Merge pull request #93 from bioinfodlsu/input

Fix display and session of genomic interval and text mining input + Revise code for clearing dcc Store data

app.py

@@ -66,13 +66,6 @@
 
     dash.page_container,
 
-    # Do NOT place inside session-container.
-    # Otherwise, the input field for genomic interval will be cleared when submitted.
-    dcc.Store(
-        id='homepage-genomic-intervals-saved-input',
-        storage_type='session'
-    ),
-
     # Session storage
     html.Div(
         id='session-container',
@@ -85,6 +78,11 @@
                 storage_type='session'
             ),
 
+            dcc.Store(
+                id='homepage-genomic-intervals-saved-input',
+                storage_type='session'
+            ),
+
             dcc.Store(
                 id='homepage-genomic-intervals-submitted-input',
                 storage_type='session'
@@ -95,6 +93,8 @@
                 storage_type='session'
             ),
 
+
+
             # ==========
             # Lift-over
             # ==========
@@ -208,16 +208,16 @@
                 id='coexpression-is-submitted',
                 storage_type='session'
             ),
+
+            # ==============================
+            # Regulatory Feature Enrichment
+            # ==============================
 
             dcc.Store(
                 id='tfbs-saved-input',
                 storage_type='session'
             ),
 
-            # ==============================
-            # Regulatory Feature Enrichment
-            # ==============================
-
             dcc.Store(
                 id='tfbs-submitted-input',
                 storage_type='session'

callbacks/coexpression/util.py

@@ -7,8 +7,7 @@
 
 import pandas as pd
 import networkx as nx
-from scipy.stats import fisher_exact
-import statsmodels.stats.multitest as sm
+from scipy.stats import fisher_exact, false_discovery_control
 
 from collections import namedtuple
 
@@ -219,8 +218,7 @@ def do_module_enrichment_analysis(implicated_gene_ids, genomic_intervals, addl_g
                     # Add 1 since user-facing module number is one-based
                     p_values_indices.append(idx + 1)
 
-            _, adj_p_values, _, _ = sm.multipletests(
-                p_values, method='fdr_bh')
+            adj_p_values = false_discovery_control(p_values, method='bh')
             significant_adj_p_values = [(p_values_indices[idx], adj_p_value) for idx, adj_p_value in enumerate(
                 adj_p_values) if adj_p_value < const.P_VALUE_CUTOFF]
             significant_adj_p_values.sort(key=lambda x: x[1])

callbacks/homepage/callbacks.py

@@ -58,24 +58,25 @@ def display_specific_analysis_page(nav_className, analysis_nav_id, analysis_layo
         State('homepage-genomic-intervals', 'value'),
 
         Input('homepage-submit', 'n_clicks'),
+        Input('homepage-genomic-intervals', 'n_submit'),
         State('session-container', 'children'),
 
         Input('homepage-reset', 'n_clicks'),
         Input('homepage-clear-cache', 'n_clicks'),
 
         prevent_initial_call=True
     )
-    def parse_input(nb_intervals_str, n_clicks, dccStore_children, *_):
+    def parse_input(nb_intervals_str, n_clicks, n_submit, dccStore_children, *_):
         if 'homepage-clear-cache' == ctx.triggered_id:
             clear_cache_folder()
 
         if 'homepage-reset' == ctx.triggered_id:
             # clear data for items in dcc.Store found in session-container
-            dccStore_children = get_cleared_dccStore_data(dccStore_children)
+            dccStore_children = get_cleared_dccStore_data_excluding_some_data(dccStore_children)
 
             return dccStore_children, None, {'display': 'none'}, False, ''
 
-        if 'homepage-submit' == ctx.triggered_id and n_clicks >= 1:
+        if n_submit >= 1 or ('homepage-submit' == ctx.triggered_id and n_clicks >= 1):
             if nb_intervals_str:
                 intervals = lift_over_util.get_genomic_intervals_from_input(
                     nb_intervals_str)
@@ -85,8 +86,8 @@ def parse_input(nb_intervals_str, n_clicks, dccStore_children, *_):
                         {'display': 'block'}, False, nb_intervals_str
                 else:
                     # clear data for items in dcc.Store found in session-container
-                    dccStore_children = get_cleared_dccStore_data(
-                        dccStore_children)
+                    dccStore_children = get_cleared_dccStore_data_excluding_some_data(
+                        dccStore_children, 'homepage-genomic-intervals-saved-input')
 
                     browse_loci_util.write_igv_tracks_to_file(nb_intervals_str)
 
@@ -120,27 +121,26 @@ def get_nipponbare_gene_ids(nb_intervals_str, homepage_is_submitted):
     @app.callback(
         Output('homepage-genomic-intervals-saved-input',
                'data', allow_duplicate=True),
-        State('homepage-genomic-intervals', 'value'),
         Input({'type': 'example-genomic-interval',
               'description': ALL}, 'n_clicks'),
-        Input('homepage-reset', 'n_clicks'),
-
         prevent_initial_call=True
     )
-    def set_input_fields(genomic_intervals, example_genomic_interval_n_clicks, *_):
-        if all(val == 0 for val in example_genomic_interval_n_clicks):
-            return ''
-
-        if ctx.triggered_id:
-            if 'homepage-reset' == ctx.triggered_id:
-                return None
-
-            if 'homepage-genomic-intervals' == ctx.triggered_id:
-                return genomic_intervals
-
+    def set_input_fields_with_preset_input(example_genomic_interval_n_clicks):
+        if ctx.triggered_id and not all(val == 0 for val in example_genomic_interval_n_clicks):
             return get_example_genomic_interval(ctx.triggered_id['description'])
 
         raise PreventUpdate
+
+
+    @app.callback(
+        Output('homepage-genomic-intervals-saved-input',
+               'data', allow_duplicate=True),
+        Input('homepage-genomic-intervals', 'value'),
+        prevent_initial_call=True
+    )
+    def set_input_fields(genomic_intervals):
+        return genomic_intervals
+
 
     @app.callback(
         Output('homepage-results-container', 'style'),

callbacks/homepage/util.py

@@ -14,9 +14,13 @@ def clear_cache_folder():
     if os.path.exists(const.TEMP):
         shutil.rmtree(const.TEMP, ignore_errors=True)
 
-def get_cleared_dccStore_data(dccStore_children):
+def get_cleared_dccStore_data_excluding_some_data(dccStore_children, *arg):
     for i in range(len(dccStore_children)):
-        dccStore_children[i]['props']['data'] = ''
+        dccStore_ID = dccStore_children[i]['props']['id']
+
+        if not dccStore_ID in arg:
+            dccStore_children[i]['props']['data'] = ''
+
     return dccStore_children
 
 def get_example_genomic_interval(description):

callbacks/lift_over/callbacks.py

@@ -308,7 +308,8 @@ def display_gene_tables(nb_intervals_str, active_tab, filter_rice_variants, othe
             if active_tab == get_tab_id('All Genes'):
                 all_genes_raw = get_all_genes(other_refs, nb_intervals)
 
-                all_genes_raw['OGI'] = get_rgi_orthogroup_link(
+                mask = (all_genes_raw['OGI'] != NULL_PLACEHOLDER)
+                all_genes_raw.loc[mask, 'OGI'] = get_rgi_orthogroup_link(
                     all_genes_raw, 'OGI')
                 if 'Nipponbare' in all_genes_raw.columns:
                     mask = (all_genes_raw['Nipponbare'] != NULL_PLACEHOLDER)
@@ -336,13 +337,16 @@ def display_gene_tables(nb_intervals_str, active_tab, filter_rice_variants, othe
                 mask = (common_genes_raw['OGI'] != NULL_PLACEHOLDER)
                 common_genes_raw.loc[mask, 'OGI'] = get_rgi_orthogroup_link(
                     common_genes_raw, 'OGI')
+
                 if 'Nipponbare' in common_genes_raw.columns:
-                    common_genes_raw['Nipponbare'] = get_rgi_genecard_link(
+                    mask = (common_genes_raw['Nipponbare'] != NULL_PLACEHOLDER)
+                    common_genes_raw.loc[mask, 'Nipponbare'] = get_rgi_genecard_link(
                         common_genes_raw, 'Nipponbare')
 
                 for cultivar in other_ref_genomes:
                     if cultivar in common_genes_raw.columns:
-                        common_genes_raw[cultivar] = get_rgi_genecard_link(
+                        mask = (common_genes_raw[cultivar] != NULL_PLACEHOLDER)
+                        common_genes_raw.loc[mask, cultivar] = get_rgi_genecard_link(
                             common_genes_raw, cultivar)
 
                 common_genes = common_genes_raw.to_dict('records')
@@ -357,9 +361,12 @@ def display_gene_tables(nb_intervals_str, active_tab, filter_rice_variants, othe
                     nb_intervals)[0].drop(
                     ['Chromosome', 'Start', 'End', 'Strand'], axis=1)
 
-                genes_from_Nb_raw['OGI'] = get_rgi_orthogroup_link(
+                mask = (genes_from_Nb_raw['OGI'] != NULL_PLACEHOLDER)
+                genes_from_Nb_raw.loc[mask, 'OGI'] = get_rgi_orthogroup_link(
                     genes_from_Nb_raw, 'OGI')
-                genes_from_Nb_raw['Name'] = get_rgi_genecard_link(
+
+                mask = (genes_from_Nb_raw['Name'] != NULL_PLACEHOLDER)
+                genes_from_Nb_raw.loc[mask, 'Name'] = get_rgi_genecard_link(
                     genes_from_Nb_raw, 'Name')
 
                 genes_from_Nb = genes_from_Nb_raw.to_dict('records')
@@ -376,9 +383,12 @@ def display_gene_tables(nb_intervals_str, active_tab, filter_rice_variants, othe
                 genes_from_other_ref_raw = get_unique_genes_in_other_ref(
                     other_ref, nb_intervals)
 
-                genes_from_other_ref_raw['OGI'] = get_rgi_orthogroup_link(
+                mask = (genes_from_other_ref_raw['OGI'] != NULL_PLACEHOLDER)
+                genes_from_other_ref_raw.loc[mask, 'OGI'] = get_rgi_orthogroup_link(
                     genes_from_other_ref_raw, 'OGI')
-                genes_from_other_ref_raw['Name'] = get_rgi_genecard_link(
+
+                mask = (genes_from_other_ref_raw['Name'] != NULL_PLACEHOLDER)
+                genes_from_other_ref_raw.loc[mask, 'Name'] = get_rgi_genecard_link(
                     genes_from_other_ref_raw, 'Name')
 
                 genes_from_other_ref = genes_from_other_ref_raw.to_dict(

callbacks/text_mining/callbacks.py

@@ -5,11 +5,6 @@
 from .util import *
 from ..lift_over import util as lift_over_util
 
-
-Text_mining_input = namedtuple(
-    'Text_mining_input', ['text_mining_query'])
-
-
 def init_callback(app):
 
     # to display user input interval in the top nav
@@ -30,19 +25,25 @@ def display_input(nb_intervals_str, homepage_is_submitted, *_):
 
     @app.callback(
         Output('text-mining-query-saved-input', 'data', allow_duplicate=True),
-        State('text-mining-query', 'value'),
         Input({'type': 'example-text-mining',
                'description': ALL}, 'n_clicks'),
         prevent_initial_call=True
     )
-    def set_input_fields(query_string, *_):
-        if ctx.triggered_id:
-            if 'text-mining-query' == ctx.triggered_id:
-                return query_string
-
+    def set_input_fields_with_preset_input(example_text_mining_n_clicks):
+        if ctx.triggered_id and not all(val == 0 for val in example_text_mining_n_clicks):
             return ctx.triggered_id['description']
 
         raise PreventUpdate
+
+
+    @app.callback(
+        Output('text-mining-query-saved-input', 'data', allow_duplicate=True),
+        Input('text-mining-query', 'value'),
+        prevent_initial_call=True
+    )
+    def set_input_fields(query_string):
+        return query_string
+
 
     @app.callback(
         Output('text-mining-query', 'value'),
@@ -52,40 +53,41 @@ def get_input_homepage_session_state(query):
         return query
 
     @app.callback(
+        Output('text-mining-input-error', 'style'),
+        Output('text-mining-input-error', 'children'),
+
         Output('text-mining-is-submitted', 'data', allow_duplicate=True),
         Output('text-mining-query-submitted-input',
                'data', allow_duplicate=True),
         Input('text-mining-submit', 'n_clicks'),
+        Input('text-mining-query', 'n_submit'),
         State('homepage-is-submitted', 'data'),
         State('text-mining-query', 'value'),
         prevent_initial_call=True
     )
-    def submit_text_mining_input(text_mining_submitted_n_clicks, homepage_is_submitted, text_mining_query):
-        if homepage_is_submitted and text_mining_submitted_n_clicks >= 1:
-            submitted_input = Text_mining_input(
-                text_mining_query)._asdict()
-
-            return True, submitted_input
+    def submit_text_mining_input(text_mining_submitted_n_clicks, text_mining_query_n_submit, homepage_is_submitted, text_mining_query):
+        if homepage_is_submitted and (text_mining_submitted_n_clicks >= 1 or text_mining_query_n_submit >= 1):
+            is_there_error, message = is_error(text_mining_query)
+
+            if not is_there_error:
+                return {'display': 'none'}, message, True, text_mining_query
+            else:
+                return {'display': 'block'}, message, False, None
 
         raise PreventUpdate
 
+
     @app.callback(
         Output('text-mining-results-container', 'style'),
-        Output('text-mining-input-error', 'style'),
-        Output('text-mining-input-error', 'children'),
-
-        State('text-mining-query', 'value'),
         Input('text-mining-is-submitted', 'data')
     )
-    def display_text_mining_output(text_mining_query, text_mining_is_submitted):
-        is_there_error, message = is_error(text_mining_query)
+    def display_coexpression_output(text_mining_is_submitted):
         if text_mining_is_submitted:
-            if not is_there_error:
-                return {'display': 'block'}, {'display': 'none'}, message
-            else:
-                return {'display': 'none'}, {'display': 'block'}, message
+            return {'display': 'block'}
+
+        else:
+            return {'display': 'none'}
 
-        return {'display': 'none'}, {'display': 'none'}, message
 
     @app.callback(
         Output('text-mining-result-table', 'data'),
@@ -98,7 +100,7 @@ def display_text_mining_output(text_mining_query, text_mining_is_submitted):
     )
     def display_text_mining_results(text_mining_is_submitted, homepage_submitted, text_mining_query_submitted_input):
         if homepage_submitted and text_mining_is_submitted:
-            query_string = text_mining_query_submitted_input['text_mining_query']
+            query_string = text_mining_query_submitted_input
 
             is_there_error, _ = is_error(query_string)
             if not is_there_error:

pages/analysis/text_mining.py

@@ -37,19 +37,23 @@
             dbc.Input(
                 id='text-mining-query',
                 type='text',
-                value=''
+                value='',
+                debounce=True,
+                n_submit=0
             ),
 
             html.Div([html.Span('Examples:', className='pe-3'),
                       html.Span('pre-harvest sprouting',
                                 id={'type': 'example-text-mining',
                                     'description': 'pre-harvest sprouting'},
-                                className='sample-genomic-interval'),
+                                className='sample-genomic-interval',
+                                n_clicks=0),
                       html.Span(',', className='sample-genomic-interval'),
                       html.Span('anaerobic germination',
                                 id={'type': 'example-text-mining',
                                     'description': 'anaerobic germination'},
-                                className='sample-genomic-interval ms-3')],
+                                className='sample-genomic-interval ms-3',
+                                n_clicks=0)],
                      className='pt-3'),
             html.Br(),
 

pages/homepage.py

@@ -114,7 +114,9 @@
     dbc.Input(
         id='homepage-genomic-intervals',
         type='text',
-        value=''
+        value='',
+        debounce=True,
+        n_submit=0
     ),
 
     html.Div([