Importer: On Mods, allow position when N or C term flag is set.

When N or C term flag is set, the position in the input will be ignored and the position will continue to hard coded in the DB to be position 1 and the length of the peptide.
yeastrc · Sep 3, 2019 · 44a9370 · 44a9370
1 parent ddb33bc
commit 44a9370
Showing 1 changed file with 48 additions and 24 deletions.
diff --git a/...strc/proxl/import_xml_to_db/pre_validate_xml/ValidateModificationsOnReportedPeptides.java b/...strc/proxl/import_xml_to_db/pre_validate_xml/ValidateModificationsOnReportedPeptides.java
@@ -86,41 +86,40 @@ public void validateModificationsOnReportedPeptides( ProxlInput proxlInput ) thr
 									}
 
 									if ( modification.isIsNTerminal() != null && modification.isIsNTerminal() ) {
+										//  Comment out to allow position
+//										if ( modification.getPosition() != null ) {
+//											String msg = "Peptide Modification Position is populated when modification is marked as 'n' terminal. Position: " + modification.getPosition().intValue()
+//													+ " Reported Peptide: " + reportedPeptide.getReportedPeptideString();
+//											log.error( msg );
+//											throw new ProxlImporterDataException( msg );
+//										}
+										//  Since allowing position, validate it.  Not really needed since will be ignored.
 										if ( modification.getPosition() != null ) {
-											String msg = "Peptide Modification Position is populated when modification is marked as 'n' terminal. Position: " + modification.getPosition().intValue()
-													+ " Reported Peptide: " + reportedPeptide.getReportedPeptideString();
-											log.error( msg );
-											throw new ProxlImporterDataException( msg );
+											validatePositionValue( modification, peptideSequenceLength, reportedPeptide);
 										}
+										//  No changed needed outside this class since in the import code the position is overlaid if the N or C terminus flag is set
 									} else if ( modification.isIsCTerminal() != null && modification.isIsCTerminal() ) {
-										if ( modification.getPosition()!= null ) {
-											String msg = "Peptide Modification Position is populated when modification is marked as 'c' terminal. Position: " + modification.getPosition().intValue()
-													+ " Reported Peptide: " + reportedPeptide.getReportedPeptideString();
-											log.error( msg );
-											throw new ProxlImporterDataException( msg );
+										//  Comment out to allow position
+//										if ( modification.getPosition()!= null ) {
+//											String msg = "Peptide Modification Position is populated when modification is marked as 'c' terminal. Position: " + modification.getPosition().intValue()
+//													+ " Reported Peptide: " + reportedPeptide.getReportedPeptideString();
+//											log.error( msg );
+//											throw new ProxlImporterDataException( msg );
+//										}
+										//  Since allowing position, validate it.  Not really needed since will be ignored.
+										if ( modification.getPosition() != null ) {
+											validatePositionValue( modification, peptideSequenceLength, reportedPeptide);
 										}
+										//  No changed needed outside this class since in the import code the position is overlaid if the N or C terminus flag is set
 									} else {
 
 										if ( modification.getPosition() == null ) {
 											String msg = "Peptide Modification Position is null or not assigned and at least one of 'is_n_terminal' or 'is_c_terminal' is not populated and true.  Reported Peptide: " + reportedPeptide.getReportedPeptideString();
 											log.error( msg );
 											throw new ProxlImporterDataException( msg );
 										}
-										if ( modification.getPosition().intValue() < 1 ) {
-											String msg = "Peptide Modification Position is < 1. peptide Modification Position: " 
-													+ modification.getPosition()
-													+ ", Reported Peptide: " + reportedPeptide.getReportedPeptideString();
-											log.error( msg );
-											throw new ProxlImporterDataException( msg );
-										}
-										if ( modification.getPosition().intValue() > peptideSequenceLength ) {
-											String msg = "Peptide Modification Position is > peptide Sequence Length. peptide Modification Position: " 
-													+ modification.getPosition()
-													+ ", peptide Sequence Length: " + peptideSequenceLength
-													+ ", Reported Peptide: " + reportedPeptide.getReportedPeptideString();
-											log.error( msg );
-											throw new ProxlImporterDataException( msg );
-										}
+
+										validatePositionValue( modification, peptideSequenceLength, reportedPeptide );
 									}
 								}
 							}
@@ -130,4 +129,29 @@ public void validateModificationsOnReportedPeptides( ProxlInput proxlInput ) thr
 			}
 		}
 	}
+
+	/**
+	 * @param modification
+	 * @param peptideSequenceLength
+	 * @param reportedPeptide
+	 * @throws ProxlImporterDataException
+	 */
+	private void validatePositionValue( Modification modification, int peptideSequenceLength, ReportedPeptide reportedPeptide ) throws ProxlImporterDataException {
+
+		if ( modification.getPosition().intValue() < 1 ) {
+			String msg = "Peptide Modification Position is < 1. peptide Modification Position: " 
+					+ modification.getPosition()
+					+ ", Reported Peptide: " + reportedPeptide.getReportedPeptideString();
+			log.error( msg );
+			throw new ProxlImporterDataException( msg );
+		}
+		if ( modification.getPosition().intValue() > peptideSequenceLength ) {
+			String msg = "Peptide Modification Position is > peptide Sequence Length. peptide Modification Position: " 
+					+ modification.getPosition()
+					+ ", peptide Sequence Length: " + peptideSequenceLength
+					+ ", Reported Peptide: " + reportedPeptide.getReportedPeptideString();
+			log.error( msg );
+			throw new ProxlImporterDataException( msg );
+		}
+	}
 }