fix: species names

app.py

@@ -39,7 +39,7 @@ if HF_TOKEN is None:
     )
 
 PLOT_TARGET_POINTS = int(os.environ.get("PLOT_TARGET_POINTS", "1500"))
-SEARCH_MAX_RESULTS = int(os.environ.get("SEARCH_MAX_RESULTS", "50"))
+SEARCH_MAX_RESULTS = int(os.environ.get("SEARCH_MAX_RESULTS", "20"))
 
 # -----------------------------
 # Load pipeline (reloadable)
@@ -249,8 +249,8 @@ def _load_track_metadata() -> dict[str, str]:
 
                 # Build display name from available fields
                 parts = []
-                if biosample_type and biosample_type != "tissue":
-                    parts.append(biosample_type)
+                # if biosample_type and biosample_type != "tissue":
+                #     parts.append(biosample_type)
                 if tissue:
                     parts.append(tissue)
                 if assay:
@@ -267,7 +267,7 @@ def _load_track_metadata() -> dict[str, str]:
                     parts.append(experiment_target)
 
                 if parts:
-                    display_name = " - ".join(parts)
+                    display_name = " ".join(parts)
                 else:
                     display_name = track_id  # Fallback to ID if no metadata
 
@@ -793,10 +793,10 @@ DEFAULT_COORDS = {
 _default_coords = DEFAULT_COORDS.get(DEFAULT_SPECIES, DEFAULT_COORDS["human"])
 
 
-# Format species names for display (replace underscores with spaces, capitalize)
+# Format species names for display (replace underscores with spaces, capitalize first letter)
 def _format_species_name(species: str) -> str:
     """Format species name for display."""
-    return species.replace("_", " ").title()
+    return species.replace("_", " ").capitalize()
 
 
 # Get all available species and format them
@@ -907,11 +907,14 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
 
     gr.Markdown("# Input DNA sequence")
 
-    # Get all available species from the pipeline
+    # Get all available species from the pipeline and format for display
     all_species = sorted(ASSEMBLY_TO_SPECIES.values())
+    # Format choices as (display_name, value) tuples so dropdown shows formatted names
+    # but returns actual species values
+    species_choices = [(_format_species_name(s), s) for s in all_species]
 
     species = gr.Dropdown(
-        choices=all_species,
+        choices=species_choices,
         value=DEFAULT_SPECIES,
         label="Species",
     )
@@ -1034,18 +1037,9 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
         visible=False,
     )
 
-    bigwig_selected = gr.CheckboxGroup(
-        choices=_init_bigwig_selected,
-        value=_init_bigwig_selected,
-        label="Selected functional tracks (used for prediction)",
-        visible=bool(
-            _init_bigwig_selected
-        ),  # Show if there are default tracks, otherwise hidden
-    )
-
     bigwig_query = gr.Textbox(
         label="Search functional tracks (auto-search while typing)",
-        placeholder="Type to search… (e.g. heart RNA-seq)",
+        placeholder="Type to search… (e.g. heart DNAse-seq)",
     )
 
     bigwig_results = gr.CheckboxGroup(
@@ -1053,6 +1047,15 @@ with gr.Blocks(title="NTv3 Tracks Demo") as demo:
         label="Results (click to add to Selected)",
     )
 
+    bigwig_selected = gr.CheckboxGroup(
+        choices=_init_bigwig_selected,
+        value=_init_bigwig_selected,
+        label="Selected functional tracks (used for prediction)",
+        visible=bool(
+            _init_bigwig_selected
+        ),  # Show if there are default tracks, otherwise hidden
+    )
+
     with gr.Row(visible=True) as bigwig_buttons_row:
         bigwig_clear_btn = gr.Button("Clear search results")
         bigwig_remove_btn = gr.Button("Remove all selected")