update to tidy final reports

phenomecentre · Aug 12, 2024 · 46423b7 · 46423b7
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commit 46423b7
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Showing 9 changed files with 49 additions and 12 deletions.
diff --git a/Tests/test_targeteddataset.py b/Tests/test_targeteddataset.py
@@ -4749,8 +4749,13 @@ def setUp(self):
 										'quantiles': tmpDataset.Attributes['quantiles'],
 										'methodName': 'Bruker Quant-UR Data',
 										'externalID': [],
-										'sampleMetadataNotExported': ['Acqu Date', 'Acqu Time', 'Sample Type'],
-										'featureMetadataNotExported': ['comment'],
+										'sampleMetadataNotExported': ["AUNM", "BF1", "BYTORDP", "Computer", "File Path", "NC_proc", "NS", "O1",
+																	  "OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
+																	  "TD", "XDIM", "Delta PPM", "ERETIC Integral","ERETIC Concentration (mM)",
+																	  "Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
+																	  "WaterPeakFail", "SolventPeakFail", "BaselineFail", "Sample Base Name", "expno",
+																	  "Acqu Date", "Acqu Time", "Sample Type"],
+										'featureMetadataNotExported': ['comment', 'Exclusion Details'],
 										'analyticalMeasurements': {'Acquired Time': 'date', 'Acquisition batch': 'categorical', 'Assay data location': 'categorical',
 																  'Assay data name': 'categorical', 'Assay protocol': 'categorical', 'AssayRole': 'categorical', 'Batch': 'categorical',
 																  'Correction Batch': 'categorical', 'Dilution': 'continuous', 'Exclusion Details': 'categorical',

diff --git a/nPYc/StudyDesigns/SOP/BrukerBI-LISA.json b/nPYc/StudyDesigns/SOP/BrukerBI-LISA.json
@@ -3,8 +3,13 @@
 	"fileNamePattern":".*?results\\.xml$",
 	"externalID":[],
 	"rsdThreshold": 30,
-	"sampleMetadataNotExported":["Acqu Date", "Acqu Time", "Sample Type"],
-	"featureMetadataNotExported":["comment"],
+	"sampleMetadataNotExported" : ["AUNM", "BF1", "BYTORDP", "Computer", "File Path", "NC_proc", "NS", "O1",
+		"OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
+		"TD", "XDIM", "Delta PPM", "ERETIC Integral","ERETIC Concentration (mM)",
+		"Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
+		"WaterPeakFail", "SolventPeakFail", "BaselineFail", "Sample Base Name", "expno",
+		"Acqu Date", "Acqu Time", "Sample Type"],
+	"featureMetadataNotExported":["comment", "Exclusion Details"],
 	"analyticalMeasurements":{"Study" : "categorical", "Instrument" : "categorical", "Re-Run" : "categorical", "Suplemental Injections" : "categorical", "Matrix" : "categorical", "Well" : "categorical", "Plate" : "categorical", "Batch" : "categorical", "Dilution" : "continuous", "Measurement Date" : "date", "Measurement Time" : "date", "Acquired Time" : "date", "Run Order" : "continuous", "Correction Batch" : "categorical", "Assay data name": "categorical", "Assay data location": "categorical", "Sample position": "categorical", "Sample batch": "categorical", "Acquisition batch": "categorical", "Plot Sample Type": "categorical", "AssayRole": "categorical", "SampleType": "categorical", "Exclusion Details": "categorical", "Skipped": "categorical", "Assay protocol": "categorical"},
 	"excludeFromPlotting":["Sample File Name", "Sample Base Name", "Batch Termini", "Study Reference", "Long-Term Reference", "Method Reference", "Dilution Series", "Skipped", "Study Sample", "File Path", "Exclusion Details", "Assay protocol", "Status", "Measurement Date", "Measurement Time", "Data Present", "LIMS Present", "LIMS Marked Missing", "Assay data name", "Assay data location", "AssayRole", "SampleType", "Sample ID", "Plot Sample Type", "SubjectInfoData", "Detector Unit", "TargetLynx Sample ID", "MassLynx Row ID"],
 	"additionalQuantParamColumns":["LOD", "Lower Reference Percentile", "Lower Reference Value", "Upper Reference Percentile", "Upper Reference Value"]

diff --git a/nPYc/StudyDesigns/SOP/BrukerBI-QUANT-PS.json b/nPYc/StudyDesigns/SOP/BrukerBI-QUANT-PS.json
@@ -3,8 +3,13 @@
 	"fileNamePattern":".*?plasma_quant_report\\.xml$",
 	"externalID":[],
 	"rsdThreshold": 30,
-	"sampleMetadataNotExported":["Acqu Date", "Acqu Time", "Sample Type"],
-	"featureMetadataNotExported":["comment"],
+	"sampleMetadataNotExported" : ["AUNM", "BF1", "BYTORDP", "Computer", "File Path", "NC_proc", "NS", "O1",
+		"OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
+		"TD", "XDIM", "Delta PPM", "ERETIC Integral","ERETIC Concentration (mM)",
+		"Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
+		"WaterPeakFail", "SolventPeakFail", "BaselineFail", "Sample Base Name", "expno",
+		"Acqu Date", "Acqu Time", "Sample Type"],
+	"featureMetadataNotExported":["comment", "Exclusion Details"],
 	"analyticalMeasurements":{"Study" : "categorical", "Instrument" : "categorical", "Re-Run" : "categorical", "Suplemental Injections" : "categorical", "Matrix" : "categorical", "Well" : "categorical", "Plate" : "categorical", "Batch" : "categorical", "Dilution" : "continuous", "Measurement Date" : "date", "Measurement Time" : "date", "Acquired Time" : "date", "Run Order" : "continuous", "Correction Batch" : "categorical", "Assay data name": "categorical", "Assay data location": "categorical", "Sample position": "categorical", "Sample batch": "categorical", "Acquisition batch": "categorical", "Plot Sample Type": "categorical", "AssayRole": "categorical", "SampleType": "categorical", "Exclusion Details": "categorical", "Skipped": "categorical", "Assay protocol": "categorical"},
 	"excludeFromPlotting":["Sample File Name", "Sample Base Name", "Batch Termini", "Study Reference", "Long-Term Reference", "Method Reference", "Dilution Series", "Skipped", "Study Sample", "File Path", "Exclusion Details", "Assay protocol", "Status", "Measurement Date", "Measurement Time", "Data Present", "LIMS Present", "LIMS Marked Missing", "Assay data name", "Assay data location", "AssayRole", "SampleType", "Sample ID", "Plot Sample Type", "SubjectInfoData", "Detector Unit", "TargetLynx Sample ID", "MassLynx Row ID"],
 	"additionalQuantParamColumns":["LOD", "Lower Reference Percentile", "Lower Reference Value", "Upper Reference Percentile", "Upper Reference Value"]

diff --git a/nPYc/StudyDesigns/SOP/BrukerQuant-UR.json b/nPYc/StudyDesigns/SOP/BrukerQuant-UR.json
@@ -3,8 +3,13 @@
 	"fileNamePattern":".*?urine_quant_report_b\\.xml$",
 	"externalID":[],
 	"rsdThreshold": 30,
-	"sampleMetadataNotExported":["Acqu Date", "Acqu Time", "Sample Type"],
-	"featureMetadataNotExported":["comment"],
+	"sampleMetadataNotExported" : ["AUNM", "BF1", "BYTORDP", "Computer", "File Path", "NC_proc", "NS", "O1",
+		"OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
+		"TD", "XDIM", "Delta PPM", "ERETIC Integral","ERETIC Concentration (mM)",
+		"Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
+		"WaterPeakFail", "SolventPeakFail", "BaselineFail", "Sample Base Name", "expno",
+		"Acqu Date", "Acqu Time", "Sample Type"],
+	"featureMetadataNotExported":["comment", "Exclusion Details"],
 	"analyticalMeasurements":{"Study" : "categorical", "Instrument" : "categorical", "Re-Run" : "categorical", "Suplemental Injections" : "categorical", "Matrix" : "categorical", "Well" : "categorical", "Plate" : "categorical", "Batch" : "categorical", "Dilution" : "continuous", "Measurement Date" : "date", "Measurement Time" : "date", "Acquired Time" : "date", "Run Order" : "continuous", "Correction Batch" : "categorical", "Assay data name": "categorical", "Assay data location": "categorical", "Sample position": "categorical", "Sample batch": "categorical", "Acquisition batch": "categorical", "Plot Sample Type": "categorical", "AssayRole": "categorical", "SampleType": "categorical", "Exclusion Details": "categorical", "Skipped": "categorical", "Assay protocol": "categorical"},
 	"excludeFromPlotting":["Sample File Name", "Sample Base Name", "Batch Termini", "Study Reference", "Long-Term Reference", "Method Reference", "Dilution Series", "Skipped", "Study Sample", "File Path", "Exclusion Details", "Assay protocol", "Status", "Measurement Date", "Measurement Time", "Data Present", "LIMS Present", "LIMS Marked Missing", "Assay data name", "Assay data location", "AssayRole", "SampleType", "Sample ID", "Plot Sample Type", "SubjectInfoData", "Detector Unit", "TargetLynx Sample ID", "MassLynx Row ID"],
 	"additionalQuantParamColumns":["LOD", "Lower Reference Percentile", "Lower Reference Value", "Upper Reference Percentile", "Upper Reference Value"]

diff --git a/nPYc/StudyDesigns/SOP/GenericNMRurine.json b/nPYc/StudyDesigns/SOP/GenericNMRurine.json
@@ -29,9 +29,9 @@
       "Long-Term Reference", "Study Sample", "Status", "Exclusion Details", "LIMS Present", "LIMS Marked Missing",
       "path", "Assay data name", "Assay data location", "Assay protocol", "titleFileContent", "SF"],
     "sampleMetadataNotExported" : ["AUNM", "BF1", "BYTORDP", "Computer", "File Path", "NC_proc", "NS", "O1",
-      "OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
+		"OFFSET", "OWNER", "P", "PROBHD", "PULPROG", "RG", "SF", "SFO1", "SI", "SW", "SW_p",
 		"TD", "XDIM", "Delta PPM", "ERETIC Integral","ERETIC Concentration (mM)",
-      "Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
-      "WaterPeakFail", "BaselineFail", "Sample Base Name", "expno"],
-	"featureMetadataNotExported":[]
+		"Line Width (Hz)", "Exclusion Details", "CalibrationFail", "LineWidthFail",
+		"WaterPeakFail", "SolventPeakFail", "BaselineFail", "Sample Base Name", "expno"],
+	"featureMetadataNotExported": ["Exclusion Details"]
 }
diff --git a/nPYc/reports/_finalReportPeakPantheR.py b/nPYc/reports/_finalReportPeakPantheR.py
@@ -133,6 +133,10 @@ def _finalReportPeakPantheR(dataset, destinationPath=None):
     if hasattr(sampleSummary['Acquired'], 'Already Excluded'):
         sampleSummary['Acquired'].rename(columns={'Already Excluded': 'Excluded'}, inplace=True)
 
+    # Drop rows where no samples present for that datatype
+    sampleSummary['Acquired'].drop(sampleSummary['Acquired'].index[sampleSummary['Acquired']['Total'].values == 0],
+                                   axis=0, inplace=True)
+
     sampleSummary['isFinalReport'] = True
     if 'StudySamples Exclusion Details' in sampleSummary:
         sampleSummary['studySamplesExcluded'] = True

diff --git a/nPYc/reports/_generateReportMS.py b/nPYc/reports/_generateReportMS.py
@@ -188,6 +188,10 @@ def _finalReport(dataset, destinationPath=None, pcaModel=None, reportType='final
     # Tidy table for final report format
     sampleSummary['Acquired'].drop('Marked for Exclusion', inplace=True, axis=1)
 
+    # Drop rows where no samples present for that datatype
+    sampleSummary['Acquired'].drop(sampleSummary['Acquired'].index[sampleSummary['Acquired']['Total'].values == 0],
+                                   axis=0, inplace=True)
+
     sampleSummary['isFinalReport'] = True
     if 'StudySamples Exclusion Details' in sampleSummary:
         sampleSummary['studySamplesExcluded'] = True

diff --git a/nPYc/reports/_generateReportNMR.py b/nPYc/reports/_generateReportNMR.py
@@ -263,6 +263,9 @@ def _finalReport(dataset, destinationPath=None, pcaModel=None):
     # Tidy table for final report format
 	sampleSummary['Acquired'].drop('Marked for Exclusion', inplace=True, axis=1)
 
+	# Drop rows where no samples present for that datatype
+	sampleSummary['Acquired'].drop(sampleSummary['Acquired'].index[sampleSummary['Acquired']['Total'].values == 0], axis=0, inplace=True)
+
 	sampleSummary['isFinalReport'] = True
 	if 'StudySamples Exclusion Details' in sampleSummary:
 		sampleSummary['studySamplesExcluded'] = True

diff --git a/nPYc/reports/_generateReportTargeted.py b/nPYc/reports/_generateReportTargeted.py
@@ -601,6 +601,9 @@ def _finalReportMS(tData, item, destinationPath, pcaModel=None, withAccPrec=True
 	# Tidy table for final report format
 	sampleSummary['Acquired'].drop('Marked for Exclusion', inplace=True, axis=1)
 
+	# Drop rows where no samples present for that datatype
+	sampleSummary['Acquired'].drop(sampleSummary['Acquired'].index[sampleSummary['Acquired']['Total'].values == 0], axis=0, inplace=True)
+
 	sampleSummary['isFinalReport'] = True
 	if 'StudySamples Exclusion Details' in sampleSummary:
 		sampleSummary['studySamplesExcluded'] = True
@@ -864,6 +867,9 @@ def _finalReportNMR(tData, item, destinationPath, pcaModel=None, withAccPrec=Tru
 	# Tidy table for final report format
 	sampleSummary['Acquired'].drop('Marked for Exclusion', inplace=True, axis=1)
 
+	# Drop rows where no samples present for that datatype
+	sampleSummary['Acquired'].drop(sampleSummary['Acquired'].index[sampleSummary['Acquired']['Total'].values == 0], axis=0, inplace=True)
+
 	sampleSummary['isFinalReport'] = True
 	if 'StudySamples Exclusion Details' in sampleSummary:
 		sampleSummary['studySamplesExcluded'] = True