remove unused yml files and fix TaggerViewer errors

environment.yml

@@ -12,7 +12,5 @@ dependencies:
   - pip: # dependencies only available through pip
       # streamlit dependencies
     - streamlit==1.29.0
-    - streamlit-plotly-events==0.0.6
-    - streamlit-aggrid==0.3.4.post3
     - st_pages==0.4.5
     - captcha==0.5.0

pages/FLASHTaggerViewer.py

@@ -222,9 +222,9 @@ def sendDataToJS(selected_data, layout_info_per_exp):
             elif comp_name == 'sequence_view':
             #    data_to_send['sequence_data'] = getFragmentDataFromSeq(st.session_state.input_sequence)
                 component_arguments = SequenceViewTagger()
-            elif comp_name == 'internal_fragment_view':
+            elif comp_name == 'internal_fragment_map':
             #    data_to_send['internal_fragment_data'] = getInternalFragmentDataFromSeq(st.session_state.input_sequence)
-                component_arguments = InternalFragmentView()
+                component_arguments = InternalFragmentMap()
 
             components_of_this_row.append(FlashViewerComponent(component_arguments))
         components.append(components_of_this_row)
@@ -266,7 +266,7 @@ def sendDataToJS(selected_data, layout_info_per_exp):
 def setSequenceViewInDefaultView():
     if 'input_sequence' in st.session_state and st.session_state.input_sequence:
         global DEFAULT_LAYOUT
-        DEFAULT_LAYOUT = DEFAULT_LAYOUT + [['sequence_view']] + [['internal_fragment_view']]
+        DEFAULT_LAYOUT = DEFAULT_LAYOUT + [['sequence_view']] + [['internal_fragment_map']]
 
 
 def content():

pages/FileUploadTagger.py

@@ -228,6 +228,8 @@ def content():
     # for error message or list of uploaded files
     deconv_files = sorted(st.session_state["deconv_dfs"].keys())
     anno_files = sorted(st.session_state["anno_dfs"].keys())
+    tag_files = sorted(st.session_state["tag_dfs"].keys())
+    db_files = sorted(st.session_state["protein_dfs"].keys())
 
     # error message if files not exist
     if len(deconv_files) == 0 and len(anno_files) == 0:
@@ -240,7 +242,7 @@ def content():
         st.error("The same number of deconvolved and annotated mzML file should be uploaded!")
     else:
         v_space(2)
-        st.session_state["experiment-df"] = getUploadedFileDF(deconv_files, anno_files)
+        st.session_state["experiment-df"] = getUploadedFileDF(deconv_files, anno_files, tag_files, db_files)
         st.markdown('**Uploaded experiments in current workspace**')
         st.dataframe(st.session_state["experiment-df"])  # show table
         v_space(1)

run_app.py

@@ -0,0 +1,7 @@
+from streamlit.web import cli
+
+if __name__ == "__main__":
+    cli._main_run_clExplicit(
+        file="app.py", command_line="streamlit run", args=["local"]
+    )  # run in local mode
+    # we will create this function inside our streamlit framework