------------
 ;; Component data (custom)
 
-(def action-btns [{:text "file"
-                   :items [{:text "new" :action #(dorun (js/console.log "test")
-                                                        (js/console.log "hi"))}
-                           {: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")}
+(def action-btns [{:text "tools" :action #(js/console.log "hi")}
+                  {:text "search" :action #((go (let [res (<! (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]"))]
+                                                  (js/console.log res))))}
                   {:text "help" :action #(js/console.log "test4")}])
 
 ;; -------------------------
diff --git a/reagent-test/src/reagent_test/ncbi.cljs b/reagent-test/src/reagent_test/ncbi.cljs
index 2ef9b06..2b7ffc1 100644
--- a/reagent-test/src/reagent_test/ncbi.cljs
+++ b/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
-  "Send search query to NCBI database.
+(def base-url "https://eutils.ncbi.nlm.nih.gov/entrez/eutils")
+
+(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]
-  (let [res (->> query
-                 (gstring/format "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%s")
-                 js/fetch
-                 take!)]
-    (js/console.log res)))
+  [db-id query]
+  (go (let [res (<! (http/get (gstring/format
+                               "%s/esearch.fcgi?db=%s&term=%s"
+                               base-url db-id query)))
+            xml-doc (loadXml 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))
diff --git a/reagent-test/src/reagent_test/ncbi_test.cljs b/reagent-test/src/reagent_test/ncbi_test.cljs
index a7350bf..d2244f4 100644
--- a/reagent-test/src/reagent_test/ncbi_test.cljs
+++ b/reagent-test/src/reagent_test/ncbi_test.cljs
@@ -1,10 +1,21 @@
 (ns reagent-test.ncbi-test
-  (:require [cljs.test :refer [deftest is async?]]
-            [clojure.core.async :refer [<! go]]
+  (:require [cljs.pprint :refer [pprint]]
+            [cljs.test :refer [deftest]]
+            [cljs.core.async :refer [<! go]]
             [reagent-test.ncbi :refer [ncbi-search]]))
 
-(deftest a-test
-  (dorun
-  (go
-    (let [res (<! (ncbi-search "science[journal]+AND+breast+cancer+AND+2008[pdat]"))]
-      (js/console.log res)))))
+;; (deftest test-ncbi-search-pubmed
+;;   (go (let [res (<! (ncbi-search "pubmed" "science[journal]+AND+breast+cancer+AND+2008[pdat]"))
+;;             status (:status res)
+;;             buf (:buf 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")))