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[Treebase-guts] SF.net SVN: treebase:[963] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/matrix/RowSegment.java
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From: <hs...@us...> - 2011-09-23 17:15:22
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Revision: 963
http://treebase.svn.sourceforge.net/treebase/?rev=963&view=rev
Author: hshyket
Date: 2011-09-23 17:15:15 +0000 (Fri, 23 Sep 2011)
Log Message:
-----------
When uploading RowSegment data, some of the fields will truncate to the column size rather than stop inserting
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java 2011-09-20 15:16:58 UTC (rev 962)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/matrix/RowSegment.java 2011-09-23 17:15:15 UTC (rev 963)
@@ -1,5 +1,6 @@
package org.cipres.treebase.domain.matrix;
+import java.lang.reflect.Method;
import java.util.List;
import java.util.Map;
@@ -335,54 +336,152 @@
for (int i = 0; i < pMappedFields.size(); i++) {
RowSegmentField mappedField = pMappedFields.get(i);
+
+ try {
- if (mappedField == RowSegmentField.TITLE) {
- setTitle(pValues.get(i));
- } else if (mappedField == RowSegmentField.TAXONLABEL) {
- String rowTaxonLabel = pValues.get(i);
+ if (mappedField == RowSegmentField.TITLE) {
+ setTitle(pValues.get(i));
+ } else if (mappedField == RowSegmentField.TAXONLABEL) {
+ String rowTaxonLabel = pValues.get(i);
- if (rowTaxonLabel != null) {
- MatrixRow row = pTaxonLabelRowMap.get(rowTaxonLabel);
- setMatrixRow(row);
+ if (rowTaxonLabel != null) {
+ MatrixRow row = pTaxonLabelRowMap.get(rowTaxonLabel);
+ setMatrixRow(row);
+ }
+ } else if (mappedField == RowSegmentField.START_INDEX) {
+ setStartIndex(Integer.parseInt(pValues.get(i)));
+ } else if (mappedField == RowSegmentField.END_INDEX) {
+ setEndIndex(Integer.parseInt(pValues.get(i)));
+ } else if (mappedField == RowSegmentField.INST_ACRONYM) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getInstAcronym");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Institutional Acroynm field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setInstAcronym(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.COLLECTION_CODE) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getCollectionCode");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Collection Code field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setCollectionCode(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.CATALOG_NUM) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getCatalogNumber");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Catalog Number field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setCatalogNumber(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.GENBANK_ACC_NUM) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getGenBankAccession");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The GenBank Accession Number field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setGenBankAccession(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.OTHER_ACC_NUM) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getOtherAccession");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Other Accession Number field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setOtherAccession(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.SAMPLE_DATE) {
+ getSpecimenLabel().setSampleDate(
+ TreebaseUtil.parseDate(pValues.get(i), true, pExecution));
+ } else if (mappedField == RowSegmentField.SAMPLE_TAXONLABEL) {
+ setSpecimenTaxonLabelStr(pValues.get(i));
+ } else if (mappedField == RowSegmentField.COLLECTOR) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getCollector");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Collector field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setCollector(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.LATITUDE) {
+ getSpecimenLabel()
+ .setLatitude(TreebaseUtil.parseDouble(pValues.get(i), pExecution));
+ } else if (mappedField == RowSegmentField.LONGITUDE) {
+ getSpecimenLabel().setLongitude(
+ TreebaseUtil.parseDouble(pValues.get(i), pExecution));
+ } else if (mappedField == RowSegmentField.ELEVATION) {
+ getSpecimenLabel().setElevation(
+ TreebaseUtil.parseDouble(pValues.get(i), pExecution));
+ } else if (mappedField == RowSegmentField.COUNTRY) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getCountry");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ int length = getColumn.length();
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Country field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setCountry(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.STATE) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getState");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The State field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setState(pValues.get(i));
+
+ } else if (mappedField == RowSegmentField.LOCALITY) {
+
+ Method getMethod = SpecimenLabel.class.getMethod("getLocality");
+ Column getColumn = getMethod.getAnnotation(Column.class);
+
+ if (pValues.get(i).length() > getColumn.length()) {
+ pValues.set(i, pValues.get(i).substring(0, getColumn.length()));
+ pExecution.addErrorMessage("The Locality field was truncated due to its length");
+ }
+
+ getSpecimenLabel().setLocality(pValues.get(i));
}
- } else if (mappedField == RowSegmentField.START_INDEX) {
- setStartIndex(Integer.parseInt(pValues.get(i)));
- } else if (mappedField == RowSegmentField.END_INDEX) {
- setEndIndex(Integer.parseInt(pValues.get(i)));
- } else if (mappedField == RowSegmentField.INST_ACRONYM) {
- getSpecimenLabel().setInstAcronym(pValues.get(i));
- } else if (mappedField == RowSegmentField.COLLECTION_CODE) {
- getSpecimenLabel().setCollectionCode(pValues.get(i));
- } else if (mappedField == RowSegmentField.CATALOG_NUM) {
- getSpecimenLabel().setCatalogNumber(pValues.get(i));
- } else if (mappedField == RowSegmentField.GENBANK_ACC_NUM) {
- getSpecimenLabel().setGenBankAccession(pValues.get(i));
- } else if (mappedField == RowSegmentField.OTHER_ACC_NUM) {
- getSpecimenLabel().setOtherAccession(pValues.get(i));
- } else if (mappedField == RowSegmentField.SAMPLE_DATE) {
- getSpecimenLabel().setSampleDate(
- TreebaseUtil.parseDate(pValues.get(i), true, pExecution));
- } else if (mappedField == RowSegmentField.SAMPLE_TAXONLABEL) {
- setSpecimenTaxonLabelStr(pValues.get(i));
- } else if (mappedField == RowSegmentField.COLLECTOR) {
- getSpecimenLabel().setCollector(pValues.get(i));
- } else if (mappedField == RowSegmentField.LATITUDE) {
- getSpecimenLabel()
- .setLatitude(TreebaseUtil.parseDouble(pValues.get(i), pExecution));
- } else if (mappedField == RowSegmentField.LONGITUDE) {
- getSpecimenLabel().setLongitude(
- TreebaseUtil.parseDouble(pValues.get(i), pExecution));
- } else if (mappedField == RowSegmentField.ELEVATION) {
- getSpecimenLabel().setElevation(
- TreebaseUtil.parseDouble(pValues.get(i), pExecution));
- } else if (mappedField == RowSegmentField.COUNTRY) {
- getSpecimenLabel().setCountry(pValues.get(i));
- } else if (mappedField == RowSegmentField.STATE) {
- getSpecimenLabel().setState(pValues.get(i));
- } else if (mappedField == RowSegmentField.LOCALITY) {
- getSpecimenLabel().setLocality(pValues.get(i));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
}
-
+
}
}
@@ -439,6 +538,7 @@
* Returns a string representation of the segment.
*
* @return
+
*/
@Transient
public String getSegmentData() {
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