[Mobies-commit] [commit] r3856 - in UDM/trunk/judm/samples: GeneTF/src/test/edu/vanderbilt/isis/genetf/test GeneTRE/src/test/edu/vanderbilt/isis/genetre/test SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test
ksmyth at redhat1.isis.vanderbilt.edu
ksmyth at redhat1.isis.vanderbilt.edu
Fri Aug 26 15:45:45 CDT 2011
Author: ksmyth
Date: Fri Aug 26 15:45:45 2011
New Revision: 3856
Log:
Fix exception handling
Modified:
UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFFileInstanceTest.java
UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFStringInstanceTest.java
UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREFileInstanceTest.java
UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREStringInstanceTest.java
UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadFileTest.java
UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadStringTest.java
UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesFileInstanceTest.java
UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesStringInstanceTest.java
Modified: UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFFileInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFFileInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFFileInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -125,7 +125,7 @@
* @param is
* @throws UdmException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
try {
@@ -133,8 +133,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -181,9 +179,10 @@
/**
* Opens an existing data network from a file and saves in a stream.
* @throws UdmException
+ * @throws IOException
*/
public void testOpenExistingFromFileSaveToStream()
- throws UdmException {
+ throws UdmException, IOException {
ContainerFileFactory gtf = FactoryRepository.getgenetfContainerFileFactory();
Container con = gtf.open(NEW_INSTANCE_FILE);
@@ -196,13 +195,10 @@
* Opens an existing data network from a stream and saves in a file.
* @throws UdmException
*/
- public void testOpenExistingFromStreamSaveToFile()
- throws UdmException {
+ public void testOpenExistingFromStreamSaveToFile() throws IOException
+ , UdmException {
InputStream xml = null;
- try {
- xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
+ xml = new FileInputStream(BM_FILE_IN);
if (xml == null) {
System.out.println(
Modified: UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFStringInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFStringInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/GeneTF/src/test/edu/vanderbilt/isis/genetf/test/GeneTFStringInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -7,6 +7,7 @@
import java.io.BufferedWriter;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
@@ -99,7 +100,7 @@
* @param is
* @throws UdmException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
try {
@@ -107,8 +108,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -136,9 +135,8 @@
* Opens an existing data network from a string.
* @throws UdmException
*/
- public void testOpenExistingFromString() throws UdmException {
+ public void testOpenExistingFromString() throws UdmException, IOException {
String xml = new String("");
- try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
String line = null;
@@ -146,8 +144,6 @@
xml += (line + "\n");
}
raf.close();
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetfContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -167,10 +163,9 @@
* Opens an existing data network from a string and saves as a stream.
* @throws UdmException
*/
- public void testOpenExistingFromStringSaveToStream()
- throws UdmException {
+ public void testOpenExistingFromStringSaveToStream() throws IOException
+ , UdmException {
String xml = new String("");
- try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
String line = null;
@@ -178,8 +173,6 @@
xml += (line + "\n");
}
raf.close();
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetfContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -212,13 +205,11 @@
/**
* Opens an existing data network from a stream.
* @throws UdmException
+ * @throws FileNotFoundException
*/
- public void testOpenExistingFromStream() throws UdmException {
+ public void testOpenExistingFromStream() throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetfContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -237,14 +228,12 @@
/**
* Opens an existing data network from a stream and saves in a string.
* @throws UdmException
+ * @throws FileNotFoundException
*/
public void testOpenExistingFromStreamSaveToString()
- throws UdmException {
+ throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetfContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
Modified: UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREFileInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREFileInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREFileInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -7,6 +7,7 @@
import java.io.BufferedWriter;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.util.Vector;
@@ -150,8 +151,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
try {
@@ -159,8 +161,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -203,9 +203,10 @@
/**
* Opens an existing data network from a file and saves in a stream.
* @throws UdmException
+ * @throws IOException
*/
public void testOpenExistingFromFileSaveToStream()
- throws UdmException {
+ throws UdmException, IOException {
ContainerFileFactory gtf = FactoryRepository.getgenetreContainerFileFactory();
Container con = gtf.open(NEW_INSTANCE_FILE);
@@ -217,14 +218,12 @@
/**
* Opens an existing data network from a stream and saves in a file.
* @throws UdmException
+ * @throws FileNotFoundException
*/
public void testOpenExistingFromStreamSaveToFile()
- throws UdmException {
+ throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
if (xml == null) {
System.out.println(
Modified: UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREStringInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREStringInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/GeneTRE/src/test/edu/vanderbilt/isis/genetre/test/GeneTREStringInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -7,6 +7,7 @@
import java.io.BufferedWriter;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.RandomAccessFile;
import java.io.IOException;
import java.io.InputStream;
@@ -152,8 +153,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
try {
@@ -161,8 +163,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -189,10 +189,10 @@
/**
* Opens an existing data network from a string.
* @throws UdmException
+ * @throws IOException
*/
- public void testOpenExistingFromString() throws UdmException {
+ public void testOpenExistingFromString() throws UdmException, IOException {
String xml = new String("");
- try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
String line = null;
@@ -200,8 +200,6 @@
xml += (line + "\n");
}
raf.close();
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetreContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -220,9 +218,10 @@
/**
* Opens an existing data network from a string and saves as a stream.
* @throws UdmException
+ * @throws IOException
*/
public void testOpenExistingFromStringSaveToStream()
- throws UdmException {
+ throws UdmException, IOException {
String xml = new String("");
try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
@@ -266,13 +265,11 @@
/**
* Opens an existing data network from a stream.
* @throws UdmException
+ * @throws FileNotFoundException
*/
- public void testOpenExistingFromStream() throws UdmException {
+ public void testOpenExistingFromStream() throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetreContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -291,14 +288,12 @@
/**
* Opens an existing data network from a stream and saves in a string.
* @throws UdmException
+ * @throws FileNotFoundException
*/
public void testOpenExistingFromStreamSaveToString()
- throws UdmException {
+ throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getgenetreContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
Modified: UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadFileTest.java
==============================================================================
--- UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadFileTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadFileTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -101,8 +101,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
@@ -112,8 +113,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
Modified: UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadStringTest.java
==============================================================================
--- UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadStringTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/SBML2Ex/src/test/edu/vanderbilt/isis/sbml2ex/test/ReadStringTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -5,6 +5,7 @@
*/
package edu.vanderbilt.isis.sbml2ex.test;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
@@ -101,8 +102,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
try {
@@ -110,8 +112,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -152,8 +152,9 @@
/**
* Opens an existing data network from a file.
* @throws UdmException
+ * @throws IOException
*/
- public void testOpenExistingFromString() throws UdmException {
+ public void testOpenExistingFromString() throws UdmException, IOException {
System.out.println("\n-----------------------------------");
System.out.println("\tOpenExistingFromString");
System.out.println("-----------------------------------");
@@ -215,21 +216,19 @@
/**
* Opens an existing data network from a file.
* @throws UdmException
+ * @throws IOException
*/
- public void readStringTest(String fileName) throws UdmException {
+ public void readStringTest(String fileName) throws UdmException, IOException {
long time1 = System.currentTimeMillis();
sbmlStringFactory gtf = FactoryRepository.getsbmlsbmlStringFactory();
StringBuffer xmlString = new StringBuffer();
- try {
RandomAccessFile ra = new RandomAccessFile(fileName, "r");
String line = "";
while ((line = ra.readLine()) != null) {
xmlString.append(line);
xmlString.append("\n");
}
- } catch (IOException iEx) {
- }
sbml root = gtf.open(xmlString.toString());
Modified: UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesFileInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesFileInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesFileInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -17,6 +17,7 @@
import junit.framework.TestCase;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@@ -95,8 +96,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
@@ -106,8 +108,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -153,9 +153,10 @@
/**
* Opens an existing data network from a file and saves in a stream.
* @throws UdmException
+ * @throws IOException
*/
public void testOpenExistingFromFileSaveToStream()
- throws UdmException {
+ throws UdmException, IOException {
ContainerFileFactory gtf = FactoryRepository.getTimeSeriesContainerFileFactory();
Container con = gtf.open(NEW_INSTANCE_FILE);
@@ -167,15 +168,13 @@
/**
* Opens an existing data network from a stream and saves in a file.
* @throws UdmException
+ * @throws FileNotFoundException
*/
public void _testOpenExistingFromStreamSaveToFile()
- throws UdmException {
+ throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
if (xml == null) {
System.out.println(
Modified: UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesStringInstanceTest.java
==============================================================================
--- UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesStringInstanceTest.java Fri Aug 26 15:08:58 2011 (r3855)
+++ UDM/trunk/judm/samples/TimeSeries/src/test/edu/vanderbilt/isis/timeseries/test/TimeSeriesStringInstanceTest.java Fri Aug 26 15:45:45 2011 (r3856)
@@ -18,6 +18,7 @@
import junit.framework.TestCase;
import java.io.FileInputStream;
+import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.RandomAccessFile;
@@ -97,8 +98,9 @@
* Prints the content of the specified input stream to the output.
* @param is
* @throws UdmException
+ * @throws IOException
*/
- protected void printInputStream(InputStream is) throws UdmException {
+ protected void printInputStream(InputStream is) throws UdmException, IOException {
java.io.DataInputStream din = new java.io.DataInputStream(is);
String xml = new String("");
@@ -108,8 +110,6 @@
while ((line = din.readLine()) != null) {
xml += (line + "\n");
}
- } catch (IOException ex) {
- System.out.println("Error reading from stream: " + ex.getMessage());
} finally {
// close stream
try {
@@ -137,10 +137,9 @@
* Opens an existing data network from a string.
* @throws UdmException
*/
- public void testOpenExistingFromString() throws UdmException {
+ public void testOpenExistingFromString() throws UdmException, IOException {
String xml = new String("");
- try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
String line = null;
@@ -149,8 +148,6 @@
}
raf.close();
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getTimeSeriesContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -171,12 +168,12 @@
/**
* Opens an existing data network from a string and saves as a stream.
* @throws UdmException
+ * @throws IOException
*/
public void testOpenExistingFromStringSaveToStream()
- throws UdmException {
+ throws UdmException, IOException {
String xml = new String("");
- try {
RandomAccessFile raf = new RandomAccessFile(BM_FILE_IN, "r");
String line = null;
@@ -185,8 +182,6 @@
}
raf.close();
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getTimeSeriesContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -220,14 +215,12 @@
/**
* Opens an existing data network from a stream.
* @throws UdmException
+ * @throws FileNotFoundException
*/
- public void testOpenExistingFromStream() throws UdmException {
+ public void testOpenExistingFromStream() throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getTimeSeriesContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
@@ -248,15 +241,13 @@
/**
* Opens an existing data network from a stream and saves in a string.
* @throws UdmException
+ * @throws FileNotFoundException
*/
public void testOpenExistingFromStreamSaveToString()
- throws UdmException {
+ throws UdmException, FileNotFoundException {
InputStream xml = null;
- try {
xml = new FileInputStream(BM_FILE_IN);
- } catch (IOException e) {
- }
ContainerStringFactory gtf = FactoryRepository.getTimeSeriesContainerStringFactory();
UdmPseudoObject rootUPO = gtf.open(xml);
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