Merge pull request #1011 from IGS/hotfix-jorvis-1211

Fixing bug where adata.X is a sparse matrix and breaking things downs…

Author: adkinsrs

.gitignore

@@ -1,20 +1,20 @@
-gear.ini
 docker/docker-compose.yml
 docker/gear.ini.docker
 NOTES
 TODO
 www/.env
 www/cgi/remove_dataset_from_profile.cgi
-www/css/dataset_manager.css
 www/include/manual/create_account.html~
-www/include/manual/dataset_manager.html~
 www/include/manual/search_gear.html~
 www/include/manual/search_results.html~
 www/include/manual/upload_dataset.html~
-www/js/dataset_curator.vue3.js
-www/js/dataset_manager.js
 www/tests/test_dataset_curator_plotly.py
 www/datasets_epigenetic/uploads/files/*
 www/.DS_Store
 www/.cache
 .DS_Store
+orthomap_inputs
+**/__pycache__
+**/*.bak
+**/*.sql
+www/nemoarchive_import/*.json

www/api/resources/mg_plotly_data.py

@@ -163,9 +163,6 @@ def post(self, dataset_id):
 
         adata.obs = order_by_time_point(adata.obs)
 
-        # quick check to ensure
-
-
         # get a map of all levels for each column
         columns = adata.obs.select_dtypes(include="category").columns.tolist()
 
@@ -242,6 +239,13 @@ def post(self, dataset_id):
             # The "try" may fail for projections as it is already in memory
             selected = adata
 
+        # convert adata.X to a dense matrix if it is sparse
+        # This prevents potential downstream issues
+        try:
+            selected.X = selected.X.todense()
+        except:
+            pass
+
         # These plot types filter to only the specific genes.
         # The other plot types use all genes and rather annotate the specific ones.
         if plot_type in ['dotplot', 'heatmap', 'mg_violin'] and gene_filter is not None:
@@ -271,7 +275,6 @@ def post(self, dataset_id):
             # Sort ensembl IDs based on the gene symbol order
             sorted_ensm = map(lambda x: gene_to_ensm[x], normalized_genes_list)
 
-
         try:
             # Reorder the categorical values in the observation dataframe
             sort_fields = []
@@ -298,11 +301,6 @@ def post(self, dataset_id):
                     except:
                         pass
 
-            # Make a composite index of all categorical types
-            #selected.obs['composite_index'] = create_composite_index_column(selected, columns)
-            #selected.obs['composite_index'] = selected.obs['composite_index'].astype('category')
-            #columns.append("composite_index")
-
             # Filter dataframe on the chosen observation filters
             if filters:
                 for field in filters.keys():
@@ -353,7 +351,6 @@ def post(self, dataset_id):
                 'message': str(pe),
             }
 
-
         var_index = selected.var.index.name
 
         if plot_type == "volcano":

www/api/resources/plotly_data.py

@@ -228,6 +228,13 @@ def post(self, dataset_id):
                 # The "try" may fail for projections as it is already in memory
                 selected = adata[:, gene_filter]
 
+            # convert adata.X to a dense matrix if it is sparse
+            # This prevents potential downstream issues
+            try:
+                selected.X = selected.X.todense()
+            except:
+                pass
+
             # Filter by obs filters
             if filters:
                 for col, values in filters.items():

www/api/resources/tsne_data.py

@@ -347,6 +347,13 @@ def post(self, dataset_id):
             # The "try" may fail for projections as it is already in memory
             selected = adata[:, gene_filter]
 
+        # convert adata.X to a dense matrix if it is sparse
+        # This prevents potential downstream issues
+        try:
+            selected.X = selected.X.todense()
+        except:
+            pass
+
         # Filter by obs filters
         if filters:
             for col, values in filters.items():