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update generated docs
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zimingd committed Mar 23, 2020
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2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: d207b110004a7eb22630cf0b6504d923
config: 829ce52db06eddc85000fe8cd4ca9f3e
tags: 645f666f9bcd5a90fca523b33c5a78b7
98 changes: 37 additions & 61 deletions docs/build/html/Activity.html
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<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Provenance &#8212; Synapse Python Client 1.9.3 documentation</title>
<meta charset="utf-8" />
<title>Provenance &#8212; Synapse Python Client 2.0.0 documentation</title>
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />

<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
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<link rel="shortcut icon" href="_static/favicon.png"/>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Annotations" href="Annotations.html" />
<link rel="prev" title="Evaluations" href="Evaluation.html" />
<meta name="viewport" content="width=device-width,initial-scale=1.0">
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<script type="text/javascript" src="_static/css3-mediaqueries.js"></script>
<script src="_static/css3-mediaqueries.js"></script>
<![endif]-->
</head><body>
<div class="header">
Expand All @@ -46,23 +45,21 @@ <h3>Navigation</h3>
<li class="right" >
<a href="Evaluation.html" title="Evaluations"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 1.9.3 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.0.0 documentation</a> &#187;</li>
</ul>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<h3 id="searchlabel">Quick search</h3>
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<input type="text" name="q" />
<input type="text" name="q" aria-labelledby="searchlabel" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
<script>$('#searchbox').show(0);</script>
<h3><a href="index.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Provenance</a><ul>
Expand Down Expand Up @@ -103,7 +100,7 @@ <h1>Provenance<a class="headerlink" href="#provenance" title="Permalink to this
combination of data and code which are either <strong>used</strong> or <strong>executed</strong>.</p>
<div class="section" id="imports">
<h2>Imports<a class="headerlink" href="#imports" title="Permalink to this headline"></a></h2>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">synapseclient</span> <span class="k">import</span> <span class="n">Activity</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">synapseclient</span> <span class="kn">import</span> <span class="n">Activity</span>
</pre></div>
</div>
</div>
Expand Down Expand Up @@ -136,7 +133,7 @@ <h2>Storing entities with provenance<a class="headerlink" href="#storing-entitie
</div>
<div class="section" id="recording-data-source">
<h2>Recording data source<a class="headerlink" href="#recording-data-source" title="Permalink to this headline"></a></h2>
<p>The <a class="reference internal" href="Client.html#synapseclient.Synapse.store" title="synapseclient.Synapse.store"><code class="xref py py-meth docutils literal notranslate"><span class="pre">synapseclient.Synapse.store()</span></code></a> has shortcuts for specifying the used and executed lists directly.
<p>The <a class="reference internal" href="index.html#synapseclient.Synapse.store" title="synapseclient.Synapse.store"><code class="xref py py-meth docutils literal notranslate"><span class="pre">synapseclient.Synapse.store()</span></code></a> has shortcuts for specifying the used and executed lists directly.
For example, when storing a data entity, it’s a good idea to record its source:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">excellent_data</span> <span class="o">=</span> <span class="n">syn</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">excellent_data</span><span class="p">,</span>
<span class="n">activityName</span><span class="o">=</span><span class="s1">&#39;data-r-us&#39;</span>
Expand All @@ -149,43 +146,40 @@ <h2>Recording data source<a class="headerlink" href="#recording-data-source" tit
<h2>Activity<a class="headerlink" href="#activity" title="Permalink to this headline"></a></h2>
<dl class="class">
<dt id="synapseclient.activity.Activity">
<em class="property">class </em><code class="descclassname">synapseclient.activity.</code><code class="descname">Activity</code><span class="sig-paren">(</span><em>name=None</em>, <em>description=None</em>, <em>used=None</em>, <em>executed=None</em>, <em>data={}</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity" title="Permalink to this definition"></a></dt>
<em class="property">class </em><code class="sig-prename descclassname">synapseclient.activity.</code><code class="sig-name descname">Activity</code><span class="sig-paren">(</span><em class="sig-param">name=None</em>, <em class="sig-param">description=None</em>, <em class="sig-param">used=None</em>, <em class="sig-param">executed=None</em>, <em class="sig-param">data={}</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity" title="Permalink to this definition"></a></dt>
<dd><p>Represents the provenance of a Synapse Entity.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>name</strong> – name of the Activity</li>
<li><strong>description</strong> – a short text description of the Activity</li>
<li><strong>used</strong> – <p>Either a list of:
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>name</strong> – name of the Activity</p></li>
<li><p><strong>description</strong> – a short text description of the Activity</p></li>
<li><p><strong>used</strong> – <p>Either a list of:
- <a class="reference external" href="http://docs.synapse.org/rest/org/sagebionetworks/repo/model/Reference.html">reference objects</a></p>
<blockquote>
<div>(e.g. <code class="docutils literal notranslate"><span class="pre">[{'targetId':'syn123456',</span> <span class="pre">'targetVersionNumber':1}]</span></code>)</div></blockquote>
<div><p>(e.g. <code class="docutils literal notranslate"><span class="pre">[{'targetId':'syn123456',</span> <span class="pre">'targetVersionNumber':1}]</span></code>)</p>
</div></blockquote>
<ul>
<li>a list of Synapse Entities or Entity IDs</li>
<li>a list of URL’s</li>
<li><p>a list of Synapse Entities or Entity IDs</p></li>
<li><p>a list of URL’s</p></li>
</ul>
</li>
<li><strong>executed</strong> – A code resource that was executed to generate the Entity.</li>
<li><strong>data</strong> – A dictionary representation of an Activity, with fields ‘name’, ‘description’ and ‘used’
(a list of reference objects)</li>
</p></li>
<li><p><strong>executed</strong> – A code resource that was executed to generate the Entity.</p></li>
<li><p><strong>data</strong> – A dictionary representation of an Activity, with fields ‘name’, ‘description’ and ‘used’
(a list of reference objects)</p></li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd>
</dl>
<p>See also: The <a class="reference external" href="http://www.w3.org/TR/prov-o/">W3C’s provenance ontology</a></p>
<dl class="method">
<dt id="synapseclient.activity.Activity.executed">
<code class="descname">executed</code><span class="sig-paren">(</span><em>target=None</em>, <em>targetVersion=None</em>, <em>url=None</em>, <em>name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.executed" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">executed</code><span class="sig-paren">(</span><em class="sig-param">target=None</em>, <em class="sig-param">targetVersion=None</em>, <em class="sig-param">url=None</em>, <em class="sig-param">name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.executed" title="Permalink to this definition"></a></dt>
<dd><p>Add a code resource that was executed during the activity.
See <a class="reference internal" href="#synapseclient.activity.Activity.used" title="synapseclient.activity.Activity.used"><code class="xref py py-func docutils literal notranslate"><span class="pre">synapseclient.activity.Activity.used()</span></code></a></p>
</dd></dl>

<dl class="method">
<dt id="synapseclient.activity.Activity.used">
<code class="descname">used</code><span class="sig-paren">(</span><em>target=None</em>, <em>targetVersion=None</em>, <em>wasExecuted=None</em>, <em>url=None</em>, <em>name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.used" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">used</code><span class="sig-paren">(</span><em class="sig-param">target=None</em>, <em class="sig-param">targetVersion=None</em>, <em class="sig-param">wasExecuted=None</em>, <em class="sig-param">url=None</em>, <em class="sig-param">name=None</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.used" title="Permalink to this definition"></a></dt>
<dd><p>Add a resource used by the activity.</p>
<p>This method tries to be as permissive as possible. It accepts a string which might be a synapse ID or a URL,
a synapse entity, a UsedEntity or UsedURL dictionary or a list containing any combination of these.</p>
Expand Down Expand Up @@ -220,24 +214,6 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
</div>
</dd></dl>

<dl class="method">
<dt id="synapseclient.activity.Activity.usedEntity">
<code class="descname">usedEntity</code><span class="sig-paren">(</span><em>target</em>, <em>targetVersion=None</em>, <em>wasExecuted=False</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.usedEntity" title="Permalink to this definition"></a></dt>
<dd><p>See <code class="xref py py-func docutils literal notranslate"><span class="pre">synapseclient.Activity.used()</span></code>.</p>
<div class="deprecated">
<p><span class="versionmodified">Deprecated since version 1.9.0: </span>This will be removed in 2.0. Please use used() instead.</p>
</div>
</dd></dl>

<dl class="method">
<dt id="synapseclient.activity.Activity.usedURL">
<code class="descname">usedURL</code><span class="sig-paren">(</span><em>url</em>, <em>name=None</em>, <em>wasExecuted=False</em><span class="sig-paren">)</span><a class="headerlink" href="#synapseclient.activity.Activity.usedURL" title="Permalink to this definition"></a></dt>
<dd><p>See <code class="xref py py-func docutils literal notranslate"><span class="pre">synapseclient.Activity.used()</span></code>.</p>
<div class="deprecated">
<p><span class="versionmodified">Deprecated since version 1.9.0: </span>This will be removed in 2.0. Please use used() instead.</p>
</div>
</dd></dl>

</dd></dl>

</div>
Expand All @@ -264,13 +240,13 @@ <h3>Navigation</h3>
<li class="right" >
<a href="Evaluation.html" title="Evaluations"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 1.9.3 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.0.0 documentation</a> &#187;</li>
</ul>
</div>
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Last updated on Jun 28, 2019.
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