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Merge pull request #888 from Sage-Bionetworks/small-updates
Add release notes to news.rst
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‎docs/build/html/Activity.html

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<div class="section" id="manifest">
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<h4>manifest<a class="headerlink" href="#manifest" title="Permalink to this headline"></a></h4>
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<p>Generate manifest for uploading directory tree to Synapse.</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">manifest</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">parentid</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">manifestFile</span> <span class="n">OUTPUT</span><span class="p">]</span> <span class="n">PATH</span>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">synapse</span> <span class="n">manifest</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span><span class="p">]</span> <span class="o">--</span><span class="n">parent</span><span class="o">-</span><span class="nb">id</span> <span class="n">syn123</span> <span class="p">[</span><span class="o">--</span><span class="n">manifest</span><span class="o">-</span><span class="n">file</span> <span class="n">OUTPUT</span><span class="p">]</span> <span class="n">PATH</span>
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</pre></div>
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<div class="section" id="Named Arguments_repeat2">
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<h5>Named Arguments<a class="headerlink" href="#Named Arguments_repeat2" title="Permalink to this headline"></a></h5>
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<dl class="option-list">
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<dt><kbd>--parentid, --parentId</kbd></dt>
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<dt><kbd>--parent-id</kbd></dt>
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<dd><p>Synapse ID of project or folder where to upload data.</p>
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</dd>
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<dt><kbd>--manifestFile</kbd></dt>
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<dd><p>A TSV output file path where the generated manifest is stored.</p>
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<dt><kbd>--manifest-file</kbd></dt>
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<dd><p>A TSV output file path where the generated manifest is stored. (default: stdout)</p>
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</ul></td>
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<td style="width: 33%; vertical-align: top;"><ul>
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<li><a href="synapseutils.html#synapseutils.describe_functions.describe">describe() (in module synapseutils.describe_functions)</a>
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<li><a href="index.html#synapseclient.DockerRepository">DockerRepository (class in synapseclient)</a>
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<li><a href="synapseutils.html#module-synapseutils.copy_functions">synapseutils.copy_functions</a>
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<li><a href="synapseutils.html#module-synapseutils.describe_functions">synapseutils.describe_functions</a>
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<li><a href="Annotations.html#module-synapseclient.annotations">module</a>
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<h3>Highlights<a class="headerlink" href="#highlights" title="Permalink to this headline"></a></h3>
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<ul>
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<li><p>Next major release (3.0.0) will remove all non-standard single dash long parameter
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cli parameter. There might also be big cosmetic changes to the cli such as getting rid
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of all camel case parameters.
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it should be <cite>–parent</cite>. <cite>–parentId</cite> might be changed to <cite>–parent-id</cite>.</p></li>
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<li><p>Added ability generate manifest file from local directory structure</p>
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<li><p>Added ability to generate a manifest file from your local directory structure.</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># from the command line</span>
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synapse manifest --parent-id syn123 --manifest-file ./manifest.tsv ./
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<span class="c1"># write the manifest to manifest.tsv</span>
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synapse manifest --parent-id syn123 --manifest-file ./manifest.tsv /path/to/local/directory
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<span class="c1"># stdout</span>
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synapse manifest --parent-id syn123 /path/to/local/directory
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</pre></div>
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<li><p>Added ability to pipe generate manifest stdout into sync function</p>
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<li><p>Added ability to pipe manifest stdout into sync function.</p>
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<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># from the command line</span>
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<span class="c1"># Pip</span>
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<li><p>Added ability to describe csv and tsv files stored in Synapse.</p>
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<li><p>Added ability to return summary statistics of csv and tsv files stored in Synapse.</p>
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import synapseclient
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synapseutils.describe<span class="o">(</span><span class="nv">syn</span><span class="o">=</span>syn, <span class="nv">entity</span><span class="o">=</span><span class="s2">&quot;syn12345&quot;</span><span class="o">)</span>
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<span class="nv">syn</span> <span class="o">=</span> synapseclient.login<span class="o">()</span>
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<span class="nv">statistics</span> <span class="o">=</span> synapseutils.describe<span class="o">(</span><span class="nv">syn</span><span class="o">=</span>syn, <span class="nv">entity</span><span class="o">=</span><span class="s2">&quot;syn12345&quot;</span><span class="o">)</span>
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print<span class="o">(</span>statistics<span class="o">)</span>
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<span class="o">{</span>
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<span class="s2">&quot;column1&quot;</span>: <span class="o">{</span>
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<span class="s2">&quot;dtype&quot;</span>: <span class="s2">&quot;object&quot;</span>,
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<span class="s2">&quot;mode&quot;</span>: <span class="s2">&quot;FOOBAR&quot;</span>
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<span class="o">}</span>,
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<span class="s2">&quot;column2&quot;</span>: <span class="o">{</span>
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<span class="s2">&quot;dtype&quot;</span>: <span class="s2">&quot;int64&quot;</span>,
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<span class="s2">&quot;mode&quot;</span>: <span class="m">1</span>,
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<span class="s2">&quot;min&quot;</span>: <span class="m">1</span>,
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<span class="s2">&quot;max&quot;</span>: <span class="m">2</span>,
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<span class="o">}</span>,
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<span class="s2">&quot;dtype&quot;</span>: <span class="s2">&quot;bool&quot;</span>,
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<span class="s2">&quot;mode&quot;</span>: false,
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<span class="s2">&quot;min&quot;</span>: false,
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<span class="o">}</span>
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<li><p>Next major release (3.0.0) there will be major cosmetic changes to the cli such as
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parameters.
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‎docs/build/html/searchindex.js

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‎docs/build/html/sftp.html

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@@ -157,7 +157,7 @@ <h3>Navigation</h3>
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<div class="footer">
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&copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
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Last updated on Oct 05, 2021.
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Last updated on Oct 14, 2021.
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Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.5.4.
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