Skip to content

Commit 8aa5216

Browse files
zimingdzimingd
committed
update generated docs
1 parent 83d90d4 commit 8aa5216

34 files changed

+15856
-4022
lines changed

‎docs/build/html/.buildinfo

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: d207b110004a7eb22630cf0b6504d923
3+
config: 829ce52db06eddc85000fe8cd4ca9f3e
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

‎docs/build/html/Activity.html

Lines changed: 37 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -4,26 +4,25 @@
44

55
<html xmlns="http://www.w3.org/1999/xhtml">
66
<head>
7-
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
8-
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
9-
<title>Provenance &#8212; Synapse Python Client 1.9.3 documentation</title>
7+
<meta charset="utf-8" />
8+
<title>Provenance &#8212; Synapse Python Client 2.0.0 documentation</title>
109
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
1110
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
1211

13-
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
14-
<script type="text/javascript" src="_static/jquery.js"></script>
15-
<script type="text/javascript" src="_static/underscore.js"></script>
16-
<script type="text/javascript" src="_static/doctools.js"></script>
17-
<script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
18-
<script type="text/javascript" src="_static/bizstyle.js"></script>
12+
<script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
13+
<script src="_static/jquery.js"></script>
14+
<script src="_static/underscore.js"></script>
15+
<script src="_static/doctools.js"></script>
16+
<script src="_static/language_data.js"></script>
17+
<script src="_static/bizstyle.js"></script>
1918
<link rel="shortcut icon" href="_static/favicon.png"/>
2019
<link rel="index" title="Index" href="genindex.html" />
2120
<link rel="search" title="Search" href="search.html" />
2221
<link rel="next" title="Annotations" href="Annotations.html" />
2322
<link rel="prev" title="Evaluations" href="Evaluation.html" />
2423
<meta name="viewport" content="width=device-width,initial-scale=1.0">
2524
<!--[if lt IE 9]>
26-
<script type="text/javascript" src="_static/css3-mediaqueries.js"></script>
25+
<script src="_static/css3-mediaqueries.js"></script>
2726
<![endif]-->
2827
</head><body>
2928
<div class="header">
@@ -46,23 +45,21 @@ <h3>Navigation</h3>
4645
<li class="right" >
4746
<a href="Evaluation.html" title="Evaluations"
4847
accesskey="P">previous</a> |</li>
49-
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 1.9.3 documentation</a> &#187;</li>
48+
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.0.0 documentation</a> &#187;</li>
5049
</ul>
5150
</div>
5251
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
5352
<div class="sphinxsidebarwrapper">
5453
<div id="searchbox" style="display: none" role="search">
55-
<h3>Quick search</h3>
54+
<h3 id="searchlabel">Quick search</h3>
5655
<div class="searchformwrapper">
5756
<form class="search" action="search.html" method="get">
58-
<input type="text" name="q" />
57+
<input type="text" name="q" aria-labelledby="searchlabel" />
5958
<input type="submit" value="Go" />
60-
<input type="hidden" name="check_keywords" value="yes" />
61-
<input type="hidden" name="area" value="default" />
6259
</form>
6360
</div>
6461
</div>
65-
<script type="text/javascript">$('#searchbox').show(0);</script>
62+
<script>$('#searchbox').show(0);</script>
6663
<h3><a href="index.html">Table of Contents</a></h3>
6764
<ul>
6865
<li><a class="reference internal" href="#">Provenance</a><ul>
@@ -103,7 +100,7 @@ <h1>Provenance<a class="headerlink" href="#provenance" title="Permalink to this
103100
combination of data and code which are either <strong>used</strong> or <strong>executed</strong>.</p>
104101
<div class="section" id="imports">
105102
<h2>Imports<a class="headerlink" href="#imports" title="Permalink to this headline"></a></h2>
106-
<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>
103+
<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>
107104
</pre></div>
108105
</div>
109106
</div>
@@ -136,7 +133,7 @@ <h2>Storing entities with provenance<a class="headerlink" href="#storing-entitie
136133
</div>
137134
<div class="section" id="recording-data-source">
138135
<h2>Recording data source<a class="headerlink" href="#recording-data-source" title="Permalink to this headline"></a></h2>
139-
<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.
136+
<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.
140137
For example, when storing a data entity, it’s a good idea to record its source:</p>
141138
<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>
142139
<span class="n">activityName</span><span class="o">=</span><span class="s1">&#39;data-r-us&#39;</span>
@@ -149,43 +146,40 @@ <h2>Recording data source<a class="headerlink" href="#recording-data-source" tit
149146
<h2>Activity<a class="headerlink" href="#activity" title="Permalink to this headline"></a></h2>
150147
<dl class="class">
151148
<dt id="synapseclient.activity.Activity">
152-
<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>
149+
<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>
153150
<dd><p>Represents the provenance of a Synapse Entity.</p>
154-
<table class="docutils field-list" frame="void" rules="none">
155-
<col class="field-name" />
156-
<col class="field-body" />
157-
<tbody valign="top">
158-
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
159-
<li><strong>name</strong> – name of the Activity</li>
160-
<li><strong>description</strong> – a short text description of the Activity</li>
161-
<li><strong>used</strong> – <p>Either a list of:
151+
<dl class="field-list simple">
152+
<dt class="field-odd">Parameters</dt>
153+
<dd class="field-odd"><ul class="simple">
154+
<li><p><strong>name</strong> – name of the Activity</p></li>
155+
<li><p><strong>description</strong> – a short text description of the Activity</p></li>
156+
<li><p><strong>used</strong> – <p>Either a list of:
162157
- <a class="reference external" href="http://docs.synapse.org/rest/org/sagebionetworks/repo/model/Reference.html">reference objects</a></p>
163158
<blockquote>
164-
<div>(e.g. <code class="docutils literal notranslate"><span class="pre">[{'targetId':'syn123456',</span> <span class="pre">'targetVersionNumber':1}]</span></code>)</div></blockquote>
159+
<div><p>(e.g. <code class="docutils literal notranslate"><span class="pre">[{'targetId':'syn123456',</span> <span class="pre">'targetVersionNumber':1}]</span></code>)</p>
160+
</div></blockquote>
165161
<ul>
166-
<li>a list of Synapse Entities or Entity IDs</li>
167-
<li>a list of URL’s</li>
162+
<li><p>a list of Synapse Entities or Entity IDs</p></li>
163+
<li><p>a list of URL’s</p></li>
168164
</ul>
169-
</li>
170-
<li><strong>executed</strong> – A code resource that was executed to generate the Entity.</li>
171-
<li><strong>data</strong> – A dictionary representation of an Activity, with fields ‘name’, ‘description’ and ‘used’
172-
(a list of reference objects)</li>
165+
</p></li>
166+
<li><p><strong>executed</strong> – A code resource that was executed to generate the Entity.</p></li>
167+
<li><p><strong>data</strong> – A dictionary representation of an Activity, with fields ‘name’, ‘description’ and ‘used’
168+
(a list of reference objects)</p></li>
173169
</ul>
174-
</td>
175-
</tr>
176-
</tbody>
177-
</table>
170+
</dd>
171+
</dl>
178172
<p>See also: The <a class="reference external" href="http://www.w3.org/TR/prov-o/">W3C’s provenance ontology</a></p>
179173
<dl class="method">
180174
<dt id="synapseclient.activity.Activity.executed">
181-
<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>
175+
<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>
182176
<dd><p>Add a code resource that was executed during the activity.
183177
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>
184178
</dd></dl>
185179

186180
<dl class="method">
187181
<dt id="synapseclient.activity.Activity.used">
188-
<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>
182+
<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>
189183
<dd><p>Add a resource used by the activity.</p>
190184
<p>This method tries to be as permissive as possible. It accepts a string which might be a synapse ID or a URL,
191185
a synapse entity, a UsedEntity or UsedURL dictionary or a list containing any combination of these.</p>
@@ -220,24 +214,6 @@ <h2>Activity<a class="headerlink" href="#activity" title="Permalink to this head
220214
</div>
221215
</dd></dl>
222216

223-
<dl class="method">
224-
<dt id="synapseclient.activity.Activity.usedEntity">
225-
<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>
226-
<dd><p>See <code class="xref py py-func docutils literal notranslate"><span class="pre">synapseclient.Activity.used()</span></code>.</p>
227-
<div class="deprecated">
228-
<p><span class="versionmodified">Deprecated since version 1.9.0: </span>This will be removed in 2.0. Please use used() instead.</p>
229-
</div>
230-
</dd></dl>
231-
232-
<dl class="method">
233-
<dt id="synapseclient.activity.Activity.usedURL">
234-
<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>
235-
<dd><p>See <code class="xref py py-func docutils literal notranslate"><span class="pre">synapseclient.Activity.used()</span></code>.</p>
236-
<div class="deprecated">
237-
<p><span class="versionmodified">Deprecated since version 1.9.0: </span>This will be removed in 2.0. Please use used() instead.</p>
238-
</div>
239-
</dd></dl>
240-
241217
</dd></dl>
242218

243219
</div>
@@ -264,13 +240,13 @@ <h3>Navigation</h3>
264240
<li class="right" >
265241
<a href="Evaluation.html" title="Evaluations"
266242
>previous</a> |</li>
267-
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 1.9.3 documentation</a> &#187;</li>
243+
<li class="nav-item nav-item-0"><a href="index.html">Synapse Python Client 2.0.0 documentation</a> &#187;</li>
268244
</ul>
269245
</div>
270246
<div class="footer">
271247
&copy; <a href="http://sagebase.org/">Sage Bionetworks</a>.
272-
Last updated on Jun 28, 2019.
273-
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
248+
Last updated on Mar 23, 2020.
249+
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.4.4.
274250
</div>
275251
<script type="text/javascript">
276252
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){

0 commit comments

Comments
 (0)