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Prevent progress bar from starting if file already exists
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@tiagofilipe12
tiagofilipe12 committed Apr 19, 2017
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48 changes: 20 additions & 28 deletions docs/bionode-ncbi.html
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Expand Up @@ -26,7 +26,7 @@ <h1 id="bionode-ncbi">bionode-ncbi</h1>
<p>Node.js module for working with the NCBI API (aka e-utils) using Streams.</p>
<p>doi: <a href="http://dx.doi.org/10.5281/zenodo.10610">10.5281/zenodo.10610</a>
author: <a href="http://bmpvieira.com">Bruno Vieira</a>
email: <a href="&#109;&#97;&#x69;&#x6c;&#116;&#111;&#58;&#x6d;&#97;&#x69;&#108;&#x40;&#x62;&#109;&#x70;&#118;&#105;&#101;&#105;&#x72;&#97;&#46;&#99;&#111;&#109;">&#x6d;&#97;&#x69;&#108;&#x40;&#x62;&#109;&#x70;&#118;&#105;&#101;&#105;&#x72;&#97;&#46;&#99;&#111;&#109;</a>
email: <a href="&#109;&#97;&#105;&#x6c;&#x74;&#111;&#x3a;&#109;&#97;&#x69;&#x6c;&#64;&#98;&#x6d;&#x70;&#118;&#x69;&#101;&#105;&#114;&#x61;&#46;&#x63;&#111;&#x6d;">&#109;&#97;&#x69;&#x6c;&#64;&#98;&#x6d;&#x70;&#118;&#x69;&#101;&#105;&#114;&#x61;&#46;&#x63;&#111;&#x6d;</a>
license: <a href="https://raw.githubusercontent.com/bionode/bionode-ncbi/master/LICENSE">MIT</a></p>
</blockquote>
<hr>
Expand Down Expand Up @@ -451,22 +451,9 @@ <h2 id="download">Download</h2>
<span class="hljs-string">'faa'</span>: <span class="hljs-function"><span class="hljs-keyword">function</span> (<span class="hljs-params"></span>) </span>{ <span class="hljs-keyword">return</span> obj.protein.faa },
<span class="hljs-string">'repeats'</span>: <span class="hljs-function"><span class="hljs-keyword">function</span> (<span class="hljs-params"></span>) </span>{ <span class="hljs-keyword">return</span> obj.rm.out },
<span class="hljs-string">'md5'</span>: <span class="hljs-function"><span class="hljs-keyword">function</span> (<span class="hljs-params"></span>) </span>{ <span class="hljs-keyword">return</span> obj.md5checksums.txt }
}</pre></div></div>

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<p>added opts.db definition here since it is a local variable in ncbi.urls</p>
}

</div>

<div class="content"><div class='highlight'><pre> <span class="hljs-keyword">var</span> opts = <span class="hljs-keyword">typeof</span> db === <span class="hljs-string">'string'</span> ? { <span class="hljs-attr">db</span>: db } : db
<span class="hljs-keyword">var</span> opts = <span class="hljs-keyword">typeof</span> db === <span class="hljs-string">'string'</span> ? { <span class="hljs-attr">db</span>: db } : db

<span class="hljs-keyword">var</span> url = extractFiles[opts.db]()

Expand All @@ -484,10 +471,16 @@ <h2 id="download">Download</h2>
debug(<span class="hljs-string">'downloading'</span>, url)
<span class="hljs-keyword">var</span> options
<span class="hljs-keyword">if</span> (opts.pretty === <span class="hljs-literal">true</span>) {
options = { <span class="hljs-attr">dir</span>: folder, <span class="hljs-attr">resume</span>: <span class="hljs-literal">true</span>, <span class="hljs-attr">quiet</span>: <span class="hljs-literal">false</span> }
<span class="hljs-keyword">if</span> (fs.existsSync(path)) {
<span class="hljs-built_in">console</span>.log(<span class="hljs-string">'File already exists in: '</span> + path + <span class="hljs-string">'\n'</span>)
options = { <span class="hljs-attr">dir</span>: folder, <span class="hljs-attr">resume</span>: <span class="hljs-literal">true</span>, <span class="hljs-attr">quiet</span>: <span class="hljs-literal">true</span> }
} <span class="hljs-keyword">else</span> {
options = { <span class="hljs-attr">dir</span>: folder, <span class="hljs-attr">resume</span>: <span class="hljs-literal">true</span>, <span class="hljs-attr">quiet</span>: <span class="hljs-literal">false</span> }
}
} <span class="hljs-keyword">else</span> {
options = { <span class="hljs-attr">dir</span>: folder, <span class="hljs-attr">resume</span>: <span class="hljs-literal">true</span>, <span class="hljs-attr">quiet</span>: <span class="hljs-literal">true</span> }
}

<span class="hljs-keyword">var</span> dld = nugget(PROXY + url, options, <span class="hljs-function"><span class="hljs-keyword">function</span> (<span class="hljs-params">err</span>) </span>{
<span class="hljs-keyword">if</span> (err) <span class="hljs-keyword">return</span> self.destroy(err)
fs.stat(path, gotStat)
Expand All @@ -497,7 +490,6 @@ <h2 id="download">Download</h2>
log.speed = <span class="hljs-string">'NA'</span>
log.size = <span class="hljs-built_in">Math</span>.round(stat.size / <span class="hljs-number">1024</span> / <span class="hljs-number">1024</span>) + <span class="hljs-string">' MB'</span>
self.push(log)
<span class="hljs-built_in">console</span>.log(<span class="hljs-string">'\nFile saved at '</span> + path)
next()
}
})
Expand All @@ -519,11 +511,11 @@ <h2 id="download">Download</h2>
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<h2 id="urls">URLs</h2>
<p>Takes a NCBI database string and a optional search term and returns as stream of dataset/sequence files URLs.
Expand Down Expand Up @@ -591,11 +583,11 @@ <h2 id="urls">URLs</h2>
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<p>NCBI seems to return GenBank and RefSeq accessions for the same thing. We only need one.</p>

Expand Down Expand Up @@ -671,11 +663,11 @@ <h2 id="urls">URLs</h2>
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<h2 id="expand">Expand</h2>
<p>Takes a property (e.g., biosample) and optional destination property
Expand Down Expand Up @@ -707,11 +699,11 @@ <h2 id="expand">Expand</h2>
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<p>Taxonomy doesn’t work just with ID number</p>

Expand Down Expand Up @@ -744,11 +736,11 @@ <h2 id="expand">Expand</h2>
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<h2 id="fetch">Fetch</h2>
<p>Allows retrieval of records from NCBI databases. Takes the database name and a search term,
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8 changes: 7 additions & 1 deletion lib/bionode-ncbi.js
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Expand Up @@ -400,10 +400,16 @@ function download (db) {
debug('downloading', url)
var options
if (opts.pretty === true) {
options = { dir: folder, resume: true, quiet: false }
if (fs.existsSync(path)) {
console.log('File already exists in: ' + path + '\n')
options = { dir: folder, resume: true, quiet: true }
} else {
options = { dir: folder, resume: true, quiet: false }
}
} else {
options = { dir: folder, resume: true, quiet: true }
}

var dld = nugget(PROXY + url, options, function (err) {
if (err) return self.destroy(err)
fs.stat(path, gotStat)
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1 change: 1 addition & 0 deletions package.json
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Expand Up @@ -15,6 +15,7 @@
"JSONStream": "^1.3.1",
"async": "^2.3.0",
"bionode-fasta": "^0.5.5",
"build-docs": "^1.0.3",
"cheerio": "^0.22.0",
"concat-stream": "~1.6.0",
"debug": "^2.6.3",
Expand Down

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