From a2a599b84a290c508a0edb6447cf40f15beab0ed Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 29 Jul 2005 12:38:47 +0000
Subject: [PATCH] chado insert & delete featureprop
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3310 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/chado/ChadoTransaction.java | 47 ++++++++++-
.../chado/ChadoTransactionManager.java | 79 ++++++++++++++++---
.../sanger/artemis/util/DatabaseDocument.java | 3 +-
3 files changed, 113 insertions(+), 16 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index befeca708..425fd4191 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -165,9 +165,50 @@ public class ChadoTransaction
}
}
}
-// else if(type == INSERT)
-// else
-
+ else if(type == INSERT)
+ {
+ sqlBuff.append("INSERT INTO "+chadoTable);
+ StringBuffer sqlKeys = new StringBuffer();
+ StringBuffer sqlValues = new StringBuffer();
+
+ sqlKeys.append("feature_id , ");
+ sqlValues.append("(SELECT feature_id FROM feature WHERE uniquename='"+uniquename+"') , ");
+
+ String name;
+ Enumeration enum_prop = properties.keys();
+ while(enum_prop.hasMoreElements())
+ {
+ name = (String)enum_prop.nextElement();
+ sqlKeys.append(name);
+ sqlValues.append((String)properties.get(name));
+ if(enum_prop.hasMoreElements())
+ {
+ sqlKeys.append(" , ");
+ sqlValues.append(" , ");
+ }
+ }
+
+ sqlBuff.append(" ( "+sqlKeys.toString()+" ) ");
+ sqlBuff.append(" values ");
+ sqlBuff.append(" ( "+sqlValues.toString()+" ) ");
+ }
+ else if(type == DELETE)
+ {
+ sqlBuff.append("DELETE FROM "+chadoTable+" WHERE ");
+
+ String name;
+ String value;
+ Enumeration enum_constraint = constraint.keys();
+ while(enum_constraint.hasMoreElements())
+ {
+ name = (String)enum_constraint.nextElement();
+ value = (String)constraint.get(name);
+ sqlBuff.append(name+"="+value+" AND ");
+ }
+ sqlBuff.append("feature_id=(SELECT feature_id FROM feature WHERE uniquename='"+
+ uniquename+"')");
+ }
+
return sqlBuff.toString();
}
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 99319e276..834d19c86 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -39,7 +39,7 @@ import uk.ac.sanger.artemis.FeatureChangeListener;
import uk.ac.sanger.artemis.FeatureChangeEvent;
import java.util.Vector;
-
+import javax.swing.JOptionPane;
/**
*
@@ -165,42 +165,97 @@ public class ChadoTransactionManager
++qualifier_index)
{
final Qualifier this_qualifier = (Qualifier)qualifiers_new.elementAt(qualifier_index);
+
if(!qualifiers_old.contains(this_qualifier))
{
String name = this_qualifier.getName();
- if(qualifiers_old.indexOfQualifierWithName(name) > -1) // update qualifier
+ int old_index = qualifiers_old.indexOfQualifierWithName(name);
+
+ Qualifier this_old_qualifier = null;
+ StringVector old_qualifier_strings = null;
+ if(old_index> -1) // update qualifier
+ {
+ this_old_qualifier = (Qualifier)qualifiers_old.elementAt(old_index);
+
+ old_qualifier_strings =
+ StreamQualifier.toStringVector(null, this_old_qualifier);
+ }
+
+ final StringVector new_qualifier_strings =
+ StreamQualifier.toStringVector(null, this_qualifier);
+
+ String cvterm_id = DatabaseDocument.getCvtermID(name).toString();
+
+ if(cvterm_id == null) // chado doesn't recognise this
+ {
+ JOptionPane.showMessageDialog(null,
+ name+" is not a valid qualifier!",
+ "Invalid Qualifier",
+ JOptionPane.WARNING_MESSAGE);
+ continue;
+ }
+
+ if(old_index > -1 &&
+ new_qualifier_strings.size() == 1 &&
+ old_qualifier_strings.size() == 1)
{
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
feature_id, "featureprop");
- final StringVector new_qualifier_strings =
- StreamQualifier.toStringVector(null, this_qualifier);
+ String qualifier_string = new_qualifier_strings.elementAt(0);
+ int index = qualifier_string.indexOf("=");
+ if(index > -1)
+ qualifier_string = qualifier_string.substring(index+1);
- String cvterm_id = DatabaseDocument.getCvtermID(name).toString();
+ tsn.addProperty("value", "'"+ stripQuotes(qualifier_string) +"'");
+ tsn.setConstraint("featureprop.type_id", cvterm_id);
+ sql.add(tsn);
+ }
+ else
+ {
+ if(old_index > -1) // delete existing featureprops
+ {
+ tsn = new ChadoTransaction(ChadoTransaction.DELETE,
+ feature_id, "featureprop");
+ tsn.setConstraint("type_id", cvterm_id);
+ sql.add(tsn);
+ System.out.println(tsn.getSqlQuery());
+ }
+
+ // insert new featureprops
for(int value_index = 0; value_index < new_qualifier_strings.size();
++value_index)
{
+ tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+ feature_id, "featureprop");
String qualifier_string = new_qualifier_strings.elementAt(value_index);
int index = qualifier_string.indexOf("=");
if(index > -1)
qualifier_string = qualifier_string.substring(index+1);
- tsn.addProperty("value", "'"+qualifier_string+"'");
+ tsn.addProperty("value", "'"+ stripQuotes(qualifier_string) +"'");
+ tsn.addProperty("type_id", "'"+cvterm_id+"'");
+ tsn.addProperty("rank", Integer.toString(value_index));
+ sql.add(tsn);
+ System.out.println(tsn.getSqlQuery());
}
- tsn.setConstraint("featureprop.type_id", cvterm_id);
- sql.add(tsn);
-
+
System.out.println("******** "+DatabaseDocument.getCvtermID(name));
- System.out.println(tsn.getSqlQuery());
}
- else // insert qualifier
- {}
}
}
}
+ private String stripQuotes(String s)
+ {
+ if(s.startsWith("\"") && s.endsWith("\""))
+ s = s.substring(1,s.length()-1);
+
+ return s;
+ }
+
/**
*
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 1463c763c..590973055 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -304,7 +304,8 @@ public class DatabaseDocument extends Document
if(name.equals(cvterm.get(key)))
return key;
}
- return new Long("-1.");
+ return null;
+// return new Long("-1.");
}
private String getCvtermName(Connection conn, long id)
--
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