Importer: Change error messages

yeastrc · Sep 5, 2018 · c0aaa49 · c0aaa49
1 parent 9acbbaa
commit c0aaa49
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Showing 4 changed files with 109 additions and 47 deletions.
diff --git a/...n_importer/org/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeCrosslink.java b/...n_importer/org/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeCrosslink.java
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -171,23 +172,39 @@ private GetCrosslinkProteinMappingsSinglePeptideData getProteinMappingForSingleP
 						reportedPeptide // for error reporting only 
 						);
 		if( proteinMap.size() < 1 ) {
-			String msg = null;
+
+			List<String> linkersToStringArray = new ArrayList<>( linkerList.size() );
+			for ( ILinker linkerItem : linkerList ) {
+				linkersToStringArray.add(  linkerItem.toString() );
+			}
+			String linkersToString = StringUtils.join( linkersToStringArray, "," );
+
+			List<Integer> peptideLinkPositions = new ArrayList<>();
+			peptideLinkPositions.add( peptideCrossLinkPosition );
+
 			if ( peptideMonolinkPositions != null && ( ! peptideMonolinkPositions.isEmpty() ) ) {
-				msg = "Could not map this peptide and link position and monolink positions to any protein in the Proxl XML file for peptide " 
-					+ peptide.getSequence()
-					+ " at crosslink position: " + peptideCrossLinkPosition 
-					+ ", monolink position(s): " + StringUtils.join( peptideMonolinkPositions, ", " )
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
-			} else {
-				msg = "Could not map this peptide and link position to any protein in the Proxl XML file for " 
-					+ peptide.getSequence()
-					+ " at crosslink position: " + peptideCrossLinkPosition 
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+
+				for ( Integer peptideMonolinkPosition : peptideMonolinkPositions ) {
+					if ( ! peptideLinkPositions.contains( peptideMonolinkPosition ) ) {
+						peptideLinkPositions.add( peptideMonolinkPosition );
+					}
+				}
 			}
-			log.error( msg );
-			throw new ProxlImporterDataException( "getCrosslinks(...): " + msg );
+
+			Collections.sort( peptideLinkPositions );
+
+			String msg = "Could not import this Proxl XML file. Either no protein in the Proxl XML contained this peptide sequence (" 
+					+ peptide.getSequence()
+					+ ") or the linked position(s) reported for the peptide (positions " 
+					+ StringUtils.join( peptideLinkPositions, ", " )
+					+ ") was not a linkable position in the matched protein for the given cross-linker(s) (["
+					+ linkersToString
+					+ "]). The whole reported peptide string was: "
+					+ reportedPeptide.getReportedPeptideString()
+					+   "\n\nThis is most-probably caused by specifying the incorrect cross-linker or the incorrect FASTA file when generating the Proxl XML file.";
+
+			log.error( "getCrosslinks(...): Msg thrown in ProxlImporterDataException: " + msg );
+			throw new ProxlImporterDataException( msg );
 		}
 		///  Data in perPeptideData for Monolinks
 		List<MonolinkContainer> monolinkContainerList = new ArrayList<>();

diff --git a/...rg/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeDimerAsDefinedByProxl.java b/...rg/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeDimerAsDefinedByProxl.java
@@ -165,18 +165,32 @@ private GetDimerProteinMappingsSinglePeptideData getProteinMappingForSinglePepti
 						);
 		if( proteinMap.size() < 1 ) {
 			String msg = null;
+
 			if ( peptideMonolinkPositions != null && ( ! peptideMonolinkPositions.isEmpty() ) ) {
-				msg = "Could not map this peptide and monolink positions to any protein in the Proxl XML file for peptide " 
-					+ peptide.getSequence()
-					+ ", monolink position(s): " + StringUtils.join( peptideMonolinkPositions, ", " )
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+
+				List<String> linkersToStringArray = new ArrayList<>( linkerList.size() );
+				for ( ILinker linkerItem : linkerList ) {
+					linkersToStringArray.add(  linkerItem.toString() );
+				}
+				String linkersToString = StringUtils.join( linkersToStringArray, "," );
+
+				msg = "Could not import this Proxl XML file. Either no protein in the Proxl XML contained this peptide sequence (" 
+						+ peptide.getSequence()
+						+ ") or the linked position(s) reported for the peptide (positions " 
+						+ StringUtils.join( peptideMonolinkPositions, ", " )
+						+ ") was not a linkable position in the matched protein for the given cross-linker(s) (["
+						+ linkersToString
+						+ "]). The whole reported peptide string was: "
+						+ reportedPeptide.getReportedPeptideString()
+						+ "  \n\nThis is most-probably caused by specifying the incorrect cross-linker or the incorrect FASTA file when generating the Proxl XML file.";
 			} else {
-				msg = "Could not map this peptide to any protein in the Proxl XML file for " 
-					+ peptide.getSequence()
-					 + ".  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+				msg = "Could not import this Proxl XML file. No protein in the Proxl XML contained this peptide sequence (" 
+						+ peptide.getSequence()
+						+ "). The whole reported peptide string was: "
+						+ reportedPeptide.getReportedPeptideString()
+						+ "  \n\nThis is most-probably caused by specifying the incorrect FASTA file when generating the Proxl XML file.";
 			}
-			log.error( "getProteinMappingForSinglePeptide(...): " + msg );
+			log.error( "getProteinMappingForSinglePeptide(...): Msg thrown in ProxlImporterDataException: " + msg );
 			throw new ProxlImporterDataException( msg );
 		}
 		///  Data in perPeptideData for Monolinks

diff --git a/...in_importer/org/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeLooplink.java b/...in_importer/org/yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeLooplink.java
@@ -2,6 +2,7 @@
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -136,22 +137,39 @@ public GetLooplinkProteinMappingsResult getLooplinkroteinMappings(
 						reportedPeptide // For error reporting only
 						);
 		if( proteinMap.size() < 1 ) {
-			String msg = null;
+
+			List<String> linkersToStringArray = new ArrayList<>( linkerList.size() );
+			for ( ILinker linkerItem : linkerList ) {
+				linkersToStringArray.add(  linkerItem.toString() );
+			}
+			String linkersToString = StringUtils.join( linkersToStringArray, "," );
+
+			List<Integer> peptideLinkPositions = new ArrayList<>();
+			peptideLinkPositions.add( peptideLinkedPosition_1 );
+			peptideLinkPositions.add( peptideLinkedPosition_2 );
+
 			if ( peptideMonolinkPositions != null && ( ! peptideMonolinkPositions.isEmpty() ) ) {
-				msg = "Could not map this peptide and link position and monolink positions to any protein in the Proxl XML file for peptide " 
-					+ peptide.getSequence()
-					+ " at looplink positions: " + peptideLinkedPosition_1 + "," + peptideLinkedPosition_2 
-					+ ", monolink position(s): " + StringUtils.join( peptideMonolinkPositions, ", " )
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
-			} else {
-				msg = "Could not map this peptide and link position to any protein in the Proxl XML file for " 
-					+ peptide.getSequence()
-					+ " at looplink positions: " + peptideLinkedPosition_1 + "," + peptideLinkedPosition_2 
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+
+				for ( Integer peptideMonolinkPosition : peptideMonolinkPositions ) {
+					if ( ! peptideLinkPositions.contains( peptideMonolinkPosition ) ) {
+						peptideLinkPositions.add( peptideMonolinkPosition );
+					}
+				}
 			}
-			log.error( "getLooplinks(...): " + msg );
+
+			Collections.sort( peptideLinkPositions );
+
+			String msg = "Could not import this Proxl XML file. Either no protein in the Proxl XML contained this peptide sequence (" 
+					+ peptide.getSequence()
+					+ ") or the linked position(s) reported for the peptide (positions " 
+					+ StringUtils.join( peptideLinkPositions, ", " )
+					+ ") was not a linkable position in the matched protein for the given cross-linker(s) (["
+					+ linkersToString
+					+ "]). The whole reported peptide string was: "
+					+ reportedPeptide.getReportedPeptideString()
+					+ "  \n\nThis is most-probably caused by specifying the incorrect cross-linker or the incorrect FASTA file when generating the Proxl XML file.";
+
+			log.error( "getLooplinks(...): Msg thrown in ProxlImporterDataException: " + msg );
 			throw new ProxlImporterDataException( msg );
 		}
 		///  Data in perPeptideData for Monolinks

diff --git a/...yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeUnlinkedAsDefinedByProxl.java b/...yeastrc/proxl/import_xml_to_db/process_input/ProcessLinkTypeUnlinkedAsDefinedByProxl.java
@@ -127,17 +127,30 @@ public GetUnlinkedProteinMappingsResult getUnlinkedroteinMappings(
 		if( proteinMap.size() < 1 ) {
 			String msg = null;
 			if ( peptideMonolinkPositions != null && ( ! peptideMonolinkPositions.isEmpty() ) ) {
-				msg = "Could not map this peptide and monolink positions to any protein in the Proxl XML file for peptide " 
-					+ peptide.getSequence()
-					+ ", monolink position(s): " + StringUtils.join( peptideMonolinkPositions, ", " )
-					+ " for "
-					 + " linker(s).  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+
+				List<String> linkersToStringArray = new ArrayList<>( linkerList.size() );
+				for ( ILinker linkerItem : linkerList ) {
+					linkersToStringArray.add(  linkerItem.toString() );
+				}
+				String linkersToString = StringUtils.join( linkersToStringArray, "," );
+
+				msg = "Could not import this Proxl XML file. Either no protein in the Proxl XML contained this peptide sequence (" 
+						+ peptide.getSequence()
+						+ ") or the linked position(s) reported for the peptide (positions " 
+						+ StringUtils.join( peptideMonolinkPositions, ", " )
+						+ ") was not a linkable position in the matched protein for the given cross-linker(s) (["
+						+ linkersToString
+						+ "]). The whole reported peptide string was: "
+						+ reportedPeptide.getReportedPeptideString()
+						+ "  \n\nThis is most-probably caused by specifying the incorrect cross-linker or the incorrect FASTA file when generating the Proxl XML file.";
 			} else {
-				msg = "Could not map this peptide to any protein in the Proxl XML file for " 
-					+ peptide.getSequence()
-					 + ".  reportedPeptide sequence: " + reportedPeptide.getReportedPeptideString();
+				msg = "Could not import this Proxl XML file. No protein in the Proxl XML contained this peptide sequence (" 
+						+ peptide.getSequence()
+						+ "). The whole reported peptide string was: "
+						+ reportedPeptide.getReportedPeptideString()
+						+ "  \n\nThis is most-probably caused by specifying the incorrect FASTA file when generating the Proxl XML file.";
 			}
-			log.error( "getUnlinkedroteinMappings(...): " + msg );
+			log.error( "getUnlinkedroteinMappings(...): Msg thrown in ProxlImporterDataException: " + msg );
 			throw new ProxlImporterDataException( msg );
 		}
 		///  Data in perPeptideData for Monolinks