Merge pull request #49 from t0mdavid-m/new_release

New release

pages/FLASHDeconvViewer.py

@@ -7,6 +7,7 @@
 from src.components import PlotlyHeatmap, PlotlyLineplot, Plotly3Dplot, Tabulator, SequenceView, InternalFragmentMap, \
                            FlashViewerComponent, flash_viewer_grid_component
 from src.sequence import getFragmentDataFromSeq, getInternalFragmentDataFromSeq
+from pages.FileUpload import initializeWorkspace, parseUploadedFiles, getUploadedFileDF
 
 
 DEFAULT_LAYOUT = [['ms1_deconv_heat_map'], ['scan_table', 'mass_table'],
@@ -119,6 +120,17 @@ def select_experiment():
     st.title("FLASHViewer")
     setSequenceViewInDefaultView()
 
+    # Parse previously uploaded files
+    input_file_types = ["deconv-mzMLs", "anno-mzMLs", "tsv-files"]
+    parsed_df_types = ["deconv_dfs", "anno_dfs", "parsed_tsv_files"]
+    initializeWorkspace(input_file_types, parsed_df_types)
+    st.session_state['progress_bar_space'] = st.container()
+    parseUploadedFiles()
+
+    deconv_files = sorted(st.session_state["deconv_dfs"].keys())
+    anno_files = sorted(st.session_state["anno_dfs"].keys())
+    st.session_state["experiment-df"] = getUploadedFileDF(deconv_files, anno_files)
+
     ### if no input file is given, show blank page
     if "experiment-df" not in st.session_state:
         st.error('Upload input files first!')

pages/FileUpload.py

@@ -165,7 +165,7 @@ def showUploadedFilesTable() -> bool:
 
 
 # for Workflow
-def postprocessingAfterUpload_FD(uploaded_files: list) -> None:
+def postprocessingAfterUpload_FD(uploaded_files: list = None) -> None:
     initializeWorkspace(input_file_types, parsed_df_types)
     #handleInputFiles(uploaded_files)
     parseUploadedFiles()

src/Workflow.py

@@ -73,7 +73,7 @@ def configure(self) -> None:
     def execution(self) -> None:
         # Get input files
         try:      
-            in_mzMLs = self.file_manager.get_files(self.params["mzML-files"])
+            in_mzmls = self.file_manager.get_files(self.params["mzML-files"])
         except ValueError:
             st.error('Please select at least one mzML file.')  
             return
@@ -103,10 +103,10 @@ def execution(self) -> None:
             threads = DEFAULT_THREADS
 
         # Process files in sequence
-        for in_mzML in in_mzMLs:
+        for in_mzml in in_mzmls:
 
             # Generate output folder
-            current_base = splitext(basename(in_mzML))[0]
+            current_base = splitext(basename(in_mzml))[0]
             current_time = time.strftime("%Y%m%d-%H%M%S")
             folder_path = join(base_path, 'FLASHTaggerOutput', '%s_%s'%(current_base, current_time))
             if exists(folder_path):
@@ -120,6 +120,19 @@ def execution(self) -> None:
             out_tag = join(base_path, self.tool_name, 'tags-tsv', f'{current_base}_{current_time}_tagged.tsv')
             out_protein = join(base_path, self.tool_name, 'proteins-tsv', f'{current_base}_{current_time}_protein.tsv')
 
+            # Additional outputs are directly written to download folder
+            out_tsv = join(folder_path, f'out.tsv')
+            out_spec1 = join(folder_path, f'spec1.tsv')
+            out_spec2 = join(folder_path, f'spec2.tsv')
+            out_spec3 = join(folder_path, f'spec3.tsv')
+            out_spec4 = join(folder_path, f'spec4.tsv')
+            out_quant = join(folder_path, f'quant.tsv')
+            out_msalign1 = join(folder_path, f'toppic_ms1.msalign')
+            out_msalign2 = join(folder_path, f'toppic_ms2.msalign')
+            out_feature1 = join(folder_path, f'toppic_ms1.feature')
+            out_feature2 = join(folder_path, f'toppic_ms2.feature')
+            out_prsm = join(folder_path, f'prsms.tsv')
+
             # Check if a decoy database needs to be generated
             tagger_params = self.executor.parameter_manager.get_parameters_from_json()['FLASHTnT']
             if ((tagger_params.get('tnt:prsm_fdr', 1) < 1) or (tagger_params.get('tnt:pro_fdr', 1) < 1)):
@@ -150,10 +163,19 @@ def execution(self) -> None:
             self.executor.run_topp(
                 'FLASHDeconv',
                 input_output={
-                    'in' : [in_mzML],
-                    'out' : ['_.tsv'],
-                    'out_annotated_mzml' :  [out_anno],
-                    'out_mzml' :  [out_deconv],
+                    'in' : [in_mzml],
+                    'out' : [out_tsv],
+                    'out_spec1' : [out_spec1],
+                    'out_spec2' : [out_spec2],
+                    'out_spec3' : [out_spec3],
+                    'out_spec4' : [out_spec4],
+                    'out_mzml' : [out_deconv],
+                    'out_quant' : [out_quant],
+                    'out_annotated_mzml' : [out_anno],
+                    'out_msalign1' : [out_msalign1],
+                    'out_msalign2' : [out_msalign2],
+                    'out_feature1' : [out_feature1],
+                    'out_feature2' : [out_feature2],
                 },
                 params_manual = {
                     'threads' : threads
@@ -168,7 +190,7 @@ def execution(self) -> None:
                     'fasta' : [out_db],
                     'out_tag' :  [out_tag],
                     'out_pro' :  [out_protein],
-                    'out_prsm' : ['_.tsv']
+                    'out_prsm' : [out_prsm]
                 },
                 params_manual = {
                     'threads' : threads
@@ -226,7 +248,7 @@ def configure(self) -> None:
     def execution(self) -> None:
         # Get input files
         try:      
-            in_mzMLs = self.file_manager.get_files(self.params["mzML-files"])
+            in_mzmls = self.file_manager.get_files(self.params["mzML-files"])
         except ValueError:
             st.error('Please select at least one mzML file.')  
             return
@@ -247,10 +269,10 @@ def execution(self) -> None:
             threads = DEFAULT_THREADS
 
         # Process files in sequence
-        for in_mzML in in_mzMLs:
+        for in_mzml in in_mzmls:
 
             # Generate output folder
-            current_base = splitext(basename(in_mzML))[0]
+            current_base = splitext(basename(in_mzml))[0]
             current_time = time.strftime("%Y%m%d-%H%M%S")
             folder_path = join(base_path, 'FLASHDeconvOutput', '%s_%s'%(current_base, current_time))
             if exists(folder_path):
@@ -259,8 +281,8 @@ def execution(self) -> None:
 
             # Define output paths for viewer
             out_tsv = join(base_path, self.tool_name, 'tsv-files', f'{current_base}_{current_time}.tsv')
-            out_mzml = join(base_path, self.tool_name, 'deconv-mzMLs', f'{current_base}_{current_time}_deconv.mzML')
-            out_annotated_mzml = join(base_path, self.tool_name, 'anno-mzMLs', f'{current_base}_{current_time}_annotated.mzML')
+            out_deconv = join(base_path, self.tool_name, 'deconv-mzMLs', f'{current_base}_{current_time}_deconv.mzML')
+            out_anno = join(base_path, self.tool_name, 'anno-mzMLs', f'{current_base}_{current_time}_annotated.mzML')
 
             # Additional outputs are directly written to download folder
             out_spec1 = join(folder_path, f'spec1.tsv')
@@ -277,15 +299,15 @@ def execution(self) -> None:
             self.executor.run_topp(
                 'FLASHDeconv',
                 input_output={
-                    'in' : [in_mzML],
+                    'in' : [in_mzml],
                     'out' : [out_tsv],
                     'out_spec1' : [out_spec1],
                     'out_spec2' : [out_spec2],
                     'out_spec3' : [out_spec3],
                     'out_spec4' : [out_spec4],
-                    'out_mzml' : [out_mzml],
+                    'out_mzml' : [out_deconv],
                     'out_quant' : [out_quant],
-                    'out_annotated_mzml' : [out_annotated_mzml],
+                    'out_annotated_mzml' : [out_anno],
                     'out_msalign1' : [out_msalign1],
                     'out_msalign2' : [out_msalign2],
                     'out_feature1' : [out_feature1],
@@ -297,8 +319,8 @@ def execution(self) -> None:
             )
 
             # Copy generated files to output            
-            copyfile(out_mzml, join(folder_path, f'out_deconv.mzML'))
-            copyfile(out_annotated_mzml, join(folder_path, f'anno_annotated.mzML'))
+            copyfile(out_deconv, join(folder_path, f'out_deconv.mzML'))
+            copyfile(out_anno, join(folder_path, f'anno_annotated.mzML'))
             copyfile(out_tsv, join(folder_path, f'out.tsv'))
 
             # Store settings

src/workflow/ParameterManager.py

@@ -1,4 +1,5 @@
 import pyopenms as poms
+import os
 import json
 import shutil
 import streamlit as st
@@ -50,12 +51,19 @@ def save_parameters(self) -> None:
         # for each TOPP tool, open the ini file
         for tool in current_topp_tools:
             json_params[tool] = {}
+            if os.path.isfile(self.params_file):
+                with open(self.params_file, "r") as f:
+                    file_params = json.load(f)
+                if tool in file_params:
+                    json_params[tool] = file_params[tool]            
             # load the param object
             param = poms.Param()
             poms.ParamXMLFile().load(str(Path(self.ini_dir, f"{tool}.ini")), param)
             # get all session state param keys and values for this tool
+            print('xxxxx')
             for key, value in st.session_state.items():
                 if key.startswith(f"{self.topp_param_prefix}{tool}:1:"):
+                    print(key, value)
                     # get ini_key
                     ini_key = key.replace(self.topp_param_prefix, "").encode()
                     # get ini (default) value by ini_key
@@ -75,7 +83,7 @@ def save_parameters(self) -> None:
                                 cast_type = str
                             value = [cast_type(v) for v in value.split("\n")]
                     # check if value is different from default
-                    if ini_value != value:
+                    if (ini_value != value) or (json_params[tool].get(key.split(":1:")[1], value) != value):
                         # store non-default value
                         json_params[tool][key.split(":1:")[1]] = value
         # Save to json file

src/workflow/StreamlitUI.py

@@ -825,7 +825,12 @@ def file_upload_section(self, custom_upload_function) -> None:
             self.zip_and_download_files(Path(self.workflow_dir, "input-files"))
 
     def parameter_section(self, custom_paramter_function) -> None:
-        st.toggle("Show advanced parameters", value=False, key="advanced")
+        if "advanced" not in st.session_state:
+            st.session_state["advanced"] = False
+        def toggle_advanced():
+            self.parameter_manager.save_parameters()
+            st.session_state["advanced"] = not st.session_state["advanced"]
+        st.toggle("Show advanced parameters", value=st.session_state["advanced"], on_change=toggle_advanced)
 
         form = st.form(
             key=f"{self.workflow_dir.stem}-input-form",