[MOBY-guts] biomoby commit
Eddie Kawas
kawas at dev.open-bio.org
Thu Nov 29 16:59:04 UTC 2007
kawas
Thu Nov 29 11:59:04 EST 2007
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended
In directory dev.open-bio.org:/tmp/cvs-serv30748/Java/src/main/org/biomoby/shared/extended
Modified Files:
NamespaceParser.java ServiceInstanceParser.java
DataTypeParser.java ServiceTypeParser.java
Log Message:
Changes include
*takes into account URIs that don't have '#' in them, but have '/'
*made code compliant with java1.5 so that warnings disappear
moby-live/Java/src/main/org/biomoby/shared/extended NamespaceParser.java,1.7,1.8 ServiceInstanceParser.java,1.20,1.21 DataTypeParser.java,1.7,1.8 ServiceTypeParser.java,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2006/04/27 14:47:37 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/NamespaceParser.java 2007/11/29 16:59:04 1.8
@@ -149,7 +149,7 @@
+ this.url);
// lets start parsing
- ArrayList list = new ArrayList();
+ ArrayList<MobyNamespace> list = new ArrayList<MobyNamespace>();
// create the model
Model model = ModelFactory.createDefaultModel();
RDFReader reader = model.getReader();
@@ -166,7 +166,9 @@
String name = "";
if (uri.indexOf("#") > 0)
name = uri.substring(uri.indexOf("#")+1);
-
+ else if(uri.lastIndexOf("/Namespaces/") > 0) {
+ name = uri.substring(uri.lastIndexOf("/Namepaces/")+"/Namespaces/".length());
+ }
MobyNamespace namespace = new MobyNamespace(name);
if (resource.hasProperty(DC_PROTEGE.identifier)) {
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2006/12/07 16:37:36 1.20
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceInstanceParser.java 2007/11/29 16:59:04 1.21
@@ -8,7 +8,6 @@
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
-import java.util.Iterator;
import java.util.Map;
import org.biomoby.client.rdf.vocabulary.DC_PROTEGE;
@@ -151,7 +150,7 @@
+ this.url);
}
// lets start parsing
- ArrayList list = new ArrayList();
+ ArrayList<MobyService> list = new ArrayList<MobyService>();
// create the model
Model model = ModelFactory.createDefaultModel();
RDFReader reader = model.getReader();
@@ -176,7 +175,7 @@
*/
public MobyService[] getMobyServicesFromRDF(Model model) throws MobyException {
// clear out any old information
- ArrayList list = new ArrayList();
+ ArrayList<MobyService> list = new ArrayList<MobyService>();
if (model != null) {
// lets start parsing
this.parsedOkay = processModel(list, model);
@@ -190,7 +189,7 @@
/**
* @param list the list to put the services in @param model the model to use
*/
- private boolean processModel(ArrayList list, Model model) {
+ private boolean processModel(ArrayList<MobyService> list, Model model) {
// clear out any old information
this.parsedOkay = false;
this.errors = new StringBuffer();
@@ -240,8 +239,10 @@
String[] parsedServiceType = serviceType.split("#");
if (parsedServiceType.length == 2)
service.setType(parsedServiceType[1]);
- else
- service.setType(parsedServiceType[0]);
+ else if(serviceType.lastIndexOf("/Services/") > 0) {
+ service.setType(serviceType.substring(serviceType.lastIndexOf("/Services/")+"/Services/".length()));
+ } else
+ service.setType(parsedServiceType[0]);
}
}
}
@@ -307,8 +308,8 @@
Resource r = (Resource) s.getObject();
StmtIterator inputs = r.listProperties(FetaVocabulary.inputParameter);
// collections to be added at the end the current scope
- Map inputCollectionMap = new HashMap();
- Map outputCollectionMap = new HashMap();
+ Map<String,MobyPrimaryDataSet> inputCollectionMap = new HashMap<String, MobyPrimaryDataSet>();
+ Map<String, MobyPrimaryDataSet> outputCollectionMap = new HashMap<String, MobyPrimaryDataSet>();
// is the current service bad?
while (inputs.hasNext()) {
@@ -367,7 +368,9 @@
if (datatype.indexOf("#") > 0)
datatype = datatype.substring(datatype.indexOf("#") + 1);
-
+ else if(datatype.lastIndexOf("/Objects/") > 0) {
+ datatype = datatype.substring(datatype.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
// extract the article name
String articlename = parameter.getProperty(
FetaVocabulary.hasParameterNameText).getObject().toString();
@@ -381,7 +384,7 @@
continue;
}
// check for namespaces
- ArrayList namespaces = new ArrayList();
+ ArrayList<String> namespaces = new ArrayList<String>();
if (parameter.hasProperty(FetaVocabulary.inNamespaces)) {
StmtIterator namespaceIterator = parameter.listProperties(FetaVocabulary.inNamespaces);
while (namespaceIterator.hasNext()) {
@@ -395,6 +398,9 @@
continue;
if (ns.indexOf("#") > 0)
ns = ns.substring(ns.indexOf("#") + 1);
+ else if(ns.lastIndexOf("/Namespaces/") > 0) {
+ ns = ns.substring(ns.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
+ }
namespaces.add(ns);
}
}
@@ -405,10 +411,8 @@
primaryInput.setDataType(new MobyDataType(datatype));
primaryInput.setName(articlename);
if (!namespaces.isEmpty()) {
- for (Iterator nsIterator = namespaces.iterator(); nsIterator
- .hasNext();) {
- primaryInput.addNamespace(new MobyNamespace((String) nsIterator
- .next()));
+ for (String ns : namespaces) {
+ primaryInput.addNamespace(new MobyNamespace(ns));
}
}
service.addInput(primaryInput);
@@ -458,6 +462,9 @@
}
if (datatype.indexOf("#") > 0)
datatype = datatype.substring(datatype.indexOf("#") + 1);
+ else if(datatype.lastIndexOf("/Objects/") > 0) {
+ datatype = datatype.substring(datatype.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
// extract the article name
String articlename = parameter.getProperty(
@@ -473,7 +480,7 @@
}
// check for namespaces
- ArrayList namespaces = new ArrayList();
+ ArrayList<String> namespaces = new ArrayList<String>();
if (parameter.hasProperty(FetaVocabulary.inNamespaces)) {
StmtIterator namespaceIterator = parameter.listProperties(FetaVocabulary.inNamespaces);
while (namespaceIterator.hasNext()) {
@@ -487,6 +494,9 @@
continue;
if (ns.indexOf("#") > 0)
ns = ns.substring(ns.indexOf("#") + 1);
+ else if(ns.lastIndexOf("/Namespaces/") > 0) {
+ ns = ns.substring(ns.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
+ }
namespaces.add(ns);
}
}
@@ -503,11 +513,9 @@
MobyPrimaryDataSimple input = new MobyPrimaryDataSimple("");
input.setDataType(new MobyDataType(datatype));
if (!namespaces.isEmpty()) {
- for (Iterator nsIterator = namespaces.iterator(); nsIterator
- .hasNext();) {
+ for (String ns : namespaces) {
input
- .addNamespace(new MobyNamespace((String) nsIterator
- .next()));
+ .addNamespace(new MobyNamespace(ns));
}
}
collection.addElement(input);
@@ -684,7 +692,9 @@
.toString();*/
if (datatype.indexOf("#") > 0)
datatype = datatype.substring(datatype.indexOf("#") + 1);
-
+ else if(datatype.lastIndexOf("/Objects/") > 0) {
+ datatype = datatype.substring(datatype.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
// extract the article name
String articlename = parameter.getProperty(
FetaVocabulary.hasParameterNameText).getObject().toString();
@@ -695,7 +705,7 @@
// article name");
}
// check for namespaces
- ArrayList namespaces = new ArrayList();
+ ArrayList<String> namespaces = new ArrayList<String>();
if (parameter.hasProperty(FetaVocabulary.inNamespaces)) {
StmtIterator namespaceIterator = parameter.listProperties(FetaVocabulary.inNamespaces);
while (namespaceIterator.hasNext()) {
@@ -709,6 +719,9 @@
continue;
if (ns.indexOf("#") > 0)
ns = ns.substring(ns.indexOf("#") + 1);
+ else if(ns.lastIndexOf("/Namespaces/") > 0) {
+ ns = ns.substring(ns.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
+ }
namespaces.add(ns);
}
}
@@ -719,10 +732,8 @@
primaryOutput.setDataType(new MobyDataType(datatype));
primaryOutput.setName(articlename);
if (!namespaces.isEmpty()) {
- for (Iterator nsIterator = namespaces.iterator(); nsIterator
- .hasNext();) {
- primaryOutput.addNamespace(new MobyNamespace(
- (String) nsIterator.next()));
+ for (String ns : namespaces) {
+ primaryOutput.addNamespace(new MobyNamespace(ns));
}
}
service.addOutput(primaryOutput);
@@ -773,7 +784,9 @@
if (datatype.indexOf("#") > 0)
datatype = datatype.substring(datatype.indexOf("#") + 1);
-
+ else if(datatype.lastIndexOf("/Objects/") > 0) {
+ datatype = datatype.substring(datatype.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
// extract the article name
String articlename = parameter.getProperty(
FetaVocabulary.hasParameterNameText).getObject().toString();
@@ -789,7 +802,7 @@
}
// check for namespaces
- ArrayList namespaces = new ArrayList();
+ ArrayList<String> namespaces = new ArrayList<String>();
if (parameter.hasProperty(FetaVocabulary.inNamespaces)) {
StmtIterator namespaceIterator = parameter.listProperties(FetaVocabulary.inNamespaces);
while (namespaceIterator.hasNext()) {
@@ -803,6 +816,9 @@
continue;
if (ns.indexOf("#") > 0)
ns = ns.substring(ns.indexOf("#") + 1);
+ else if(ns.lastIndexOf("/Namespaces/") > 0) {
+ ns= ns.substring(ns.lastIndexOf("/Namespaces/")+"/Namespaces/".length());
+ }
namespaces.add(ns);
}
}
@@ -819,10 +835,8 @@
MobyPrimaryDataSimple output = new MobyPrimaryDataSimple("");
output.setDataType(new MobyDataType(datatype));
if (!namespaces.isEmpty()) {
- for (Iterator nsIterator = namespaces.iterator(); nsIterator
- .hasNext();) {
- output.addNamespace(new MobyNamespace((String) nsIterator
- .next()));
+ for (String ns : namespaces) {
+ output.addNamespace(new MobyNamespace(ns));
}
}
collection.addElement(output);
@@ -832,14 +846,11 @@
}
// add the collections to the service
- Iterator it = null;
- for (it = inputCollectionMap.keySet().iterator(); it.hasNext();) {
- service.addInput((MobyPrimaryDataSet) inputCollectionMap
- .get((String) it.next()));
+ for (String key : inputCollectionMap.keySet()) {
+ service.addInput((MobyPrimaryDataSet) inputCollectionMap.get(key));
}
- for (it = outputCollectionMap.keySet().iterator(); it.hasNext();) {
- service.addOutput((MobyPrimaryDataSet) outputCollectionMap.get((String) it
- .next()));
+ for (String key : outputCollectionMap.keySet()) {
+ service.addOutput((MobyPrimaryDataSet) outputCollectionMap.get(key));
}
}
if (!currentlyBad)
@@ -859,7 +870,7 @@
public MobyService[] getMobyServicesFromRDF(String rdf) throws MobyException {
// lets start parsing
- ArrayList list = new ArrayList();
+ ArrayList<MobyService> list = new ArrayList<MobyService>();
// create the model
Model model = ModelFactory.createDefaultModel();
RDFReader reader = model.getReader();
@@ -960,8 +971,9 @@
public static void main(String[] args) throws MobyException, MalformedURLException, IOException {
// show how to use this class
- ServiceInstanceParser p = new ServiceInstanceParser("http://localhost/ServiceInstance.rdf");
+ ServiceInstanceParser p = new ServiceInstanceParser("http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances");
MobyService[] services = p.getMobyServicesFromRDF();
+ System.out.println(services.length);
if (!p.isRDFValid()) {
System.out.println("One or more services in the RDF were invalid");
System.out.println("The errors are the following:");
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2007/07/17 18:11:42 1.7
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/DataTypeParser.java 2007/11/29 16:59:04 1.8
@@ -154,7 +154,7 @@
+ this.url);
// lets start parsing
- ArrayList list = new ArrayList();
+ ArrayList<MobyDataType> list = new ArrayList<MobyDataType>();
// create the model
Model model = ModelFactory.createDefaultModel();
RDFReader reader = model.getReader();
@@ -173,12 +173,17 @@
String name = "";
if (uri.indexOf("#") > 0)
name = uri.substring(uri.indexOf("#")+1);
-
+ else if(uri.lastIndexOf("/Objects/") > 0) {
+ name = uri.substring(uri.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
String parent = null;
if (resource.hasProperty(RDFS.subClassOf)) {
parent = ((Resource)resource.getProperty(RDFS.subClassOf).getObject()).getURI();
if (parent.indexOf("#") > 0)
parent = parent.substring(parent.indexOf("#")+1);
+ else if(parent.lastIndexOf("/Objects/") > 0) {
+ parent = parent.substring(parent.lastIndexOf("/Objects/")+"/Objects/".length());
+ }
}
String description = resource.getProperty(RDFS.comment).getLiteral().getString();
// create the base datatype without container relationships
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2006/04/27 14:47:37 1.8
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/extended/ServiceTypeParser.java 2007/11/29 16:59:04 1.9
@@ -147,7 +147,7 @@
+ this.url);
// lets start parsing
- ArrayList list = new ArrayList();
+ ArrayList<MobyServiceType> list = new ArrayList<MobyServiceType>();
// create the model
Model model = ModelFactory.createDefaultModel();
RDFReader reader = model.getReader();
@@ -163,7 +163,9 @@
String name = "";
if (uri.indexOf("#") > 0)
name = uri.substring(uri.indexOf("#")+1);
-
+ else if(uri.lastIndexOf("/Services/") > 0) {
+ name = uri.substring(uri.lastIndexOf("/Services/")+"/Services/".length());
+ }
MobyServiceType servicetype = new MobyServiceType(name);
if (resource.hasProperty(DC_PROTEGE.identifier)) {
@@ -177,6 +179,9 @@
String parent = resource.getProperty(RDFS.subClassOf).getObject().toString();
if (parent.indexOf("#") > 0)
parent = parent.substring(parent.indexOf("#")+1);
+ else if(parent.lastIndexOf("/Services/") > 0) {
+ parent = parent.substring(parent.lastIndexOf("/Services/")+"/Services/".length());
+ }
servicetype.setParentNames(new String[] {parent});
String description = resource.getProperty(RDFS.comment).getLiteral().getString();
servicetype.setDescription(description);
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