Merge pull request #461 from Proteobench/save_raw_input

Change saving from intermediate to raw input

proteobench/modules/quant_base/quant_base_module.py

@@ -2,6 +2,7 @@
 
 import logging
 import os
+import shutil
 from tempfile import TemporaryDirectory
 from typing import Any, Optional
 
@@ -19,15 +20,17 @@
 from proteobench.io.params.alphadia import extract_params as extract_params_alphadia
 from proteobench.io.params.alphapept import extract_params as extract_params_alphapept
 from proteobench.io.params.diann import extract_params as extract_params_diann
-from proteobench.io.params.spectronaut import read_spectronaut_settings as extract_params_spectronaut
 from proteobench.io.params.fragger import extract_params as extract_params_fragger
 from proteobench.io.params.i2masschroq import (
     extract_params as extract_params_i2masschroq,
 )
 from proteobench.io.params.maxquant import extract_params as extract_params_maxquant
+from proteobench.io.params.msaid import extract_params as extract_params_msaid
 from proteobench.io.params.proline import extract_params as extract_params_proline
 from proteobench.io.params.sage import extract_params as extract_params_sage
-from proteobench.io.params.msaid import extract_params as extract_params_msaid
+from proteobench.io.params.spectronaut import (
+    read_spectronaut_settings as extract_params_spectronaut,
+)
 from proteobench.io.parsing.parse_ion import load_input_file
 from proteobench.io.parsing.parse_settings_ion import ParseSettingsBuilder
 from proteobench.score.quant.quantscores import QuantScores
@@ -161,8 +164,6 @@ def filter_data_point(all_datapoints: pd.DataFrame, default_val_slider: int = 3)
         pd.DataFrame
             All data points with the filtered data points.
         """
-        print(all_datapoints)
-
         all_datapoints["median_abs_epsilon"] = [
             filter_df_numquant_median_abs_epsilon(v, min_quant=default_val_slider) for v in all_datapoints["results"]
         ]
@@ -355,33 +356,42 @@ def write_json_local_development(self, temporary_datapoints: pd.DataFrame, datap
 
         return os.path.join(self.t_dir_pr, "results.json")
 
-    def write_intermediate_raw(self, dir: str, ident: str, input_df: pd.DataFrame, result_performance, param_loc):
+    def write_intermediate_raw(
+        self, dir: str, ident: str, input_file_path: str, result_performance: pd.DataFrame, param_loc
+    ):
         """
         Write intermediate and raw data to a directory.
 
         Parameters
         ----------
-        dir
+        dir : str
             Directory to write to.
-        ident
-            Intermediate hash of the submission.
-        input_df
-            Input DataFrame.
-        result_performance
-            Result performance DataFrame.
+        ident : str
+            Identifier (e.g., hash) to create a subdirectory for this submission.
+        input_file_path : str
+            Location to temp file of raw-input
+        result_performance : pd.DataFrame
+            Result performance DataFrame to be saved.
+        param_loc : list of str
+            List of paths to parameter files that need to be copied to the directory.
         """
 
+        # Create the target directory
         path_write = os.path.join(dir, ident)
         try:
-            os.mkdir(path_write)
-        except:
-            logging.warning(f"Could not make directory: {path_write}")
+            os.makedirs(path_write, exist_ok=True)
+        except Exception as e:
+            logging.warning(f"Could not create directory: {path_write}. Error: {e}")
+
+        try:
+            shutil.copy(input_file_path, dir)
+        except Exception as e:
+            logging.error(f"Failed to save input file to {input_file_path}. Error: {e}")
 
         # TODO: save parameters file "locally" together with the raw and intermediate?
-        with open(os.path.join(path_write, "params.csv"), "w") as f:
+        with open(os.path.join(path_write, "params_without_extension"), "w") as f:
             f.write(",\n".join(_file.getvalue().decode("utf-8") for _file in param_loc))
 
-        input_df.to_csv(os.path.join(path_write, "input_df.csv"))
         result_performance.to_csv(os.path.join(path_write, "result_performance.csv"))
 
     def load_params_file(self, input_file: list[str], input_format: str) -> ProteoBenchParameters:
@@ -400,9 +410,6 @@ def load_params_file(self, input_file: list[str], input_format: str) -> ProteoBe
         ProteoBenchParameters
             Parameters for the module.
         """
-
-        # ! adapted to be able to parse more than one file.
-        # ! how to ensure orrect order?
         params = self.EXTRACT_PARAMS_DICT[input_format](*input_file)
         params.software_name = input_format
         return params

webinterface/pages/base_pages/quant.py

@@ -413,11 +413,13 @@ def save_intermediate_submission_data(self, pr_url: str) -> None:
             ].iloc[-1, :]["intermediate_hash"]
         )
 
+        self.user_input["input_csv"].getbuffer()
+
         if "storage" in st.secrets.keys():
             self.ionmodule.write_intermediate_raw(
                 st.secrets["storage"]["dir"],
                 id,
-                st.session_state[self.variables_quant.input_df_submission],
+                self.user_input["input_csv"],
                 st.session_state[self.variables_quant.result_performance_submission],
                 self.user_input[self.variables_quant.meta_data],
             )