✨ manually add scout to json and hint to use it

Also update Makeifle and add markdown to requirements.
Sequence description is now tracking the previously discarded rules sub key.

The hard coded scout entry illustrates where data is stored and pulled from.

entity_ux/Makefile

@@ -1,5 +1,9 @@
+bids-table_ver-1.10.0dev.json:  make_json.py requirements.txt
+	./make_json.py
+
+serve:
+	python3 -m http.server
+
 bids-specification/:
 	git clone https://github.com/bids-standard/bids-specification
 
-bids-table_ver-1.10.0dev.json:
-	./make_json.py

entity_ux/index.html

@@ -194,9 +194,18 @@
   </div>
   <div id="reproin">
     <h2>Create a <a href="https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html">ReproIn </a>spec conforming sequence name</h2>
-        Pick a DataType and Suffix label to dynamically generate a name within the cockpit image below (text is selectable and copyable). <br>See <a href="#suffix-options"> enumerated descriptions </a> below for more info. <br> <span style=font-size:smaller> Suffix and entities details are described in <a href="https://bids-specification.readthedocs.io/en/stable/glossary.html">BIDS glossary</a>. Entity requirements are also tabulated in adjacent <a href="https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html"> BIDS entity table</a> documentation.</span>
+        Pick a DataType and Suffix label to dynamically generate a name within the cockpit image below (text is selectable and copyable). <br>
+        See <a href="#suffix-options"> enumerated descriptions </a> below for more info. <br>
+        <!-- TODO: scout index hard coded at 37. will need to change  -->
+        <span style=font-size:smaller> Suffix and entities details are described in <a href="https://bids-specification.readthedocs.io/en/stable/glossary.html">BIDS glossary</a>.
+        Entity requirements are also tabulated in adjacent <a href="https://bids-specification.readthedocs.io/en/stable/appendices/entity-table.html"> BIDS entity table</a> documentation.
+
+       </span>
 <br>
-    <b style="font-size:smaller">Hint: hover your mouse over label options or entity text boxes to see the tooltip description</b></br>
+    <b style="font-size:smaller">Hints:<br>
+      hover your mouse over label options or entity text boxes to see the tooltip description<br>
+      Consider using <i>scout</i><a onclick="choose('anat', '37')" href="#">(choose)</a> to label the session (<a href="https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L629">ref source code</a>).
+</b></br>
     <div id="all-reproin-inputs">
       <div id=cont-datatype class=column>
         <label for=datatype> 1. Select DataType ("seqtype")</label></br>
@@ -220,7 +229,8 @@ <h2>Create a <a href="https://dbic-handbook.readthedocs.io/en/latest/mri/reproin
     <br>
 
     <h2>ReproIn specification</h2>
-    Defined on  <a href="https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html">dbic-handbook</a>. Parsed from DICOM to <a href="https://bids.neuroimaging.io/">BIDS</a> conforming nifti+json file hierarchy by <a href="https://heudiconv.readthedocs.io/en/latest/">heudiconv</a> in <a href="https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py">reproin.py</a> or via <a href="https://docs.flywheel.io/User_Guides/user_bids_study-design_spreadsheet/">Flywheel's</a> <a href="https://gitlab.com/flywheel-io/public/bids-client/-/blob/master/flywheel_bids/templates/reproin.json">curation template<a>, ready to be input for <a href="https://bids-apps.neuroimaging.io/apps/">BIDS Apps</a>.
+    Defined on  <a href="https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html">dbic-handbook</a>.
+    Parsed from DICOM to <a href="https://bids.neuroimaging.io/">BIDS</a> conforming nifti+json file hierarchy by <a href="https://heudiconv.readthedocs.io/en/latest/">heudiconv</a> in <a href="https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py">reproin.py</a> or via <a href="https://docs.flywheel.io/User_Guides/user_bids_study-design_spreadsheet/">Flywheel's</a> <a href="https://gitlab.com/flywheel-io/public/bids-client/-/blob/master/flywheel_bids/templates/reproin.json">curation template<a>, ready to be input for <a href="https://bids-apps.neuroimaging.io/apps/">BIDS Apps</a>.
     <pre><code>
       &lt;seqtype[-label]&gt;[_ses-&lt;SESID&gt;]
       [_task-&lt;TASKID&gt;][_acq-&lt;ACQLABEL&gt;][_run-&lt;RUNID&gt;][_dir-&lt;DIR&gt;][&lt;more BIDS&gt;]

entity_ux/make_json.py

@@ -34,20 +34,37 @@ def write_json(fname, data):
         bids_dict['objects'][obj][k]['description'] = markdown(bids_dict['objects'][obj][k]['description'])
 
 table = dict()
+# add reproin specific 'scout'
+bids_dict['objects']['suffixes']['scout'] = \
+    {"value": "scout",
+     "display_name": "Scout localizer",
+     "description": "ReproIn specific entity label for easily labeling a session. Using heudiconv, labeling this sequence session only is sufficent. You do not need to put <code>ses</code> on every sequence name! See <a href=https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L629>source reference</a>",
+     "unit": "arbitrary"}
+bids_dict['rules']['files']['raw']['anat']['scout'] = \
+     {"suffixes": ["scout"], "extensions": ['.dcm'],
+      "datatypes": ['anat'],
+      "entities": {"session": "optional", "acquisition": "optional"}}
+
 for keydesc, rules in bids_dict['rules']['files']['raw'].items():
-    for rule in rules.values():
+    # subkey is like nonparametric (anat), fmap (func)
+    # only used to add to description
+    for subkey, rule in rules.items():
 
         # only care about nifti files (MR data)
-        if '.nii' not in rule['extensions']:
+        if '.nii' not in rule.get('extensions') and subkey != 'scout':
             continue
 
         # get full entity information. repeats a lot of info but easy to query
         entities = {k: {**bids_dict['objects']['entities'][k], 'required': v}
                     for  k,v in rule['entities'].items()}
+
         # repeat entities and pull full object (desc, unit, display_name) for each suffix
         suffix_full = [{'entities': entities,
                         **bids_dict['objects']['suffixes'][i]} for i in rule['suffixes']]
 
+        for suffix in suffix_full:
+           suffix['description'] += f'\n<br><code>{subkey}</code>'
+
         # NB. currently all datatypes of interest are only in one datatype?
         # shouldn't epi be repeated for fmap and func? sbref for func and dwi?
         for datatype in rule['datatypes']:

entity_ux/requirements.txt

@@ -1,2 +1,2 @@
 bidsschematools >= 0.8.0
-
+markdown >= 3.6