fix(reports): improve generalization across software packages

- release a ``defaultconfig.json`` to initiate ``Report``s
- release a default report template (``report.tpl``)
- make config and packagename optional

Author: oesteban

niworkflows/data/tests/work/config.json renamed to niworkflows/viz/defaultconfig.json

@@ -30,7 +30,8 @@
             "space": ".*",
             "suffix": "T1w"
           },
-          "caption": "Nonlinear mapping of the T1w image into {space} space. Hover on the panel with the mouse to transition between both spaces.",
+          "description": "Results of nonlinear alignment of the T1w image to template space. Hover on the panel with the mouse to transition between both spaces.",
+          "caption": "Spatial normalization of the T1w image to the <code>{space}</code> template.",
           "title": "Spatial normalization"
         },
         {

niworkflows/data/tests/work/report.tpl renamed to niworkflows/viz/report.tpl

@@ -17,6 +17,10 @@ h2 { padding-top: 20px; }
 h3 { padding-top: 15px; }
 
 .elem-desc {}
+.elem-caption {
+    margin-top: 15px
+    margin-bottom: 0;
+}
 .elem-filename {}
 
 div.elem-image {
@@ -82,11 +86,11 @@ div#boilerplate pre {
     <h1 class="sub-report-title">{{ sub_report.name }}</h1>
     {% for run_report in sub_report.reportlets %}
         <div id="{{run_report.name}}">
-            {% if run_report.title %}<h2 class="run-title">Reports for {{ run_report.title }}</h2>{% endif %}
+            {% if run_report.title %}<h2 class="run-title">{{ run_report.title }}</h2>{% endif %}
             {% if run_report.description %}<p class="elem-desc">{{ run_report.description }}</p>{% endif %}
             {% for elem in run_report.components %}
                 {% if elem[0] %}
-                    {% if elem[1] %}<p class="elem-desc">{{ elem[1] }}</p>{% endif %}
+                    {% if elem[1] %}<p class="elem-caption">{{ elem[1] }}</p>{% endif %}
                     {{ elem[0] }}
                 {% endif %}
             {% endfor %}
@@ -99,8 +103,8 @@ div#boilerplate pre {
 <div id="boilerplate">
     <h1 class="sub-report-title">Methods</h1>
     {% if boilerplate %}
-    <p>We kindly ask to report results preprocessed with fMRIPrep using the following
-       boilerplate</p>
+    <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">
@@ -116,7 +120,6 @@ div#boilerplate pre {
     {% else %}
     <p class="text-danger">Failed to generate the boilerplate</p>
     {% endif %}
-    <p>Alternatively, an interactive <a href="http://fmriprep.readthedocs.io/en/latest/citing.html">boilerplate generator</a> is available in the <a href="https://fmriprep.org">documentation website</a>.</p>
 </div>
 
 <div id="errors">

niworkflows/viz/reports.py

@@ -19,6 +19,7 @@
 import jinja2
 from nipype.utils.filemanip import copyfile
 
+
 add_config_paths(figures=pkgrf('niworkflows', 'viz/figures.json'))
 LAYOUT_GET = defaultdict(str('s').format, [('echo', 'es')])
 SVG_SNIPPET = """\
@@ -190,8 +191,7 @@ class Report(object):
 
     .. doctest::
 
-    >>> robj = Report(testdir / 'work' / 'reportlets',
-    ...               'work/config.json', testdir / 'out',
+    >>> robj = Report(testdir / 'work' / 'reportlets', testdir / 'out',
     ...               'madeoutuuid', subject_id='01')
     >>> robj.layout.get(subject='01', desc='reconall')
     [<BIDSFile filename='fmriprep/sub-01/anat/sub-01_desc-reconall_T1w.svg'>]
@@ -203,7 +203,7 @@ class Report(object):
 
     """
 
-    def __init__(self, reportlets_dir, config, out_dir, run_uuid,
+    def __init__(self, reportlets_dir, out_dir, run_uuid, config=None,
                  subject_id=None, out_filename='report.html',
                  packagename=None):
         self.root = reportlets_dir
@@ -226,6 +226,8 @@ def __init__(self, reportlets_dir, config, out_dir, run_uuid,
         if self.subject_id is not None:
             self.out_filename = 'sub-{}.html'.format(self.subject_id)
 
+        if config is None:
+            config = pkgrf('niworkflows', 'viz/defaultconfig.json')
         self._load_config(Path(config))
 
     def _load_config(self, config):
@@ -328,7 +330,8 @@ def generate_report(self):
         return len(self.errors)
 
 
-def run_reports(reportlets_dir, out_dir, subject_label, run_uuid, config):
+def run_reports(reportlets_dir, out_dir, subject_label, run_uuid, config=None,
+                packagename=None):
     """
     Runs the reports
 
@@ -347,27 +350,28 @@ def run_reports(reportlets_dir, out_dir, subject_label, run_uuid, config):
     .. doctest::
 
     >>> run_reports(str(testdir / 'work' / 'reportlets'),
-    ...             str(testdir / 'out'), '01', 'madeoutuuid',
-    ...             'work/config.json')
+    ...             str(testdir / 'out'), '01', 'madeoutuuid')
     0
 
     .. testcleanup::
 
     >>> tmpdir.cleanup()
 
     """
-    report = Report(Path(reportlets_dir), config, out_dir, run_uuid,
-                    subject_id=subject_label)
+    report = Report(Path(reportlets_dir), out_dir, run_uuid, config=config,
+                    subject_id=subject_label, packagename=packagename)
     return report.generate_report()
 
 
-def generate_reports(subject_list, output_dir, work_dir, run_uuid, config):
+def generate_reports(subject_list, output_dir, work_dir, run_uuid, config=None,
+                     packagename=None):
     """
     A wrapper to run_reports on a given ``subject_list``
     """
     reports_dir = str(Path(work_dir) / 'reportlets')
     report_errors = [
-        run_reports(reports_dir, output_dir, subject_label, run_uuid, config)
+        run_reports(reports_dir, output_dir, subject_label, run_uuid,
+                    config, packagename=packagename)
         for subject_label in subject_list
     ]
 

setup.py

@@ -33,6 +33,8 @@ def main():
         'niworkflows': [
             'data/t1-mni_registration*.json',
             'data/bold-mni_registration*.json',
+            'viz/*.json',
+            'viz/report.tpl',
         ]}
 
     root_dir = op.dirname(op.abspath(getfile(currentframe())))