nipreps · oesteban · Mar 21, 2023 · Mar 15, 2023 · Mar 19, 2023 · Mar 19, 2023
diff --git a/nireports/assembler/__init__.py b/nireports/assembler/__init__.py
@@ -1,3 +0,0 @@
-"""
-Aggregate reports into an HTML document.
-"""

diff --git a/nireports/assembler/data/default.yml b/nireports/assembler/data/default.yml
@@ -1,4 +1,4 @@
-package: nireports
+packagename: nireports
 sections:
 - name: Summary
   reportlets:
@@ -173,5 +173,37 @@ sections:
       in green; noise components in red.
     subtitle: ICA Components classified by AROMA
 - name: About
+  nested: true
   reportlets:
-  - bids: {datatype: figures, desc: about, suffix: T1w}
+  - custom: boilerplate
+    path: '{reportlets_dir}/sub-{subject_id}/'
+    bibfile: ['nireports.assembler', 'data/tests/boilerplate.bib']
+    caption: We kindly ask to report results preprocessed with this tool using the following boilerplate.
+    title: Methods
+  - custom: errors
+    path: '{reportlets_dir}/sub-{subject_id}/log/{run_uuid}'
+    captions: <em>NiReports</em> may have recorded failure conditions.
+    title: Errors
+  - metadata:
+      Execution provenance:
+        NiReports version: '23.0.1'
+        NiReports command: |
+          <code>/opt/conda/bin/fmriprep /data /out participant --sloppy --write-graph
+          --mem-mb 14336 --nthreads 4 -vv --anat-derivatives /opt/smriprep/subjects
+          -w /scratch --output-spaces fsaverage5</code>
+        Date processed: '2023-03-12 03:15:45 +0000'
+      Dataset information:
+        Dataset name: 'Test example'
+        Participant ID: '00017'
+        Split Nested_key1: value1
+        Split Nested_key2: value1
+    settings:
+      # By default, only the first dictionary will be expanded.
+      # If folded is true, all will be folded. If false all expanded.
+      folded: true
+      # If an ID is not provided, one should be generated automatically
+      id: 'about-metadata'
+    caption: |
+      Thanks for using <em>NiReports</em>. The following information may assist in
+      reconstructing the provenance of the corresponding derivatives.
+    title: Reproducibility and provenance information
diff --git a/nireports/assembler/data/report.tpl b/nireports/assembler/data/report.tpl
@@ -5,9 +5,8 @@
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="Docutils 0.12: http://docutils.sourceforge.net/" />
 <title></title>
-<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-EVSTQN3/azprG1Anm3QDgpJLIm9Nao0Yz1ztcQTwFspd3yD65VohhpuuCOmLASjC" crossorigin="anonymous">
-<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.2/dist/js/bootstrap.bundle.min.js" integrity="sha384-MrcW6ZMFYlzcLA8Nl+NtUVF0sA7MsXsP1UyJoMp4YLEuNSfAP+JcXn/tWtIaxVXM" crossorigin="anonymous"></script>
 <script src="https://code.jquery.com/jquery-3.6.0.min.js" integrity="sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4=" crossorigin="anonymous"></script>
+
 <style type="text/css">
 .sub-report-title {}
 .run-title {}
@@ -53,33 +52,38 @@ div#boilerplate pre {
     padding-left: 1em;
 }
 </style>
+
+<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-rbsA2VBKQhggwzxH7pPCaAqO46MgnOM80zW1RWuH61DGLwZJEdK2Kadq2F9CUG65" crossorigin="anonymous">
+<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.2.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-kenU1KFdBIe4zVF0s0G1M5b4hcpxyD9F7jL+jjXkk+Q2h455rYXK/7HAuoJl+0I4" crossorigin="anonymous"></script>
+
 </head>
 <body>
 
-
-<nav class="navbar fixed-top navbar-expand-lg navbar-light bg-light">
-<div class="collapse navbar-collapse">
-    <ul class="navbar-nav">
+<nav class="navbar fixed-top navbar-expand-lg bg-light">
+<div class="container-fluid">
+<div class="collapse navbar-collapse" id="navbarSupportedContent">
+    <ul class="navbar-nav me-auto mb-2 mb-lg-0">
     {% for sub_report in sections %}
         {% if sub_report.isnested %}
         <li class="nav-item dropdown">
-            <a class="nav-link dropdown-toggle" id="navbar{{ sub_report.name }}" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false" href="#">{{ sub_report.name }}</a>
-            <div class="dropdown-menu" aria-labelledby="navbar{{ sub_report.name }}">
-                {% for run_report in sub_report.reportlets %}
-                    {% if run_report.title %}
-                    <a class="dropdown-item" href="#{{run_report.name}}">{{run_report.title}}</a>
-                    {% endif %}
-                {% endfor %}
-            </div>
+            <a class="nav-link dropdown-toggle" id="navbar{{ sub_report.name }}" role="button" data-bs-toggle="dropdown" aria-expanded="false" href="#{{sub_report.name}}">
+            {{ sub_report.name }}
+            </a>
+            <ul class="dropdown-menu">
+            {% for run_report in sub_report.reportlets %}
+                {% if run_report.title %}
+                <li><a class="dropdown-item" href="#{{run_report.name}}">{{run_report.title}}</a></li>
+                {% endif %}
+            {% endfor %}
+            </ul>
         </li>
         {% else %}
         <li class="nav-item"><a class="nav-link" href="#{{sub_report.name}}">{{sub_report.name}}</a></li>
         {% endif %}
     {% endfor %}
-        <li class="nav-item"><a class="nav-link" href="#boilerplate">Methods</a></li>
-        <li class="nav-item"><a class="nav-link" href="#errors">Errors</a></li>
     </ul>
 </div>
+</div>
 </nav>
 <noscript>
     <h1 class="text-danger"> The navigation menu uses Javascript. Without it this report might not work as expected </h1>
@@ -106,59 +110,19 @@ div#boilerplate pre {
     {% endif %}
 {% endfor %}
 
-<div id="boilerplate">
-    <h1 class="sub-report-title">Methods</h1>
-    {% if boilerplate %}
-    <p>We kindly ask to report results preprocessed with this tool using the following
-       boilerplate.</p>
-    <ul class="nav nav-tabs" id="myTab" role="tablist">
-        {% for b in boilerplate %}
-        <li class="nav-item">
-            <a class="nav-link {% if b[0] == 0 %}active{% endif %}" id="{{ b[1] }}-tab" data-toggle="tab" href="#{{ b[1] }}" role="tab" aria-controls="{{ b[1] }}" aria-selected="{% if b[0] == 0 %}true{%else%}false{% endif %}">{{ b[1] }}</a>
-        </li>
-        {% endfor %}
-    </ul>
-    <div class="tab-content" id="myTabContent">
-      {% for b in boilerplate %}
-      <div class="tab-pane fade {% if b[0] == 0 %}active show{% endif %}" id="{{ b[1] }}" role="tabpanel" aria-labelledby="{{ b[1] }}-tab">{{ b[2] }}</div>
-      {% endfor %}
-    </div>
-    {% else %}
-    <p class="text-danger">Failed to generate the boilerplate</p>
-    {% endif %}
-</div>
-
-<div id="errors">
-    <h1 class="sub-report-title">Errors</h1>
-    {% for error in errors %}
-    <details>
-        <summary>Node Name: {{ error.node }}</summary><br>
-        <div>
-            File: <code>{{ error.file }}</code><br>
-            Working Directory: <code>{{ error.node_dir }}</code><br>
-            Inputs: <br>
-            <ul>
-            {% for name, spec in error.inputs %}
-                <li>{{ name }}: <code>{{ spec }}</code></li>
-            {% endfor %}
-            </ul>
-            <pre>{{ error.traceback }}</pre>
-        </div>
-    </details>
-    {% else %}
-    <p>No errors to report!</p>
-    {% endfor %}
-</div>
-
-
 <script type="text/javascript">
-    function toggle(id) {
-        var element = document.getElementById(id);
-        if(element.style.display == 'block')
-            element.style.display = 'none';
-        else
-            element.style.display = 'block';
-    }
+function toggle(id) {
+    var element = document.getElementById(id);
+    if(element.style.display == 'block')
+        element.style.display = 'none';
+    else
+        element.style.display = 'block';
+}
+
+<!-- $(".nav .nav-link").on("click", function(){
+   $(".nav").find(".active").removeClass("active");
+   $(this).addClass("active");
+}); -->
 </script>
 </body>
 </html>