Merge pull request #33 from mmzdouc/dev_mmz

v0.3.2

CHANGELOG.md

@@ -10,6 +10,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 N/A
 
+## [0.3.2] 05-06-2024
+
+### Fixed
+
+- Corrected erroneous assignment of 'True' to 'module_passed' for FragmentAnnotator and NeutralLossAnnotator if no MS/MS information was provided
+
 ## [0.3.1] 05-06-2024
 
 ### Changed

example_data/minimal.params.json

@@ -0,0 +1,9 @@
+{
+  "files": {
+    "peaktable": {
+      "filepath": "example_data/case_study_peak_table_quant_full.csv",
+      "format": "mzmine3",
+      "polarity": "positive"
+    }
+  }
+}

fermo_core/data_analysis/annotation_manager/class_adduct_annotator.py

@@ -78,7 +78,7 @@ def run_analysis(self: Self):
             for s_name in self.stats.samples:
                 self.annotate_adducts_pos(s_name)
         else:
-            logger.warning(
+            logger.info(
                 "'AnnotationManager/AdductAnnotator': negative ion mode detected. "
                 "Attempt to annotate for negative ion mode adducts."
             )

fermo_core/data_analysis/annotation_manager/class_annotation_manager.py

@@ -268,8 +268,7 @@ def run_neutral_loss_annotation(self: Self):
                 samples=self.samples,
             )
             neutralloss_annotator.run_analysis()
-            self.features = neutralloss_annotator.return_features()
-            self.params.NeutralLossParameters.module_passed = True
+            self.features, self.params = neutralloss_annotator.return_attributes()
         except Exception as e:
             logger.error(str(e))
             logger.error(
@@ -292,8 +291,7 @@ def run_fragment_annotation(self: Self):
                 samples=self.samples,
             )
             fragment_annotator.run_analysis()
-            self.features = fragment_annotator.return_features()
-            self.params.FragmentAnnParameters.module_passed = True
+            self.features, self.params = fragment_annotator.return_attributes()
         except Exception as e:
             logger.error(str(e))
             logger.error(

fermo_core/data_analysis/annotation_manager/class_fragment_annotator.py

@@ -57,13 +57,13 @@ class FragmentAnnotator(BaseModel):
     samples: Repository
     frags: CharFragments = CharFragments()
 
-    def return_features(self: Self) -> Repository:
-        """Returns modified Feature objects in Repository object instance
+    def return_attributes(self: Self) -> tuple[Repository, ParameterManager]:
+        """Returns modified object instance
 
         Returns:
-            Modified Feature Repository object.
+            Modified Feature Repository and ParameterManager objects.
         """
-        return self.features
+        return self.features, self.params
 
     @staticmethod
     def add_annotation(feature: Feature) -> Feature:
@@ -154,3 +154,5 @@ def run_analysis(self: Self):
                 "SKIP"
             )
             return
+
+        self.params.FragmentAnnParameters.module_passed = True

fermo_core/data_analysis/annotation_manager/class_neutral_loss_annotator.py

@@ -57,13 +57,13 @@ class NeutralLossAnnotator(BaseModel):
     samples: Repository
     mass: NeutralLosses = NeutralLosses()
 
-    def return_features(self: Self) -> Repository:
-        """Returns modified Feature objects in Repository object instance
+    def return_attributes(self: Self) -> tuple[Repository, ParameterManager]:
+        """Returns modified attributes
 
         Returns:
-            Modified Feature Repository object.
+            Modified Feature and Params object
         """
-        return self.features
+        return self.features, self.params
 
     def annotate_feature_neg(self: Self, f_id: int):
         """Annotate neutral losses of feature and store data in General Feature
@@ -325,3 +325,5 @@ def run_analysis(self: Self):
             )
             for f_id in self.stats.active_features:
                 self.annotate_feature_neg(f_id)
+
+        self.params.NeutralLossParameters.module_passed = True

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fermo_core"
-version = "0.3.1"
+version = "0.3.2"
 description = "Data processing/analysis functionality of metabolomics dashboard FERMO"
 readme = "README.md"
 requires-python = ">=3.11,<3.12"