From 85d63898226c93e3e7eed2bbe63c6827f44ff742 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Aug 2018 09:05:05 -0700
Subject: [PATCH 1/5] basis

---
 mriqc/data/reports/individual.html | 160 ++++++++++-------------------
 1 file changed, 52 insertions(+), 108 deletions(-)

diff --git a/mriqc/data/reports/individual.html b/mriqc/data/reports/individual.html
index 884fcce29..90910f081 100644
--- a/mriqc/data/reports/individual.html
+++ b/mriqc/data/reports/individual.html
@@ -9,6 +9,35 @@
 <script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
 <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/js/bootstrap.min.js" integrity="sha384-ChfqqxuZUCnJSK3+MXmPNIyE6ZbWh2IMqE241rYiqJxyMiZ6OW/JmZQ5stwEULTy" crossorigin="anonymous"></script>
 <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
+<script>
+function download() {
+    var ds = "{{ dataset }}"
+    var sub = "{{ bids_name }}"
+    var reportlets = []
+
+    var els = document.getElementsByClassName("rating-form")
+    for (var elid = 0; elid < els.length; elid++) {
+        // Do stuff here
+        var thisrep = {}
+        for (var i = 0; i < els[elid].children.length; i++) {
+            thisrep[els[elid].children[i].name] = els[elid].children[i].value
+        }
+
+        reportlets.push(thisrep)
+    };
+
+    var file = new Blob([JSON.stringify({
+        'dataset': ds,
+        'subject': sub,
+        'reports': reportlets}
+    )], {type: 'text/json'});
+
+    var a = document.getElementById("a");
+    a.href = URL.createObjectURL(file);
+    a.download = ds + "_" + sub + ".json";
+    a.style.visibility = "visible"
+}
+</script>
 <style type="text/css">
 body {
   font-family: helvetica;
@@ -166,119 +195,34 @@ <h5 class="mb-0">
 
 {% if provenance %}
 <h2 id="feedback">Rate Image</h2>
-<div class="container">
-<form action="javascript:sendRating()">
-    <div class="form-group">
-        <input id="ratingField" type="hidden" required>
-        <div class="radio"><label><input type="radio" name="inlineRadio" id="inlineRating0" value="0" required> Invalid</label></div>
-        <div class="radio"><label><input type="radio" name="inlineRadio" id="inlineRating1" value="1"> Exclude</label></div>
-        <div class="radio"><label><input type="radio" name="inlineRadio" id="inlineRating2" value="2"> Usable</label></div>
-        <div class="radio"><label><input type="radio" name="inlineRadio" id="inlineRating3" value="3"> Good</label></div>
-        Name: <br><input id="ratingName" type="text" class="form-control"><br>
-        Comments: <br><textarea rows="4" id="ratingComment" type="text" class="form-control"></textarea><br>
-        <input type="submit" value="Submit">
-    </div>
-</form>
-<div id="submitResAlert" role="alert" class="d-none alert alert-success">Submitted</div>
-<div class="d-none" id="allRatingsDiv">
-<table class="table table-striped">
-<thead>
-    <tr>
-        <td>Rating</td>
-        <td>Count</td>
-    </tr>
-<tbody>
-    <tr>
-        <td>Invalid</td>
-        <td id="allRatings0"></td>
-    </tr>
-    <tr>
-        <td>Exclude</td>
-        <td id="allRatings1"></td>
-    </tr>
-    <tr>
-        <td>Usable</td>
-        <td id="allRatings2"></td>
-    </tr>
-    <tr>
-        <td>Good</td>
-        <td id="allRatings3"></td>
-    </tr>
-</tbody>
-</thead>
-</table>
-
-{% endif %}
 
-<p>For details on the IQMs (image quality metrics) and further information on
-the enclosed plots, please read the
-<a class="reference external" href="http://mriqc.readthedocs.io/en/stable/measures.html">documentation</a>.</p>
+<div class="rating-form">
+<input type="hidden" value="overall" name="name" />
+<select name="rating">
+  <option value="-1">(unrated)</option>
+  <option value="0">Useless</option>
+  <option value="1">Poor result</option>
+  <option value="2">Acceptable</option>
+  <option value="3">Exceptional</option>
+</select>
+<textarea rows="2" cols="100" name="comment">
+</textarea>
 </div>
-{% if provenance %}
-<script type="text/javascript">
-var sentOnce = false;
 
-function setAllRatings(allRatings) {
-    allRatings['_items'].sort(function(a, b) {
-        if(a['_id'] < b['_id']) return -1;
-        if(a['_id'] > b['_id']) return 1;
-        return 0;
-    });
-    console.log(allRatings);
-    document.getElementById("allRatings0").textContent = allRatings['_items'][0]['count'];
-    document.getElementById("allRatings1").textContent = allRatings['_items'][1]['count'];
-    document.getElementById("allRatings2").textContent = allRatings['_items'][2]['count'];
-    document.getElementById("allRatings3").textContent = allRatings['_items'][3]['count'];
-    document.getElementById("allRatingsDiv").classList.remove("d-none");
-};
+<button onclick="download()">Create file</button>
+<a href="" id="a" style="visibility:hidden">Save your ratings</a>
+<br />
+<br />
 
-function sendRating() {
-    var allRatings;
-    var rating;
-    var radios = document.getElementsByName("inlineRadio");
-    for (var i = 0; i < radios.length; i++) {
-        if (radios[i].checked) {
-            rating = radios[i].value;
-            break;
-        }
-    }
-    var md5sum = "{{ md5sum }}";
-    var name = document.getElementById("ratingName").value;
-    var comment = document.getElementById("ratingComment").value;
-    var params = {'rating': rating, 'md5sum': md5sum, 'name': name, 'comment': comment};
-
-    var ratingReq = new XMLHttpRequest();
-    var allRatingsReq = new XMLHttpRequest();
-    var aggParam = '{\"$value\":\"' + md5sum + '\"}';
-    allRatingsReq.open("GET", "{{ webapi_url }}/rating_counts?aggregate=" + aggParam);
-    allRatingsReq.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
-    allRatingsReq.setRequestHeader("Authorization", "<secret_token>");
-    ratingReq.open("POST", "{{ webapi_url }}/rating");
-    ratingReq.setRequestHeader("Content-Type", "application/json;charset=UTF-8");
-    ratingReq.setRequestHeader("Authorization", "<secret_token>");
-    ratingReq.onload = function () {
-        status = ratingReq.status;
-        if (status === "201") {
-            sentOnce = true;
-            allRatingsReq.send();
-            setAlert();
-        }
-    };
-    allRatingsReq.onload = function () {
-        console.log(allRatingsReq.response);
-        allRatings = JSON.parse(allRatingsReq.response);
-        setAllRatings(allRatings);
-    };
-    ratingReq.send(JSON.stringify(params));
-};
-
-function setAlert() {
-    alertElem = document.getElementById("submitResAlert");
-    alertElem.className.classList.remove("d-none");
-
-};
 
+<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';
+    }
 </script>
-{% endif %}
 </body>
 </html>

From a4a9c5665eadc934a1738f6e0dd732062c61e0a5 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Aug 2018 18:07:49 -0700
Subject: [PATCH 2/5] stringfy comment

this new feature relates to #719, as it enables the rating to be
downloaded locally.
---
 mriqc/data/reports/individual.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/mriqc/data/reports/individual.html b/mriqc/data/reports/individual.html
index 9c17ba4be..5e0a88145 100644
--- a/mriqc/data/reports/individual.html
+++ b/mriqc/data/reports/individual.html
@@ -37,7 +37,7 @@
         'rating': payload['rating'],
         'md5sum': md5sum,
         'name': "",
-        'comment': payload['artifacts']
+        'comment': JSON.stringify(payload['artifacts'])
     };
 
     // disable developement releases

From 36daaf6d53be008c35a90b36736543524b7303fd Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Aug 2018 19:32:25 -0700
Subject: [PATCH 3/5] add ``--dsname`` argument

---
 .circleci/config.yml          | 4 ++--
 mriqc/bin/mriqc_run.py        | 7 +++++--
 mriqc/interfaces/bids.py      | 4 ++++
 mriqc/workflows/anatomical.py | 3 ++-
 mriqc/workflows/functional.py | 3 ++-
 5 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 98a380ab9..c3e9c3c38 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -275,7 +275,7 @@ jobs:
                        -v $PWD:/scratch -w /scratch \
                        poldracklab/mriqc:latest \
                        /data derivatives/ participant \
-                       -vv --verbose-reports --profile -m T1w \
+                       -vv --verbose-reports --profile -m T1w --dsname circletests \
                        --n_procs 2 --ants-nthreads 1 --ants-float \
                        --webapi-url http://$( hostname -I | awk '{print $1}' )/api/v1 --upload-strict
       - run:
@@ -385,7 +385,7 @@ jobs:
                        -v $PWD:/scratch -w /scratch \
                        poldracklab/mriqc:latest \
                        /data derivatives/ participant \
-                       -vv --verbose-reports --profile -m bold \
+                       -vv --verbose-reports --profile -m bold --dsname circletests \
                        --n_procs 2 --ants-nthreads 1 --ants-float \
                        --testing --ica \
                        --webapi-url http://$( hostname -I | awk '{print $1}' )/api/v1 --upload-strict
diff --git a/mriqc/bin/mriqc_run.py b/mriqc/bin/mriqc_run.py
index aac616e55..d0256acf7 100644
--- a/mriqc/bin/mriqc_run.py
+++ b/mriqc/bin/mriqc_run.py
@@ -67,6 +67,7 @@ def get_parser():
     g_bids.add_argument('-m', '--modalities', action='store', nargs='*',
                         choices=['T1w', 'bold', 'T2w'], default=['T1w', 'bold', 'T2w'],
                         help='filter input dataset by MRI type ("T1w", "T2w", or "bold")')
+    g_bids.add_argument('--dsname', type=str, help='a dataset name')
 
     # Control instruments
     g_outputs = parser.add_argument_group('Instrumental options')
@@ -86,8 +87,7 @@ def get_parser():
                                 'to MRIQC\'s metrics repository.')
     g_outputs.add_argument('--email', action='store', default='', type=str,
                            help='Email address to include with quality metric submission.')
-    g_outputs.add_argument("-v", "--verbose", dest="verbose_count",
-                           action="count", default=0,
+    g_outputs.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
                            help="increases log verbosity for each occurence, debug level is -vvv")
 
     g_outputs.add_argument(
@@ -348,6 +348,9 @@ def init_mriqc(opts, retval):
     if opts.ants_settings:
         settings['ants_settings'] = opts.ants_settings
 
+    if opts.dsname:
+        settings['dataset_name'] = opts.dsname
+
     log_dir = settings['output_dir'] / 'logs'
 
     # Create directories
diff --git a/mriqc/interfaces/bids.py b/mriqc/interfaces/bids.py
index 370eaf027..e8e54cb9b 100644
--- a/mriqc/interfaces/bids.py
+++ b/mriqc/interfaces/bids.py
@@ -75,6 +75,7 @@ class IQMFileSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
     acq_id = traits.Either(None, Str, usedefault=True)
     rec_id = traits.Either(None, Str, usedefault=True)
     run_id = traits.Either(None, Str, usedefault=True)
+    dataset = Str(desc='dataset identifier')
     metadata = traits.Dict()
     provenance = traits.Dict()
 
@@ -179,6 +180,9 @@ def _run_interface(self, runtime):
             self._out_dict['bids_meta'] = {}
         self._out_dict['bids_meta'].update(id_dict)
 
+        if isdefined(self.inputs.dataset):
+            self._out_dict['bids_meta']['dataset'] = self.inputs.dataset
+
         # Fill in the "provenance" key
         # Predict QA from IQMs and add to metadata
         prov_dict = {}
diff --git a/mriqc/workflows/anatomical.py b/mriqc/workflows/anatomical.py
index f15599d66..69f5787d8 100644
--- a/mriqc/workflows/anatomical.py
+++ b/mriqc/workflows/anatomical.py
@@ -259,7 +259,8 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
                                for fname in ['1mm_tpm_csf', '1mm_tpm_gm', '1mm_tpm_wm']]
 
     datasink = pe.Node(IQMFileSink(
-        modality=modality, out_dir=str(settings['output_dir'])),
+        modality=modality, out_dir=str(settings['output_dir']),
+        dataset=settings['dataset_name']),
         name='datasink', run_without_submitting=True)
     datasink.inputs.modality = modality
 
diff --git a/mriqc/workflows/functional.py b/mriqc/workflows/functional.py
index 9c1cd6dc4..4028b57b2 100644
--- a/mriqc/workflows/functional.py
+++ b/mriqc/workflows/functional.py
@@ -264,7 +264,8 @@ def compute_iqms(settings, name='ComputeIQMs'):
 
     # Save to JSON file
     datasink = pe.Node(IQMFileSink(
-        modality='bold', out_dir=str(settings['output_dir'])),
+        modality='bold', out_dir=str(settings['output_dir']),
+        dataset=settings['dataset_name']),
         name='datasink', run_without_submitting=True)
 
     workflow.connect([

From f037d87cd65c6d3c14b103ddb40750f924d8abc9 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Aug 2018 21:55:18 -0700
Subject: [PATCH 4/5] fix error of dataset name

---
 mriqc/workflows/anatomical.py | 2 +-
 mriqc/workflows/functional.py | 8 +++++---
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/mriqc/workflows/anatomical.py b/mriqc/workflows/anatomical.py
index 69f5787d8..d90cb26e7 100644
--- a/mriqc/workflows/anatomical.py
+++ b/mriqc/workflows/anatomical.py
@@ -260,7 +260,7 @@ def compute_iqms(settings, modality='T1w', name='ComputeIQMs'):
 
     datasink = pe.Node(IQMFileSink(
         modality=modality, out_dir=str(settings['output_dir']),
-        dataset=settings['dataset_name']),
+        dataset=settings.get('dataset_name', 'unknown')),
         name='datasink', run_without_submitting=True)
     datasink.inputs.modality = modality
 
diff --git a/mriqc/workflows/functional.py b/mriqc/workflows/functional.py
index 4028b57b2..a9336d662 100644
--- a/mriqc/workflows/functional.py
+++ b/mriqc/workflows/functional.py
@@ -255,8 +255,10 @@ def compute_iqms(settings, name='ComputeIQMs'):
     ])
 
     # Add metadata
-    meta = pe.Node(ReadSidecarJSON(), name='metadata')
-    addprov = pe.Node(niu.Function(function=_add_provenance), name='provenance')
+    meta = pe.Node(ReadSidecarJSON(), name='metadata',
+                   run_without_submitting=True)
+    addprov = pe.Node(niu.Function(function=_add_provenance), name='provenance',
+                      run_without_submitting=True)
     addprov.inputs.settings = {
         'fd_thres': settings.get('fd_thres', 0.2),
         'hmc_fsl': settings.get('hmc_fsl', True),
@@ -265,7 +267,7 @@ def compute_iqms(settings, name='ComputeIQMs'):
     # Save to JSON file
     datasink = pe.Node(IQMFileSink(
         modality='bold', out_dir=str(settings['output_dir']),
-        dataset=settings['dataset_name']),
+        dataset=settings.get('dataset_name', 'unknown')),
         name='datasink', run_without_submitting=True)
 
     workflow.connect([

From 8907acb7b4e34d91ef32a37dfa4beb687f094542 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 16 Aug 2018 21:59:29 -0700
Subject: [PATCH 5/5] add new artifacts

---
 mriqc/data/reports/individual.html | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/mriqc/data/reports/individual.html b/mriqc/data/reports/individual.html
index 5e0a88145..11e2f73f2 100644
--- a/mriqc/data/reports/individual.html
+++ b/mriqc/data/reports/individual.html
@@ -277,7 +277,7 @@ <h2 id="other" class="mt-5 mb-2">Other</h2>
     </div>
     <div class="form-check">
         <input class="form-check-input" type="checkbox" name="wrap-around" id="art8">
-        <label class="form-check-label" for="art8">Wrap-around</label>
+        <label class="form-check-label" for="art8">Problematic FoV prescription / Wrap-around</label>
     </div>
     <div class="form-check">
         <input class="form-check-input" type="checkbox" name="ghost-aliasing" id="art9">
@@ -296,8 +296,12 @@ <h2 id="other" class="mt-5 mb-2">Other</h2>
         <label class="form-check-label" for="art12">Temporal field variation</label>
     </div>
     <div class="form-check">
-        <input class="form-check-input" type="checkbox" name="uncategorized" id="art13">
-        <label class="form-check-label" for="art13">Uncategorized artifact</label>
+        <input class="form-check-input" type="checkbox" name="postprocessing" id="art13">
+        <label class="form-check-label" for="art13">Reconstruction and postprocessing (e.g. denoising, defacing, resamplings)</label>
+    </div>
+    <div class="form-check">
+        <input class="form-check-input" type="checkbox" name="uncategorized" id="art0">
+        <label class="form-check-label" for="art0">Uncategorized artifact</label>
     </div>
 </fieldset>
 <a class="btn btn-primary disabled" id="btn-download" href="">Download</a>