Merge pull request #420 from AmpliconSuite/search_fix

fix for search

Author: liefeld

caper/caper/views.py

@@ -63,6 +63,9 @@
 # imports for coamp graph
 from .neo4j_utils import load_graph, fetch_subgraph
 
+# Import search function
+from .search import perform_search
+
 import subprocess
 import shutil
 import caper.sample_plot as sample_plot
@@ -2869,62 +2872,46 @@ def search_results(request):
         # Get the combined cancer/tissue field
         cancer_tissue = request.POST.get("metadata_cancer_tissue", "").upper()
 
-        # Gene Search
-        if request.user.is_authenticated:
-            username = request.user.username
-            useremail = request.user.email
-            query_obj = {'private': True, "$or": [{"project_members": username}, {"project_members": useremail}],
-                         'Oncogenes': gen_query, 'delete': False}
-
-            private_projects = list(collection_handle.find(query_obj))
-            # private_projects = get_projects_close_cursor(query_obj)
-        else:
-            private_projects = []
-
-        public_projects = list(collection_handle.find({'private': False, 'Oncogenes': gen_query, 'delete': False}))
-        # public_projects = get_projects_close_cursor({'private' : False, 'Oncogenes' : gen_query, 'delete': False})
+        # We'll set both parameters to the same value for the backend search
+        cancer_type = cancer_tissue
+        tissue_origin = ""  # Leave empty to avoid duplicate filtering
+
+        extra_metadata = request.POST.get('metadata_extra', "").upper()
+
+        # Store user query for persistence in the form
+        user_query = {
+            "genequery": gene_search,
+            "project_name": project_name,
+            "classquery": classifications,
+            "metadata_sample_name": sample_name,
+            "metadata_sample_type": sample_type,
+            "metadata_cancer_tissue": cancer_tissue,  # New field
+            'extra_metadata': extra_metadata
+        }
 
-        for proj in private_projects:
-            prepare_project_linkid(proj)
-        for proj in public_projects:
-            prepare_project_linkid(proj)
+        # Debugging logs
+        logging.info(f'Search terms: Gene={gene_search}, Project={project_name}, Class={classifications}, '
+                     f'Sample Name={sample_name}, Sample Type={sample_type}, Cancer/Tissue={cancer_tissue},'
+                     f' Extra Metadata={extra_metadata}')
+
+        # Run the search function
+        search_results = perform_search(
+            genequery=gene_search,
+            project_name=project_name,
+            classquery=classifications,
+            metadata_sample_name=sample_name,
+            metadata_sample_type=sample_type,
+            metadata_cancer_type=cancer_tissue,  # Use the combined term
+            metadata_tissue_origin=tissue_origin,  # Leave this empty
+            extra_metadata=extra_metadata,
+            user=request.user
+        )
 
-        def collect_class_data(projects):
-            sample_data = []
-            for project in projects:
-                project_name = project['project_name']
-                project_linkid = project['_id']
-                features = project['runs']
-                features_list = replace_space_to_underscore(features)
-                data = sample_data_from_feature_list(features_list)
-
-                for sample in data:
-                    sample['project_name'] = project_name
-                    sample['project_linkid'] = project_linkid
-
-                    # Gene and classification checks
-                    gene_match = (genequery in sample['Oncogenes'] or len(genequery) == 0)
-                    upperclass = list(map(str.upper, sample['Classifications']))
-                    class_match = (classquery in upperclass or len(classquery) == 0)
-
-                    # Cancer type or tissue of origin check
-                    cancer_tissue_match = True  # Default to True if no filter
-                    if metadata_cancer_tissue:
-                        cancer_type = sample.get('Cancer_type', '').lower()
-                        tissue_origin = sample.get('Tissue_of_origin', '').lower()
-                        cancer_tissue_match = (
-                                metadata_cancer_tissue.lower() in cancer_type or
-                                metadata_cancer_tissue.lower() in tissue_origin
-                        )
-
-                    # Only add the sample if all filters match
-                    if gene_match and class_match and cancer_tissue_match:
-                        sample_data.append(sample)
-
-            return sample_data
-
-        public_sample_data = collect_class_data(public_projects)
-        private_sample_data = collect_class_data(private_projects)
+        # Count the number of matches for each category
+        public_projects_count = len(search_results["public_projects"])
+        private_projects_count = len(search_results["private_projects"])
+        public_samples_count = len(search_results["public_sample_data"])
+        private_samples_count = len(search_results["private_sample_data"])
 
         # Calculate project filter data with counts
         def get_project_filters(sample_data):
@@ -2943,8 +2930,8 @@ def get_project_filters(sample_data):
             # Sort by project name
             return sorted(project_counts.values(), key=lambda x: x['name'])
 
-        public_project_filters = get_project_filters(public_sample_data)
-        private_project_filters = get_project_filters(private_sample_data)
+        public_project_filters = get_project_filters(search_results["public_sample_data"])
+        private_project_filters = get_project_filters(search_results["private_sample_data"])
 
         query_info = {
             "Gene Name": gene_search,