fix SpectronautLoader.py

MannLabs · Oct 28, 2024 · 84718ca · 84718ca
1 parent 6f8fc80
commit 84718ca
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/alphastats/gui/utils/ui_helper.py b/alphastats/gui/utils/ui_helper.py
@@ -96,9 +96,8 @@ def init_session_state() -> None:
 class StateKeys:
     ## 02_Data Import
     # on 1st run
-    ORGANISM = "organism"
+    ORGANISM = "organism"  # TODO this is essentially a constant
     USER_SESSION_ID = "user_session_id"
-    LOADER = "loader"
     # on sample run (function load_sample_data), removed on new session click
     DATASET = "dataset"  # functions upload_metadatafile
 

diff --git a/alphastats/loader/SpectronautLoader.py b/alphastats/loader/SpectronautLoader.py
@@ -88,7 +88,7 @@ def _reshape_long_to_wide(self):
         other proteomics softwares use a wide format (column for each sample)
         reshape to a wider format
         """
-        self.rawinput["sample"] = (
+        self.rawinput["tmp_sample"] = (
             self.rawinput[self.sample_column]
             + SPECTRONAUT_COLUMN_DELIM
             + self.intensity_column
@@ -98,9 +98,11 @@ def _reshape_long_to_wide(self):
             indexing_columns.append(self.gene_names_column)
 
         df = self.rawinput.pivot(
-            columns="sample", index=indexing_columns, values=self.intensity_column
+            columns="tmp_sample", index=indexing_columns, values=self.intensity_column
         )
         df.reset_index(inplace=True)
+        # get rid of tmp_sample again, which can cause troubles when working with indices downstream
+        df.rename_axis(columns=None, inplace=True)
 
         return df