Merge branch 'ui-v2' of https://github.com/IGS/gEAR into ui-v2

lib/gear/metadata.py

@@ -70,7 +70,6 @@ def __init__(self, metadata=None, file_path=None):
 
 
     def read_file(self, file_path=None):
-        print(f'DEBUG: Reading metadata file: {file_path}', file=sys.stderr)
         """
         Reads dataset_metadata.xlsx or dataset_metadata.json into a pandas dataframe
 
@@ -267,7 +266,7 @@ def get_field_value(self, field=None):
 
         return fv
 
-    def save_to_mysql(self, status=None):
+    def save_to_mysql(self, status=None, is_public=0):
         """
         Saves metadata to gEAR MySQL table 'dataset'. If present, also saves tags.
 
@@ -302,16 +301,6 @@ def save_to_mysql(self, status=None):
             organism_id = id
 
         geo_id = str( get_value_from_df(df, 'geo_accession') ).strip()
-
-        # Make all datasets private if not specified in the metadata
-        try:
-            is_public = get_value_from_df(df, 'is_public')
-
-            if is_public != 1:
-                is_public = 0
-        except:
-            is_public = 0
-
         ldesc = get_value_from_df(df, 'summary')
         dtype = get_value_from_df(df, 'dataset_type')
         schematic_image = get_value_from_df(df, 'schematic_image')

www/cgi/finalize_uploaded_expression_dataset.cgi

@@ -25,6 +25,7 @@ result = {
 import cgi
 import json
 import os, sys
+import shutil
 
 lib_path = os.path.abspath(os.path.join('..', '..', 'lib'))
 sys.path.append(lib_path)
@@ -50,6 +51,16 @@ def main():
     share_uid = form.getvalue('share_uid')
     session_id = form.getvalue('session_id')
     dataset_id = form.getvalue('dataset_uid')
+    dataset_visibility = form.getvalue('dataset_visibility')
+
+    if dataset_visibility == 'private':
+        is_public = 0
+    elif dataset_visibility == 'public':
+        is_public = 1
+    else:
+        result['message'] = 'Invalid dataset visibility.'
+        print(json.dumps(result))
+        sys.exit(0)
 
     user = geardb.get_user_from_session_id(session_id)
     if user is None:
@@ -78,7 +89,7 @@ def main():
     # Load the metadata into the database
     metadata = Metadata(file_path=metadata_file)
     try:
-        metadata.save_to_mysql(status='complete')
+        metadata.save_to_mysql(status='complete', is_public=is_public)
         result['metadata_loaded'] = 1
     except Exception as e:
         result['message'] = 'Error saving metadata to MySQL: {}'.format(str(e))
@@ -87,13 +98,12 @@ def main():
 
     # migrate the H5AD file
     h5ad_file = os.path.join(dataset_upload_dir, f'{share_uid}.h5ad')
+    h5ad_dest = os.path.join(dataset_final_dir, f'{dataset_id}.h5ad')
     if not os.path.exists(h5ad_file):
         result['message'] = 'H5AD file not found: {}'.format(h5ad_file)
         print(json.dumps(result))
         sys.exit(0)
 
-    h5ad_dest = os.path.join(dataset_final_dir, f'{dataset_id}.h5ad')
-
     try:
         os.rename(h5ad_file, h5ad_dest)
         result['h5ad_migrated'] = 1
@@ -102,16 +112,25 @@ def main():
         print(json.dumps(result))
         sys.exit(0)
 
+    # migrate the tarball
+    tarball_file = os.path.join(dataset_upload_dir, f'{share_uid}.tar.gz')
+    tarball_dest = os.path.join(dataset_final_dir, f'{dataset_id}.tar.gz')
+
+    try:
+        os.rename(tarball_file, tarball_dest)
+        result['tarball_migrated'] = 1
+    except Exception as e:
+        result['message'] = 'Error migrating tarball file: {}'.format(str(e))
+        print(json.dumps(result))
+        sys.exit(0)
 
     # if we made it this far, all is well, so return success
     result['success'] = 1
     result['message'] = 'All steps completed successfully.'
     print(json.dumps(result))
 
-
-
-
-
+    # now delete the entire upload directory
+    shutil.rmtree(dataset_upload_dir)
 
 if __name__ == '__main__':
     main()

www/include/primary_nav.html

@@ -128,7 +128,7 @@
                   </a>
                 </span>
               </li>
-              <!--
+
               <li>
                 <span class="icon-text is-align-items-center is-flex">
                   <a class="icon-link-part" tool="upload_dataset" href="./upload_dataset.html">
@@ -137,7 +137,7 @@
                   </a>
                 </span>
               </li>
-            -->
+
             </ul>
             <p class="menu-label mb-0 is-capitalized has-text-primary-light">
               <span class="menu-label-text">Support</span>

www/js/upload_dataset.js

@@ -67,6 +67,13 @@ window.onload=function() {
         stepTo('finalize-dataset');
     });
 
+    document.getElementById('dataset-curate-submit').addEventListener('click', (event) => {
+        event.preventDefault();
+
+        let url = `/dataset_curator.html?dataset_id=${dataset_uid}`;
+        window.location.href = url;
+    });
+
     document.getElementById('metadata-form-submit').addEventListener('click', (event) => {
         event.preventDefault();
         let errored_fields = validateMetadataForm();
@@ -195,6 +202,9 @@ const finalizeUpload = async () => {
     formData.append('session_id', CURRENT_USER.session_id);
     formData.append('dataset_uid', dataset_uid);
 
+    const dataset_visibility = document.querySelector('input[name=dataset-visibility]:checked').value;
+    formData.append('dataset_visibility', dataset_visibility);
+
     const data = await apiCallsMixin.finalizeExpressionUpload(formData);
 
     if (data['metadata_loaded']) {
@@ -214,8 +224,10 @@ const finalizeUpload = async () => {
     }
 
     if (data.success) {
-        console.log("SUCCESS");
-        console.log(data);
+        // Not actually doing anything further with access rights after the initial insert,
+        // so can set it as successful here
+        document.getElementById('finalize-setting-access').classList.remove('mdi-checkbox-blank-outline');
+        document.getElementById('finalize-setting-access').classList.add('mdi-checkbox-marked');
         document.getElementById('dataset-finalize-next-step').disabled = false;
     } else {
         console.log("ERROR");

www/upload_dataset.html

@@ -859,7 +859,7 @@ <h3>Steps being performed:</h3>
                           <li>
                             <span class="icon-text">
                               <span class="icon">
-                              <i class="mdi mdi-checkbox-blank-outline"></i>
+                                <i id="finalize-setting-access" class="mdi mdi-checkbox-blank-outline"></i>
                               </span>
                               <span>Setting access rights</span>
                             </span>
@@ -881,6 +881,30 @@ <h3>Steps being performed:</h3>
                   </div>
                 </div>
                 <div id="step-curate-dataset-c" class="step-c is-hidden">
+                  <h1>Step - Curate dataset</h1>
+                  <p>
+                    Your dataset has been submitted and is now available in the Dataset Explorer. 
+                  </p>
+                  <hr />
+                  <div class="columns">
+                    <div class="column">
+                      <h3>What is curation?</h3>
+                      <p>
+                        Right now your dataset is stored in the system but there 
+                        are no visualizations created so users can explore it. Curation is the process
+                        of creating these visualizations, which can include things like bar charts, UMAPs,
+                        heatmaps, etc.
+                      </p>
+                      <div class="field mt-6">
+                        <div class="control">
+                          <button class="button is-primary" id="dataset-curate-submit">Curate dataset</button>
+                        </div>
+                      </div>
+                    </div>
+                    <div class="column">
+                      <img class="img-fluid" src="/img/gear_plot_type_examples.png" alt="Dataset curation examples" />
+                    </div>
+                  </div>
                 </div>
               </div> 
             </div> <!-- end #logged-in-c -->