Merge pull request #81 from MannLabs/gui_fixes

Release 0.2.7

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.6
+current_version = 0.2.7
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

HISTORY.md

@@ -1,5 +1,8 @@
 # Changelog
 
+## 0.2.7
+* Fix warning when loading DIA-NN GUI
+
 ## 0.2.6
 * Bug fix when importing data in GUI
 * version binning

alphastats/__init__.py

@@ -1,5 +1,5 @@
 __project__ = "alphastats"
-__version__ = "0.2.6"
+__version__ = "0.2.7"
 __license__ = "Apache"
 __description__ = "An open-source Python package for Mass Spectrometry Analysis"
 __author__ = "Mann Labs"

alphastats/gui/pages/02_Import Data.py

@@ -39,12 +39,9 @@ def check_software_file(df, software):
 
     elif software == "DIANN":
         expected_columns = [
-            "PG.Quantity",
             "Protein.Group",
         ]
 
-        st.write(set(expected_columns).issubset(set(df.columns.to_list())))
-
         if (set(expected_columns).issubset(set(df.columns.to_list()))) == False:
             st.error("This is not a valid DIA-NN file.")
 
@@ -98,7 +95,7 @@ def load_proteomics_data(uploaded_file, intensity_column, index_column, software
     return loader
 
 
-def select_sample_column_metadata(df):
+def select_sample_column_metadata(df, software):
     samples_proteomics_data = get_sample_names_from_software_file()
     valid_sample_columns = []
 
@@ -114,7 +111,7 @@ def select_sample_column_metadata(df):
 
     st.write(
         f"Select column that contains sample IDs matching the sample names described"
-        + f"in {software_options.get(st.session_state.loader.software).get('import_file')}"
+        + f"in {software_options.get(software).get('import_file')}"
     )
 
     with st.form("sample_column"):
@@ -161,7 +158,7 @@ def upload_softwarefile(software):
             st.session_state["loader"] = loader
 
 
-def upload_metadatafile():
+def upload_metadatafile(software):
 
     st.write("\n\n")
     st.markdown("### 3. Upload corresponding metadata.")
@@ -180,7 +177,7 @@ def upload_metadatafile():
         st.dataframe(metadatafile_df.head(5))
         # pick sample column
 
-        if select_sample_column_metadata(metadatafile_df):
+        if select_sample_column_metadata(metadatafile_df, software):
             # create dataset
             st.session_state["dataset"] = DataSet(
                 loader=st.session_state.loader,
@@ -237,7 +234,7 @@ def import_data():
         upload_softwarefile(software=software)
 
     if "loader" in st.session_state:
-        upload_metadatafile()
+        upload_metadatafile(software)
 
 
 def display_loaded_dataset():
@@ -332,5 +329,7 @@ def empty_session_state():
 
         import_data()
 
-    display_loaded_dataset()
+    if "dataset" in st.session_state: 
+
+        display_loaded_dataset()
 

alphastats/gui/utils/analysis_helper.py

@@ -5,8 +5,6 @@
 from datetime import datetime
 
 
-
-
 def check_if_options_are_loaded(f):
     # decorator to check for missing values
     def inner(*args, **kwargs):

alphastats/loader/DIANNLoader.py

@@ -25,7 +25,7 @@ def __init__(
         """
 
         super().__init__(file, intensity_column, index_column, sep)
-        self.software = "DIA-NN"
+        self.software = "DIANN"
         self.no_sample_column = [
             "PG.Q.value",
             "Global.PG.Q.value",

docs/conf.py

@@ -23,7 +23,7 @@
 author = "Elena Krismer"
 
 # The full version, including alpha/beta/rc tags
-release = "0.2.6"
+release = "0.2.7"
 
 
 # -- General configuration ---------------------------------------------------

setup.py

@@ -46,7 +46,7 @@ def create_pip_wheel():
     requirements, extra_requirements = get_requirements()
     setuptools.setup(
         name="alphastats",
-        version="0.2.6",
+        version="0.2.7",
         license="Apache",
         description="An open-source Python package for Mass Spectrometry Analysis",
         long_description=get_long_description(),