git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
e04c427
)
JAL-972 JAL-1084 propagate reference to local authentication provider so it can be...
author
jprocter
<jprocter@compbio.dundee.ac.uk>
Thu, 10 May 2012 16:14:26 +0000
(17:14 +0100)
committer
jprocter
<jprocter@compbio.dundee.ac.uk>
Thu, 10 May 2012 16:14:26 +0000
(17:14 +0100)
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
patch
|
blob
|
history
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
patch
|
blob
|
history
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
patch
|
blob
|
history
diff --git
a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index
7a78d8d
..
4f053aa
100644
(file)
--- a/
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/
src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@
-25,8
+25,10
@@
import java.util.Map;
import java.util.StringTokenizer;
\r
import java.util.Vector;
\r
\r
import java.util.StringTokenizer;
\r
import java.util.Vector;
\r
\r
+import org.biodas.jdas.client.ConnectionPropertyProviderI;
\r
import org.biodas.jdas.client.SequenceClient;
\r
import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
\r
import org.biodas.jdas.client.SequenceClient;
\r
import org.biodas.jdas.client.adapters.sequence.DasSequenceAdapter;
\r
+import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
\r
import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
\r
import org.biodas.jdas.schema.sequence.SEQUENCE;
\r
import org.biodas.jdas.schema.sources.COORDINATES;
\r
import org.biodas.jdas.client.threads.SequenceClientMultipleSources;
\r
import org.biodas.jdas.schema.sequence.SEQUENCE;
\r
import org.biodas.jdas.schema.sources.COORDINATES;
\r
@@
-65,7
+67,7
@@
public class DasSequenceSource extends DbSourceProxyImpl implements
protected String dbname = "DASCS";
\r
\r
protected String dbrefname = "das:source";
\r
protected String dbname = "DASCS";
\r
\r
protected String dbrefname = "das:source";
\r
-
\r
+ protected MultipleConnectionPropertyProviderI connprops=null;
\r
/**
\r
* create a new DbSource proxy for a DAS 1 source
\r
*
\r
/**
\r
* create a new DbSource proxy for a DAS 1 source
\r
*
\r
@@
-82,9
+84,9
@@
public class DasSequenceSource extends DbSourceProxyImpl implements
* if source is not capable of the 'sequence' command
\r
*/
\r
public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
\r
* if source is not capable of the 'sequence' command
\r
*/
\r
public DasSequenceSource(String dbname, String dbrefname, SOURCE source,
\r
- VERSION version, COORDINATES coordsys) throws Exception
\r
+ VERSION version, COORDINATES coordsys, MultipleConnectionPropertyProviderI connprops) throws Exception
\r
{
\r
{
\r
- if (!(jsrc = new JalviewSource(source, false)).isSequenceSource())
\r
+ if (!(jsrc = new JalviewSource(source, connprops, false)).isSequenceSource())
\r
{
\r
throw new Exception("Source " + source.getTitle()
\r
+ " does not support the sequence command.");
\r
{
\r
throw new Exception("Source " + source.getTitle()
\r
+ " does not support the sequence command.");
\r
@@
-93,6
+95,7
@@
public class DasSequenceSource extends DbSourceProxyImpl implements
this.dbname = dbname;
\r
this.dbrefname = dbrefname;
\r
this.coordsys = coordsys;
\r
this.dbname = dbname;
\r
this.dbrefname = dbrefname;
\r
this.coordsys = coordsys;
\r
+ this.connprops=connprops;
\r
}
\r
\r
public String getAccessionSeparator()
\r
}
\r
\r
public String getAccessionSeparator()
\r
@@
-149,8
+152,7
@@
public class DasSequenceSource extends DbSourceProxyImpl implements
System.err
\r
.println("Retrieving IDs individually from das source: "
\r
+ sr);
\r
System.err
\r
.println("Retrieving IDs individually from das source: "
\r
+ sr);
\r
- // todo : get conn property provider
\r
- org.biodas.jdas.client.SequenceClient sq = new SequenceClient();
\r
+ org.biodas.jdas.client.SequenceClient sq = new SequenceClient(connprops.getConnectionPropertyProviderFor(sr));
\r
for (String q : toks)
\r
{
\r
List<String> qset = Arrays.asList(new String[]
\r
for (String q : toks)
\r
{
\r
List<String> qset = Arrays.asList(new String[]
\r
diff --git
a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index
2bc33b6
..
3ed597e
100644
(file)
--- a/
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/
src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@
-83,7
+83,7
@@
public class DasSourceRegistry implements DasSourceRegistryI,
private List<jalviewSourceI> getDASSources()
{
private List<jalviewSourceI> getDASSources()
{
- return getDASSources(getDasRegistryURL());
+ return getDASSources(getDasRegistryURL(), this);
}
/**
}
/**
@@
-92,7
+92,7
@@
public class DasSourceRegistry implements DasSourceRegistryI,
* @param registryURL
* return sources from registryURL
*/
* @param registryURL
* return sources from registryURL
*/
- private static List<jalviewSourceI> getDASSources(String registryURL)
+ private static List<jalviewSourceI> getDASSources(String registryURL, MultipleConnectionPropertyProviderI registry)
{
try
{
{
try
{
@@
-108,7
+108,7
@@
public class DasSourceRegistry implements DasSourceRegistryI,
Integer latest;
for (SOURCE src : dassources)
{
Integer latest;
for (SOURCE src : dassources)
{
- JalviewSource jsrc=new JalviewSource(src, false);
+ JalviewSource jsrc=new JalviewSource(src, registry, false);
latest=latests.get(jsrc.getSourceURL());
if (latest!=null)
{
latest=latests.get(jsrc.getSourceURL());
if (latest!=null)
{
@@
-223,7
+223,7
@@
public class DasSourceRegistry implements DasSourceRegistryI,
{
localSources = new Hashtable<String, jalviewSourceI>();
}
{
localSources = new Hashtable<String, jalviewSourceI>();
}
- jalviewSourceI src = new JalviewSource(local, true);
+ jalviewSourceI src = new JalviewSource(local, this, true);
localSources.put(local.getTitle(), src);
return src;
}
localSources.put(local.getTitle(), src);
return src;
}
diff --git
a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index
c9caf6e
..
11bdf02
100644
(file)
--- a/
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/
src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@
-7,6
+7,7
@@
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
import java.util.List;
import java.util.Map;
+import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
import org.biodas.jdas.dassources.Capabilities;
import org.biodas.jdas.dassources.utils.DasTimeFormat;
import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
import org.biodas.jdas.dassources.Capabilities;
import org.biodas.jdas.dassources.utils.DasTimeFormat;
import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
@@
-23,9
+24,10
@@
import jalview.ws.seqfetcher.DbSourceProxy;
public class JalviewSource implements jalviewSourceI
{
SOURCE source;
public class JalviewSource implements jalviewSourceI
{
SOURCE source;
-
- public JalviewSource(SOURCE local2, boolean local)
+ MultipleConnectionPropertyProviderI connprov;
+ public JalviewSource(SOURCE local2, MultipleConnectionPropertyProviderI connprov, boolean local)
{
{
+ this.connprov=connprov;
this.local = local;
source = local2;
}
this.local = local;
source = local2;
}
@@
-257,7
+259,7
@@
public class JalviewSource implements jalviewSourceI
seqsources.add(ds = new DasSequenceSource(getTitle() + " ("
+ cs.getAuthority() + " " + cs.getSource()
+ (cs.getVersion() != null ? " " + cs.getVersion() : "")
seqsources.add(ds = new DasSequenceSource(getTitle() + " ("
+ cs.getAuthority() + " " + cs.getSource()
+ (cs.getVersion() != null ? " " + cs.getVersion() : "")
- + ")", cs.getAuthority(), source, v, cs));
+ + ")", cs.getAuthority(), source, v, cs, connprov));
if (seqsources.size() > 1)
{
System.err.println("Added another sequence DB source for "
if (seqsources.size() > 1)
{
System.err.println("Added another sequence DB source for "
@@
-277,7
+279,7
@@
public class JalviewSource implements jalviewSourceI
try
{
seqsources.add(new DasSequenceSource(getTitle(), getTitle(),
try
{
seqsources.add(new DasSequenceSource(getTitle(), getTitle(),
- source, getVersion(), null));
+ source, getVersion(), null, connprov));
} catch (Exception e)
{
// TODO Auto-generated catch block
} catch (Exception e)
{
// TODO Auto-generated catch block