Merge pull request #29 from mmzdouc/dev_mmz

Fixed bug in SummaryWriter
mmzdouc · May 26, 2024 · 82cde8e · 82cde8e
2 parents 8882ac8 + 7540251
commit 82cde8e
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Showing 3 changed files with 43 additions and 30 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 N/A
 
+## [0.2.1] 26-05-2024
+
+### Fixed
+
+- Fixed bug in "SummaryWriter": implemented error catching.
+
 ## [0.2.0] 26-05-2024
 
 ### Changed

diff --git a/fermo_core/input_output/class_summary_writer.py b/fermo_core/input_output/class_summary_writer.py
@@ -133,9 +133,9 @@ def summarize_featurefilteringparameters(self: Self):
                 self.summary.append(
                     f"Molecular features were filtered and only retained if they were "
                     f"inside the relative area range of "
-                    f"'{self.params.FeatureFilteringParameters.filter_rel_int_range[0]}"
+                    f"'{self.params.FeatureFilteringParameters.filter_rel_area_range[0]}"
                     f"-"
-                    f"{self.params.FeatureFilteringParameters.filter_rel_int_range[1]}'"
+                    f"{self.params.FeatureFilteringParameters.filter_rel_area_range[1]}'"
                     f" in at least one sample (relative to the feature with the "
                     f"highest area in the sample)."
                 )
@@ -349,30 +349,37 @@ def summarize_askcbdeepscorematchingparams(self: Self):
 
     def assemble_summary(self: Self):
         """Call methods to assemble the summary file"""
-        logger.debug("'SummaryWriter': Started summary: files")
-        self.summarize_peaktableparameters()
-        self.summarize_msmsparameters()
-        self.summarize_phenotypeparameters()
-        self.summarize_groupmetadataparameters()
-        self.summarize_speclibparameters()
-        self.summarize_ms2queryresultsparameters()
-        self.summarize_asresultsparameters()
-        logger.debug("'SummaryWriter': Completed summary: files")
-        logger.debug("'SummaryWriter': Started summary: analysis modules")
-        self.summarize_featurefilteringparameters()
-        self.summarize_adductannotationparameters()
-        self.summarize_neutrallossparameters()
-        self.summarize_fragmentannparameters()
-        self.summarize_specsimnetworkcosineparameters()
-        self.summarize_specsimnetworkdeepscoreparameters()
-        self.summarize_blankassignmentparameters()
-        self.summarize_groupfactassignmentparameters()
-        self.summarize_phenoqualassgnparams()
-        self.summarize_phenoquantpercentassgnparams()
-        self.summarize_phenoquantconcassgnparams()
-        self.summarize_spectrallibmatchingcosineparameters()
-        self.summarize_spectrallibmatchingdeepscoreparameters()
-        self.summarize_ms2queryannotationparameters()
-        self.summarize_askcbcosinematchingparams()
-        self.summarize_askcbdeepscorematchingparams()
-        logger.debug("'SummaryWriter': Completed summary: analysis modules")
+        try:
+            logger.debug("'SummaryWriter': Started summary: files")
+            self.summarize_peaktableparameters()
+            self.summarize_msmsparameters()
+            self.summarize_phenotypeparameters()
+            self.summarize_groupmetadataparameters()
+            self.summarize_speclibparameters()
+            self.summarize_ms2queryresultsparameters()
+            self.summarize_asresultsparameters()
+            logger.debug("'SummaryWriter': Completed summary: files")
+            logger.debug("'SummaryWriter': Started summary: analysis modules")
+            self.summarize_featurefilteringparameters()
+            self.summarize_adductannotationparameters()
+            self.summarize_neutrallossparameters()
+            self.summarize_fragmentannparameters()
+            self.summarize_specsimnetworkcosineparameters()
+            self.summarize_specsimnetworkdeepscoreparameters()
+            self.summarize_blankassignmentparameters()
+            self.summarize_groupfactassignmentparameters()
+            self.summarize_phenoqualassgnparams()
+            self.summarize_phenoquantpercentassgnparams()
+            self.summarize_phenoquantconcassgnparams()
+            self.summarize_spectrallibmatchingcosineparameters()
+            self.summarize_spectrallibmatchingdeepscoreparameters()
+            self.summarize_ms2queryannotationparameters()
+            self.summarize_askcbcosinematchingparams()
+            self.summarize_askcbdeepscorematchingparams()
+            logger.debug("'SummaryWriter': Completed summary: analysis modules")
+        except Exception as e:
+            logger.error(str(e))
+            logger.error(
+                "SummaryWriter: error occurred during writing of summary. "
+                "Write steps until error occurred."
+            )
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "fermo_core"
-version = "0.2.0"
+version = "0.2.1"
 description = "Data processing/analysis functionality of metabolomics dashboard FERMO"
 readme = "README.md"
 requires-python = ">=3.11,<3.12"