From 818cb811b12a9d63ea3c2a076d499ac6504dcc2a Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 16 Mar 2010 10:36:34 +0000
Subject: [PATCH] changes to handle semi-colon separators in the qualifier
field of a history term
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13484 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../chado/ChadoTransactionManager.java | 6 ++-
.../genebuilder/cv/AbstractCvBox.java | 53 +++++++++++++++++--
.../components/genebuilder/cv/HistoryBox.java | 11 ++--
3 files changed, 61 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 9e8e269a2..cad6d435d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -2440,7 +2440,11 @@ public class ChadoTransactionManager
String prop = this_qualifier_part.substring(index+1);
logger4j.debug("FeatureCvTermProp = "+this_qualifier_part_lowercase);
- CvTerm cvTerm = getCvTerm(this_qualifier_part.substring(0,index), null);
+ CvTerm cvTerm;
+ if(index == -1 && cvName.equals(HISTORY_CV))
+ cvTerm = getCvTerm("qualifier", null);
+ else
+ cvTerm = getCvTerm(this_qualifier_part.substring(0,index), null);
if(cvTerm == null)
JOptionPane.showMessageDialog(null,
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java
index d24cfeb08..70381ab2d 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/AbstractCvBox.java
@@ -60,6 +60,41 @@ abstract class AbstractCvBox
return field;
}
+ /**
+ * Strip out the value of a field of interest from a qualifier string
+ * by splitting on '='.
+ * @param fieldName
+ * @param qualifierString
+ * @return
+ */
+ protected static String getFieldIgnoreSeparator(final String fieldName, final String qualifierString)
+ {
+ String[] parts = qualifierString.split("=");
+ StringBuffer buff = null;
+ for(int i=0; i<parts.length; i++)
+ {
+ if(parts[i].endsWith(fieldName) && i<parts.length-1)
+ {
+ if(buff == null)
+ buff = new StringBuffer();
+ else
+ buff.append("; ");
+
+ String part = parts[i+1];
+ if(i<parts.length-2)
+ {
+ int ind = part.lastIndexOf(';');
+ buff.append(part.substring(0, ind));
+ }
+ else
+ buff.append(part);
+ }
+ }
+ if(buff != null)
+ return buff.toString();
+ return getField(fieldName, qualifierString);
+ }
+
/**
* Strip out the value of a field of interest from a qualifier string
*
@@ -108,6 +143,21 @@ abstract class AbstractCvBox
return newQualifierString;
}
+/* protected String replace(String str, String pattern, String replace)
+ {
+ int s = 0;
+ int e = 0;
+ StringBuffer result = new StringBuffer();
+ while ((e = str.indexOf(pattern, s)) >= 0)
+ {
+ result.append(str.substring(s, e));
+ result.append(replace);
+ s = e+pattern.length();
+ }
+ result.append(str.substring(s));
+ return result.toString();
+ } */
+
/**
* Get a Date object from a date string in the format 20061129
* @param dateStr
@@ -130,9 +180,6 @@ abstract class AbstractCvBox
return cal.getTime();
}
-
-
-
protected abstract boolean isQualifierChanged();
protected abstract void updateQualifier(final QualifierVector qv);
}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java b/uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java
index 2690f808d..9359e31e2 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/cv/HistoryBox.java
@@ -104,7 +104,7 @@ class HistoryBox extends AbstractCvBox
curatorNameField.setCaretPosition(0);
xBox.add(curatorNameField);
- qual = getField("qualifier=", qualifierString);
+ qual = getFieldIgnoreSeparator("qualifier", qualifierString);
qualfTextField = new JTextField(qual);
qualfTextField.setToolTipText("qualifier column");
Dimension dimension2 = new Dimension(dimension.width*2, dimension.height);
@@ -126,7 +126,7 @@ class HistoryBox extends AbstractCvBox
if(!old.equals(termCombo.getSelectedItem()))
return true;
- old = getField("qualifier=", origQualifierString);
+ old = getFieldIgnoreSeparator("qualifier", origQualifierString);
if(!old.equals(qualfTextField.getText()))
return true;
@@ -238,11 +238,12 @@ class HistoryBox extends AbstractCvBox
newQualifierString);
}
- old = getField("qualifier=", origQualifierString);
+ old = getFieldIgnoreSeparator("qualifier", origQualifierString);
if(!old.equals(qualfTextField.getText()))
{
- newQualifierString = changeField("qualifier=", qualfTextField.getText().trim(),
- newQualifierString);
+ newQualifierString = newQualifierString.replaceAll("qualifier=[^;]+", "");
+ newQualifierString = newQualifierString.replaceAll("[;]+", ";");
+ newQualifierString += ";qualifier="+qualfTextField.getText().trim();
}
return newQualifierString;
--
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