Merge branch 'master' into ModelingGenerator

.gitignore

@@ -13,3 +13,9 @@ bin/iBioSim.jar
 .settings/
 **/.project
 /.metadata/
+
+# intellij artefacts
+out
+*.iws
+*.ipr
+*.iml

conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java

@@ -336,7 +336,7 @@ public class SBML2SBOL {
 					}
 				}
 			}
-			compDef_type.add(ComponentDefinition.DNA);
+			compDef_type.add(ComponentDefinition.DNA_REGION);
 			compDef_role.add(SequenceOntology.PROMOTER);
 		} 
 		else 
@@ -357,10 +357,10 @@ public class SBML2SBOL {
 			if (species.isSetSBOTerm()) {
 				if (species.getSBOTermID().equals(GlobalConstants.SBO_DNA) ||
 						species.getSBOTermID().equals(GlobalConstants.SBO_DNA_SEGMENT)) {
-					compDef_type.add(ComponentDefinition.DNA);
+					compDef_type.add(ComponentDefinition.DNA_REGION);
 				} else if (species.getSBOTermID().equals(GlobalConstants.SBO_RNA) ||
 						species.getSBOTermID().equals(GlobalConstants.SBO_RNA_SEGMENT)) {
-					compDef_type.add(ComponentDefinition.RNA);
+					compDef_type.add(ComponentDefinition.RNA_REGION);
 				} else if (species.getSBOTermID().equals(GlobalConstants.SBO_PROTEIN)) {
 					compDef_type.add(ComponentDefinition.PROTEIN);
 				} else if (species.getSBOTermID().equals(GlobalConstants.SBO_NONCOVALENT_COMPLEX) ||

dataModels/pom.xml

@@ -71,7 +71,7 @@
 		<dependency>
 			<groupId>org.sbml.jsbml</groupId>
 			<artifactId>jsbml</artifactId>
-			<version>1.3-SNAPSHOT</version>
+			<version>1.4</version>
 		</dependency>
 
 		<dependency>
@@ -84,7 +84,7 @@
 		<dependency>
 			<groupId>org.sbolstandard</groupId>
 			<artifactId>libSBOLj</artifactId>
-			<version>2.3.2-SNAPSHOT</version>
+			<version>2.4.1-SNAPSHOT</version>
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/AbstractResponseHandler.java

@@ -0,0 +1,64 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import com.google.gson.Gson;
+import com.google.gson.GsonBuilder;
+import org.apache.http.Header;
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpResponse;
+import org.apache.http.StatusLine;
+import org.apache.http.client.ClientProtocolException;
+import org.apache.http.client.HttpResponseException;
+import org.apache.http.client.ResponseHandler;
+import org.apache.http.entity.ContentType;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+@SuppressWarnings("WeakerAccess")
+public abstract class AbstractResponseHandler<T> implements ResponseHandler<T> {
+
+    @Override
+    public T handleResponse(HttpResponse response) throws IOException {
+        StatusLine statusLine = response.getStatusLine();
+        HttpEntity entity = response.getEntity();
+        if (statusLine.getStatusCode() == 307) {
+            //noinspection unused
+            final Header location = response.getFirstHeader("Location");
+            // TODO follow the redirection if location is not null
+        }
+        return parseResponse(statusLine, entity, getObjectMappingClass());
+    }
+
+    protected abstract Class<T> getObjectMappingClass();
+
+    protected T parseResponse(StatusLine statusLine, HttpEntity entity, Class<T> pojoClass)
+            throws IOException {
+        if (statusLine.getStatusCode() >= 400) {
+            throw new HttpResponseException(
+                    statusLine.getStatusCode(),
+                    statusLine.getReasonPhrase());
+        }
+        if (entity == null) {
+            throw new ClientProtocolException("Response contains no content");
+        }
+        ContentType contentType = ContentType.getOrDefault(entity);
+        Charset charset = contentType.getCharset() != null ? contentType.getCharset() :
+                StandardCharsets.UTF_8;
+
+        try (BufferedReader reader = new BufferedReader(
+                new InputStreamReader(entity.getContent(), charset))) {
+            return unmarshallContent(reader, pojoClass);
+        }
+    }
+
+    protected T unmarshallContent(BufferedReader reader, Class<T> type) {
+        Gson gson = new GsonBuilder().create();
+        return gson.fromJson(reader, type);
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/BioModelsConnectionService.java

@@ -0,0 +1,101 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+
+import static edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.Requests.SEARCH_RESULTS_PER_PAGE;
+
+import java.io.IOException;
+import java.util.Objects;
+import java.util.Set;
+import java.util.TreeSet;
+import java.util.stream.Collectors;
+import java.util.stream.IntStream;
+import java.util.stream.Stream;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+@SuppressWarnings("WeakerAccess")
+public class BioModelsConnectionService implements AutoCloseable {
+    private final CloseableHttpClient client;
+
+    public BioModelsConnectionService() {
+        this(HttpClients.createDefault());
+    }
+
+    public BioModelsConnectionService(CloseableHttpClient client) {
+        this.client = Objects.requireNonNull(client, "The HttpClient cannot be null");
+    }
+
+    public ModelResponse getModel(String m) {
+        final HttpGet request = Requests.newGetModelRequest(m);
+        return performRequest(request, new GetModelResponseHandler());
+    }
+
+    public CuratedModelsResponse getCuratedModelSet() {
+        final HttpGet request = Requests.newCuratedModelSearchRequest();
+        CuratedModelsResponse firstPage = performRequest(request, new CuratedModelsResponseHandler());
+        if (null == firstPage) return null;
+
+        return doGetAllCuratedModels(firstPage);
+    }
+
+    public String getModelFileName(String model) {
+        HttpGet filesRequest = Requests.newGetFilesRequest(model);
+
+        ModelFilesResponse files = performRequest(filesRequest, new GetFilesResponseHandler());
+        if (null == files) return null;
+
+        return files.getMainFileName();
+    }
+
+    public ModelFileResponse getModelFile(String model) {
+        String mainFileName = getModelFileName(model);
+        if (mainFileName == null) return null;
+        HttpGet modelFileRequest = Requests.newGetModelFileRequest(model, mainFileName);
+        return performRequest(modelFileRequest, new GetModelFileResponseHandler());
+    }
+
+    @Override
+    public void close() {
+        try {
+            client.close();
+        } catch (IOException e) {
+            System.err.printf("Could not close the HttpClient instance: %s%n", e);
+        }
+    }
+
+    private CuratedModelsResponse doGetAllCuratedModels(CuratedModelsResponse firstPage) {
+        int total = firstPage.getMatches();
+        int pageCount = (int) Math.ceil(((double) total) / SEARCH_RESULTS_PER_PAGE);
+        Stream<ModelSummary> remainder = IntStream.range(1, pageCount)
+                .mapToObj(this::getSearchResultsPage)
+                .filter(p -> p != null) // requests that threw exceptions return null
+                .flatMap(CuratedModelsResponse::getModelsStream);
+
+        Set<ModelSummary> responses = Stream.concat(firstPage.getModelsStream(), remainder)
+                .collect(Collectors.toCollection(TreeSet::new));
+
+        return new CuratedModelsResponse(responses);
+    }
+
+    private <T> T performRequest(HttpGet request, AbstractResponseHandler<T> responseHandler) {
+        try {
+            return client.execute(request, responseHandler);
+        } catch (IOException e) {
+            System.err.printf("I/O exception encountered while performing request %s: %s%n",
+                    request.getURI().toString(), e);
+        }
+        return null;
+    }
+
+    private CuratedModelsResponse getSearchResultsPage(int page) {
+        if (page < 1) throw new IllegalArgumentException(String.valueOf(page));
+
+        final int offset = page * SEARCH_RESULTS_PER_PAGE;
+        HttpGet request = Requests.newCuratedModelSearchRequest(offset);
+        return performRequest(request, new CuratedModelsResponseHandler());
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/CuratedModelsResponse.java

@@ -0,0 +1,37 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import java.util.Set;
+import java.util.stream.Stream;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+@SuppressWarnings("unused")
+public class CuratedModelsResponse {
+    private int matches;
+    private Set<ModelSummary> models;
+
+    public CuratedModelsResponse() {
+    }
+
+    public CuratedModelsResponse(Set<ModelSummary> models) {
+        this.models = models;
+        if (null == models) {
+            matches = 0;
+        } else {
+            matches = models.size();
+        }
+    }
+
+    public Stream<ModelSummary> getModelsStream() {
+        return models.parallelStream();
+    }
+
+    public int getMatches() {
+        return matches;
+    }
+
+    public Set<ModelSummary> getModels() {
+        return models;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/CuratedModelsResponseHandler.java

@@ -0,0 +1,11 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public class CuratedModelsResponseHandler extends AbstractResponseHandler<CuratedModelsResponse> {
+    @Override
+    protected Class<CuratedModelsResponse> getObjectMappingClass() {
+        return CuratedModelsResponse.class;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/GetFilesResponseHandler.java

@@ -0,0 +1,11 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public class GetFilesResponseHandler extends AbstractResponseHandler<ModelFilesResponse> {
+    @Override
+    protected Class<ModelFilesResponse> getObjectMappingClass() {
+        return ModelFilesResponse.class;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/GetModelFileResponseHandler.java

@@ -0,0 +1,18 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import java.io.BufferedReader;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public class GetModelFileResponseHandler extends AbstractResponseHandler<ModelFileResponse> {
+    @Override
+    protected Class<ModelFileResponse> getObjectMappingClass() {
+        return ModelFileResponse.class;
+    }
+
+    @Override
+    protected ModelFileResponse unmarshallContent(BufferedReader reader, Class<ModelFileResponse> type) {
+        return ModelFileResponse.parse(reader);
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/GetModelResponseHandler.java

@@ -0,0 +1,12 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public final class GetModelResponseHandler extends AbstractResponseHandler<ModelResponse> {
+
+    @Override
+    protected Class<ModelResponse> getObjectMappingClass() {
+        return ModelResponse.class;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/ModelFileResponse.java

@@ -0,0 +1,35 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk>
+ */
+public class ModelFileResponse {
+    private String fileContent;
+
+    public static ModelFileResponse parse(BufferedReader reader) {
+        ModelFileResponse response = new ModelFileResponse();
+
+        StringWriter stringWriter = new StringWriter(8192);
+        try (PrintWriter writer = new PrintWriter(stringWriter)) {
+            String currentLine;
+            while ((currentLine = reader.readLine()) != null) {
+                writer.write(currentLine);
+                writer.println();
+            }
+            response.fileContent = stringWriter.toString();
+        } catch (IOException e) {
+            throw new IllegalStateException("Failed to read model file contents", e);
+        }
+
+        return response;
+    }
+
+    public String getFileContent() {
+        return fileContent;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/ModelFilesResponse.java

@@ -0,0 +1,20 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import java.util.List;
+
+@SuppressWarnings("WeakerAccess,unused")
+public class ModelFilesResponse {
+    @SuppressWarnings("MismatchedQueryAndUpdateOfCollection")
+    private List<RepositoryFile> main;
+    private List<RepositoryFile> additional;
+
+    public static final class RepositoryFile {
+        private String name;
+        private String description;
+        private int fileSize;
+    }
+
+    public String getMainFileName() {
+        return main.get(0).name;
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/ModelResponse.java

@@ -0,0 +1,35 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import java.util.Optional;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public class ModelResponse {
+    private String name;
+    private String submissionId;
+    private Publication publication;
+
+    private class Publication {
+        private String link;
+    }
+
+    public String getPublicationLink() {
+        if (null == publication) return null;
+
+        return publication.link;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder response = new StringBuilder();
+
+        response.append("Model id ")
+                .append(submissionId)
+                .append(" (")
+                .append(name)
+                .append(")");
+
+        return response.toString();
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/ModelSummary.java

@@ -0,0 +1,33 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+@SuppressWarnings("unused")
+public class ModelSummary implements Comparable<ModelSummary> {
+    private String id;
+    private String name;
+    private Publication publication;
+
+    public static class Publication {
+        private String link;
+    }
+
+    public String getPublicationLink() {
+        return null == publication ? null : publication.link;
+    }
+
+    public String toString() {
+        return id + ' ' + name;
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    @Override
+    public int compareTo(ModelSummary o) {
+        return id.compareTo(o.getId());
+    }
+
+    public boolean equals(Object o) {
+        return (o instanceof ModelSummary) && ((ModelSummary) o).getId().equals(id);
+    }
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/ebiBiomodels/Requests.java

@@ -0,0 +1,56 @@
+package edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels;
+
+import org.apache.http.client.methods.HttpGet;
+
+import java.util.Objects;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+@SuppressWarnings("WeakerAccess")
+public final class Requests {
+    // can also use the Caltech instance: http://biomodels.caltech.edu/
+    public static final String BIOMODELS_EBI_BASE = "https://www.ebi.ac.uk/biomodels/";
+    public static final String SEARCH_CMD =
+            "search?query=curationstatus%3AManually%20curated&sort=id-desc";
+    public static final String GET_FILES_CMD = "model/files/";
+    public static final String DLD_MODEL_CMD = "model/download/";
+    public static final int SEARCH_RESULTS_PER_PAGE = 100;
+
+    public static HttpGet newGetModelRequest(String model) {
+        final String url = String.format("%s%s", BIOMODELS_EBI_BASE,
+                Objects.requireNonNull(model, "Model identifier (e.g. BIOMD0000000001) required"));
+        return constructSignedJsonGetRequest(url);
+    }
+
+    public static HttpGet newCuratedModelSearchRequest() {
+        return newCuratedModelSearchRequest(0);
+    }
+
+    public static HttpGet newCuratedModelSearchRequest(int offset) {
+        String url = String.format("%s%s&offset=%d&numResults=%d", BIOMODELS_EBI_BASE,
+                SEARCH_CMD, offset, SEARCH_RESULTS_PER_PAGE);
+        return constructSignedJsonGetRequest(url);
+    }
+
+    public static HttpGet newGetModelFileRequest(String modelId, String fileName) {
+        String url = String.format("%s%s%s?filename=%s", BIOMODELS_EBI_BASE, DLD_MODEL_CMD,
+                Objects.requireNonNull(modelId, "The model identifier is required"),
+                Objects.requireNonNull(fileName, "Model file name is required"));
+        return constructSignedJsonGetRequest(url);
+    }
+
+    public static HttpGet newGetFilesRequest(String modelId) {
+        String getFilesUrl = String.format("%s%s%s", BIOMODELS_EBI_BASE, GET_FILES_CMD,
+                Objects.requireNonNull(modelId, "The model identifier is required"));
+        return constructSignedJsonGetRequest(getFilesUrl);
+    }
+
+    private static HttpGet constructSignedJsonGetRequest(String uri) {
+        final HttpGet request = new HttpGet(uri);
+        request.setHeader("User-Agent", "iBioSim <https://github.com/MyersResearchGroup/iBioSim>");
+        request.setHeader("Accept", "application/json");
+
+        return request;
+    }
+}

dataModels/src/test/java/edu/utah/ece/async/ibiosim/biomodels/BioModelsConnectionServiceTest.java

@@ -0,0 +1,80 @@
+package edu.utah.ece.async.ibiosim.biomodels;
+
+import org.apache.http.impl.client.HttpClients;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.BioModelsConnectionService;
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.CuratedModelsResponse;
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.ModelFileResponse;
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.ModelResponse;
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.ModelSummary;
+
+import java.util.Optional;
+
+import static org.junit.Assert.*;
+
+/**
+ * @author Mihai Glon\u021b mglont@ebi.ac.uk
+ */
+public class BioModelsConnectionServiceTest {
+    private BioModelsConnectionService service;
+
+    @Before
+    public void setUp() {
+        service = new BioModelsConnectionService(HttpClients.createMinimal());
+    }
+
+    @After
+    public void tearDown() throws Exception {
+        Optional.ofNullable(service).ifPresent(BioModelsConnectionService::close);
+    }
+
+    @Test
+    public void shouldRetrieveAModel() {
+        String expected = "Model id MODEL6615119181 (Kholodenko2000 - " +
+                "Ultrasensitivity and negative feedback bring oscillations in MAPK cascade)";
+        ModelResponse response = service.getModel("MODEL6615119181");
+
+        assertEquals("the correct model is retrieved", expected, response.toString());
+    }
+
+    @Test
+    public void shouldGetCuratedModelSet() {
+        CuratedModelsResponse response = service.getCuratedModelSet();
+        assertNotNull("the response object is defined", response);
+        assertTrue("Have at least 700 models", response.getMatches() > 700);
+        assertTrue(response.getModels().size() == response.getMatches());
+
+        String biomd738 = "BIOMD0000000738 Mouse Iron Distribution - Rich iron diet (No Tracer)";
+        Optional<ModelSummary> match = response.getModelsStream()
+                .filter(summary -> summary.toString().equals(biomd738))
+                .findAny();
+        assertTrue("BIOMD0000000738 is in the search results", match.isPresent());
+
+        /*response.getModelsStream()
+                .map(ModelSummary::getId)
+                .forEachOrdered(System.out::println);*/
+    }
+
+    @Test
+    public void shouldRetrieveModelFileNameForAKnownModel() {
+        String name = service.getModelFileName("BIOMD0000000044");
+        assertEquals("BIOMD0000000044_url.xml is the model file name", "BIOMD0000000044_url.xml", name);
+    }
+
+    @Test
+    public void shouldRetrieveModelFileContents() {
+        ModelFileResponse response = service.getModelFile("BIOMD0000000044");
+
+        assertNotNull(response);
+        String content = response.getFileContent();
+        assertNotNull(content);
+    }
+
+    @Test(expected = NullPointerException.class)
+    public void shouldThrowExceptionWhenRetrievingFilesForUndefinedModel() {
+        service.getModelFileName(null);
+    }
+}

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java

@@ -104,6 +104,7 @@ import javax.xml.xpath.XPathExpressionException;
 import org.antlr.runtime.ANTLRFileStream;
 import org.antlr.runtime.CommonTokenStream;
 import org.antlr.runtime.TokenStream;
+import org.apache.http.impl.client.HttpClients;
 import org.jdom2.JDOMException;
 import org.jlibsedml.AbstractTask;
 import org.jlibsedml.ArchiveComponents;
@@ -175,7 +176,6 @@ import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
 import edu.utah.ece.async.sboldesigner.sbol.editor.SynBioHubFrontends;
 import edu.utah.ece.async.sboldesigner.sbol.editor.dialog.RegistryInputDialog;
 import uk.ac.ebi.biomodels.ws.BioModelsWSClient;
-import uk.ac.ebi.biomodels.ws.BioModelsWSException;
 import de.unirostock.sems.cbarchive.ArchiveEntry;
 import de.unirostock.sems.cbarchive.CombineArchive;
 import de.unirostock.sems.cbarchive.CombineArchiveException;
@@ -200,6 +200,7 @@ import edu.utah.ece.async.ibiosim.dataModels.util.Message;
 import edu.utah.ece.async.ibiosim.dataModels.util.SEDMLutilities;
 import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
 import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObserver;
+import edu.utah.ece.async.ibiosim.dataModels.ebiBiomodels.*;
 import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
 import edu.utah.ece.async.ibiosim.gui.analysisView.AnalysisView;
 import edu.utah.ece.async.ibiosim.gui.graphEditor.Graph;
@@ -306,13 +307,11 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 
 	protected String viewer;
 
-	protected boolean runGetNames;
-
 	// protected boolean showParts = false;
 
 	// protected Thread getPartsThread = null;
 
-	private String[] BioModelIds = null;
+	private ModelSummary[] BioModelIds = null;
 
 	// protected Parts allVirtualParts = null;
 
@@ -2758,20 +2757,44 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		}
 	}
 
+	private ModelSummary[] retrieveCuratedBioModels() {
+		try(BioModelsConnectionService service = new BioModelsConnectionService()) {
+			CuratedModelsResponse response = service.getCuratedModelSet();
+			Set<ModelSummary> summaries = response.getModels();
+			return summaries.toArray(new ModelSummary[summaries.size()]);
+		}
+	}
+
+	private String getBioModelsModelFile(String modelId) {
+		try(BioModelsConnectionService service = new BioModelsConnectionService()) {
+			ModelFileResponse response = service.getModelFile(modelId);
+			return response.getFileContent();
+		}
+	}
+
+	private String getPublicationLinkForModel(String modelId) {
+		try (BioModelsConnectionService service = new BioModelsConnectionService()) {
+			ModelResponse modelInformation = service.getModel(modelId);
+			if (null == modelInformation) {
+				System.err.println("No entry found in BioModels for " + modelId);
+				return null;
+			}
+			return modelInformation.getPublicationLink();
+		}
+	}
+
 	private void downloadBioModel() {
-		final BioModelsWSClient client = new BioModelsWSClient();
 		if (BioModelIds == null) {
 			try {
-				BioModelIds = client.getAllCuratedModelsId();
+				BioModelIds = retrieveCuratedBioModels();
-			} catch (BioModelsWSException e2) {
+			} catch (Exception e2) {
-				JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
+				JOptionPane.showMessageDialog(frame, "Error Contacting BioModels", "Error",
 						JOptionPane.ERROR_MESSAGE);
 				return;
 			}
 		}
 		final JPanel BioModelsPanel = new JPanel(new BorderLayout());
-		final JList ListOfBioModels = new JList();
+		final JList<ModelSummary> ListOfBioModels = new JList<>();
-		edu.utah.ece.async.ibiosim.dataModels.biomodel.util.Utility.sort(BioModelIds);
 		ListOfBioModels.setListData(BioModelIds);
 		ListOfBioModels.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 		JLabel TextBioModels = new JLabel("List of BioModels");
@@ -2780,65 +2803,28 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		ScrollBioModels.setPreferredSize(new Dimension(552, 250));
 		ScrollBioModels.setViewportView(ListOfBioModels);
 		JPanel GetButtons = new JPanel();
-		JButton GetNames = new JButton("Get Names");
 		JButton GetDescription = new JButton("Get Description");
 		JButton GetReference = new JButton("Get Reference");
 		final JProgressBar progressBar = new JProgressBar(0, 100);
 		progressBar.setStringPainted(true);
 		progressBar.setValue(0);
-		runGetNames = true;
+
-		final Thread getNamesThread = new Thread(new Runnable() {
-			@Override
-			public void run() {
-				Preferences biosimrc = Preferences.userRoot();
-				for (int i = 0; i < BioModelIds.length && runGetNames; i++) {
-					try {
-						progressBar.setValue(100 * i / BioModelIds.length);
-						if (!BioModelIds[i].contains(" ")) {
-							if (!biosimrc.get(BioModelIds[i], "").equals("")) {
-								BioModelIds[i] += " " + biosimrc.get(BioModelIds[i], "");
-							} else {
-								String name = client.getModelNameById(BioModelIds[i]);
-								biosimrc.put(BioModelIds[i], name);
-								BioModelIds[i] += " " + name;
-							}
-							ListOfBioModels.setListData(BioModelIds);
-							ListOfBioModels.revalidate();
-							ListOfBioModels.repaint();
-						}
-					} catch (BioModelsWSException e1) {
-						JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
-								JOptionPane.ERROR_MESSAGE);
-						runGetNames = false;
-					}
-				}
-				progressBar.setValue(100);
-				ListOfBioModels.setListData(BioModelIds);
-				runGetNames = false;
-			}
-		});
-		GetNames.addActionListener(new ActionListener() {
-			@Override
-			public void actionPerformed(ActionEvent e) {
-				if (runGetNames && !getNamesThread.isAlive()) {
-					getNamesThread.start();
-				}
-			}
-		});
 		GetDescription.addActionListener(new ActionListener() {
 			@Override
 			public void actionPerformed(ActionEvent e) {
 				if (ListOfBioModels.isSelectionEmpty()) {
 					return;
 				}
-				String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
+				String selectedModel = ListOfBioModels.getSelectedValue().getId();
 				Preferences biosimrc = Preferences.userRoot();
 				String command = biosimrc.get("biosim.general.browser", "");
-				command = command + " http://www.ebi.ac.uk/compneur-srv/biomodels-main/" + SelectedModel;
+				command = command + " http://identifiers.org/biomodels.db/" + selectedModel;
+				progressBar.setValue(25);
 				log.addText("Executing:\n" + command + "\n");
 				Runtime exec = Runtime.getRuntime();
 				try {
 					exec.exec(command);
+					progressBar.setValue(100);
 				} catch (IOException e1) {
 					JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error",
 							JOptionPane.ERROR_MESSAGE);
@@ -2851,25 +2837,31 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 				if (ListOfBioModels.isSelectionEmpty()) {
 					return;
 				}
-				String SelectedModel = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
+				ModelSummary model = ListOfBioModels.getSelectedValue();
+				String modelId = model.getId();
 				try {
-					String Pub = (client.getSimpleModelById(SelectedModel)).getPublicationId();
+					String pub = getPublicationLinkForModel(modelId);
+					progressBar.setValue(25);
+					progressBar.repaint();
+					if (null == pub) {
+						JOptionPane.showMessageDialog(frame,
+								"Could not find publication information in BioModels for " + modelId,
+								"Warning", JOptionPane.WARNING_MESSAGE);
+						return;
+					}
 					Preferences biosimrc = Preferences.userRoot();
 					String command = biosimrc.get("biosim.general.browser", "");
-					command = command + " http://www.ncbi.nlm.nih.gov/pubmed/?term=" + Pub;
+					command = command + ' ' + pub;
 					log.addText("Executing:\n" + command + "\n");
 					Runtime exec = Runtime.getRuntime();
 					exec.exec(command);
-				} catch (BioModelsWSException e2) {
+					progressBar.setValue(100);
-					JOptionPane.showMessageDialog(frame, "Error Contacting BioModels Database", "Error",
-							JOptionPane.ERROR_MESSAGE);
 				} catch (IOException e1) {
 					JOptionPane.showMessageDialog(frame, "Unable to open model description.", "Error",
 							JOptionPane.ERROR_MESSAGE);
 				}
 			}
 		});
-		GetButtons.add(GetNames);
 		GetButtons.add(GetDescription);
 		GetButtons.add(GetReference);
 		GetButtons.add(progressBar);
@@ -2879,17 +2871,16 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		Object[] options = { "OK", "Cancel" };
 		int value = JOptionPane.showOptionDialog(frame, BioModelsPanel, "List of BioModels", JOptionPane.YES_NO_OPTION,
 				JOptionPane.PLAIN_MESSAGE, null, options, options[0]);
-		runGetNames = false;
 		if (value == JOptionPane.YES_OPTION && ListOfBioModels.getSelectedValue() != null) {
-			String ModelId = ((String) ListOfBioModels.getSelectedValue()).split(" ")[0];
+			String modelId = ListOfBioModels.getSelectedValue().getId();
-			String filename = ModelId + ".xml";
+			String filename = modelId + ".xml";
 			try {
 				if (overwrite(root + File.separator + filename, filename)) {
-					String model = client.getModelSBMLById(ModelId);
+					String model = getBioModelsModelFile(modelId);
-					Writer out = new BufferedWriter(new OutputStreamWriter(
+					try (Writer out = new BufferedWriter(new OutputStreamWriter(
-							new FileOutputStream(root + File.separator + filename), "UTF-8"));
+							new FileOutputStream(root + File.separator + filename), "UTF-8"))) {
 						out.write(model);
-					out.close();
+					}
 					String[] file = GlobalConstants.splitPath(filename.trim());
 					SBMLDocument document = SBMLutilities.readSBML(root + File.separator + filename.trim(), null, this);
 					Utils.check(root + File.separator + filename.trim(), document, false, null, this);
@@ -6147,7 +6138,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 				try 
 				{
 					ComponentDefinition cd = getSBOLDocument().createComponentDefinition(partId, "1",
-							ComponentDefinition.DNA);
+							ComponentDefinition.DNA_REGION);
 					cd.addRole(SequenceOntology.ENGINEERED_REGION);
 					writeSBOLDocument();
 					Set<ComponentDefinition> selectedDesign = new HashSet<ComponentDefinition>();

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/sbol/SBOLField2.java

@@ -304,11 +304,11 @@ public class SBOLField2 extends JPanel implements ActionListener {
 	 */
 	private String getSpeciesSBOTerm(URI sbolSBOTerm)
 	{
-		if(sbolSBOTerm.equals(ComponentDefinition.DNA))
+		if(sbolSBOTerm.equals(ComponentDefinition.DNA_REGION))
 		{
 			return GlobalConstants.SBO_DNA_SEGMENT;
 		}
-		else if(sbolSBOTerm.equals(ComponentDefinition.RNA))
+		else if(sbolSBOTerm.equals(ComponentDefinition.RNA_REGION))
 		{
 			return GlobalConstants.SBO_RNA_SEGMENT;
 		}

synthesis/src/main/java/edu/utah/ece/async/ibiosim/synthesis/assembly/Assembler2.java

@@ -107,7 +107,7 @@ public class Assembler2
 //		assembledComp.setDnaSequence(synthSeq); 
 		
 //		ComponentDefinition  assembledComp = new ComponentDefinition(GlobalConstants.SBOL_AUTHORITY_DEFAULT, "assembledComp", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
-		ComponentDefinition  assembledComp = sbolDoc.createComponentDefinition(defaultURIPrefix, "assembledComp", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
+		ComponentDefinition  assembledComp = sbolDoc.createComponentDefinition(defaultURIPrefix, "assembledComp", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA_REGION)));
 		assembledComp.addRole(SequenceOntology.ENGINEERED_REGION);
 		Sequence synthSeq = sbolDoc.createSequence(defaultURIPrefix, "synthSeq", "", "", Sequence.IUPAC_DNA);
 		assembledComp.addSequence(synthSeq);