master
michael 2023-02-04 14:49:44 -08:00
parent bcc8513890
commit bfbf2ff239
17 changed files with 1211 additions and 0 deletions

130
ncbi-api-test/.gitignore vendored Normal file
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# Logs
logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
lerna-debug.log*
.pnpm-debug.log*
# Diagnostic reports (https://nodejs.org/api/report.html)
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
# Runtime data
pids
*.pid
*.seed
*.pid.lock
# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov
# Coverage directory used by tools like istanbul
coverage
*.lcov
# nyc test coverage
.nyc_output
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
.grunt
# Bower dependency directory (https://bower.io/)
bower_components
# node-waf configuration
.lock-wscript
# Compiled binary addons (https://nodejs.org/api/addons.html)
build/Release
# Dependency directories
node_modules/
jspm_packages/
# Snowpack dependency directory (https://snowpack.dev/)
web_modules/
# TypeScript cache
*.tsbuildinfo
# Optional npm cache directory
.npm
# Optional eslint cache
.eslintcache
# Optional stylelint cache
.stylelintcache
# Microbundle cache
.rpt2_cache/
.rts2_cache_cjs/
.rts2_cache_es/
.rts2_cache_umd/
# Optional REPL history
.node_repl_history
# Output of 'npm pack'
*.tgz
# Yarn Integrity file
.yarn-integrity
# dotenv environment variable files
.env
.env.development.local
.env.test.local
.env.production.local
.env.local
# parcel-bundler cache (https://parceljs.org/)
.cache
.parcel-cache
# Next.js build output
.next
out
# Nuxt.js build / generate output
.nuxt
dist
# Gatsby files
.cache/
# Comment in the public line in if your project uses Gatsby and not Next.js
# https://nextjs.org/blog/next-9-1#public-directory-support
# public
# vuepress build output
.vuepress/dist
# vuepress v2.x temp and cache directory
.temp
.cache
# Docusaurus cache and generated files
.docusaurus
# Serverless directories
.serverless/
# FuseBox cache
.fusebox/
# DynamoDB Local files
.dynamodb/
# TernJS port file
.tern-port
# Stores VSCode versions used for testing VSCode extensions
.vscode-test
# yarn v2
.yarn/cache
.yarn/unplugged
.yarn/build-state.yml
.yarn/install-state.gz
.pnp.*

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ncbi-api-test/index.js Normal file
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searchQuery = "science[journal]+AND+breast+cancer+AND+2008[pdat]";
function testSearch(query) {
fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/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));
})
// }
})
}
testSearch(searchQuery);

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{
"name": "ncbi-api-test",
"version": "0.0.1",
"main": "index.js",
"license": "MIT",
"scripts": {
"start": "node index.js"
}
}

4
ncbi-api-test/yarn.lock Normal file
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# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
# yarn lockfile v1

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reagent-test/.gitignore vendored Normal file
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# tests
tests-out
# clojure/cljs
/target
/classes
/checkouts
profiles.clj
pom.xml
pom.xml.asc
*.jar
*.class
/.lein-*
/.nrepl-port
/resources/public/js
/public/js
/out
/.repl
*.log
/.env
.lsp
.shadow-cljs
.clj-kondo
# Logs
logs
*.log
npm-debug.log*
yarn-debug.log*
yarn-error.log*
lerna-debug.log*
.pnpm-debug.log*
# Diagnostic reports (https://nodejs.org/api/report.html)
report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
# Runtime data
pids
*.pid
*.seed
*.pid.lock
# Directory for instrumented libs generated by jscoverage/JSCover
lib-cov
# Coverage directory used by tools like istanbul
coverage
*.lcov
# nyc test coverage
.nyc_output
# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
.grunt
# Bower dependency directory (https://bower.io/)
bower_components
# node-waf configuration
.lock-wscript
# Compiled binary addons (https://nodejs.org/api/addons.html)
build/Release
# Dependency directories
node_modules/
jspm_packages/
# Snowpack dependency directory (https://snowpack.dev/)
web_modules/
# TypeScript cache
*.tsbuildinfo
# Optional npm cache directory
.npm
# Optional eslint cache
.eslintcache
# Optional stylelint cache
.stylelintcache
# Microbundle cache
.rpt2_cache/
.rts2_cache_cjs/
.rts2_cache_es/
.rts2_cache_umd/
# Optional REPL history
.node_repl_history
# Output of 'npm pack'
*.tgz
# Yarn Integrity file
.yarn-integrity
# dotenv environment variable files
.env
.env.development.local
.env.test.local
.env.production.local
.env.local
# parcel-bundler cache (https://parceljs.org/)
.cache
.parcel-cache
# Next.js build output
.next
out
# Nuxt.js build / generate output
.nuxt
dist
# Gatsby files
.cache/
# Comment in the public line in if your project uses Gatsby and not Next.js
# https://nextjs.org/blog/next-9-1#public-directory-support
# public
# vuepress build output
.vuepress/dist
# vuepress v2.x temp and cache directory
.temp
.cache
# Docusaurus cache and generated files
.docusaurus
# Serverless directories
.serverless/
# FuseBox cache
.fusebox/
# DynamoDB Local files
.dynamodb/
# TernJS port file
.tern-port
# Stores VSCode versions used for testing VSCode extensions
.vscode-test
# yarn v2
.yarn/cache
.yarn/unplugged
.yarn/build-state.yml
.yarn/install-state.gz
.pnp.*

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reagent-test/README.md Normal file
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# Reagent JBrowse Plugin Test
## Development
```bash
# Install dependencies
yarn
# Run dev server on port 3000
yarn shadow-cljs watch app
```
Start a ClojureScript REPL
```
npx shadow-cljs browser-repl
```
### Building for production
```
npx shadow-cljs release app
```

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reagent-test/index.html Normal file
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<!DOCTYPE html>
<html><head><title>shadow.test.browser</title><meta charset="utf-8"></head><body><script src="/js/test.js"></script><script>shadow.test.browser.init();</script></body></html>

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reagent-test/package.json Normal file
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{
"scripts": {
"test": "shadow-cljs compile tests",
"repl": "shadow-cljs node-repl"
},
"devDependencies": {
"shadow-cljs": "^2.19.2"
},
"dependencies": {
"react": "^17.0.2",
"react-dom": "^17.0.2"
}
}

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body {
font-family: 'Helvetica Neue', Verdana, Helvetica, Arial, sans-serif;
max-width: 600px;
margin: 0 auto;
padding-top: 72px;
-webkit-font-smoothing: antialiased;
font-size: 1.125em;
color: #333;
line-height: 1.5em;
}
h1, h2, h3 {
color: #000;
}
h1 {
font-size: 2.5em
}
h2 {
font-size: 2em
}
h3 {
font-size: 1.5em
}
a {
text-decoration: none;
color: #09f;
}
a:hover {
text-decoration: underline;
}
.button-container {
display: flex;
flex-direction: row;
}
.menu {
position: absolute;
}
.menu-item {
width: 5rem;
}

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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta content="width=device-width, initial-scale=1" name="viewport">
<link href="/css/site.css" rel="stylesheet" type="text/css">
</head>
<body>
<div id="app">
<h3>ClojureScript has not been compiled!</h3>
<p>please run <b>npx shadow-cljs watch app</b> in order to start the compiler</p>
</div>
<script src="/js/app.js" type="text/javascript"></script>
<script type="text/javascript">reagent_test.core.init_BANG_();</script>
</body>
</html>

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{:source-paths ["src"]
:dependencies [[binaryage/devtools "1.0.6"]
[nrepl "1.0.0"]
[reagent "1.1.1"]]
:builds {:app {:target :browser
:output-dir "public/js"
:asset-path "/js"
:modules {:app {:entries [reagent-test.core]}}
:devtools {:after-load reagent-test.core/mount-root}}
:tests {:target :node-test
:output-to "tests-out/tests.js"
:output-dir "tests-out/output"
:modules {:app {:entries [reagent-test.core-test
reagent-test.ncbi-test]}}
:autorun true}}
:dev-http {3000 {:root "public"}}}

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(ns reagent-test.core
(:require
[reagent.core :as r]
[reagent.dom :as d]
[reagent-test.ncbi :refer [ncbi-search]]))
;; -------------------------
;; 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")}
{:text "help" :action #(js/console.log "test4")}])
;; -------------------------
;; Menus
(defn dropdown-or-action
"Render dropdown menu for an action button/menu"
[btn-item is-dropdown]
[:button {:class (if is-dropdown "menu-button" "")}
:text (:text btn-item)
:on-click (let [action (:action btn-item)]
(if (nil? action)
#(dropdown-or-action btn-item true)
action))])
;; -------------------------
;; Views
(defn home-page []
[:div
[:h2 "Reagent Playground"]
[:p "A groundbreaking, revolutionary app that does stuff."]
[:div {:class "button-container"}
(map (fn [btn] [:button
{:on-click #(dropdown-or-action btn false)}
(:text btn)]) action-btns)]])
;; -------------------------
;; Initialize app
(defn mount-root []
(d/render [home-page] (.getElementById js/document "app")))
(defn ^:export init! []
(mount-root))

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;; (ns reagent-test.core-test
;; (:require [reagent-test.core]
;; [cljs.test :refer (deftest is)]))
;; (deftest )

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(ns reagent-test.ncbi
(:require [clojure.core.async :refer [take!]]
[goog.string :as gstring]
[goog.string.format]))
(defn ncbi-search
"Send search query to NCBI database.
[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)))

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(ns reagent-test.ncbi-test
(:require [cljs.test :refer [deftest is async?]]
[clojure.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)))))

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@ -0,0 +1,7 @@
(ns user
(:require
[shadow.cljs.devtools.api :as shadow]
[ring.middleware.resource :refer [wrap-resource]]))
(defn cljs []
(shadow/repl :app))

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reagent-test/yarn.lock Normal file
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string_decoder "~1.1.1"
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object-assign "^4.1.1"
setimmediate@^1.0.4:
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shadow-cljs-jar@1.3.2:
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which "^1.3.1"
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source-map-support@^0.4.15:
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xtend "^4.0.0"
string_decoder@^1.0.0, string_decoder@^1.1.1:
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timers-browserify@^2.0.4:
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querystring "0.2.0"
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ws@^7.4.6:
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