Merge pull request #173 from mwang87/chromatogram-support

mwang87 · web-flow · commit a8ca71b36a7d · 2021-03-11T10:53:22.000-08:00
Chromatogram Support
diff --git a/app.py b/app.py
@@ -68,6 +68,7 @@
 
 # Importing layout for HTML
 from layout_misc import EXAMPLE_DASHBOARD, SYCHRONIZATION_MODAL, SPECTRUM_DETAILS_MODAL, ADVANCED_VISUALIZATION_MODAL, ADVANCED_IMPORT_MODAL, ADVANCED_REPLAY_MODAL
+from layout_xic_options import ADVANCED_XIC_MODAL
 
 server = Flask(__name__)
 app = dash.Dash(__name__, server=server, external_stylesheets=[dbc.themes.BOOTSTRAP])
@@ -199,7 +200,10 @@
         dbc.CardBody(dbc.Row(
             [   ## Left Panel
                 dbc.Col([
-                    html.H5(children='File Selection'),
+                    dbc.Row(
+                        dbc.Col(html.H5(children='File Selection')),
+                    ),
+                    html.Hr(),
                     dbc.InputGroup(
                         [
                             dbc.InputGroupAddon("GNPS USI", addon_type="prepend"),
@@ -388,7 +392,20 @@
                 ], className="col-sm"),
                 ## Right Panel
                 dbc.Col([
-                    html.H5(children='XIC Options'),
+                    dbc.Row([
+                        dbc.Col(html.H5(children='XIC Options')),
+                        dbc.Col(
+                            dbc.Button("Advanced XIC Options", 
+                                id="advanced_xic_modal_button", 
+                                color="info", size="sm", 
+                                className="mr-1", 
+                                style={
+                                    "float" : "right"
+                                }
+                            ),
+                        ),
+                    ]),
+                    html.Hr(),
                     dbc.Row([
                         dbc.Col(
                             dbc.InputGroup(
@@ -407,16 +424,7 @@
                                 ],
                                 className="mb-3",
                             ),
-                        ),
-                        dbc.Col(
-                            dbc.InputGroup(
-                                [
-                                    dbc.InputGroupAddon("XIC Peptide", addon_type="prepend"),
-                                    dbc.Input(id='xic_peptide', placeholder="Enter Peptide to XIC", value=""),
-                                ],
-                                className="mb-3",
-                            ),
-                        ),
+                        )
                     ]),
                     dbc.Row([
                         dbc.Col(
@@ -1368,6 +1376,7 @@
         dbc.Row(ADVANCED_IMPORT_MODAL),
         dbc.Row(ADVANCED_REPLAY_MODAL),
         dbc.Row(ADVANCED_VISUALIZATION_MODAL),
+        dbc.Row(ADVANCED_XIC_MODAL),
         
     ],
     fluid=True,
@@ -1623,6 +1632,8 @@ def draw_spectrum(usi, ms2_identifier, export_format, plot_theme, xic_mz):
                 Output("feature_finding_rt_tolerance", "value"),
                 Output("sychronization_session_id", "value"),
 
+                Output("chromatogram_options", "value"),
+
                 Output("comment", "value"),
 
                 Output("map_plot_color_scale", "value"),
@@ -1673,6 +1684,8 @@ def draw_spectrum(usi, ms2_identifier, export_format, plot_theme, xic_mz):
                   
                   State('sychronization_session_id', 'value'),
 
+                  State("chromatogram_options", "value"),
+
                   State("comment", 'value'),
 
                   State('map_plot_color_scale', 'value'),
@@ -1725,6 +1738,8 @@ def determine_url_only_parameters(  search,
 
                                     existing_sychronization_session_id,
 
+                                    existing_chromatogram_options,
+
                                     existing_comment,
                                     
                                     existing_map_plot_color_scale,
@@ -1798,6 +1813,9 @@ def determine_url_only_parameters(  search,
         default_session_id = existing_sychronization_session_id
     sychronization_session_id = _get_param_from_url(search, "", "sychronization_session_id", default_session_id, session_dict=session_dict, old_value=existing_sychronization_session_id, no_change_default=dash.no_update)
 
+    # Chromatogram Options
+    chromatogram_options = _get_param_from_url(search, "", "chromatogram_options", dash.no_update, session_dict=session_dict, old_value=existing_chromatogram_options, no_change_default=dash.no_update)
+
     # Comment
     comment = _get_param_from_url(search, "", "comment", dash.no_update, session_dict=session_dict, old_value=existing_comment, no_change_default=dash.no_update)
 
@@ -1838,6 +1856,11 @@ def determine_url_only_parameters(  search,
             show_lcms_2nd_map = dash.no_update
     except:
         pass
+
+    try:
+        chromatogram_options = json.loads(chromatogram_options)
+    except:
+        pass    
     
     return [xic_formula, 
             xic_peptide, 
@@ -1853,6 +1876,7 @@ def determine_url_only_parameters(  search,
             overlay_usi, overlay_mz, overlay_rt, overlay_color, overlay_size, overlay_hover, overlay_filter_column, overlay_filter_value,
             feature_finding_type, feature_finding_ppm, feature_finding_noise, feature_finding_min_peak_rt, feature_finding_max_peak_rt, feature_finding_rt_tolerance,
             sychronization_session_id,
+            chromatogram_options, 
             comment,
             map_plot_color_scale,
             map_plot_quantization_level]
@@ -2488,8 +2512,21 @@ def _perform_batch_xic(usi_list, usi1_list, usi2_list, xic_norm, all_xic_values,
             pass
 
     merged_df_long = pd.concat(df_long_list)
+
     return merged_df_long, ms2_data
 
+def _perform_chromatogram_extraction(usi_list, chromatogram_list):
+    usi = usi_list[0]
+    remote_link, local_filename = _resolve_usi(usi)
+
+    df_list = []
+    for chromatogram_value in chromatogram_list:
+        chromatogram_df = xic.get_chromatogram(local_filename, chromatogram_value)
+        chromatogram_df["USI"] = usi
+        df_list.append(chromatogram_df)
+
+    merged_df = pd.concat(df_list)
+    return merged_df
 
 def _is_worker_up():
     """Gives us utility function to tell is celery is up and running
@@ -2528,6 +2565,27 @@ def _integrate_files(long_data_df, xic_integration_type):
 
     return grouped_df
 
+##################################
+# XIC Chromatogram Options
+##################################
+@app.callback(Output('chromatogram_options', 'options'),
+              [
+                  Input('usi', 'value'), 
+                  Input('usi2', 'value'), 
+              ])
+def create_chromatogram_options(usi, usi2):
+    all_usi = usi.split("\n")
+    remote_link, local_filename = _resolve_usi(all_usi[0])
+
+    chromatogram_list = tasks.task_chromatogram_options(local_filename)
+
+    options = []
+    for term in chromatogram_list:
+        options.append({'label': term, 'value': term})
+
+    return options
+
+
 # Creating XIC plot
 @app.callback([
                 Output('xic-plot', 'figure'), 
@@ -2540,20 +2598,21 @@ def _integrate_files(long_data_df, xic_integration_type):
                   Input('usi', 'value'), 
                   Input('usi2', 'value'), 
                   Input('xic_mz', 'value'), 
-                Input('xic_formula', 'value'), 
-                Input('xic_peptide', 'value'), 
-                Input('xic_tolerance', 'value'),
-                Input('xic_ppm_tolerance', 'value'),
-                Input('xic_tolerance_unit', 'value'),
-                Input('xic_rt_window', 'value'),
-                Input('xic_integration_type', 'value'),
-                Input('xic_norm', 'value'),
-                Input('xic_file_grouping', 'value'),
-                Input('polarity_filtering', 'value'),
-                Input('image_export_format', 'value'), 
-                Input("plot_theme", "value")
+                  Input('xic_formula', 'value'), 
+                  Input('xic_peptide', 'value'), 
+                  Input('xic_tolerance', 'value'),
+                  Input('xic_ppm_tolerance', 'value'),
+                  Input('xic_tolerance_unit', 'value'),
+                  Input('xic_rt_window', 'value'),
+                  Input('xic_integration_type', 'value'),
+                  Input('xic_norm', 'value'),
+                  Input('xic_file_grouping', 'value'),
+                  Input("chromatogram_options", "value"),
+                  Input('polarity_filtering', 'value'),
+                  Input('image_export_format', 'value'), 
+                  Input("plot_theme", "value"),
               ])
-def draw_xic(usi, usi2, xic_mz, xic_formula, xic_peptide, xic_tolerance, xic_ppm_tolerance, xic_tolerance_unit, xic_rt_window, xic_integration_type, xic_norm, xic_file_grouping, polarity_filter, export_format, plot_theme):
+def draw_xic(usi, usi2, xic_mz, xic_formula, xic_peptide, xic_tolerance, xic_ppm_tolerance, xic_tolerance_unit, xic_rt_window, xic_integration_type, xic_norm, xic_file_grouping, chromatogram_list, polarity_filter, export_format, plot_theme):
     triggered_id = [p['prop_id'] for p in dash.callback_context.triggered][0]
     print("TRIGGERED XIC PLOT", triggered_id, file=sys.stderr)
 
@@ -2633,11 +2692,18 @@ def draw_xic(usi, usi2, xic_mz, xic_formula, xic_peptide, xic_tolerance, xic_ppm
             pass
 
     # Exiting if we don't have any valid XIC values
-    if len(all_xic_values) == 0:
+    if len(all_xic_values) == 0 and len(chromatogram_list) == 0:
         return [placeholder_xic_plot, graph_config, dash.no_update, dash.no_update, dash.no_update]
 
-    # Performing XIC for all USI in the list
-    merged_df_long, ms2_data = _perform_batch_xic(usi_list, usi1_list, usi2_list, xic_norm, all_xic_values, parsed_xic_da_tolerance, parsed_xic_ppm_tolerance, xic_tolerance_unit, rt_min, rt_max, polarity_filter)
+    merged_df_long = pd.DataFrame()
+    if len(all_xic_values) > 0:
+        # Performing XIC for all USI in the list
+        merged_df_long, ms2_data = _perform_batch_xic(usi_list, usi1_list, usi2_list, xic_norm, all_xic_values, parsed_xic_da_tolerance, parsed_xic_ppm_tolerance, xic_tolerance_unit, rt_min, rt_max, polarity_filter)
+
+    # Looking at chromatograms only if a single file exists
+    if len(usi_list) == 1 and len(chromatogram_list) > 0:
+        chrom_df = _perform_chromatogram_extraction(usi_list, chromatogram_list)
+        merged_df_long = pd.concat([merged_df_long, chrom_df])
 
     # Limit the plotting USIs, but not the integrals below
     plotting_df = merged_df_long
@@ -3077,6 +3143,8 @@ def create_gnps_mzmine2_link(usi, usi2, feature_finding_type, feature_finding_pp
                 Input("sychronization_session_id", "value"),
                 Input("synchronization_leader_token", "value"),
 
+                Input("chromatogram_options", "value"),
+
                 Input("comment", "value"),
 
                 Input("map_plot_color_scale", "value"),
@@ -3091,6 +3159,7 @@ def create_link(usi, usi2, xic_mz, xic_formula, xic_peptide,
                 overlay_usi, overlay_mz, overlay_rt, overlay_color, overlay_size, overlay_hover, overlay_filter_column, overlay_filter_value,
                 feature_finding_type, feature_finding_ppm, feature_finding_noise, feature_finding_min_peak_rt, feature_finding_max_peak_rt, feature_finding_rt_tolerance,
                 sychronization_save_session_button_clicks, sychronization_session_id, synchronization_leader_token, 
+                chromatogram_options, 
                 comment,
                 map_plot_color_scale, map_plot_quantization_level,
                 synchronization_type):
@@ -3135,6 +3204,9 @@ def create_link(usi, usi2, xic_mz, xic_formula, xic_peptide,
     # Sychronization Options
     url_params["sychronization_session_id"] = sychronization_session_id
 
+    # mzML Chromatogram Options
+    url_params["chromatogram_options"] = json.dumps(chromatogram_options)
+
     # Comment
     url_params["comment"] = comment
 
@@ -3405,6 +3477,7 @@ def create_sychronization_link(sychronization_session_id, synchronization_leader
 
 
 
+
 @app.callback(Output('network-link-button', 'children'),
               [
                   Input('usi', 'value'), 
@@ -3546,6 +3619,7 @@ def get_overlay_options(overlay_usi):
 
 
 
+
 # Sychronization Section for callbacks
 @app.callback([
                 Output('synchronization_leader_token', 'value'),
@@ -3759,6 +3833,13 @@ def toggle_modal(n1, n2, is_open):
     [State("advanced_replay_modal", "is_open")],
 )(toggle_modal)
 
+app.callback(
+    Output("advanced_xic_modal", "is_open"),
+    [Input("advanced_xic_modal_button", "n_clicks"), Input("advanced_xic_modal_close", "n_clicks")],
+    [State("advanced_xic_modal", "is_open")],
+)(toggle_modal)
+
+
 # Helping to toggle the panels
 def toggle_panel(n1, is_open):
     if n1:
diff --git a/layout_misc.py b/layout_misc.py
@@ -9,9 +9,8 @@
 import dash_daq as daq
 
 # Plotly Imports
-
 import plotly.express as px
-import plotly.graph_objects as go 
+import plotly.graph_objects as go
 
 EXAMPLE_DASHBOARD = [
     dbc.CardHeader(html.H5("Example Exploration Dashboards")),
diff --git a/layout_xic_options.py b/layout_xic_options.py
@@ -0,0 +1,55 @@
+# Dash imports
+
+import dash
+import dash_core_components as dcc
+import dash_bootstrap_components as dbc
+import dash_html_components as html
+import dash_table
+from dash.dependencies import Input, Output, State
+import dash_daq as daq
+
+# Plotly Imports
+import plotly.express as px
+import plotly.graph_objects as go
+
+ADVANCED_XIC_MODAL = [
+    dbc.Modal(
+        [
+            dbc.ModalHeader("XIC Options"),
+            dbc.ModalBody([
+                dbc.Row([
+                    dbc.Col(
+                            dbc.InputGroup(
+                                [
+                                    dbc.InputGroupAddon("XIC Peptide", addon_type="prepend"),
+                                    dbc.Input(id='xic_peptide', placeholder="Enter Peptide to XIC", value=""),
+                                ],
+                                className="mb-3",
+                            ),
+                        ),
+                ]),
+                dbc.Row([
+                    dbc.Col([
+                        html.H5("mzML Chromatograms"),
+                        dcc.Dropdown(
+                            id='chromatogram_options',
+                            options=[],
+                            searchable=False,
+                            clearable=True,
+                            multi=True,
+                            value=[],
+                            style={
+                                "width":"100%"
+                            }
+                        ),
+                    ]),
+                ])
+            ]),
+            dbc.ModalFooter(
+                dbc.Button("Close", id="advanced_xic_modal_close", className="ml-auto")
+            ),
+        ],
+        id="advanced_xic_modal",
+        size="xl",
+    ),
+]
diff --git a/tasks.py b/tasks.py
@@ -54,6 +54,14 @@ def task_xic(local_filename, all_xic_values, xic_tolerance, xic_ppm_tolerance, x
     xic_df, ms2_data = xic_file(local_filename, all_xic_values, xic_tolerance, xic_ppm_tolerance, xic_tolerance_unit, rt_min, rt_max, polarity_filter, get_ms2=get_ms2)
     return xic_df.to_dict(orient="records"), ms2_data
 
+@celery_instance.task(time_limit=60)
+def task_chromatogram_options(local_filename):
+    # Caching
+    chromatograms_list = memory.cache(xic.chromatograms_list)
+
+    options = chromatograms_list(local_filename)
+    return options
+
 @celery_instance.task(time_limit=90)
 def task_featurefinding(filename, params):
     feature_df = feature_finding.perform_feature_finding(filename, params, timeout=80)
diff --git a/test/test_debug.py b/test/test_debug.py
@@ -10,10 +10,18 @@
 import download
 
 
-def test_scan_in_usi():
-    usi = "mzspec:PXD023650:03552_GA1_P_041575_P00_A00_30min_R1.raw"
-    remote_link = download._resolve_usi_remotelink(usi)
-    print(remote_link)
+# def test_scan_in_usi():
+#     usi = "mzspec:PXD023650:03552_GA1_P_041575_P00_A00_30min_R1.raw"
+#     remote_link = download._resolve_usi_remotelink(usi)
+#     print(remote_link)
+
+#     remote_link, local_filename = download._resolve_usi(usi, cleanup=False)
+#     print(remote_link, local_filename)
+
+def test_chromatograms():
+    local_filename = "std1_022721.mzML"
+    chrom_list = xic.chromatograms_list(local_filename)
+    xic_df = xic.get_chromatogram(local_filename, chrom_list[0])
+
+    print(xic_df)
 
-    remote_link, local_filename = download._resolve_usi(usi, cleanup=False)
-    print(remote_link, local_filename)
diff --git a/xic.py b/xic.py
