Merge branch 'fix_merging_issues' of github.com:JeeH-K/FLASHViewer in…

…to fix_merging_issues

pages/FLASHDeconvWorkflow.py

@@ -1,8 +1,6 @@
 import streamlit as st
 from src.common import page_setup
-from src.workflow.WorkflowManager import WorkflowManager
-from src.Workflow import DeconvWorkflow, Workflow
-import pyopenms as oms
+from src.Workflow import DeconvWorkflow
 
 
 # The rest of the page can, but does not have to be changed

pages/FLASHTaggerWorkflow.py

@@ -1,8 +1,6 @@
 import streamlit as st
 from src.common import page_setup
-from src.workflow.WorkflowManager import WorkflowManager
-from src.Workflow import TagWorkflow, Workflow
-import pyopenms as oms
+from src.Workflow import TagWorkflow
 
 
 # The rest of the page can, but does not have to be changed

pages/FileUpload.py

@@ -8,6 +8,10 @@
 from src.common import page_setup, v_space, save_params, reset_directory
 
 
+input_file_types = ["deconv-mzMLs", "anno-mzMLs"]
+parsed_df_types = ["deconv_dfs", "anno_dfs"]
+
+
 def initializeWorkspace(input_file_types_: list, parsed_df_types_: list) -> None:
     """
     Set up the required directory and session states
@@ -135,14 +139,45 @@ def parseUploadedFiles():
             st.success('Done parsing the experiment %s!' % exp_name)
 
 
+def showUploadedFilesTable() -> bool:
+    ''' return: if showing without error '''
+    # 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())
+
+    # error message if files not exist
+    if len(deconv_files) == 0 and len(anno_files) == 0:
+        st.info('No mzML added yet!', icon="ℹ️")
+    elif len(deconv_files) == 0:
+        st.error("FLASHDeconv deconvolved mzML file is not added yet!")
+    elif len(anno_files) == 0:
+        st.error("FLASHDeconv annotated mzML file is not added yet!")
+    elif len(deconv_files) != len(anno_files):
+        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.markdown('**Uploaded experiments in current workspace**')
+        st.dataframe(st.session_state["experiment-df"])  # show table
+        v_space(1)
+        return True
+    return False
+
+
+# for Workflow
+def postprocessingAfterUpload_FD(uploaded_files: list) -> None:
+    initializeWorkspace(input_file_types, parsed_df_types)
+    handleInputFiles(uploaded_files)
+    parseUploadedFiles(reparse=True)
+    showUploadedFilesTable()
+
+
 if __name__ == '__main__':
 
     # page initialization
     params = page_setup()
 
     # make directory to store deconv and anno mzML files & initialize data storage
-    input_file_types = ["deconv-mzMLs", "anno-mzMLs"]
-    parsed_df_types = ["deconv_dfs", "anno_dfs"]
     initializeWorkspace(input_file_types, parsed_df_types)
 
     st.title("FLASHDeconv output files Upload")
@@ -203,26 +238,7 @@ def parseUploadedFiles():
     st.session_state['progress_bar_space'] = st.container()
     parseUploadedFiles()
 
-    # 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())
-
-    # error message if files not exist
-    if len(deconv_files) == 0 and len(anno_files) == 0:
-        st.info('No mzML added yet!', icon="ℹ️")
-    elif len(deconv_files) == 0:
-        st.error("FLASHDeconv deconvolved mzML file is not added yet!")
-    elif len(anno_files) == 0:
-        st.error("FLASHDeconv annotated mzML file is not added yet!")
-    elif len(deconv_files) != len(anno_files):
-        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.markdown('**Uploaded experiments in current workspace**')
-        st.dataframe(st.session_state["experiment-df"])  # show table
-        v_space(1)
-
+    if showUploadedFilesTable():
         # Remove files
         with st.expander("🗑️ Remove mzML files"):
             to_remove = st.multiselect(

pages/FileUploadTagger.py

@@ -8,6 +8,10 @@
 from pages.FileUpload import remove_selected_mzML_files
 
 
+input_file_types = ["deconv-mzMLs", "anno-mzMLs", "tags-tsv", "proteins-tsv"]
+parsed_df_types = ["deconv_dfs", "anno_dfs", "tag_dfs", "protein_dfs"]
+
+
 def initializeWorkspace(input_file_types_: list, parsed_df_types_: list) -> None:
     """
     Set up the required directory and session states
@@ -167,13 +171,20 @@ def content():
     parsed_df_types = ["deconv_dfs", "anno_dfs", "tag_dfs", "protein_dfs"]
     initializeWorkspace(input_types, parsed_df_types)
 
+
+# for Workflow
+def postprocessingAfterUpload_Tagger(uploaded_files: list) -> None:
+    initializeWorkspace(input_file_types, parsed_df_types)
+    handleInputFiles(uploaded_files)
+    parseUploadedFiles(reparse=True)
+    showUploadedFilesTable()
+
+
 if __name__ == '__main__':
 
     params = page_setup()
 
     # make directory to store deconv and anno mzML files & initialize data storage
-    input_file_types = ["deconv-mzMLs", "anno-mzMLs", "tags-tsv", "proteins-tsv"]
-    parsed_df_types = ["deconv_dfs", "anno_dfs", "tag_dfs", "protein_dfs"]
     initializeWorkspace(input_file_types, parsed_df_types)
 
     st.title("File Upload")

src/Workflow.py

@@ -1,9 +1,8 @@
 import streamlit as st
 import time
 from .workflow.WorkflowManager import WorkflowManager
-from pages.FileUploadTagger import handleInputFiles
-from pages.FileUploadTagger import parseUploadedFiles
-from pages.FileUploadTagger import initializeWorkspace, showUploadedFilesTable
+from pages.FileUploadTagger import postprocessingAfterUpload_Tagger
+from pages.FileUpload import postprocessingAfterUpload_FD
 
 from os.path import join, splitext, basename, exists, dirname
 from os import makedirs
@@ -182,13 +181,7 @@ def pp(self) -> None:
 
 
         # make directory to store deconv and anno mzML files & initialize data storage
-        input_types = ["deconv-mzMLs", "anno-mzMLs", "tags-tsv", "proteins-tsv"]
-        parsed_df_types = ["deconv_dfs", "anno_dfs", "tag_dfs", "protein_dfs"]
-        initializeWorkspace(input_types, parsed_df_types)
-        handleInputFiles(uploaded_files)
-        parseUploadedFiles(reparse=True)
-        showUploadedFilesTable()
-
+        postprocessingAfterUpload_Tagger(uploaded_files)
 
 
 
@@ -343,7 +336,35 @@ def configure(self) -> None:
             ],
             display_subsections=True
         )
-
+
+
+    def pp(self) -> None:
+        st.session_state['progress_bar_space'] = st.container()
+
+        try:
+            in_mzMLs = self.file_manager.get_files(self.params["mzML-files"])
+        except:
+            st.error('Please select at least one mzML file.')
+            return
+
+        base_path = dirname(self.workflow_dir)
+
+        uploaded_files = []
+        for in_mzML in in_mzMLs:
+            current_base = splitext(basename(in_mzML))[0]
+            current_time = time.strftime("%Y%m%d-%H%M%S")
+
+            out_anno = join(base_path, 'anno-mzMLs', f'{current_base}_{current_time}_annotated.mzML')
+            out_deconv = join(base_path, 'deconv-mzMLs', f'{current_base}_{current_time}_deconv.mzML')
+
+            #uploaded_files.append(out_db)
+            uploaded_files.append(out_anno)
+            uploaded_files.append(out_deconv)
+
+        # make directory to store deconv and anno mzML files & initialize data storage
+        postprocessingAfterUpload_FD(uploaded_files)
+
+
     def execution(self) -> None:
         # Get mzML input files from self.params.
         # Can be done without file manager, however, it ensures everything is correct.