inline file uploader

alphastats/gui/pages/02_Import Data.py

@@ -6,13 +6,13 @@
 from alphastats.gui.utils.import_helper import (
     load_example_data,
     empty_session_state,
-    load_softwarefile_df,
-    show_metadata_file_uploader,
+    uploaded_file_to_df,
     show_loader_columns_selection,
     load_proteomics_data,
     load_options,
     show_select_sample_column_for_metadata,
     init_session_state,
+    show_button_download_metadata_template_file,
 )
 from alphastats.gui.utils.ui_helper import sidebar_info
 
@@ -80,7 +80,7 @@
 if softwarefile is None:
     st.stop()
 
-softwarefile_df = load_softwarefile_df(software, softwarefile)
+softwarefile_df = uploaded_file_to_df(softwarefile, software)
 
 intensity_column, index_column = show_loader_columns_selection(
     software=software, softwarefile_df=softwarefile_df
@@ -96,12 +96,26 @@
 
 # ##########  Load Metadata File
 st.markdown("##### 3. Prepare Metadata (optional)")
-sample_column = None
-metadatafile_df = show_metadata_file_uploader(loader)
-if metadatafile_df is not None:
-    sample_column = show_select_sample_column_for_metadata(
-        metadatafile_df, software, loader
-    )
+
+st.write(
+    "Download the template file and add additional information "
+    + "to your samples as columns (e.g. 'disease group'). "
+    + "Then upload the updated metadata file."
+)
+show_button_download_metadata_template_file(loader)
+
+metadatafile_upload = st.file_uploader(
+    "Upload metadata file with information about your samples",
+)
+
+if metadatafile_upload is None:
+    st.stop()
+
+metadatafile_df = uploaded_file_to_df(metadatafile_upload)
+
+sample_column = show_select_sample_column_for_metadata(
+    metadatafile_df, software, loader
+)
 
 
 # ##########  Create dataset

alphastats/gui/utils/analysis_helper.py

@@ -86,7 +86,10 @@ def download_preprocessing_info(plot):
 
 
 def _read_file_to_df(file: UploadedFile, decimal: str = ".") -> Optional[pd.DataFrame]:
-    """Read file to DataFrame based on file extension."""
+    """Read file to DataFrame based on file extension.
+
+    TODO rename: softwarefile -> data_file
+    """
 
     extension = Path(file.name).suffix
 

alphastats/gui/utils/import_helper.py

@@ -45,51 +45,25 @@ def load_proteomics_data(uploaded_file, intensity_column, index_column, software
     return loader
 
 
-def load_softwarefile_df(software: str, softwarefile: UploadedFile) -> pd.DataFrame:
-    """Load software file into pandas DataFrame.
+def uploaded_file_to_df(
+    uploaded_file: UploadedFile, software: str = None
+) -> pd.DataFrame:
+    """Load uploaded file into pandas DataFrame. If `software` is given, do some additional checks."""
+    df = _read_file_to_df(uploaded_file)
 
-    TODO rename: softwarefile -> data_file
-    """
-    softwarefile_df = _read_file_to_df(softwarefile)
-
-    _check_softwarefile_df(softwarefile_df, software)
-
-    st.write(
-        f"File successfully uploaded. Number of rows: {softwarefile_df.shape[0]}"
-        f", Number of columns: {softwarefile_df.shape[1]}."
-    )
-
-    st.write("Preview:")
-    st.dataframe(softwarefile_df.head(5))
+    if software is not None:
+        # assuming it's a softwarefile
+        _check_softwarefile_df(df, software)
 
-    return softwarefile_df
-
-
-def show_metadata_file_uploader(loader: BaseLoader) -> Optional[pd.DataFrame]:
-    """Show the 'upload metadata file' component and return the data."""
     st.write(
-        "Download the template file and add additional information "
-        + "to your samples as columns (e.g. 'disease group'). "
-        + "Then upload the updated metadata file."
-    )
-    show_button_download_metadata_template_file(loader)
-
-    metadatafile_upload = st.file_uploader(
-        "Upload metadata file with information about your samples",
+        f"File successfully uploaded. Number of rows: {df.shape[0]}"
+        f", Number of columns: {df.shape[1]}."
     )
 
-    if metadatafile_upload is None:
-        return None
-
-    metadatafile_df = _read_file_to_df(metadatafile_upload)
-    st.write(
-        f"File successfully uploaded. Number of rows: {metadatafile_df.shape[0]}"
-        f", Number of columns: {metadatafile_df.shape[1]}."
-    )
     st.write("Preview:")
-    st.dataframe(metadatafile_df.head(5))
+    st.dataframe(df.head(5))
 
-    return metadatafile_df
+    return df
 
 
 def load_example_data():