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Added lipidomics draft semantic validation file.
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Nils Hoffmann
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Jan 7, 2020
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -24,7 +24,6 @@ | |
| import de.isas.mztab2.model.MzTab; | ||
| import de.isas.mztab2.model.ValidationMessage; | ||
| import de.isas.mztab2.validation.CvMappingValidator; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.io.StringWriter; | ||
| import java.nio.file.Path; | ||
|
|
@@ -37,15 +36,19 @@ | |
| import java.util.logging.Logger; | ||
| import javax.xml.bind.JAXBException; | ||
| import de.isas.mztab2.io.MzTabFileParser; | ||
| import java.io.PrintWriter; | ||
| import java.util.Optional; | ||
| import lombok.extern.slf4j.Slf4j; | ||
| import uk.ac.ebi.pride.jmztab2.model.MZTabConstants; | ||
| import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException; | ||
| import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList; | ||
| import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType; | ||
| import uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException; | ||
|
|
||
| /** | ||
| * | ||
| * @author Nils Hoffmann <[email protected]> | ||
| */ | ||
| @Slf4j | ||
| public class IsasValidator implements WebValidator { | ||
|
|
||
| private final CvParameterLookupService lookupService; | ||
|
|
@@ -56,51 +59,49 @@ public IsasValidator(CvParameterLookupService lookupService) { | |
|
|
||
| @Override | ||
| public List<ValidationMessage> validate(Path filepath, | ||
| String validationLevel, int maxErrors, boolean checkCvMapping, Path validationFile) throws IllegalStateException, IOException { | ||
| String validationLevel, int maxErrors, boolean checkCvMapping, Path validationFile) throws IllegalStateException, IOException { | ||
| MzTabFileParser parser = null; | ||
| List<ValidationMessage> validationResults = new ArrayList<>(); | ||
| try { | ||
| parser = new MzTabFileParser(filepath.toFile()); | ||
| parser.parse( | ||
| System.out, MZTabErrorType.findLevel(validationLevel), maxErrors); | ||
| } catch (MZTabErrorOverflowException ex) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| MZTabErrorList errorList = parser.parse( | ||
| System.out, MZTabErrorType.findLevel(validationLevel), maxErrors); | ||
| errorList.convertToValidationMessages(); | ||
| } catch (Exception e) { | ||
| log.error("Caught Exception in IsasValidator:", e); | ||
| ValidationMessage vm = new ValidationMessage(); | ||
| vm.setCategory(ValidationMessage.CategoryEnum.CROSS_CHECK); | ||
| vm.setCategory( | ||
| ValidationMessage.CategoryEnum.FORMAT); | ||
| vm.setCode(""); | ||
| vm.setLineNumber(-1l); | ||
| vm.setMessageType( | ||
| ValidationMessage.MessageTypeEnum.ERROR); | ||
| vm.setMessage(ex.getMessage()); | ||
| ValidationMessage.MessageTypeEnum.ERROR); | ||
| StringWriter sw = new StringWriter(); | ||
| PrintWriter pw = new PrintWriter(sw); | ||
| e.printStackTrace(pw); | ||
| vm.setMessage(e.getMessage()!=null?e.getMessage():"Caught an Exception while parsing '"+filepath.getFileName()+"'. Please check your file's tabular structure and inspect further validation messages!" + "\n" +sw.toString()); | ||
| validationResults.add(vm); | ||
| } finally { | ||
| if (parser != null) { | ||
| validationResults.addAll(parser.getErrorList(). | ||
| convertToValidationMessages()); | ||
| convertToValidationMessages()); | ||
| if (checkCvMapping) { | ||
| try { | ||
| CvMappingValidator cvValidator = CvMappingValidator.of( | ||
| // IsasValidator.class.getResource( | ||
| // "/static/examples/mzTab-M-mapping.xml"), | ||
| validationFile.toFile(), | ||
| lookupService, checkCvMapping); | ||
| validationResults.addAll(cvValidator.validate(parser. | ||
| getMZTabFile())); | ||
| } catch (JAXBException ex) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| throw new IOException(ex); | ||
| } catch (IllegalArgumentException iae) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, iae); | ||
| validationFile.toFile(), | ||
| lookupService, checkCvMapping); | ||
| List<ValidationMessage> messages = cvValidator.validate(parser. | ||
| getMZTabFile()); | ||
| validationResults.addAll(Optional.ofNullable(messages).orElse(Collections.emptyList())); | ||
| } catch (JAXBException | IllegalArgumentException iae) { | ||
| log.error("Caught Exception in IsasValidator, semantic validation:", iae); | ||
| ValidationMessage vm = new ValidationMessage(); | ||
| vm.setCategory( | ||
| ValidationMessage.CategoryEnum.CROSS_CHECK); | ||
| ValidationMessage.CategoryEnum.FORMAT); | ||
| vm.setCode(""); | ||
| vm.setLineNumber(-1l); | ||
| vm.setMessageType( | ||
| ValidationMessage.MessageTypeEnum.ERROR); | ||
| ValidationMessage.MessageTypeEnum.ERROR); | ||
| vm.setMessage(iae.getMessage()); | ||
| validationResults.add(vm); | ||
| } | ||
|
|
@@ -112,39 +113,39 @@ public List<ValidationMessage> validate(Path filepath, | |
|
|
||
| @Override | ||
| public Map<String, List<Map<String, String>>> parse(Path filepath, | ||
| String validationLevel, int maxErrors) throws IOException { | ||
| String validationLevel, int maxErrors) throws IOException { | ||
| MzTabFileParser parser = new MzTabFileParser(filepath.toFile()); | ||
| try { | ||
| parser.parse( | ||
| System.out, MZTabErrorType.findLevel(validationLevel), maxErrors); | ||
| System.out, MZTabErrorType.findLevel(validationLevel), maxErrors); | ||
| } finally { | ||
| MzTab mzTabFile = parser.getMZTabFile(); | ||
| if (mzTabFile != null) { | ||
| MzTabWriterDefaults writerDefaults = new MzTabWriterDefaults(); | ||
| CsvMapper mapper = writerDefaults.metadataMapper(); | ||
| CsvSchema schema = writerDefaults.metaDataSchema(mapper); | ||
| if (mzTabFile.getMetadata(). | ||
| getMzTabVersion() == null) { | ||
| getMzTabVersion() == null) { | ||
| //set default version if not set | ||
| mzTabFile.getMetadata(). | ||
| mzTabVersion(MZTabConstants.VERSION_MZTAB_M); | ||
| mzTabVersion(MZTabConstants.VERSION_MZTAB_M); | ||
| } | ||
| StringWriter writer = new StringWriter(); | ||
| try { | ||
| mapper.writer(schema). | ||
| writeValue(writer, mzTabFile.getMetadata()); | ||
| writeValue(writer, mzTabFile.getMetadata()); | ||
| } catch (JsonProcessingException ex) { | ||
| Logger.getLogger(MzTabNonValidatingWriter.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| } | ||
| Map<String, List<Map<String, String>>> mzTabLines = new LinkedHashMap<>(); | ||
| String[] metaDataLines = writer.toString(). | ||
| split(MZTabConstants.NEW_LINE); | ||
| split(MZTabConstants.NEW_LINE); | ||
| List<Map<String, String>> metaData = new ArrayList<>(); | ||
| int lineNumber = 1; | ||
| for (int i = 0; i < metaDataLines.length; i++) { | ||
| String[] metaDataLine = metaDataLines[i].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| Map<String, String> lineMap = new LinkedHashMap<>(); | ||
| lineMap.put("LINE_NUMBER", lineNumber + ""); | ||
| lineMap.put("PREFIX", metaDataLine[0]); | ||
|
|
@@ -158,29 +159,29 @@ public Map<String, List<Map<String, String>>> parse(Path filepath, | |
| mapper = writerDefaults.smallMoleculeSummaryMapper(); | ||
| try { | ||
| schema = writerDefaults. | ||
| smallMoleculeSummarySchema(mapper, mzTabFile); | ||
| smallMoleculeSummarySchema(mapper, mzTabFile); | ||
| writer = new StringWriter(); | ||
| mapper.writer(schema). | ||
| writeValue(writer, mzTabFile.getSmallMoleculeSummary()); | ||
| writeValue(writer, mzTabFile.getSmallMoleculeSummary()); | ||
| } catch (JsonProcessingException ex) { | ||
| Logger.getLogger(MzTabNonValidatingWriter.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| } catch (MZTabException ex) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| throw new IOException(ex); | ||
| } | ||
|
|
||
| String[] summaryDataLines = writer.toString(). | ||
| split(MZTabConstants.NEW_LINE); | ||
| split(MZTabConstants.NEW_LINE); | ||
| String[] summaryHeader = summaryDataLines[0].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| List<Map<String, String>> summaryData = new ArrayList<>(); | ||
| //due to the header | ||
| lineNumber++; | ||
| for (int i = 1; i < summaryDataLines.length; i++) { | ||
| String[] dataLine = summaryDataLines[i].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| Map<String, String> lineMap = new LinkedHashMap<>(); | ||
| lineMap.put("LINE_NUMBER", lineNumber + ""); | ||
| for (int j = 0; j < summaryHeader.length; j++) { | ||
|
|
@@ -194,28 +195,28 @@ public Map<String, List<Map<String, String>>> parse(Path filepath, | |
| mapper = writerDefaults.smallMoleculeFeatureMapper(); | ||
| try { | ||
| schema = writerDefaults. | ||
| smallMoleculeFeatureSchema(mapper, mzTabFile); | ||
| smallMoleculeFeatureSchema(mapper, mzTabFile); | ||
| writer = new StringWriter(); | ||
| mapper.writer(schema). | ||
| writeValue(writer, mzTabFile.getSmallMoleculeFeature()); | ||
| writeValue(writer, mzTabFile.getSmallMoleculeFeature()); | ||
| } catch (JsonProcessingException ex) { | ||
| Logger.getLogger(MzTabNonValidatingWriter.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| } catch (MZTabException ex) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| throw new IOException(ex); | ||
| } | ||
| String[] featureDataLines = writer.toString(). | ||
| split(MZTabConstants.NEW_LINE); | ||
| split(MZTabConstants.NEW_LINE); | ||
| String[] featureHeader = featureDataLines[0].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| List<Map<String, String>> featureData = new ArrayList<>(); | ||
| //due to the header | ||
| lineNumber++; | ||
| for (int i = 1; i < featureDataLines.length; i++) { | ||
| String[] dataLine = featureDataLines[i].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| Map<String, String> lineMap = new LinkedHashMap<>(); | ||
| lineMap.put("LINE_NUMBER", lineNumber + ""); | ||
| for (int j = 0; j < featureHeader.length; j++) { | ||
|
|
@@ -229,28 +230,28 @@ public Map<String, List<Map<String, String>>> parse(Path filepath, | |
| mapper = writerDefaults.smallMoleculeEvidenceMapper(); | ||
| try { | ||
| schema = writerDefaults.smallMoleculeEvidenceSchema(mapper, | ||
| mzTabFile); | ||
| mzTabFile); | ||
| writer = new StringWriter(); | ||
| mapper.writer(schema). | ||
| writeValue(writer, mzTabFile.getSmallMoleculeEvidence()); | ||
| writeValue(writer, mzTabFile.getSmallMoleculeEvidence()); | ||
| } catch (JsonProcessingException ex) { | ||
| Logger.getLogger(MzTabNonValidatingWriter.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| } catch (MZTabException ex) { | ||
| Logger.getLogger(IsasValidator.class.getName()). | ||
| log(Level.SEVERE, null, ex); | ||
| log(Level.SEVERE, null, ex); | ||
| throw new IOException(ex); | ||
| } | ||
| String[] evidenceDataLines = writer.toString(). | ||
| split(MZTabConstants.NEW_LINE); | ||
| split(MZTabConstants.NEW_LINE); | ||
| String[] evidenceHeader = evidenceDataLines[0].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| List<Map<String, String>> evidenceData = new ArrayList<>(); | ||
| //due to the header | ||
| lineNumber++; | ||
| for (int i = 1; i < evidenceDataLines.length; i++) { | ||
| String[] dataLine = evidenceDataLines[i].split( | ||
| MZTabConstants.TAB_STRING); | ||
| MZTabConstants.TAB_STRING); | ||
| Map<String, String> lineMap = new LinkedHashMap<>(); | ||
| lineMap.put("LINE_NUMBER", lineNumber + ""); | ||
| for (int j = 0; j < evidenceHeader.length; j++) { | ||
|
|
||
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