Author: jgao
Date: 2010-09-02 18:34:42 -0700 (Thu, 02 Sep 2010)
New Revision: 21682
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
Log:
CyThesaurus: more commands
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
2010-09-03 00:29:14 UTC (rev 21681)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/CyThesaurusNamespace.java
2010-09-03 01:34:42 UTC (rev 21682)
@@ -37,6 +37,9 @@
import csplugins.id.mapping.IDMapperClientManager;
import csplugins.id.mapping.ui.IDMappingSourceConfigDialog;
import csplugins.id.mapping.ui.CyThesaurusDialog;
+import csplugins.id.mapping.AttributeBasedIDMapping;
+import csplugins.id.mapping.AttributeBasedIDMappingImpl;
+import csplugins.id.mapping.util.DataSourceWrapper;
import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
@@ -49,17 +52,19 @@
import cytoscape.command.CyCommandResult;
import cytoscape.layout.Tunable;
-import cytoscape.logger.CyLogger;
-import cytoscape.view.CyNetworkView;
-import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
import java.util.HashSet;
-import java.util.List;
import java.util.Map;
import java.util.Set;
import org.bridgedb.DataSource;
+import org.bridgedb.DataSourcePatterns;
+import org.bridgedb.IDMapperCapabilities;
+import org.bridgedb.IDMapperStack;
+import org.bridgedb.Xref;
/**
*
@@ -79,7 +84,11 @@
private static final String DESELECT_RESOURCE = "deselect resource";
private static final String GET_SRC_ID_TYPES = "get source id types";
private static final String GET_TGT_ID_TYPES = "get target id types";
- private static final String IS_MAPPING_SUPPORT = "is mapping supported";
+ private static final String CHECK_MAPPING_SUPPORT = "check mapping
supported";
+ private static final String ATTRIBUTE_BASED_MAPPING = "attribute based
mapping";
+ private static final String GENERAL_MAPPING = "general mapping";
+ private static final String CHECK_ID_EXIST = "check id exist";
+ private static final String GUESS_TYPE = "guess id type";
// Arguments
private static final String CLASS_PATH = "classpath";
@@ -87,6 +96,10 @@
private static final String DISPLAY_NAME = "displayname";
private static final String SOURCE_TYPE = "sourcetype";
private static final String TARGET_TYPE = "targettype";
+ private static final String NETWORK_LIST = "networklist";
+ private static final String SOURCE_ATTR = "sourceattr";
+ private static final String TARGET_ATTR = "targetattr";
+ private static final String SOURCE_ID = "sourceid";
protected CyThesaurusNamespace(CyCommandNamespace ns) {
super(ns);
@@ -123,10 +136,31 @@
addArgument(GET_TGT_ID_TYPES);
addDescription(GET_TGT_ID_TYPES, "Get supported target ID types");
- addArgument(IS_MAPPING_SUPPORT);
- addArgument(IS_MAPPING_SUPPORT, SOURCE_TYPE);
- addArgument(IS_MAPPING_SUPPORT, TARGET_TYPE);
- addDescription(IS_MAPPING_SUPPORT, "Check if ID mapping between two ID
types is supported");
+// addArgument(IS_MAPPING_SUPPORT);
+ addArgument(CHECK_MAPPING_SUPPORT, SOURCE_TYPE);
+ addArgument(CHECK_MAPPING_SUPPORT, TARGET_TYPE);
+ addDescription(CHECK_MAPPING_SUPPORT, "Check if ID mapping between two
ID types is supported");
+
+ addArgument(ATTRIBUTE_BASED_MAPPING, NETWORK_LIST); //optional
+ addArgument(ATTRIBUTE_BASED_MAPPING, SOURCE_ATTR); // required
+ addArgument(ATTRIBUTE_BASED_MAPPING, TARGET_ATTR); // optional
+ addArgument(ATTRIBUTE_BASED_MAPPING, SOURCE_TYPE); // optional
+ addArgument(ATTRIBUTE_BASED_MAPPING, TARGET_TYPE); // required
+ addDescription(ATTRIBUTE_BASED_MAPPING, "Mapping IDs of the
sourceidtype(s) in "
+ + "sourceattribute to IDs of the targetidtype and save them to
targetattribute.");
+
+ addArgument(GENERAL_MAPPING, SOURCE_ID);
+ addArgument(GENERAL_MAPPING, SOURCE_TYPE);
+ addArgument(GENERAL_MAPPING, TARGET_TYPE);
+ addDescription(GENERAL_MAPPING, "Mapping sourceid(s) of sourcetype to
targettype.");
+
+ addArgument(CHECK_ID_EXIST, SOURCE_ID);
+ addArgument(CHECK_ID_EXIST, SOURCE_TYPE);
+ addDescription(CHECK_ID_EXIST, "Check if ID exists.");
+
+ addArgument(GUESS_TYPE, SOURCE_ID);
+ addDescription(CHECK_ID_EXIST, "Guess ID types from a set of IDs.");
+
}
@@ -143,187 +177,577 @@
}
public CyCommandResult execute(String command, Map<String, Object>args)
throws CyCommandException {
+ if (command.equals(VERSION))
+ return version(command, args);
+ if (command.equals(MAIN_DIALOG))
+ return mainDialog(command, args);
+ if (command.equals(RESOURCE_DIALOG))
+ return resourcesDialog(command, args);
+ if (command.equals(LIST_RESOURCE))
+ return listResources(command, args);
+ if (command.equals(LIST_SELECTED_RESOURCE))
+ return listSelectedResources(command, args);
+ if (command.equals(ADD_RESOURCE))
+ return addResource(command, args);
+ if (command.equals(REMOVE_RESOURCE))
+ remvoeResource(command, args);
+ if (command.equals(SELECT_RESOURCE))
+ return selectResource(command, args);
+ if (command.equals(DESELECT_RESOURCE))
+ return deselectResource(command, args);
+ if (command.equals(GET_SRC_ID_TYPES))
+ return getSrcIdTypes(command, args);
+ if (command.equals(GET_TGT_ID_TYPES))
+ return getTgtIdTypes(command, args);
+ if (command.equals(CHECK_MAPPING_SUPPORT))
+ return isMappingSupported(command, args);
+ if (command.equals(ATTRIBUTE_BASED_MAPPING))
+ return attributeBasedMapping(command, args);
+ if (command.equals(GENERAL_MAPPING))
+ return generalMapping(command, args);
+ if (command.equals(CHECK_ID_EXIST))
+ return idExists(command, args);
+ if (command.equals(GUESS_TYPE))
+ return guessIDTypes(command, args);
+ throw new CyCommandException(getHandlerName()+": unknown command
"+command);
+ }
+
+ private CyCommandResult version(String command, Map<String, Object>args)
throws CyCommandException {
CyCommandResult result = new CyCommandResult();
+ result.addResult(CyThesaurusPlugin.VERSION);
+ return result;
+ }
- if (command.equals(VERSION)) {
- result.addResult(CyThesaurusPlugin.VERSION);
- } else if (command.equals(MAIN_DIALOG)) {
- final CyThesaurusDialog dialog = new
CyThesaurusDialog(Cytoscape.getDesktop(), true);
- dialog.setLocationRelativeTo(Cytoscape.getDesktop());
- dialog.setMapSrcAttrIDTypes(CyThesaurusPlugin.mapSrcAttrIDTypes);
- dialog.setVisible(true);
- } else if (command.equals(RESOURCE_DIALOG)) {
- IDMappingSourceConfigDialog srcConfDialog
- = new IDMappingSourceConfigDialog(Cytoscape.getDesktop(),
true);
- srcConfDialog.setVisible(true);
- } else if (command.equals(LIST_RESOURCE)) {
- Set<String> mappers = new HashSet();
- Set<IDMapperClient> clients = IDMapperClientManager.allClients();
- String message = "There are "+clients.size()+" ID mapping
resources:\n";
+ private CyCommandResult mainDialog(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ final CyThesaurusDialog dialog = new
CyThesaurusDialog(Cytoscape.getDesktop(), true);
+ dialog.setLocationRelativeTo(Cytoscape.getDesktop());
+ dialog.setMapSrcAttrIDTypes(CyThesaurusPlugin.mapSrcAttrIDTypes);
+ dialog.setVisible(true);
+ return result;
+ }
- for (IDMapperClient client : clients) {
- String connStr = client.getConnectionString();
- mappers.add(connStr);
- message += "\t"+connStr+"[class:
"+client.getClassString()+"]"+"\n";
- }
+ private CyCommandResult resourcesDialog(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ IDMappingSourceConfigDialog srcConfDialog
+ = new IDMappingSourceConfigDialog(Cytoscape.getDesktop(),
true);
+ srcConfDialog.setVisible(true);
+ return result;
+ }
- result.addMessage(message);
- result.addResult(mappers);
- } else if (command.equals(LIST_SELECTED_RESOURCE)) {
- Set<String> mappers = new HashSet();
- Set<IDMapperClient> clients =
IDMapperClientManager.selectedClients();
- String message = "There are selected "+clients.size()+" ID mapping
resources:\n";
+ private CyCommandResult listResources(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Set<String> mappers = new HashSet();
+ Set<IDMapperClient> clients = IDMapperClientManager.allClients();
+ String message = "There are "+clients.size()+" ID mapping
resources:\n";
- for (IDMapperClient client : clients) {
- String connStr = client.getConnectionString();
- mappers.add(connStr);
- message += "\t"+connStr+"[class:
"+client.getClassString()+"]"+"\n";
+ for (IDMapperClient client : clients) {
+ String connStr = client.getConnectionString();
+ mappers.add(connStr);
+ message += "\t"+connStr+"[class:
"+client.getClassString()+"]"+"\n";
+ }
+
+ result.addMessage(message);
+ result.addResult(mappers);
+ return result;
+ }
+
+ private CyCommandResult listSelectedResources(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Set<String> mappers = new HashSet();
+ Set<IDMapperClient> clients = IDMapperClientManager.selectedClients();
+ String message = "There are selected "+clients.size()+" ID mapping
resources:\n";
+
+ for (IDMapperClient client : clients) {
+ String connStr = client.getConnectionString();
+ mappers.add(connStr);
+ message += "\t"+connStr+"[class:
"+client.getClassString()+"]"+"\n";
+ }
+
+ result.addMessage(message);
+ result.addResult(mappers);
+ return result;
+ }
+
+ private CyCommandResult addResource(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ String classPath = getArg(command, CLASS_PATH, args);
+ String connString = getArg(command, CONN_STRING, args);
+ String displayName = getArg(command, DISPLAY_NAME, args);
+ if (connString == null || classPath==null)
+ throw new CyCommandException(CLASS_PATH + " and " +
CONN_STRING + " cannot be null.");
+
+ if (displayName==null)
+ displayName = connString;
+
+ try {
+ IDMapperClient client = new IDMapperClientImplTunables
+ .Builder(connString, classPath)
+ .displayName(displayName)
+ .build();
+ IDMapperClientManager.registerClient(client);
+ result.addMessage("Successfully registered");
+ } catch (Exception e) {
+ // throw new CyCommandException(e);
+ result.addError("Failed to add the resource\n"+e.getMessage());
+ }
+ return result;
+ }
+
+ private CyCommandResult remvoeResource(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ String connString = getArg(command, CONN_STRING, args);
+ if (connString == null)
+ throw new CyCommandException(CONN_STRING + " cannot be null.");
+
+ try {
+ if (IDMapperClientManager.removeClient(connString)) {
+ result.addResult(Boolean.TRUE);
+ result.addMessage("Successfully unregistered");
+ } else {
+ result.addResult(Boolean.FALSE);
+ result.addMessage("Could not unregister. The specific ID
mapping resource might not exist.");
}
- result.addMessage(message);
- result.addResult(mappers);
- } else if (command.equals(ADD_RESOURCE)) {
- String classPath = getArg(command, CLASS_PATH, args);
- String connString = getArg(command, CONN_STRING, args);
- String displayName = getArg(command, DISPLAY_NAME, args);
- if (connString == null || classPath==null)
- throw new CyCommandException(CLASS_PATH + " and " +
CONN_STRING + " cannot be null.");
+ } catch (Exception e) {
+ // throw new CyCommandException(e);
+ result.addError("Failed to remove the resource\n"+e.getMessage());
+ }
+ return result;
+ }
- if (displayName==null)
- displayName = connString;
+ private CyCommandResult selectResource(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ String connString = getArg(command, CONN_STRING, args);
+ if (connString == null)
+ throw new CyCommandException(CONN_STRING + " cannot be null.");
- try {
- IDMapperClient client = new IDMapperClientImplTunables
- .Builder(connString, classPath)
- .displayName(displayName)
- .build();
- IDMapperClientManager.registerClient(client);
- result.addMessage("Successfully registered");
- } catch (Exception e) {
- // throw new CyCommandException(e);
- result.addError("Failed to add the resource\n"+e.getMessage());
+ try {
+ IDMapperClient client =
IDMapperClientManager.getClient(connString);
+ if (client == null) {
+ result.addResult(Boolean.FALSE);
+ result.addMessage("Could not select the specific ID mapping
resource since it did not exist.");
+ } else {
+ client.setSelected(true);
+ result.addResult(Boolean.TRUE);
+ result.addMessage("Selected.");
}
- } else if (command.equals(REMOVE_RESOURCE)) {
- String connString = getArg(command, CONN_STRING, args);
- if (connString == null)
- throw new CyCommandException(CONN_STRING + " cannot be
null.");
+ } catch (Exception e) {
+ // throw new CyCommandException(e);
+ result.addError("Failed to remove the resource\n"+e.getMessage());
+ }
+ return result;
+ }
- try {
- if (IDMapperClientManager.removeClient(connString)) {
- result.addResult(Boolean.TRUE);
- result.addMessage("Successfully unregistered");
- } else {
- result.addResult(Boolean.FALSE);
- result.addMessage("Could not unregister. The specific ID
mapping resource might not exist.");
- }
+ private CyCommandResult deselectResource(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ String connString = getArg(command, CONN_STRING, args);
+ if (connString == null)
+ throw new CyCommandException(CONN_STRING + "cannot be null.");
- } catch (Exception e) {
- // throw new CyCommandException(e);
- result.addError("Failed to remove the
resource\n"+e.getMessage());
+ try {
+ IDMapperClient client =
IDMapperClientManager.getClient(connString);
+ if (client == null) {
+ result.addResult(Boolean.FALSE);
+ result.addMessage("Could not deselect the specific ID mapping
resource since it did not exist.");
+ } else {
+ client.setSelected(false);
+ result.addResult(Boolean.TRUE);
+ result.addMessage("Deselected.");
}
- } else if (command.equals(SELECT_RESOURCE)) {
- String connString = getArg(command, CONN_STRING, args);
- if (connString == null)
- throw new CyCommandException(CONN_STRING + " cannot be
null.");
+ } catch (Exception e) {
+ // throw new CyCommandException(e);
+ result.addError("Failed to remove the resource\n"+e.getMessage());
+ }
+ return result;
+ }
- try {
- IDMapperClient client =
IDMapperClientManager.getClient(connString);
- if (client == null) {
- result.addResult(Boolean.FALSE);
- result.addMessage("Could not select the specific ID
mapping resource since it did not exist.");
+ private CyCommandResult getSrcIdTypes(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Set<String> types = new HashSet();
+ Set<DataSource> dss;
+ try {
+ dss = IDMapperClientManager.selectedIDMapperStack().
+ getCapabilities().getSupportedSrcDataSources();
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+
+ String message = "There are "+dss.size()+" supported source ID
types:\n";
+
+ for (DataSource ds : dss) {
+ types.add(ds.getFullName());
+ message += "\t"+ds.getFullName()+"\n";
+ }
+
+ result.addMessage(message);
+ result.addResult(types);
+ return result;
+ }
+
+ private CyCommandResult getTgtIdTypes(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Set<String> types = new HashSet();
+ Set<DataSource> dss;
+ try {
+ dss = IDMapperClientManager.selectedIDMapperStack().
+ getCapabilities().getSupportedTgtDataSources();
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+
+ String message = "There are "+dss.size()+" supported target ID
types:\n";
+
+ for (DataSource ds : dss) {
+ types.add(ds.getFullName());
+ message += "\t"+ds.getFullName()+"\n";
+ }
+
+ result.addMessage(message);
+ result.addResult(types);
+ return result;
+ }
+
+ private CyCommandResult isMappingSupported(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ String srctype = getArg(command, SOURCE_TYPE, args);
+ String tgttype = getArg(command, TARGET_TYPE, args);
+ if (srctype == null || tgttype==null)
+ throw new CyCommandException(SOURCE_TYPE + " and " +
TARGET_TYPE + " cannot be null.");
+
+ DataSource srcds = DataSource.getByFullName(srctype);
+ DataSource tgtds = DataSource.getByFullName(tgttype);
+ try {
+ if (IDMapperClientManager.selectedIDMapperStack().
+ getCapabilities().isMappingSupported(srcds, tgtds)) {
+ result.addResult(Boolean.TRUE);
+ result.addMessage("Yes, mapping from "+srctype+" to
"+tgttype+" is supported.");
+ } else {
+ result.addResult(Boolean.FALSE);
+ result.addMessage("No, mapping from "+srctype+" to
"+tgttype+" is not supported.");
+ }
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+ return result;
+ }
+
+ private CyCommandResult attributeBasedMapping(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ Set<CyNetwork> networks = new HashSet();
+
+ // parse networks
+ Object obj = args.get(NETWORK_LIST);
+ if (obj==null) {
+ //succ = false;
+ //error.append("Message content does not contain field \"" +
NETWORK_ID +"\"\n");
+ // maping id for all networks
+ networks.addAll(Cytoscape.getNetworkSet());
+ if (networks.isEmpty()) {
+ throw new CyCommandException("No network available");
+ }
+ }else{
+ if (obj instanceof CyNetwork) {
+ networks.add((CyNetwork)obj);
+ } else if (obj instanceof String) {
+ String netId = (String)obj;
+ CyNetwork network = Cytoscape.getNetwork(netId);
+ if (network!=null && network!=Cytoscape.getNullNetwork()) {
+ networks.add(network);
} else {
- client.setSelected(true);
- result.addResult(Boolean.TRUE);
- result.addMessage("Selected.");
+ throw new CyCommandException("Network "+netId+" does not
exist.");
}
- } catch (Exception e) {
- // throw new CyCommandException(e);
- result.addError("Failed to remove the
resource\n"+e.getMessage());
+ } else if (obj instanceof Collection) {
+ Collection nets = (Collection)obj;
+ for (Object net : nets) {
+ if (net instanceof CyNetwork) {
+ networks.add((CyNetwork)net);
+ } else if (net instanceof String) {
+ String netId = (String)obj;
+ CyNetwork network = Cytoscape.getNetwork(netId);
+ if (network!=null &&
network!=Cytoscape.getNullNetwork()) {
+ networks.add(network);
+ } else {
+ throw new CyCommandException("Network "+netId+"
does not exist.");
+ }
+ }
+ }
+ } else {
+ throw new CyCommandException(NETWORK_LIST+" must be String or
Collection<String> "
+ + "or CyNetwork or Collection<CyNetwork>.\n");
}
- } else if (command.equals(DESELECT_RESOURCE)) {
- String connString = getArg(command, CONN_STRING, args);
- if (connString == null)
- throw new CyCommandException(CONN_STRING + "cannot be
null.");
- try {
- IDMapperClient client =
IDMapperClientManager.getClient(connString);
- if (client == null) {
- result.addResult(Boolean.FALSE);
- result.addMessage("Could not deselect the specific ID
mapping resource since it did not exist.");
+ if (networks.isEmpty()) {
+ throw new CyCommandException("No network to work on.");
+ }
+ }
+
+ Set<String> attributes = new HashSet();
+ attributes.add("ID"); //TODO: remove in Cy3
+
attributes.addAll(java.util.Arrays.asList(Cytoscape.getNodeAttributes().getAttributeNames()));
+
+ // parse source attributes
+ Set<String> srcAttrs = new HashSet();
+ obj = args.get(SOURCE_ATTR);
+ if (obj==null) {
+ throw new CyCommandException("Message content does not contain
field \"" + SOURCE_ATTR +"\"");
+ }else{
+ if (obj instanceof String) {
+ String attr = (String)obj;
+ if (attributes.contains(attr)) {
+ srcAttrs.add(attr);
} else {
- client.setSelected(false);
- result.addResult(Boolean.TRUE);
- result.addMessage("Deselected.");
+ throw new CyCommandException("Node attribute "+attr+" does
not exist.");
}
- } catch (Exception e) {
- // throw new CyCommandException(e);
- result.addError("Failed to remove the
resource\n"+e.getMessage());
+ } else if (obj instanceof Collection) {
+ Collection<String> attrs = (Collection)obj;
+ for (String attr : attrs) {
+ if (attributes.contains(attr)) {
+ srcAttrs.add(attr);
+ } else {
+ throw new CyCommandException("Node attribute "+attr+"
does not exist.");
+ }
+ }
+ } else {
+ throw new CyCommandException(SOURCE_ATTR+" must be String or
Collection<String>.\n");
}
- } else if (command.equals(GET_SRC_ID_TYPES)) {
- Set<String> types = new HashSet();
- Set<DataSource> dss;
- try {
- dss = IDMapperClientManager.selectedIDMapperStack().
- getCapabilities().getSupportedSrcDataSources();
- } catch (Exception e) {
- throw new CyCommandException(e);
+
+ if (srcAttrs.isEmpty()) {
+ throw new CyCommandException("No network to work on.");
}
+ }
- String message = "There are "+dss.size()+" supported source ID
types:\n";
+ Set<DataSource> srcDataSources = null;
+ Set<DataSource> tgtDataSources = null;
+ try {
+ IDMapperCapabilities cap
+ =
IDMapperClientManager.selectedIDMapperStack().getCapabilities();
+ srcDataSources = cap.getSupportedSrcDataSources();
+ tgtDataSources = cap.getSupportedTgtDataSources();
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
- for (DataSource ds : dss) {
- types.add(ds.getFullName());
- message += "\t"+ds.getFullName()+"\n";
+ if (srcDataSources==null || srcDataSources.isEmpty()
+ || tgtDataSources==null || tgtDataSources.isEmpty()) {
+ throw new CyCommandException("No supported source or target id
type. Please select mapping resources first.");
+ }
+
+ Set<String> supportedSrcTypes = new HashSet(srcDataSources.size());
+ for (DataSource ds : srcDataSources) {
+ String fullName = ds.getFullName();
+ if (fullName!=null) {
+ supportedSrcTypes.add(ds.getFullName());
+ } else {
+ // TODO: how to deal?
}
+ }
- result.addMessage(message);
- result.addResult(types);
- } else if (command.equals(GET_TGT_ID_TYPES)) {
- Set<String> types = new HashSet();
- Set<DataSource> dss;
- try {
- dss = IDMapperClientManager.selectedIDMapperStack().
- getCapabilities().getSupportedTgtDataSources();
- } catch (Exception e) {
- throw new CyCommandException(e);
+ Set<String> supportedTgtTypes = new HashSet(tgtDataSources.size());
+ for (DataSource ds : tgtDataSources) {
+ String fullName = ds.getFullName();
+ if (fullName!=null) {
+ supportedTgtTypes.add(ds.getFullName());
+ } else {
+ // TODO: how to deal?
}
+ }
- String message = "There are "+dss.size()+" supported target ID
types:\n";
+ // parse source type
+ Set<String> srcTypes = new HashSet();
+ obj = args.get(SOURCE_TYPE);
+ if (obj==null) {
+ srcTypes.addAll(supportedSrcTypes);
+ }else{
+ if (obj instanceof String) {
+ String type = (String)obj;
+ if (supportedSrcTypes.contains(type)) {
+ srcTypes.add(type);
+ } else {
+ throw new CyCommandException("Source ID type "+type+" does
not exist.");
+ }
+ } else if (obj instanceof Set) {
+ for (String type : (Set<String>)obj) {
+ if (supportedSrcTypes.contains(type)) {
+ srcTypes.add(type);
+ } else {
+ throw new CyCommandException("Source ID type "+type+"
does not exist.");
+ }
+ }
- for (DataSource ds : dss) {
- types.add(ds.getFullName());
- message += "\t"+ds.getFullName()+"\n";
+ if (srcTypes.isEmpty()) {
+ throw new CyCommandException("No source ID type to work
on.");
+ }
+ } else {
+ throw new CyCommandException(SOURCE_TYPE+" must be String or
Collection<String>.");
}
+ }
- result.addMessage(message);
- result.addResult(types);
- } else if (command.equals(IS_MAPPING_SUPPORT)) {
- String srctype = getArg(command, SOURCE_TYPE, args);
- String tgttype = getArg(command, TARGET_TYPE, args);
- if (srctype == null || tgttype==null)
- throw new CyCommandException(SOURCE_TYPE + " and " +
TARGET_TYPE + " cannot be null.");
+ //parse target id type
+ String tgtType = getArg(command, TARGET_TYPE, args);
+ if (!supportedTgtTypes.contains(tgtType)) {
+ throw new CyCommandException("Please specified a supported target
ID type.");
+ }
- DataSource srcds = DataSource.getByFullName(srctype);
- DataSource tgtds = DataSource.getByFullName(tgttype);
- try {
- if (IDMapperClientManager.selectedIDMapperStack().
- getCapabilities().isMappingSupported(srcds, tgtds)) {
- result.addResult(Boolean.TRUE);
- result.addMessage("Yes, mapping from "+srctype+" to
"+tgttype+" is supported.");
- } else {
- result.addResult(Boolean.FALSE);
- result.addMessage("No, mapping from "+srctype+" to
"+tgttype+" is not supported.");
- }
- } catch (Exception e) {
- throw new CyCommandException(e);
+ String tgtAttr = getArg(command, TARGET_ATTR, args);
+ Set<String> usedName = new HashSet();
+ usedName.add("ID"); //TODO remove in Cy3
+
usedName.addAll(java.util.Arrays.asList(Cytoscape.getNodeAttributes().getAttributeNames()));
+
+ // mapping ids
+ AttributeBasedIDMapping service
+ = new AttributeBasedIDMappingImpl();
+ Map<String,Set<DataSourceWrapper>> mapAttrTypes = new HashMap();
+ for (String attr : srcAttrs) {
+ Set<DataSourceWrapper> dsws = new HashSet(srcTypes.size());
+ for (String srcType : srcTypes) {
+ dsws.add(DataSourceWrapper.getInstance(srcType,
+ DataSourceWrapper.DsAttr.DATASOURCE));
}
+ mapAttrTypes.put(attr, dsws);
+ }
+
+ DataSourceWrapper dsw = DataSourceWrapper.getInstance(tgtType,
+ DataSourceWrapper.DsAttr.DATASOURCE);
+ Map<String,DataSourceWrapper> mapTgtTypeAttr =
Collections.singletonMap(tgtAttr, dsw);
+
+ try {
+ service.map(networks, mapAttrTypes, mapTgtTypeAttr);
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+
+ result.addMessage(service.getReport());
+
+ return result;
+ }
+
+ private CyCommandResult generalMapping(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+ Set<String> srcIDs = null;
+ Object obj = args.get(SOURCE_ID);
+ if (obj instanceof String) {
+ srcIDs = Collections.singleton((String)obj);
+ } else if (obj instanceof Collection) {
+ srcIDs = new HashSet((Collection<String>)obj);
+ }
+
+ String srcType = getArg(command, SOURCE_TYPE, args);
+ String tgtType = getArg(command, TARGET_TYPE, args);
+
+ if (srcIDs==null || srcType==null || tgtType==null) {
+ throw new CyCommandException("Message content must contain " +
+ "Source_ID, SOURCE_ID_TYPE and TARGET_ID_TYPE.");
+ }
+
+ if (!DataSource.getFullNames().contains(srcType)) {
+ throw new CyCommandException("Source type \""+srcType+"\" does not
exist.");
+ }
+
+ if (!DataSource.getFullNames().contains(tgtType)) {
+ throw new CyCommandException("Target type \""+tgtType+"\" does not
exist.");
+ }
+
+ IDMapperStack stack = IDMapperClientManager.selectedIDMapperStack();
+
+ IDMapperCapabilities caps = stack.getCapabilities();
+ DataSource srcDs = DataSource.getByFullName(srcType);
+ DataSource tgtDs = DataSource.getByFullName(tgtType);
+ boolean supported = false;
+ try {
+ supported = caps.isMappingSupported(srcDs, tgtDs);
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+
+ if (!supported)
+ throw new CyCommandException("Mapping from \""+srcDs+"\" to
\""+tgtDs+"\" is not supported.");
+
+ Set<Xref> srcXrefs = new HashSet(srcIDs.size());
+ for (String id : srcIDs) {
+ srcXrefs.add(new Xref(id, srcDs));
+ }
+
+ DataSource[] tgtDataSources = {tgtDs};
+
+ Map<Xref,Set<Xref>> mapping = null;
+ try {
+ mapping = stack.mapID(srcXrefs, tgtDataSources);
+ } catch (Exception e) {
+ throw new CyCommandException(e);
+ }
+
+ if (mapping==null) {
+ result.addError("No mapping was performed.");
} else {
- throw new CyCommandException(getHandlerName()+": unknown
command "+command);
+ Map<String, Set<String>> mapSrcIdTargetIDs = new
HashMap(mapping.size());
+ for (Xref srcXref : mapping.keySet()) {
+ Set<Xref> tgtXrefs = mapping.get(srcXref);
+ if (tgtXrefs!=null) {
+ Set<String> tgtIds = new HashSet();
+ for (Xref tgtXref : tgtXrefs) {
+ tgtIds.add(tgtXref.getId());
+ }
+ mapSrcIdTargetIDs.put(srcXref.getId(), tgtIds);
+ }
+ }
+
+ result.addResult(mapSrcIdTargetIDs);
+ result.addMessage(""+mapSrcIdTargetIDs.size()+"out of
"+srcIDs.size()
+ +" source IDs was mapping from type: "+srcType+" to
type:"+tgtType);
}
return result;
}
+ private CyCommandResult idExists(String command, Map<String, Object>args)
throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ Set<String> srcIDs = null;
+ Object obj = args.get(SOURCE_ID);
+ if (obj instanceof String) {
+ srcIDs = Collections.singleton((String)obj);
+ } else if (obj instanceof Collection) {
+ srcIDs = new HashSet((Collection<String>)obj);
+ }
+
+ if (srcIDs==null || srcIDs.isEmpty()) {
+ throw new CyCommandException("Parameter "+SOURCE_ID+" must
contains one or more source IDs.");
+ }
+
+ Set<String> types = new HashSet<String>();
+ for (String id : srcIDs) {
+ Set<DataSource> dss = DataSourcePatterns.getDataSourceMatches(id);
+ for (DataSource ds : dss)
+ types.add(ds.getFullName());
+ }
+
+ result.addResult(types);
+
+ StringBuilder sb = new StringBuilder();
+ sb.append(types.size());
+ sb.append(" ID types matchs:\n");
+ for (String type : types) {
+ sb.append("\t");
+ sb.append(type);
+ sb.append("\n");
+ }
+ result.addMessage(sb.toString());
+
+ return result;
+ }
+
+ private CyCommandResult guessIDTypes(String command, Map<String,
Object>args) throws CyCommandException {
+ CyCommandResult result = new CyCommandResult();
+
+ String id = getArg(command, SOURCE_ID, args);
+ String type = getArg(command, SOURCE_TYPE, args);
+
+
+ return result;
+ }
+
public static CyCommandHandler register(String namespace) throws
RuntimeException {
// Get the namespace
CyCommandNamespace ns =
CyCommandManager.reserveNamespace(namespace);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java
2010-09-03 00:29:14 UTC (rev 21681)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/service/IDMappingServiceSuppport.java
2010-09-03 01:34:42 UTC (rev 21682)
@@ -440,10 +440,9 @@
} else {
DataSource ds = DataSource.getByFullName(type);
IDMapperStack stack =
IDMapperClientManager.selectedIDMapperStack();
- boolean exist = false;
try {
- exist = stack.xrefExists(new Xref(id, ds));
- content.put(SUCCESS, true);
+ if (stack.xrefExists(new Xref(id, ds)))
+ content.put(SUCCESS, true);
} catch (Exception e) {
e.printStackTrace();
content.put(SUCCESS, false);
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form
2010-09-03 00:29:14 UTC (rev 21681)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.form
2010-09-03 01:34:42 UTC (rev 21682)
@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="UTF-8" ?>
+<?xml version="1.1" encoding="UTF-8" ?>
<Form version="1.5" maxVersion="1.7"
type="org.netbeans.modules.form.forminfo.JDialogFormInfo">
<Properties>
@@ -48,8 +48,9 @@
<SubComponents>
<Container class="javax.swing.JSplitPane" name="sourceDescSplitPane">
<Properties>
+ <Property name="dividerLocation" type="int" value="300"/>
<Property name="preferredSize" type="java.awt.Dimension"
editor="org.netbeans.beaninfo.editors.DimensionEditor">
- <Dimension value="[800, 150]"/>
+ <Dimension value="[800, 500]"/>
</Property>
</Properties>
<AuxValues>
@@ -66,6 +67,9 @@
<SubComponents>
<Container class="javax.swing.JScrollPane"
name="srcTreeScrollPane">
<Properties>
+ <Property name="minimumSize" type="java.awt.Dimension"
editor="org.netbeans.beaninfo.editors.DimensionEditor">
+ <Dimension value="[200, 200]"/>
+ </Property>
<Property name="preferredSize" type="java.awt.Dimension"
editor="org.netbeans.beaninfo.editors.DimensionEditor">
<Dimension value="[300, 500]"/>
</Property>
Modified:
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
===================================================================
---
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
2010-09-03 00:29:14 UTC (rev 21681)
+++
csplugins/trunk/soc/jgao/IDMapping/src/csplugins/id/mapping/ui/IDMappingSourceConfigDialog.java
2010-09-03 01:34:42 UTC (rev 21682)
@@ -154,8 +154,10 @@
sourceConfPanel.setPreferredSize(new java.awt.Dimension(833, 542));
sourceConfPanel.setLayout(new java.awt.GridBagLayout());
- sourceDescSplitPane.setPreferredSize(new java.awt.Dimension(800, 150));
+ sourceDescSplitPane.setDividerLocation(300);
+ sourceDescSplitPane.setPreferredSize(new java.awt.Dimension(800, 500));
+ srcTreeScrollPane.setMinimumSize(new java.awt.Dimension(200, 200));
srcTreeScrollPane.setPreferredSize(new java.awt.Dimension(300, 500));
srcTree = new IDMappingSourceSelectionTree(this);
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
