Merge branch 'development' into enhancement/announcements-reorder

src/modules/site-v2/base/views/tools/phenotype_database.py

@@ -12,7 +12,7 @@
 from extensions import cache, compress
 from sqlalchemy import or_, func
 
-from caendr.api.phenotype import query_phenotype_metadata, get_trait, filter_trait_query_by_text, filter_trait_query_by_tags
+from caendr.api.phenotype import query_phenotype_metadata, get_trait_categories
 from caendr.services.cloud.postgresql import rollback_on_error_handler
 
 from caendr.services.logger import logger
@@ -56,42 +56,11 @@ def phenotype_database():
     Phenotype Database table (non-bulk)
   """
   form = EmptyForm()
-  
-  # Get the list of traits for non-bulk files
+
+  # Get the list of unique tags
   try:
-    query = query_phenotype_metadata()
-
-    # Get the list of unique tags
-    tags = [ tr.tags.split(', ') for tr in query if tr.tags ]
-    tags_list = [tg for tr_tag in tags for tg in tr_tag]
-    unique_tags = list(set(tags_list))
-
-    if request.method == 'POST':
-      selected_tags = request.json.get('selected_tags', [])
-      search_val = request.json.get('search_val', '')
-      page = int(request.json.get('page', 1))
-      current_page = int(request.json.get('current_page', 1))
-      per_page = 10
-
-      # Filter by search value and tags, if provided
-      query = filter_trait_query_by_text(query, search_val)
-      query = filter_trait_query_by_tags(query, selected_tags)
-
-      # Paginate the query, rolling back on error
-      with rollback_on_error_handler():
-        pagination = query.paginate(page=page, per_page=per_page)
-
-      json_data = [ tr.to_json() for tr in pagination.items ]
-      pagination_data = {
-        'has_next':     pagination.has_next,
-        'has_prev':     pagination.has_prev,
-        'prev_num':     pagination.prev_num,
-        'next_num':     pagination.next_num,
-        'total_pages':  pagination.pages,
-        'current_page': current_page
-      }
-      return jsonify({'data': json_data, 'pagination': pagination_data })
-
+    categories = get_trait_categories()
+
   except Exception as ex:
     logger.error(f'Failed to retrieve the list of traits: {ex}')
     abort(500, description='Failed to retrieve the list of traits')
@@ -102,73 +71,11 @@ def phenotype_database():
     "tool_alt_parent_breadcrumb": { "title": "Tools", "url": url_for('tools.tools') },
 
     # Data
-    'categories': unique_tags,
+    'categories': categories,
     'form': form
   })
 
 
-@phenotype_database_bp.route('/traits-zhang')
-@cache.memoize(60*60)
-@compress.compressed()
-def get_zhang_traits_json():
-  """
-    Phenotype Database table (bulk)
-    Fetch table content by request for each page and render the data for Datatables()
-  """
-  try:
-    # get parameters for query
-    draw = request.args.get('draw', type=int)
-    start = request.args.get('start', type=int)
-    length = request.args.get('length', type=int)
-    search_value = bleach.clean(request.args.get('search[value]', '')).lower()
-
-    query = query_phenotype_metadata(is_bulk_file=True)
-    total_records = query.count()
-
-    # Filter by search value, if provided
-    query = filter_trait_query_by_text(query, search_value)
-
-    # Query PhenotypeMetadata (include phenotype values for each trait)
-    with rollback_on_error_handler():
-      data = query.offset(start).limit(length).from_self().\
-        join(PhenotypeMetadata.phenotype_values).all()
-
-    json_data = [ trait.to_json_with_values() for trait in data ]
-
-    filtered_records = query.count()
-
-    response_data = {
-        "draw": draw,
-        "recordsTotal": total_records,
-        "recordsFiltered": filtered_records,
-        "data": json_data
-    }
-
-  except Exception as ex:
-    logger.error(f'Failed to retrieve the list of traits: {ex}')
-    response_data = []
-  return jsonify(response_data)
-
-@phenotype_database_bp.route('/traits-list', methods=['POST'])
-@cache.memoize(60*60)
-@compress.compressed()
-def get_traits_json():
-  """
-    Get traits data for non-bulk files in JSON format (include phenotype values)
-  """
-  trait_id = request.json.get('trait_id')
-  err_msg = f'Failed to retrieve metadata for trait {trait_id}'
-
-  if trait_id:
-    try:
-      trait = get_trait(trait_id).to_json_with_values()
-      return jsonify(trait)
-
-    except Exception as ex:
-      logger.error(f'{err_msg}: {ex}')
-
-  return jsonify({ 'message': err_msg }), 404
-
 
 #
 # Submission Flow
@@ -191,14 +98,13 @@ def submit_traits():
 
   # Check for URL vars specifying an initial trait
   # These will be inherited from submit_start
-  initial_trait_name = request.args.get('trait')
-  initial_trait_set  = request.args.get('dataset')
+  initial_trait_id = request.args.get('trait')
 
   # Try looking up the specified trait
-  if initial_trait_name:
+  if initial_trait_id:
     try:
-      initial_trait = Trait(dataset=initial_trait_set, trait_name=initial_trait_name)
-    except NotFoundError:
+      initial_trait = Trait.from_id(initial_trait_id)
+    except (NotFoundError, ValueError):
       flash('That trait could not be found.', 'danger')
       initial_trait = None
   else: