add Download section to FLASHTagger

app.py

@@ -47,6 +47,7 @@ def flashtagPages():
         Page("pages/FileUploadTagger.py", "File Upload", "📁"),
         Page("pages/LayoutManagerTagger.py", "Layout Manager", "📝️"),
         Page("pages/FLASHTaggerViewer.py", "Viewer", "👀"),
+        Page("pages/FLASHTaggerDownload.py", "Download", "⬇️"),
     ])
 
 

pages/FLASHTaggerDownload.py

@@ -0,0 +1,61 @@
+import streamlit as st
+
+from os.path import join, exists, dirname, isfile, basename
+from os import listdir
+
+from src.common import page_setup
+from io import StringIO, BytesIO
+from zipfile import ZipFile, ZIP_DEFLATED
+
+
+def content():
+    page_setup("TaggerViewer")
+
+    dirpath = join(st.session_state["workspace"], 'FLASHTaggerOutput')
+
+    if exists(dirpath):
+        directories = sorted(
+            [entry for entry in listdir(dirpath) if not isfile(entry)]
+        )
+    else:
+        directories = []
+
+    if len(directories) == 0:
+        st.error('No results to show yet. Please run a workflow first!')
+        return
+
+    # Table Header
+    columns = st.columns((0.4, 0.6))
+    columns[0].write('**Run**')
+    columns[1].write('**Download**')
+
+    # Table Body
+    for i, directory in enumerate(directories):
+        st.divider()
+        columns = st.columns((0.4, 0.6))
+        columns[0].empty().write(directory)
+
+        with columns[1]:
+            button_placeholder = st.empty()
+
+            clicked = button_placeholder.button('Prepare Download', key=i)
+            if clicked:
+                button_placeholder.empty()
+                with st.spinner():
+                    out_zip = join(dirpath, directory, 'output.zip')
+                    if not exists(out_zip):
+                        with ZipFile(out_zip, 'w', ZIP_DEFLATED) as zip_file:
+                            for output in listdir(join(dirpath, directory)):
+                                try:
+                                    with open(join(dirpath, directory, output), 'r') as f:
+                                        zip_file.writestr(basename(output), f.read())
+                                except:
+                                    continue
+                    with open(out_zip, 'rb') as f:
+                        button_placeholder.download_button(
+                            "Download ⬇️", f, 
+                            file_name = f'{directory}.zip'
+                        )
+
+if __name__ == "__main__":
+    content()

pages/FLASHTaggerViewer.py

@@ -232,26 +232,26 @@ def content():
                 sendDataToJS(selected_exp, layout_info, 'flash_viewer_grid_%d' % exp_index)
 
 
-    selected_tags = selected_exp0.iloc[0]['Tag Files']
-    selected_proteins = selected_exp0.iloc[0]['Protein Files']
-    tag_df = st.session_state['tag_dfs_tagger'][selected_tags]
-    protein_df = st.session_state['protein_dfs_tagger'][selected_proteins]
-
-    tag_buffer = StringIO()
-    tag_df.to_csv(tag_buffer, sep='\t', index=False)
-    tag_buffer.seek(0)
-
-    protein_buffer = StringIO()
-    protein_df.to_csv(protein_buffer, sep='\t', index=False)
-    protein_buffer.seek(0)
-
-    zip_buffer = BytesIO()
-    with ZipFile(zip_buffer, 'w', ZIP_DEFLATED) as zip_file:
-        zip_file.writestr('tags.tsv', tag_buffer.getvalue())
-        zip_file.writestr('proteins.tsv', protein_buffer.getvalue())
-    zip_buffer.seek(0)
+    # selected_tags = selected_exp0.iloc[0]['Tag Files']
+    # selected_proteins = selected_exp0.iloc[0]['Protein Files']
+    # tag_df = st.session_state['tag_dfs_tagger'][selected_tags]
+    # protein_df = st.session_state['protein_dfs_tagger'][selected_proteins]
+
+    # tag_buffer = StringIO()
+    # tag_df.to_csv(tag_buffer, sep='\t', index=False)
+    # tag_buffer.seek(0)
+
+    # protein_buffer = StringIO()
+    # protein_df.to_csv(protein_buffer, sep='\t', index=False)
+    # protein_buffer.seek(0)
+
+    # zip_buffer = BytesIO()
+    # with ZipFile(zip_buffer, 'w', ZIP_DEFLATED) as zip_file:
+    #     zip_file.writestr('tags.tsv', tag_buffer.getvalue())
+    #     zip_file.writestr('proteins.tsv', protein_buffer.getvalue())
+    # zip_buffer.seek(0)
 
-    st.download_button("Download ⬇️", zip_buffer, file_name=f'{st.session_state.selected_experiment0}.zip')
+    # st.download_button("Download ⬇️", zip_buffer, file_name=f'{st.session_state.selected_experiment0}.zip')
 
 
 if __name__ == "__main__":

src/Workflow.py

@@ -232,6 +232,14 @@ def execution(self) -> None:
             out_tag = join(base_path, 'tags-tsv', f'{current_base}_{current_time}_tagged.tsv')
             out_protein = join(base_path, 'proteins-tsv', f'{current_base}_{current_time}_protein.tsv')
             #decoy_db = join(temp_path, f'{current_base}_db.fasta')
+
+            # Get folder name
+            folder_path = join(base_path, 'FLASHTaggerOutput', '%s_%s'%(current_base, current_time))
+
+            if exists(folder_path):
+                rmtree(folder_path)
+            makedirs(folder_path)
+
 
             if self.executor.parameter_manager.get_parameters_from_json()['generate_decoys']:
                 if self.executor.parameter_manager.get_parameters_from_json()['few_proteins']:
@@ -279,6 +287,12 @@ def execution(self) -> None:
             uploaded_files.append(out_tag)
             uploaded_files.append(out_protein)
 
+            copyfile(out_db, join(folder_path, 'database.fasta'))
+            copyfile(out_anno, join(folder_path, 'annotated.mzML'))
+            copyfile(out_deconv, join(folder_path, 'out.mzML'))
+            copyfile(out_tag, join(folder_path, 'tags.tsv'))
+            copyfile(out_protein, join(folder_path, 'proteins.tsv'))
+
 
         # make directory to store deconv and anno mzML files & initialize data storage
         # input_types = ["deconv-mzMLs", "anno-mzMLs", "tags-tsv", "db-fasta"]