added filename

bichkd · Jan 24, 2023 · c4b2746 · c4b2746
1 parent 6a05ed3
commit c4b2746
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Showing 4 changed files with 6 additions and 9 deletions.
diff --git a/client/src/components/LeftSidePanel/LeftSidePanel.tsx b/client/src/components/LeftSidePanel/LeftSidePanel.tsx
@@ -91,9 +91,8 @@ const viewLinks = [
     {icon: CellTypeMarkerIcon, label: 'Cell type marker analysis', link: 'CellMarkerAnalysis'},
     {icon: ExpressionAnalysisIcon, label: 'Expression analysis', link: 'ExpressionAnalysis'},
     {icon: CoExpressionAnalysisIcon, label: 'Co-Expression analysis', link: 'CoexpressionAnalysis'},
-    {icon: CoExpressionAnalysisIcon, label: 'Interactive Celltype Discovery', link: 'CelltypeDiscovery'},
+    {icon: UserAnnotationIcon, label: 'Interactive cell type annotation', link: 'CelltypeDiscovery'},
     {icon: CompareAnnotationsIcon, label: 'Compare annotations', link: 'AnnotationComparison'},
-    {icon: UserAnnotationIcon, label: 'User annotations', link: 'UserAnnotation'},
 ];
 
 type Props = {

diff --git a/client/src/index.css b/client/src/index.css
@@ -25,8 +25,3 @@ code {
   font-family: 'Exo-Bold';
   src: local('Exo-Bold'), url('./fonts/Exo-Bold.ttf') format('truetype');
 }
-
-@font-face {
-  font-family: 'Rubik';
-  src: local('Rubik'), url('./fonts/Rubik-VariableFont_wght.ttf') format('truetype');
-}
diff --git a/data_import/study_import.py b/data_import/study_import.py
@@ -1,5 +1,6 @@
 import argparse
 import logging
+from pathlib import Path
 from typing import List
 
 import numpy as np
@@ -228,9 +229,10 @@ def import_differential_expression(study_id: int, adata_genes_df, adata: AnnData
 def import_study(filename: str) -> int:
     adata = sc.read_h5ad(filename)
     with engine.connect() as connection:
-        r = connection.execute(text("""INSERT INTO study (study_name, description, tissue_ncit_ids, disease_mesh_ids, organism_tax_id)
-            VALUES (:study_name, :description, :tissue_ncit_ids, :disease_mesh_ids, :organism_tax_id)
+        r = connection.execute(text("""INSERT INTO study (filename, study_name, description, tissue_ncit_ids, disease_mesh_ids, organism_tax_id)
+            VALUES (:filename, :study_name, :description, :tissue_ncit_ids, :disease_mesh_ids, :organism_tax_id)
             RETURNING study_id"""), {
+            'filename': (Path('/h5ad_store') / Path(filename).name).as_posix(),
             'study_name': adata.uns['cellenium']['title'],
             'description': adata.uns['cellenium']['description'],
             'tissue_ncit_ids': adata.uns['cellenium']['ncit_tissue_ids'].tolist(),

diff --git a/database_schema/3-cellenium.sql b/database_schema/3-cellenium.sql
@@ -1,5 +1,6 @@
 CREATE TABLE study
 (
+    filename         text,
     study_id          serial primary key,
     study_name        text not null,
     description       text,