Merge pull request #117 from bioinfodlsu/input

Sanitize browse loci input + Add coexpression node data div
bioinfodlsu · Sep 12, 2023 · 1d19771 · 1d19771
2 parents b3d2a9d + a8872a9
commit 1d19771
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Showing 4 changed files with 23 additions and 3 deletions.
diff --git a/callbacks/browse_loci/callbacks.py b/callbacks/browse_loci/callbacks.py
@@ -110,7 +110,8 @@ def send_open_chromatin_panicle_url(filename):
     )
     def display_selected_genomic_intervals(nb_intervals_str, homepage_is_submitted, selected_nb_interval):
         if homepage_is_submitted:
-            igv_options = nb_intervals_str.split(';')
+            igv_options = util.sanitize_nb_intervals_str(nb_intervals_str) 
+            igv_options = igv_options.split(';')
 
             if not selected_nb_interval:
                 selected_nb_interval = igv_options[0]
@@ -171,6 +172,9 @@ def display_igv(selected_nb_intervals_str, selected_tracks, homepage_is_submitte
             display_tracks = [
                 track for track in track_info if selected_tracks and track['name'] in selected_tracks]
 
+            selected_nb_intervals_str = lift_over_util.to_genomic_interval(selected_nb_intervals_str)
+            selected_nb_intervals_str = str(selected_nb_intervals_str.chrom) + ':' + str(selected_nb_intervals_str.start) + '-' + str(selected_nb_intervals_str.stop)
+
             return html.Div([
                 dashbio.Igv(
                     id='igv-Nipponbare-local',

diff --git a/callbacks/browse_loci/util.py b/callbacks/browse_loci/util.py
@@ -23,7 +23,9 @@ def write_igv_tracks_to_file(nb_intervals_str):
 
 def write_gff_igv_track_to_file(source_dir, source_file, nb_intervals_str):
     if path_exists(source_dir):
-        loci_list = nb_intervals_str.split(';')
+        loci_list = util.sanitize_nb_intervals_str(nb_intervals_str) 
+        loci_list = loci_list.split(';')
+
         genomic_interval_list = util.get_genomic_intervals_from_input(
             nb_intervals_str)
 

diff --git a/callbacks/coexpression/callbacks.py b/callbacks/coexpression/callbacks.py
@@ -6,6 +6,8 @@
 from ..lift_over import util as lift_over_util
 from ..branch import *
 
+import json
+
 Input_parameter_module = namedtuple('Input_parameter_module', [
     'param_slider_marks', 'param_slider_value'])
 
@@ -532,8 +534,18 @@ def download_coexpression_table_to_csv(download_n_clicks, coexpression_df, genom
         State('coexpression-module-graph', 'elements'),
         State('homepage-genomic-intervals-submitted-input', 'data')
     )
-    def download_coexpression_table_to_csv(download_n_clicks, coexpression_dict, genomic_intervals):
+    def download_coexpression_graph_to_csv(download_n_clicks, coexpression_dict, genomic_intervals):
         if download_n_clicks >= 1:
             return dict(content='Hello world!', filename=f'[{genomic_intervals}] Co-Expression Network Analysis Graph.txt')
 
         raise PreventUpdate
+
+    @app.callback(
+        Output('coexpression-module-graph-node-data', 'children'),
+        Input('coexpression-module-graph', 'tapNodeData')
+    )
+    def display_node_data(node_data):
+        if node_data:
+            return json.dumps(node_data)
+
+        raise PreventUpdate
diff --git a/pages/analysis/co_expr.py b/pages/analysis/co_expr.py
@@ -495,6 +495,8 @@
                             ]
                         ),
 
+                        html.Div(id='coexpression-module-graph-node-data', hidden=True),
+
                         dcc.Loading([
                             cyto.Cytoscape(
                                 id='coexpression-module-graph',