Merge pull request #464 from ImagingDataCommons/sprint-15-sp

Sprint 15

Author: s-paquette

idc/settings.py

@@ -80,6 +80,8 @@
 GCLOUD_PROJECT_NUMBER          = os.environ.get('GCLOUD_PROJECT_NUMBER', '')
 BIGQUERY_PROJECT_ID            = os.environ.get('BIGQUERY_PROJECT_ID', GCLOUD_PROJECT_ID)
 BIGQUERY_DATA_PROJECT_ID       = os.environ.get('BIGQUERY_DATA_PROJECT_ID', GCLOUD_PROJECT_ID)
+BIGQUERY_USER_MANIFEST_DATASET = os.environ.get('BIGQUERY_USER_MANIFEST_DATASET', 'dev_user_dataset')
+BIGQUERY_PIVOT_TABLE           = os.environ.get('BIGQUERY_PIVOT_TABLE', 'idc-dev.metadata.dicom_pivot_wave1')
 
 # Deployment module
 CRON_MODULE             = os.environ.get('CRON_MODULE')

static/js/cohorts/cohort-details.js

@@ -58,7 +58,7 @@ require([
     tippy('.manifest-size-warning',{
         content: 'Your cohort is too large to be downloaded in its entirety, and will be truncated at 65,000 records ' +
         'ordered by PatientID, CollectionID, StudyInstanceUID, SeriesInstanceUID, SOPInstanceUID, SourceDOI, ' +
-            'CRDCInstanceUUID, and GCSPath.',
+            'CRDCInstanceUUID, and GCS_URL.',
         theme: 'light',
         placement: 'left',
         arrow: false,
@@ -92,14 +92,16 @@ require([
     update_export_option("file-manifest");
 
     var download_manifest = function(file_type, clicked_button, e) {
+        let manifest_type = $('input[name="manifest-type"]:checked').val();
+
         $('#unallowed-chars-alert').hide();
         $('#name-too-long-alert-modal').hide();
 
         var name = $('#export-manifest-name').val();
         var unallowed = (name.match(base.blacklist) || []);
 
         if (name.length == 0) {
-            $('#download-csv').prop('title','Please input the name.');
+            $('#download-csv').prop('title','Please provide a file name.');
             $('#export-manifest-name')[0].focus();
             e.preventDefault();
             return false;
@@ -123,20 +125,22 @@ require([
             return false;
         }
 
-        $('#export-manifest-form').submit();
-
         $('#download-csv').attr('disabled','disabled');
         $('#download-tsv').attr('disabled','disabled');
         $('#download-json').attr('disabled','disabled');
-
-        $('#download-in-progress').modal('show');
-
-        base.blockResubmit(function() {
-            $('#download-csv').removeAttr('disabled');
-            $('#download-tsv').removeAttr('disabled');
-            $('#download-json').removeAttr('disabled');
-            $('#download-in-progress').modal('hide');
-        },downloadToken, 'downloadToken');
+        $('#get-bq-table').attr('disabled','disabled');
+
+        $('#manifest-in-progress').modal('show');
+
+        if(manifest_type == 'file-manifest') {
+            base.blockResubmit(function () {
+                $('#download-csv').removeAttr('disabled');
+                $('#download-tsv').removeAttr('disabled');
+                $('#download-json').removeAttr('disabled');
+                $('#get-bq-table').removeAttr('disabled');
+                $('#manifest-in-progress').modal('hide');
+            }, downloadToken, 'downloadToken');
+        }
 
         var checked_fields = [];
         $('.field-checkbox').each(function()
@@ -158,25 +162,52 @@ require([
            }
         });
 
-        var include_header = $('#include-header-checkbox')[0].checked;
-
-        var url = BASE_URL + '/cohorts/download_manifest/' + cohort_id + '/';
-        url += ("?file_type=" + file_type);
-        url += ("&include_header=" + include_header);
-        url += ("&file_name=" + name);
-        url += ("&header_fields=" + JSON.stringify(checked_fields));
-        url += ("&columns=" + JSON.stringify(checked_columns));
-        url += ("&downloadToken=" + downloadToken);
+        $('input[name="file_type"]').val(file_type);
+        $('input[name="header_fields"]').val(JSON.stringify(checked_fields));
+        $('input[name="columns"]').val(JSON.stringify(checked_columns));
+        $('input[name="downloadToken"]').val(downloadToken);
+        $('input[name="include_header"]').val($('#include-header-checkbox').is(':checked') ? 'true': 'false');
 
         var select_box_div = $('#file-part-select-box');
         var select_box = select_box_div.find('select');
-        if (select_box_div.is(":visible"))
-        {
+        if (select_box_div.is(":visible")) {
             var selected_file_part = select_box.children("option:selected").val();
-            url += ("&file_part=" + selected_file_part);
+            $('input[name="file_part"]').val(selected_file_part);
+        } else {
+            $('input[name="file_part"]').val("");
         }
 
-        location.href = url;
+        if(manifest_type == 'file-manifest') {
+            $('#export-manifest-form').submit();
+        } else {
+            $.ajax({
+                url: $('#export-manifest-form').attr('action'),
+                data: $('#export-manifest-form').serialize(),
+                method: 'GET',
+                success: function (data) {
+                    if(data.message) {
+                        base.showJsMessage("info",data.message,true);
+                    }
+                },
+                error: function (xhr) {
+                    console.log(xhr);
+                    var responseJSON = $.parseJSON(xhr.responseText);
+                    // If we received a redirect, honor that
+                    if(responseJSON.redirect) {
+                        base.setReloadMsg(responseJSON.level || "error",responseJSON.message);
+                        window.location = responseJSON.redirect;
+                    } else {
+                        base.showJsMessage(responseJSON.level || "error",responseJSON.message,true);
+                    }
+                },
+                complete: function(xhr, status) {
+                    $('#manifest-in-progress').modal('hide');
+                    $('#get-bq-table').removeAttr('disabled');
+                    $('#export-manifest-modal').modal('hide');
+                    $('#export-manifest-form')[0].reset();
+                }
+            });
+        }
     };
 
     $('.column-checkbox').change(function() {
@@ -213,4 +244,9 @@ require([
     };
 
     update_download_manifest_buttons();
+
+    $('#get-bq-table').on('click',function(){
+        download_manifest('',$(this));
+    });
+
 });

templates/cohorts/cohort_details.html

@@ -68,12 +68,12 @@ <h3 class="pull-left" role="heading" aria-level="1">Cohort Name: {{ cohort.name
 {% endwith %}
 
     <!-- Download In Progress Modal -->
-<div class="modal fade" id="download-in-progress" tabindex="-1" role="dialog" data-backdrop="static" aria-hidden="true">
+<div class="modal fade" id="manifest-in-progress" tabindex="-1" role="dialog" data-backdrop="static" aria-hidden="true">
     <div class="modal-dialog">
         <div class="modal-content">
             <div class="modal-header"></div>
             <div class="modal-body">
-                <p><i class="fa fa-cog fa-spin"></i> Preparing manifest for download...</p>
+                <p><i class="fa fa-cog fa-spin"></i> Preparing cohort manifest...</p>
             </div>
             <div class="modal-footer"></div>
         </div>

templates/cohorts/export-manifest-modal.html

@@ -21,13 +21,13 @@ <h4 class="modal-title" id="exportManifestModal">Export Cohort Manifest</h4>
                 </div>
             </div>
 
-            <form id="export-manifest-form">
+            <form id="export-manifest-form" method="get" action="{% url 'cohort_manifest' cohort_id %}">
                 <div class="modal-body">
                     <div class="form-group">
                         <!-- Name -->
                         <div>
                             <label for="export-manifest-name">Name</label>
-                            <input class="form-control" type="text" id="export-manifest-name" name="name" value="{{ cohort.name }}_{{ cohort.id }}_{% now "Ymd_Gis" %}" required />
+                            <input class="form-control" type="text" id="export-manifest-name" name="file_name" value="{{ cohort.name }}_{{ cohort.id }}_{% now "Ymd_Gis" %}" required />
                         </div>
                         <br>
 
@@ -61,7 +61,7 @@ <h4 class="modal-title" id="exportManifestModal">Export Cohort Manifest</h4>
                             <li class="checkbox"><label>
                                 <input class="field-checkbox" type="checkbox" value="total_records" checked>
                                 <span class="value">Total Records</span>
-                            </label></li>
+                            </label></li>0
                         </div>
                         <br>
 
@@ -108,24 +108,26 @@ <h4 class="modal-title" id="exportManifestModal">Export Cohort Manifest</h4>
                             </label></li>
 
                             <li class="checkbox"><label>
-                                <input class="column-checkbox" type="checkbox" value="gcs_path" checked>
+                                <input class="column-checkbox" type="checkbox" value="gcs_url" checked>
                                 <span class="value">GCS URL </span>
                             </label></li>
                         </div>
                         <br>
 
                         <!-- Export Option -->
                         <div class="export-option">
-                            <span class="value"><input type="radio" name="colorRadio" value="file-manifest" checked> Files</span>
-                            <span style="margin-left:10px" class="value"><input type="radio" name="colorRadio" value="bq-manifest"> BigQuery</span>
+                            <span class="value"><input type="radio" name="manifest-type" value="file-manifest" checked> Files</span>
+                            <span style="margin-left:10px" class="value" {% if not is_social %}title="Export to BigQuery is only available with a Google Account."{% endif %}>
+                                <input type="radio" name="manifest-type" value="bq-manifest" {% if not is_social %}disabled{% endif %}> BigQuery</span>
                         </div>
                         <br>
-
+                        {% if is_social %}
                         <div id="bq-manifest">
                             <a id="get-bq-table" class="btn btn-primary" title="Get BQ Table of this manifest.">
                                Get BQ Table
                             </a>
                         </div>
+                        {% endif %}
                         <div id="file-manifest">
                             <div id="file-part-select-box">
                                 <select class="form-control">
@@ -150,6 +152,12 @@ <h4 class="modal-title" id="exportManifestModal">Export Cohort Manifest</h4>
                         </div>
                     </div>
                 </div>
+                <input type="hidden" name="downloadToken">
+                <input type="hidden" name="file_type">
+                <input type="hidden" name="file_part">
+                <input type="hidden" name="columns">
+                <input type="hidden" name="header_fields">
+                <input type="hidden" name="include_header">
             </form>
         </div>
     </div>