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JAL-2071 improvement to get column data files as InputStream
author
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 26 Apr 2016 12:00:43 +0000
(13:00 +0100)
committer
tcofoegbu
<tcnofoegbu@dundee.ac.uk>
Tue, 26 Apr 2016 12:00:43 +0000
(13:00 +0100)
src/jalview/fts/core/FTSRestClient.java
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src/jalview/fts/service/pdb/PDBFTSRestClient.java
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src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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test/jalview/fts/core/FTSRestClientTest.java
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diff --git
a/src/jalview/fts/core/FTSRestClient.java
b/src/jalview/fts/core/FTSRestClient.java
index
f611d5b
..
0605fef
100644
(file)
--- a/
src/jalview/fts/core/FTSRestClient.java
+++ b/
src/jalview/fts/core/FTSRestClient.java
@@
-5,8
+5,9
@@
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
import java.io.BufferedReader;
import jalview.fts.api.FTSRestClientI;
import java.io.BufferedReader;
-import java.io.FileReader;
import java.io.IOException;
import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Objects;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Objects;
@@
-43,7
+44,10
@@
public abstract class FTSRestClient implements FTSRestClientI
public void parseDataColumnsConfigFile()
{
String fileName = getColumnDataConfigFileName();
public void parseDataColumnsConfigFile()
{
String fileName = getColumnDataConfigFileName();
- try (BufferedReader br = new BufferedReader(new FileReader(fileName)))
+
+ InputStream in = getClass().getResourceAsStream(fileName);
+
+ try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
{
String line;
while ((line = br.readLine()) != null)
{
String line;
while ((line = br.readLine()) != null)
diff --git
a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index
28e06d2
..
08803b0
100644
(file)
--- a/
src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/
src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@
-413,7
+413,7
@@
public class PDBFTSRestClient extends FTSRestClient
@Override
public String getColumnDataConfigFileName()
{
@Override
public String getColumnDataConfigFileName()
{
- return getResourceFile("/fts/pdb_data_columns.txt");
+ return "/fts/pdb_data_columns.txt";
}
}
diff --git
a/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
b/src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
index
15c699e
..
c8e21e0
100644
(file)
--- a/
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
+++ b/
src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
@@
-217,7
+217,7
@@
public class UniProtFTSRestClient extends FTSRestClient
@Override
public String getColumnDataConfigFileName()
{
@Override
public String getColumnDataConfigFileName()
{
- return getResourceFile("/fts/uniprot_data_columns.txt");
+ return "/fts/uniprot_data_columns.txt";
}
}
}
}
diff --git
a/test/jalview/fts/core/FTSRestClientTest.java
b/test/jalview/fts/core/FTSRestClientTest.java
index
4a90c4e
..
a5c6390
100644
(file)
--- a/
test/jalview/fts/core/FTSRestClientTest.java
+++ b/
test/jalview/fts/core/FTSRestClientTest.java
@@
-24,7
+24,7
@@
public class FTSRestClientTest
@Override
public String getColumnDataConfigFileName()
{
@Override
public String getColumnDataConfigFileName()
{
- return "examples/testdata/test_fts_data_columns.conf";
+ return "/fts/uniprot_data_columns.txt";
}
@Override
}
@Override
@@
-272,7
+272,7
@@
public class FTSRestClientTest
}
String actualResourseFile = ftsRestClient
}
String actualResourseFile = ftsRestClient
- .getResourceFile("fts/uniprot_data_columns.conf");
+ .getResourceFile("/fts/uniprot_data_columns.txt");
Assert.assertNotNull(actualResourseFile);
Assert.assertTrue(actualResourseFile.length() > 31);
}
Assert.assertNotNull(actualResourseFile);
Assert.assertTrue(actualResourseFile.length() > 31);
}