Merge pull request #79 from wasade/per-sample-summary

Per sample summary

microsetta_admin/server.py

@@ -326,6 +326,52 @@ def urlify_account_id(id_):
                            projects=projects)
 
 
+@app.route('/per_sample_summary', methods=['GET', 'POST'])
+def per_sample_summary():
+    strip_sampleid = request.form.get('strip_sampleid', 'off')
+    strip_sampleid = strip_sampleid.lower() == 'on'
+
+    if request.method == 'GET':
+        sample_barcode = request.args.get('sample_barcode')
+        if sample_barcode is None:
+            return render_template('per_sample_summary.html',
+                                   resource=None,
+                                   **build_login_variables())
+        sample_barcodes = [sample_barcode, ]
+    elif request.method == 'POST':
+        sample_barcodes, upload_err = upload_util.parse_request_csv_col(
+                                                            request,
+                                                            'file',
+                                                            'sample_name'
+        )
+        if upload_err is not None:
+            return render_template('per_sample_summary.html',
+                                   resource=None,
+                                   **build_login_variables(),
+                                   search_error=[{'error': upload_err}])
+
+    payload = {'sample_barcodes': sample_barcodes}
+    status, result = APIRequest.post('/api/admin/account_barcode_summary?'
+                                     'strip_sampleid=%s' % str(strip_sampleid),
+                                     json=payload)
+    if status != 200:
+        return render_template('per_sample_summary.html',
+                               resource=None,
+                               error_message=result,
+                               **build_login_variables())
+    else:
+        resource = pd.DataFrame(result)
+        order = ['sampleid', 'project', 'account-email', 'source-email',
+                 'source-type', 'site-sampled', 'sample-status',
+                 'sample-received', 'ffq-taken', 'ffq-complete',
+                 'vioscreen_username']
+        order.extend(sorted(set(resource.columns) - set(order)))
+        resource = resource[order]
+        return render_template('per_sample_summary.html',
+                               resource=resource,
+                               **build_login_variables())
+
+
 @app.route('/create_kits', methods=['GET', 'POST'])
 def new_kits():
     _, result = _get_projects(include_stats=False, is_active=True)

microsetta_admin/templates/per_sample_summary.html

@@ -0,0 +1,64 @@
+{% extends "sitebase.html" %}
+{% block head %}
+<link rel="stylesheet" type="text/css" href="/static/vendor/DataTables/DataTables-1.10.21/css/jquery.dataTables.css">
+<script src="/static/vendor/DataTables/DataTables-1.10.21/js/jquery.dataTables.js"></script>
+<script src="/static/vendor/DataTables/Buttons-1.6.2/js/dataTables.buttons.min.js"></script>
+<script src="/static/vendor/DataTables/Buttons-1.6.2/js/buttons.html5.min.js"></script>
+<script>
+    function remove_error_messages () {
+        block = document.getElementById("search_errors");
+        if (block !== null) {
+            block.innerHTML = "";
+        }
+    };
+    $(document).ready(function() {
+        {% if resource is not none %}
+            $('#search_results').DataTable({
+                // more information on "dom" can be found here:
+                // https://datatables.net/reference/option/dom
+                dom: 'Bfrtip',
+                buttons: ['csv']
+                }
+            );
+        {% endif %}
+    } );
+</script>
+{% endblock %}
+{% block content %}
+<h3>Microsetta Per Sample Summary</h3>
+<div style="height: 400px;">
+    {% if error_message %}
+        <p style="color:red">
+            {{ error_message |e }}
+        </p>
+    {% endif %}
+    <form name="search_form" id="search_form" method="GET">
+        <table>
+            <tr>
+                <td><label for="sample_barcode">Barcode: </label></td>
+                <td><input type="text" name="sample_barcode" id="sample_barcode" {% if info %} value="{{info.barcode}}"{% endif %}></td>
+                <td></td>
+                <td><input type="submit" value="Retrieve Summary"></td>
+            </tr>
+        </table>
+        <script>
+           document.search_form.sample_barcode.focus()
+        </script>
+    </form>
+    <br/>
+    Or upload a file of barcodes listed in the column "sample_name" (max: 1000)
+    <br/>
+    <form name="upload_csv" id="search_csv" method="POST" enctype="multipart/form-data" onsubmit="return remove_error_messages()">
+      <input type="checkbox" id="strip_sampleid" name="strip_sampleid">
+      <label for="strip_sampleid"> Check to remove sample IDs from summary</label><br/>
+      <input type=file name=file><br/>
+      <input type=submit value=Upload>
+    </form>
+    {% if resource is not none %}
+    <div class="result_container">
+    {{resource.to_html(table_id="search_results", classes=["display"], render_links=True, escape=False) |safe}}
+    </div>
+</div>
+{% endif %}
+{{blob}}
+{% endblock %}

microsetta_admin/templates/sitebase.html

@@ -49,6 +49,7 @@ <h3>Microsetta Utilities</h3>
             <li><a href="/create_kits">Create Kit</a></li>
             <li><a href="/scan">Scan Barcode</a></li>
             <li><a href="/metadata_pulldown">Retrieve Metadata</a></li>
+            <li><a href="/per_sample_summary">Per sample summary</a></li>
             <li><a href="/submit_daklapack_order">Submit Daklapack Order</a></li>
             <li><a href="{{authrocket_url}}/logout?redirect_uri={{endpoint}}/logout">Log Out <br> ({{email |e}})</a></li>
             {% else %}