Runtime - Turn-key research data management repository

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md-icon"></span> </label> <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_7_8_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_7_8"> <span class="md-nav__icon md-icon"></span> REST API </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="../../../reference/rest_api_index/" class="md-nav__link"> <span class="md-ellipsis"> Overview </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_quickstart/" class="md-nav__link"> <span class="md-ellipsis"> Quickstart </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_communities/" class="md-nav__link"> <span class="md-ellipsis"> Communities </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_drafts_records/" class="md-nav__link"> <span class="md-ellipsis"> Drafts and Records </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_groups/" class="md-nav__link"> <span class="md-ellipsis"> Groups </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_members/" class="md-nav__link"> <span class="md-ellipsis"> Members </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_requests/" class="md-nav__link"> <span class="md-ellipsis"> Requests </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_users/" class="md-nav__link"> <span class="md-ellipsis"> Users </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_reviews/" class="md-nav__link"> <span class="md-ellipsis"> Reviews </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_vocabularies/" class="md-nav__link"> <span class="md-ellipsis"> Vocabularies </span> </a> </li> <li class="md-nav__item"> <a href="../../../reference/rest_api_names/" class="md-nav__link"> <span class="md-ellipsis"> Names </span> </a> </li> <li class="md-nav__item"> <a 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md-icon"></span> </label> <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_8_8_2_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_8_8_2"> <span class="md-nav__icon md-icon"></span> Version v8.0 </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="../../../releases/v8/version-v8.0.0/" class="md-nav__link"> <span class="md-ellipsis"> Release Notes v8.0 </span> </a> </li> <li class="md-nav__item"> <a href="../../../releases/v8/upgrade-v8.0/" class="md-nav__link"> <span class="md-ellipsis"> Upgrade from v7 to v8 </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8_8_3" > <label class="md-nav__link" for="__nav_8_8_3" id="__nav_8_8_3_label" tabindex="0"> <span class="md-ellipsis"> Version v7.0 </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_8_8_3_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_8_8_3"> <span class="md-nav__icon md-icon"></span> Version v7.0 </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="../../../releases/v7/version-v7.0.0/" class="md-nav__link"> <span class="md-ellipsis"> Release Notes v7.0 </span> </a> </li> <li class="md-nav__item"> <a href="../../../releases/v7/upgrade-v7.0/" class="md-nav__link"> <span class="md-ellipsis"> Upgrade from v6 to v7 </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_8_8_4" > <label class="md-nav__link" for="__nav_8_8_4" id="__nav_8_8_4_label" tabindex="0"> <span class="md-ellipsis"> Version v6.0.5 </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_8_8_4_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_8_8_4"> <span class="md-nav__icon 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class="md-nav__item md-nav__item--nested"> <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_9" > <label class="md-nav__link" for="__nav_9" id="__nav_9_label" tabindex="0"> <span class="md-ellipsis"> Maintainers </span> <span class="md-nav__icon md-icon"></span> </label> <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_9_label" aria-expanded="false"> <label class="md-nav__title" for="__nav_9"> <span class="md-nav__icon md-icon"></span> Maintainers </label> <ul class="md-nav__list" data-md-scrollfix> <li class="md-nav__item"> <a href="../../../maintenance/" class="md-nav__link"> <span class="md-ellipsis"> Overview </span> </a> </li> <li class="md-nav__item"> <a href="../../../maintenance/newcomers/" class="md-nav__link"> <span class="md-ellipsis"> Newcomers </span> </a> </li> <li class="md-nav__item"> <a href="../../../maintenance/board-workflow/" class="md-nav__link"> <span class="md-ellipsis"> Sprintboard workflow </span> </a> </li> <li 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md-nav--secondary" aria-label="Table of contents"> <label class="md-nav__title" for="__toc"> <span class="md-nav__icon md-icon"></span> Table of contents </label> <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix> <li class="md-nav__item"> <a href="#core-concepts" class="md-nav__link"> <span class="md-ellipsis"> Core concepts </span> </a> <nav class="md-nav" aria-label="Core concepts"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#application-and-blueprint" class="md-nav__link"> <span class="md-ellipsis"> Application and blueprint </span> </a> </li> <li class="md-nav__item"> <a href="#flask-extensions" class="md-nav__link"> <span class="md-ellipsis"> Flask extensions </span> </a> </li> <li class="md-nav__item"> <a href="#application-and-request-context" class="md-nav__link"> <span class="md-ellipsis"> Application and request context </span> </a> </li> </ul> </nav> </li> <li class="md-nav__item"> <a href="#interfaces-wsgi-cli-and-celery" class="md-nav__link"> <span class="md-ellipsis"> Interfaces: WSGI, CLI and Celery </span> </a> </li> <li class="md-nav__item"> <a href="#application-assembly" class="md-nav__link"> <span class="md-ellipsis"> Application assembly </span> </a> <nav class="md-nav" aria-label="Application assembly"> <ul class="md-nav__list"> <li class="md-nav__item"> <a href="#assembly-phases" class="md-nav__link"> <span class="md-ellipsis"> Assembly phases </span> </a> </li> <li class="md-nav__item"> <a href="#module-discovery" class="md-nav__link"> <span class="md-ellipsis"> Module discovery </span> </a> </li> <li class="md-nav__item"> <a href="#wsgi-ui-and-rest" class="md-nav__link"> <span class="md-ellipsis"> WSGI: UI and REST </span> </a> </li> <li class="md-nav__item"> <a href="#implementation" class="md-nav__link"> <span class="md-ellipsis"> Implementation </span> </a> </li> </ul> </nav> </li> </ul> </nav> </div> </div> </div> <div class="md-content" data-md-component="content"> <article class="md-content__inner md-typeset"> <h1 id="runtime-architecture">Runtime architecture<a class="headerlink" href="#runtime-architecture" title="Permanent link">¶</a></h1> <p>At its core Invenio is an application built on-top of the Flask web development framework, and fully understanding Invenio's architectural design requires you to understand core concepts of Flask which will be covered in brief here.</p> <p>The Flask application is exposed via different <em>application interfaces</em> depending on if the application is running in a web server, CLI or job queue.</p> <p>Invenio adds a powerful <em>application factory</em> on top of Flask, which takes care of dynamically assembling an Invenio application from the many individual modules that make up Invenio, and which also allow you to easily extend Invenio with your own modules.</p> <h2 id="core-concepts">Core concepts<a class="headerlink" href="#core-concepts" title="Permanent link">¶</a></h2> <p>We will explain the core Flask concepts using a simple Flask application:</p> <div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">flask</span> <span class="kn">import</span> <span class="n">Blueprint</span><span class="p">,</span> <span class="n">Flask</span><span class="p">,</span> <span class="n">request</span> <span class="c1"># Blueprint</span> <span class="n">bp</span> <span class="o">=</span> <span class="n">Blueprint</span><span class="p">(</span><span class="s1">'bp'</span><span class="p">,</span> <span class="vm">__name__</span><span class="p">)</span> <span class="nd">@bp</span><span class="o">.</span><span class="n">route</span><span class="p">(</span><span class="s1">'/'</span><span class="p">)</span> <span class="k">def</span> <span class="nf">my_user_agent</span><span class="p">():</span> <span class="c1"># Executing inside request context</span> <span class="k">return</span> <span class="n">request</span><span class="o">.</span><span class="n">headers</span><span class="p">[</span><span class="s1">'User-Agent'</span><span class="p">]</span> <span class="c1"># Extension</span> <span class="k">class</span> <span class="nc">MyExtension</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">app</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> <span class="k">if</span> <span class="n">app</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">init_app</span><span class="p">(</span><span class="n">app</span><span class="p">)</span> <span class="k">def</span> <span class="nf">init_app</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">app</span><span class="p">):</span> <span class="n">app</span><span class="o">.</span><span class="n">config</span><span class="o">.</span><span class="n">setdefault</span><span class="p">(</span><span class="s1">'MYCONF'</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span> <span class="c1"># Application</span> <span class="n">app</span> <span class="o">=</span> <span class="n">Flask</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span> <span class="n">ext</span> <span class="o">=</span> <span class="n">MyExtension</span><span class="p">(</span><span class="n">app</span><span class="p">)</span> <span class="n">app</span><span class="o">.</span><span class="n">register_blueprint</span><span class="p">(</span><span class="n">bp</span><span class="p">)</span> </code></pre></div> <p>You can save above code in a file <code>app.py</code> and run the application:</p> <div class="highlight"><pre><span></span><code><span class="gp">$ </span>pip<span class="w"> </span>install<span class="w"> </span>Flask <span class="gp">$ </span><span class="nb">export</span><span class="w"> </span><span class="nv">FLASK_APP</span><span class="o">=</span>app.py<span class="w"> </span>flask<span class="w"> </span>run </code></pre></div> <h3 id="application-and-blueprint">Application and blueprint<a class="headerlink" href="#application-and-blueprint" title="Permanent link">¶</a></h3> <p>Invenio is a large application built up of many smaller individual modules. The way Flask allows you to build modular applications is via <em>blueprints</em>. In above example we have a small blueprint with just one <em>view</em> (<code>my_user_agent</code>), which returns the browser's user agent sting.</p> <p>This blueprint is <em>registered</em> on the <em>Flask application</em>. This allows you to reuse the blueprint in another Flask application.</p> <h3 id="flask-extensions">Flask extensions<a class="headerlink" href="#flask-extensions" title="Permanent link">¶</a></h3> <p>Like blueprints allow you to modularise your Flask application's views, Flask extensions allow you to modularise the initialization of your application that is not specific to views (e.g. providing database connectivity).</p> <p>Flask extensions are just objects like the one in the example above, which has an <code>init_app</code> method.</p> <h3 id="application-and-request-context">Application and request context<a class="headerlink" href="#application-and-request-context" title="Permanent link">¶</a></h3> <p>Code in a Flask application can be executed in two "states":</p> <ul> <li><em>Application context</em>: when the application is e.g. being used via a CLI or running in a job queue (i.e. not handling requests).</li> <li><em>Request context</em>: when the application is handling a request from a user.</li> </ul> <p>In the above example, the code inside the view <code>my_user_agent</code> is executed during a request, and thus you can have access to the browser's user agent string. On the other hand, if you tried to access <code>request.headers</code> outside the view, the application would fail as no request is being processed.</p> <p>The <code>request</code> object is a proxy object which points to the current request being processed. There is some magic happening behind the scenes in order to make this thread safe.</p> <h2 id="interfaces-wsgi-cli-and-celery">Interfaces: WSGI, CLI and Celery<a class="headerlink" href="#interfaces-wsgi-cli-and-celery" title="Permanent link">¶</a></h2> <p>Overall the Flask application runs via three different application interfaces:</p> <ul> <li><strong>WSGI:</strong> The frontend web server interfaces with Flask via Flask's WSGI application.</li> <li><strong>CLI:</strong> The command-line interface is made using Click and takes care of executing commands inside the Flask application.</li> <li><strong>Celery:</strong> The distributed job queue is made using Celery and takes care of executing jobs inside the Flask application.</li> </ul> <h2 id="application-assembly">Application assembly<a class="headerlink" href="#application-assembly" title="Permanent link">¶</a></h2> <p>In each of the above interfaces, a Flask application needs to be created. A common pattern for large Flask applications is to move the application creation into a factory function, named an <strong>application factory</strong>.</p> <p>Invenio provides a powerful application factory for Flask which is capable of dynamically assembling an application. In order to illustrate the basics of what the Invenio application factory does, have a look at the following example:</p> <div class="highlight"><pre><span></span><code><span class="kn">from</span> <span class="nn">flask</span> <span class="kn">import</span> <span class="n">Flask</span><span class="p">,</span> <span class="n">Blueprint</span> <span class="c1"># Module 1</span> <span class="n">bp1</span> <span class="o">=</span> <span class="n">Blueprint</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">'bp1'</span><span class="p">)</span> <span class="nd">@bp1</span><span class="o">.</span><span class="n">route</span><span class="p">(</span><span class="s1">'/'</span><span class="p">)</span> <span class="k">def</span> <span class="nf">hello</span><span class="p">():</span> <span class="k">return</span> <span class="s1">'Hello'</span> <span class="c1"># Module 2</span> <span class="n">bp2</span> <span class="o">=</span> <span class="n">Blueprint</span><span class="p">(</span><span class="vm">__name__</span><span class="p">,</span> <span class="s1">'bp2'</span><span class="p">)</span> <span class="nd">@bp2</span><span class="o">.</span><span class="n">route</span><span class="p">(</span><span class="s1">'/'</span><span class="p">)</span> <span class="k">def</span> <span class="nf">world</span><span class="p">():</span> <span class="k">return</span> <span class="s1">'World'</span> <span class="c1"># Application factory</span> <span class="k">def</span> <span class="nf">create_app</span><span class="p">():</span> <span class="n">app</span> <span class="o">=</span> <span class="n">Flask</span><span class="p">(</span><span class="vm">__name__</span><span class="p">)</span> <span class="n">app</span><span class="o">.</span><span class="n">register_blueprint</span><span class="p">(</span><span class="n">bp1</span><span class="p">)</span> <span class="n">app</span><span class="o">.</span><span class="n">register_blueprint</span><span class="p">(</span><span class="n">bp2</span><span class="p">)</span> <span class="k">return</span> <span class="n">app</span> </code></pre></div> <p>The example illustrates two blueprints, which are statically registered on the Flask application blueprint inside the application factory. It is essentially this part that the Invenio application factory takes care of for you. Invenio will automatically discover all your installed Invenio modules and register them on your application.</p> <h3 id="assembly-phases">Assembly phases<a class="headerlink" href="#assembly-phases" title="Permanent link">¶</a></h3> <p>The Invenio application factory assembles your application in five phases:</p> <ol> <li><strong>Application creation</strong>: Besides creating the Flask application object, this phase will also ensure your instance folder exists, as well as route Python warnings through the Flask application logger.</li> <li><strong>Configuration loading</strong>: In this phase your application will load your instance configuration. This essentially sets all the configuration variables for which you don't want to use the default values, e.g. the database host configuration.</li> <li><strong>URL converter loading</strong>: In this phase, the application will load any of your URL converters. This phase is usually only needed for some few specific cases.</li> <li><strong>Flask extensions loading</strong>: In this phase all the Invenio modules which provide Flask extensions will initialize the extension. Usually the extensions will provide default configuration values they need, unless the user already set them.</li> <li><strong>Blueprints loading</strong>: After all extensions have been loaded, the factory will end with registering all the blueprints provided by the Invenio modules on the application.</li> </ol> <p>Understanding the above application assembly phases, what they do, and how you can plug into them is essential for fully mastering Invenio development.</p> <div class="admonition note"> <p class="admonition-title">Note</p> <p><strong>No loading order within a phase</strong></p> <p>It's very important to know that, within each phase, there is <strong>no order</strong> in how the Invenio modules are loaded. Say, within the Flask extensions loading phase, there's no way to specify that one extension has to be loaded before another extension.</p> <p>You only have the order of the phases to work with, so e.g. Flask extensions are loaded before any blueprints are loaded.</p> </div> <h3 id="module-discovery">Module discovery<a class="headerlink" href="#module-discovery" title="Permanent link">¶</a></h3> <p>In each of the application assembly phases, the Invenio factory automatically discovers your installed Invenio modules. This works via Python <strong>entry points</strong>. When you install the Python package for an Invenio module, the package describes via entry points which Flask extensions, blueprints etc. it provides.</p> <h3 id="wsgi-ui-and-rest">WSGI: UI and REST<a class="headerlink" href="#wsgi-ui-and-rest" title="Permanent link">¶</a></h3> <p>Each of the application interfaces (WSGI, CLI, Celery) may need slightly different Flask applications. The Invenio application factory is in charge of assembling these applications, which is done through the five assembly phases.</p> <p>The WSGI application is however also split up into two Flask applications:</p> <ul> <li><strong>UI:</strong> Flask application responsible for processing all user facing views.</li> <li><strong>REST:</strong> Flask application responsible for processing all REST API requests.</li> </ul> <p>The reason to split the frontend part of Invenio into two separate applications is partly</p> <ul> <li>to be able to run the REST API on one domain (<code>api.example.org</code>) and the UI app on another domain (<code>www.example.org</code>)</li> <li>because UI and REST API applications usually have vastly different requirements.</li> </ul> <p>As an example, a <code>404 Not found</code> HTTP error, usually needs to render a template in the UI application, but returns a JSON response in the REST API application.</p> <h3 id="implementation">Implementation<a class="headerlink" href="#implementation" title="Permanent link">¶</a></h3> <p>The following Invenio modules are each responsible for implementing parts of the above application architecture, and it is highly advisable to dig deeper into these modules for a better understanding of the Invenio application architecture:</p> <ul> <li><a href="https://invenio-base.readthedocs.io">Invenio-Base</a>: Implements the Invenio application factory.</li> <li><a href="https://invenio-config.readthedocs.io">Invenio-Config</a>: Implements the configuration loading phase.</li> <li><a href="https://invenio-app.readthedocs.io">Invenio-App</a>: Implements default applications for WSGI, CLI and Celery.</li> </ul> </article> </div> <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script> </div> </main> <footer class="md-footer"> <nav class="md-footer__inner md-grid" aria-label="Footer" > <a href="../software/" 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