Merge pull request #243 from Jhsmit/folding

Add folding/rfu app

Author: Jhsmit

MANIFEST.in

@@ -12,7 +12,7 @@ recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif
 include versioneer.py
 include pyhdx/_version.py
 include pyhdx/web/*.html
-include pyhdx/web/*.yaml
+include pyhdx/web/apps/*.yaml
 include pyhdx/config.ini
 
 graft pyhdx/web/static 

dev/gui/dev_gui_rfu.py

@@ -0,0 +1,167 @@
+"""
+Reload folding data and GUI
+Run local_cluster.py in anothor thread
+
+"""
+
+import sys
+from pathlib import Path
+
+import pandas as pd
+import panel as pn
+import yaml
+
+from pyhdx.batch_processing import yaml_to_hdxm
+from pyhdx.fileIO import csv_to_dataframe, load_fitresult
+from pyhdx.fileIO import csv_to_protein
+from pyhdx.web.apps import rfu_app
+from pyhdx.web.base import STATIC_DIR
+from pyhdx.web.utils import load_state, fix_multiindex_dtypes
+
+sys._excepthook = sys.excepthook
+
+import traceback as tb
+def my_exception_hook(exctype, value, traceback):
+    # Print the error and traceback
+    # https://stackoverflow.com/questions/43039048/pyqt5-fails-with-cryptic-message/43039363#43039363
+    tb.print_tb(traceback, file=sys.stdout)
+    print(exctype, value, traceback)
+
+    tb.print_stack()
+    print(traceback.format_exc())
+    # or
+    print(sys.exc_info()[2])
+    # Call the normal Exception hook after
+    sys._excepthook(exctype, value, traceback)
+    sys.exit(1)
+
+
+
+# Set the exception hook to our wrapping function
+sys.excepthook = my_exception_hook
+
+
+ctrl, tmpl = rfu_app()
+
+
+cwd = Path(__file__).parent.resolve()
+# root_dir = cwd.parent.parent
+# test_dir = cwd / 'test_data'
+#
+# fpath_1 = root_dir / 'tests' / 'test_data' / 'ecSecB_apo.csv'
+# fpath_2 = root_dir / 'tests' / 'test_data' / 'ecSecB_dimer.csv'
+# fitresult_dir = root_dir / 'tests' / 'test_data' / 'output' / 'ecsecb_tetramer_dimer'
+#
+#
+# data_dir = root_dir / 'tests' / 'test_data' / 'input'
+# #data_dir = cwd / 'rinky_data'
+#
+# yaml_dict = yaml.safe_load(Path(data_dir / 'data_states.yaml').read_text())
+# pdb_string = (test_dir / '1qyn.pdb').read_text()
+
+
+
+def reload_tables():
+    test_dir = cwd / 'test_data'
+    src = ctrl.sources['main']
+
+    df = csv_to_dataframe(test_dir / 'peptides.csv')
+    # names = df.columns.names
+    # df = df.convert_dtypes()
+    # df.columns.names = names
+    table_names = [
+            'rfu_residues.csv',
+            'rates.csv',
+            'peptides.csv',
+            'dG_fits.csv',
+            'ddG_comparison.csv',
+            'd_calc.csv',
+            'loss.csv',
+            'peptide_mse.csv'
+    ]
+    for name in table_names:
+        try:
+            df = csv_to_dataframe(test_dir / name)
+            df.columns = fix_multiindex_dtypes(df.columns)
+            src.tables[name.split('.')[0]] = df
+        except Exception as e:
+            print(e)
+            print('not loaded:', name)
+
+    src.param.trigger('updated')
+
+
+    #ctrl.views['protein'].object = pdb_string
+
+#ctrl.views['protein'].object = pdb_string
+
+
+def reload_dashboard():
+    data_objs = {k: yaml_to_hdxm(v, data_dir=data_dir) for k, v in yaml_dict.items()}
+    for k, v in data_objs.items():
+        v.metadata['name'] = k
+
+    source = ctrl.sources['main']
+    for ds in ['peptides', 'peptides_mse', 'd_calc', 'rfu', 'rates', 'global_fit', 'losses']:
+        df = csv_to_protein(test_dir / f'{ds}.csv')
+        source.add_df(df, ds)
+
+    #Temporary workaround for comment characters in csv files
+    ds = 'colors'
+    df = pd.read_csv(test_dir / f'{ds}.csv', header=[0, 1, 2], index_col=0,
+                     skiprows=3)
+    source.add_df(df, ds)
+
+
+def init_dashboard():
+    for k, v in yaml_dict.items():
+        load_state(ctrl, v, data_dir=data_dir, name=k)
+
+    # k = next(iter(yaml_dict.keys()))
+    # load_state(ctrl, yaml_dict[k], data_dir=data_dir, name=k)
+
+    src = ctrl.sources['main']
+    fit_control = ctrl.control_panels['FitControl']
+
+    fit_control.r1 = 0.05
+    fit_control.r2 = 0.1
+    fit_control.epochs = 200
+    fit_control.patience = 100
+
+
+    # ngl = ctrl.views['protein']
+    # ngl._ngl.pdb_string = Path(test_dir / '1qyn.pdb').read_text()
+    fit_result = load_fitresult(fitresult_dir)
+
+    src.add(fit_result, 'gibbs_fit_1')
+
+    pdb_src = ctrl.sources['pdb']
+    pdb_src.add_from_string(pdb_string, '1qyn')
+
+    diff = ctrl.control_panels['DifferentialControl']
+    #diff._action_add_comparison()
+
+    # ctrl.views['protein'].object = pdb_string
+    #
+    # fit_result = load_fitresult(fitresult_dir)
+    # src.add(fit_result, 'fit_1')
+
+
+#if __name__ == '__main__':
+#pn.state.onload(reload_dashboard)
+#pn.state.onload(reload_tables)
+#pn.state.onload(init_dashboard)
+
+if __name__ == '__main__':
+
+    #init_dashboard()
+
+    pn.serve(tmpl, show=True, static_dirs={'pyhdx': STATIC_DIR})
+
+elif __name__.startswith('bokeh_app'):
+    tmpl.servable()
+
+#ctrl.template.servable()
+
+
+# panel serve --show --autoreload --static-dirs pyhdx=C:\Users\jhsmi\pp\PyHDX\pyhdx\web\static

images/pyhdx_header.png

@@ -35,7 +35,7 @@ def main():
         print(f"Started new Dask LocalCluster at {scheduler_address}")
 
     if args.serve:
-        serve.run_main()
+        serve.run_apps()
 
 
 if __name__ == '__main__':

pyhdx/cli.py

@@ -12,24 +12,25 @@
 
 #cache = HybridHDFCache(file_path ='test123.h5')
 
+
+fmt = {
+    'header_color': '#ffffff',  # this is the text
+    'header_background': '#00407A',
+    'accent_base_color': '#00407A',
+    'theme_toggle': False
+}
+
 @logger('pyhdx')
 def main_app():
     cwd = Path(__file__).parent.resolve()
-    yaml_dict = yaml.safe_load((cwd / 'pyhdx_app.yaml').read_text(encoding='utf-8'))
+    yaml_dict = yaml.safe_load((cwd / 'apps' / 'pyhdx_app.yaml').read_text(encoding='utf-8'))
 
     ctr = AppConstructor(loggers={'pyhdx': main_app.logger}, cache=cache)
 
     ctrl = ctr.parse(yaml_dict)
 
     ctrl.start()
 
-    fmt = {
-        'header_color': '#ffffff',  # this is the text
-        'header_background': '#00407A',
-        'accent_base_color': '#00407A',
-        'theme_toggle': False
-    }
-
     tmpl = pn.template.FastGridTemplate(title=f'{VERSION_STRING}', **fmt)
     controllers = ctrl.control_panels.values()
     controls = pn.Accordion(*[controller.panel for controller in controllers], toggle=True)
@@ -45,7 +46,6 @@ def main_app():
         'rates',
         'gibbs_overlay',
         'peptide_mse',
-        #'peptide_scatter',
         'peptide_overlay',
         'loss_lines'
         ]
@@ -85,4 +85,60 @@ def get_view(name):
     tmpl.main[3:5, 0:6] = log_tab
     tmpl.main[3:5, 6:12] = peptide_tab
 
+    return ctrl, tmpl
+
+
+@logger('pyhdx')
+def rfu_app():
+    cwd = Path(__file__).parent.resolve()
+    yaml_dict = yaml.safe_load((cwd / 'apps' / 'rfu_app.yaml').read_text(encoding='utf-8'))
+
+    ctr = AppConstructor(loggers={'pyhdx': rfu_app.logger}, cache=cache)
+
+    ctrl = ctr.parse(yaml_dict)
+
+    ctrl.start()
+
+
+
+    tmpl = pn.template.FastGridTemplate(title=f'{VERSION_STRING}', **fmt)
+    controllers = ctrl.control_panels.values()
+    controls = pn.Accordion(*[controller.panel for controller in controllers], toggle=True)
+    tmpl.sidebar.append(controls)
+
+    views_names = [
+        'rfu_scatter',
+        'coverage',
+        'logging_info',
+        'logging_debug',
+        'protein',
+        ]
+
+    views = {v: ctrl.views[v] for v in views_names}
+    [v.update() for v in views.values()]
+
+    # this should be on the view intances probably
+    def get_view(name):
+        return pn.Column(views[name].panel, sizing_mode='stretch_both')
+
+    cov_tab = pn.Tabs(
+        ('Coverage', get_view('coverage')),
+        ('Protein', get_view('protein')),
+    )
+
+    scatter_tab = pn.Tabs(
+        ('RFU', get_view('rfu_scatter')),
+    )
+
+    log_tab = pn.Tabs(
+        ('Info log', views['logging_info'].panel),
+        ('Debug log', views['logging_debug'].panel)
+    )
+
+
+    tmpl.main[0:3, 0:6] = cov_tab
+    tmpl.main[0:3, 6:12] = scatter_tab
+    tmpl.main[3:5, 0:6] = log_tab
+    #tmpl.main[3:5, 6:12] = peptide_tab
+
     return ctrl, tmpl