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Posted to commits@taverna.apache.org by st...@apache.org on 2018/06/29 10:55:01 UTC
[14/27] incubator-taverna-plugin-component git commit: package rename
folders
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/BaseProfileLocator.java
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diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/BaseProfileLocator.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/BaseProfileLocator.java
new file mode 100644
index 0000000..989f411
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/BaseProfileLocator.java
@@ -0,0 +1,154 @@
+package io.github.taverna_extras.component.profile;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import static java.util.Locale.UK;
+import static org.apache.commons.httpclient.HttpStatus.SC_OK;
+import static org.apache.commons.io.FileUtils.writeStringToFile;
+import static org.apache.log4j.Logger.getLogger;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+
+import org.apache.commons.httpclient.Header;
+import org.apache.commons.httpclient.HttpClient;
+import org.apache.commons.httpclient.HttpException;
+import org.apache.commons.httpclient.HttpMethod;
+import org.apache.commons.httpclient.methods.GetMethod;
+import org.apache.commons.httpclient.params.HttpClientParams;
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import org.apache.taverna.configuration.app.ApplicationConfiguration;
+
+public class BaseProfileLocator {
+ private static final String BASE_PROFILE_PATH = "BaseProfile.xml";
+ private static final String BASE_PROFILE_URI = "http://build.mygrid.org.uk/taverna/BaseProfile.xml";
+ private static final int TIMEOUT = 5000;
+ private static final String pattern = "EEE, dd MMM yyyy HH:mm:ss z";
+ private static final SimpleDateFormat format = new SimpleDateFormat(
+ pattern, UK);
+
+ private Logger logger = getLogger(BaseProfileLocator.class);
+ private ApplicationConfiguration appConfig;
+ private ComponentProfileImpl profile;
+
+ private void locateBaseProfile() {
+ File baseProfileFile = getBaseProfileFile();
+ @SuppressWarnings("unused")
+ boolean load = false;
+ Long remoteBaseProfileTime = null;
+ long localBaseProfileTime = -1;
+
+ HttpClientParams params = new HttpClientParams();
+ params.setConnectionManagerTimeout(TIMEOUT);
+ params.setSoTimeout(TIMEOUT);
+ HttpClient client = new HttpClient(params);
+
+ try {
+ remoteBaseProfileTime = getRemoteBaseProfileTimestamp(client);
+ logger.info("NoticeTime is " + remoteBaseProfileTime);
+ } catch (URISyntaxException e) {
+ logger.error("URI problem", e);
+ } catch (IOException e) {
+ logger.info("Could not read base profile", e);
+ } catch (ParseException e) {
+ logger.error("Could not parse last-modified time", e);
+ }
+ if (baseProfileFile.exists())
+ localBaseProfileTime = baseProfileFile.lastModified();
+
+ try {
+ if ((remoteBaseProfileTime != null)
+ && (remoteBaseProfileTime > localBaseProfileTime)) {
+ profile = new ComponentProfileImpl(null, new URL(BASE_PROFILE_URI),
+ null);
+ writeStringToFile(baseProfileFile, profile.getXML());
+ }
+ } catch (MalformedURLException e) {
+ logger.error("URI problem", e);
+ profile = null;
+ } catch (ComponentException e) {
+ logger.error("Component Registry problem", e);
+ profile = null;
+ } catch (IOException e) {
+ logger.error("Unable to write profile", e);
+ profile = null;
+ }
+
+ try {
+ if ((profile == null) && baseProfileFile.exists())
+ profile = new ComponentProfileImpl(null, baseProfileFile.toURI()
+ .toURL(), null);
+ } catch (Exception e) {
+ logger.error("URI problem", e);
+ profile = null;
+ }
+ }
+
+ private long parseTime(String timestamp) throws ParseException {
+ timestamp = timestamp.trim();
+ if (timestamp.endsWith(" GMT"))
+ timestamp = timestamp.substring(0, timestamp.length() - 3)
+ + " +0000";
+ else if (timestamp.endsWith(" BST"))
+ timestamp = timestamp.substring(0, timestamp.length() - 3)
+ + " +0100";
+ return format.parse(timestamp).getTime();
+ }
+
+ private long getRemoteBaseProfileTimestamp(HttpClient client)
+ throws URISyntaxException, IOException, HttpException,
+ ParseException {
+ URI baseProfileURI = new URI(BASE_PROFILE_URI);
+ HttpMethod method = new GetMethod(baseProfileURI.toString());
+ int statusCode = client.executeMethod(method);
+ if (statusCode != SC_OK) {
+ logger.warn("HTTP status " + statusCode + " while getting "
+ + baseProfileURI);
+ return -1;
+ }
+ Header h = method.getResponseHeader("Last-Modified");
+ if (h == null)
+ return -1;
+ return parseTime(h.getValue());
+ }
+
+ private File getBaseProfileFile() {
+ File config = new File(appConfig.getApplicationHomeDir().toFile(), "conf");
+ if (!config.exists())
+ config.mkdir();
+ return new File(config, BASE_PROFILE_PATH);
+ }
+
+ public synchronized ComponentProfileImpl getProfile() {
+ if (profile == null)
+ locateBaseProfile();
+ return profile;
+ }
+
+ public void setAppConfig(ApplicationConfiguration appConfig) {
+ this.appConfig = appConfig;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ComponentProfileImpl.java
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diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ComponentProfileImpl.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ComponentProfileImpl.java
new file mode 100644
index 0000000..6c7a5b0
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ComponentProfileImpl.java
@@ -0,0 +1,683 @@
+package io.github.taverna_extras.component.profile;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import static org.apache.jena.rdf.model.ModelFactory.createOntologyModel;
+import static java.lang.System.identityHashCode;
+import static java.util.Collections.emptyList;
+import static java.util.Collections.emptyMap;
+import static org.apache.log4j.Logger.getLogger;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.io.StringWriter;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.TreeMap;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.transform.stream.StreamSource;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Registry;
+import io.github.taverna_extras.component.api.profile.ActivityProfile;
+import io.github.taverna_extras.component.api.profile.ExceptionHandling;
+import io.github.taverna_extras.component.api.profile.PortProfile;
+import io.github.taverna_extras.component.api.profile.SemanticAnnotationProfile;
+
+import io.github.taverna_extras.component.api.profile.doc.Activity;
+import io.github.taverna_extras.component.api.profile.doc.Ontology;
+import io.github.taverna_extras.component.api.profile.doc.Port;
+import io.github.taverna_extras.component.api.profile.doc.Profile;
+import io.github.taverna_extras.component.api.profile.doc.SemanticAnnotation;
+
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntProperty;
+import static org.apache.taverna.workflowmodel.health.HealthCheck.NO_PROBLEM;
+import org.apache.taverna.workflowmodel.health.RemoteHealthChecker;
+
+/**
+ * A ComponentProfile specifies the inputs, outputs and semantic annotations
+ * that a Component must contain.
+ *
+ * @author David Withers
+ */
+public class ComponentProfileImpl implements
+ io.github.taverna_extras.component.api.profile.Profile {
+ private static final Logger logger = getLogger(ComponentProfileImpl.class);
+ private static final Map<String, OntModel> ontologyModels = new HashMap<>();
+ private static final JAXBContext jaxbContext;
+ private BaseProfileLocator base;
+ static {
+ try {
+ jaxbContext = JAXBContext.newInstance(Profile.class);
+ } catch (JAXBException e) {
+ // Should never happen! Represents a critical error
+ throw new Error(
+ "Failed to initialize profile deserialization engine", e);
+ }
+ }
+ private io.github.taverna_extras.component.api.profile.Profile parent;
+ private Profile profileDoc;
+ private ExceptionHandling exceptionHandling;
+ private Registry parentRegistry = null;
+ private final Object lock = new Object();
+ private Exception loaderException = null;
+ protected volatile boolean loaded = false;
+
+ public ComponentProfileImpl(URL profileURL, BaseProfileLocator base)
+ throws ComponentException {
+ this(null, profileURL, base);
+ }
+
+ public ComponentProfileImpl(String profileString, BaseProfileLocator base)
+ throws ComponentException {
+ this(null, profileString, base);
+ }
+
+ public ComponentProfileImpl(Registry registry, URI profileURI,
+ BaseProfileLocator base) throws ComponentException,
+ MalformedURLException {
+ this(registry, profileURI.toURL(), base);
+ }
+
+ public ComponentProfileImpl(Registry registry, URL profileURL,
+ BaseProfileLocator base) throws ComponentException {
+ logger.info("Loading profile in " + identityHashCode(this) + " from "
+ + profileURL);
+ this.base = base;
+ try {
+ URL url = profileURL;
+ if (url.getProtocol().startsWith("http"))
+ url = new URI(url.getProtocol(), url.getAuthority(),
+ url.getPath(), url.getQuery(), url.getRef()).toURL();
+ loadProfile(this, url, base);
+ } catch (MalformedURLException e) {
+ logger.warn("Malformed URL? " + profileURL);
+ } catch (URISyntaxException e) {
+ logger.warn("Malformed URL? " + profileURL);
+ }
+ parentRegistry = registry;
+ }
+
+ public ComponentProfileImpl(Registry registry, String profileString,
+ BaseProfileLocator base) throws ComponentException {
+ logger.info("Loading profile in " + identityHashCode(this)
+ + " from string");
+ this.base = base;
+ loadProfile(this, profileString, base);
+ this.parentRegistry = registry;
+ }
+
+ private static void loadProfile(final ComponentProfileImpl profile,
+ final Object source, BaseProfileLocator base) {
+ Runnable r = new Runnable() {
+ @Override
+ public void run() {
+ Date start = new Date();
+ if (source instanceof URL)
+ loadProfileFromURL(profile, (URL) source);
+ else if (source instanceof String)
+ loadProfileFromString(profile, (String) source);
+ else
+ throw new IllegalArgumentException(
+ "Bad type of profile source: " + source.getClass());
+ Date end = new Date();
+ logger.info("Loaded profile in " + identityHashCode(profile)
+ + " (in " + (end.getTime() - start.getTime())
+ + " msec)");
+ }
+ };
+ if (base.getProfile() == null)
+ // Must load the base profile synchronously, to avoid deadlock
+ r.run();
+ else
+ new Thread(r).start();
+ }
+
+ private static void loadProfileFromURL(ComponentProfileImpl profile, URL source) {
+ try {
+ URLConnection conn = source.openConnection();
+ try {
+ conn.addRequestProperty("Accept", "application/xml,*/*;q=0.1");
+ } catch (Exception e) {
+ }
+ try (InputStream is = conn.getInputStream()) {
+ profile.profileDoc = jaxbContext.createUnmarshaller()
+ .unmarshal(new StreamSource(is), Profile.class)
+ .getValue();
+ }
+ } catch (FileNotFoundException e) {
+ profile.loaderException = e;
+ logger.warn("URL not readable: " + source);
+ } catch (Exception e) {
+ profile.loaderException = e;
+ logger.warn("Failed to load profile.", e);
+ }
+ synchronized (profile.lock) {
+ profile.loaded = true;
+ profile.lock.notifyAll();
+ }
+ }
+
+ private static void loadProfileFromString(ComponentProfileImpl profile,
+ String source) {
+ try {
+ profile.profileDoc = jaxbContext
+ .createUnmarshaller()
+ .unmarshal(new StreamSource(new StringReader(source)),
+ Profile.class).getValue();
+ } catch (Exception e) {
+ profile.loaderException = e;
+ logger.warn("Failed to load profile.", e);
+ }
+ synchronized (profile.lock) {
+ profile.loaded = true;
+ profile.lock.notifyAll();
+ }
+ }
+
+ @Override
+ public Registry getComponentRegistry() {
+ return parentRegistry;
+ }
+
+ @Override
+ public String getXML() throws ComponentException {
+ try {
+ StringWriter stringWriter = new StringWriter();
+ jaxbContext.createMarshaller().marshal(getProfileDocument(),
+ stringWriter);
+ return stringWriter.toString();
+ } catch (JAXBException e) {
+ throw new ComponentException("Unable to serialize profile.", e);
+ }
+ }
+
+ @Override
+ public Profile getProfileDocument() throws ComponentException {
+ try {
+ synchronized (lock) {
+ while (!loaded)
+ lock.wait();
+ if (loaderException != null) {
+ if (loaderException instanceof FileNotFoundException)
+ throw new ComponentException(
+ "Profile not found/readable: "
+ + loaderException.getMessage(),
+ loaderException);
+ throw new ComponentException(
+ "Problem loading profile definition: "
+ + loaderException.getMessage(),
+ loaderException);
+ }
+ return profileDoc;
+ }
+ } catch (InterruptedException e) {
+ logger.info("Interrupted during wait for lock.", e);
+ return null;
+ }
+ }
+
+ @Override
+ public String getId() {
+ try {
+ return getProfileDocument().getId();
+ } catch (ComponentException e) {
+ return null;
+ }
+ }
+
+ @Override
+ public String getName() {
+ try {
+ return getProfileDocument().getName();
+ } catch (ComponentException e) {
+ return null;
+ }
+ }
+
+ @Override
+ public String getDescription() {
+ try {
+ return getProfileDocument().getDescription();
+ } catch (ComponentException e) {
+ return null;
+ }
+ }
+
+ /**
+ * @return Is this the base profile?
+ */
+ private boolean isBase() {
+ if (base == null)
+ return true;
+ Object o = base.getProfile();
+ return o == null || o == this;
+ }
+
+ private synchronized io.github.taverna_extras.component.api.profile.Profile parent()
+ throws ComponentException {
+ if (parent == null) {
+ try {
+ if (!isBase() && getProfileDocument().getExtends() != null
+ && parentRegistry != null) {
+ parent = parentRegistry
+ .getComponentProfile(getProfileDocument()
+ .getExtends().getProfileId());
+ if (parent != null)
+ return parent;
+ }
+ } catch (ComponentException e) {
+ }
+ parent = new EmptyProfile();
+ }
+ return parent;
+ }
+
+ @Override
+ public String getOntologyLocation(String ontologyId) {
+ String ontologyURI = null;
+ try {
+ for (Ontology ontology : getProfileDocument().getOntology())
+ if (ontology.getId().equals(ontologyId))
+ ontologyURI = ontology.getValue();
+ } catch (ComponentException e) {
+ }
+ if ((ontologyURI == null) && !isBase())
+ ontologyURI = base.getProfile().getOntologyLocation(ontologyId);
+ return ontologyURI;
+ }
+
+ private Map<String, String> internalGetPrefixMap()
+ throws ComponentException {
+ Map<String, String> result = new TreeMap<>();
+ try {
+ for (Ontology ontology : getProfileDocument().getOntology())
+ result.put(ontology.getId(), ontology.getValue());
+ } catch (ComponentException e) {
+ }
+ result.putAll(parent().getPrefixMap());
+ return result;
+ }
+
+ @Override
+ public Map<String, String> getPrefixMap() throws ComponentException {
+ Map<String, String> result = internalGetPrefixMap();
+ if (!isBase())
+ result.putAll(base.getProfile().getPrefixMap());
+ return result;
+ }
+
+ private OntModel readOntologyFromURI(String ontologyId, String ontologyURI) {
+ logger.info("Reading ontology for " + ontologyId + " from "
+ + ontologyURI);
+ OntModel model = createOntologyModel();
+ try {
+ URL url = new URL(ontologyURI);
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+ // CRITICAL: must be retrieved as correct content type
+ conn.addRequestProperty("Accept",
+ "application/rdf+xml,application/xml;q=0.9");
+ try (InputStream in = conn.getInputStream()) {
+ // TODO Consider whether the encoding is handled right
+ // ontologyModel.read(in, url.toString());
+ model.read(new StringReader(IOUtils.toString(in, "UTF-8")),
+ url.toString());
+ }
+ } catch (MalformedURLException e) {
+ logger.error("Problem reading ontology " + ontologyId, e);
+ return null;
+ } catch (IOException e) {
+ logger.error("Problem reading ontology " + ontologyId, e);
+ return null;
+ } catch (NullPointerException e) {
+ // TODO Why is this different?
+ logger.error("Problem reading ontology " + ontologyId, e);
+ model = createOntologyModel();
+ }
+ return model;
+ }
+
+ private boolean isAccessible(String ontologyURI) {
+ return RemoteHealthChecker.contactEndpoint(null, ontologyURI).getResultId() == NO_PROBLEM;
+ }
+
+ @Override
+ public OntModel getOntology(String ontologyId) {
+ String ontologyURI = getOntologyLocation(ontologyId);
+ synchronized (ontologyModels) {
+ if (ontologyModels.containsKey(ontologyURI))
+ return ontologyModels.get(ontologyURI);
+ }
+
+ // Drop out of critical section while we do I/O
+ if (!isAccessible(ontologyURI)) {
+ logger.warn("Catastrophic problem contacting ontology source.");
+ // Catastrophic problem?!
+ synchronized (ontologyModels) {
+ ontologyModels.put(ontologyURI, null);
+ }
+ return null;
+ }
+ OntModel model = readOntologyFromURI(ontologyId, ontologyURI);
+
+ synchronized (ontologyModels) {
+ if (model != null && !ontologyModels.containsKey(ontologyURI)) {
+ ontologyModels.put(ontologyURI, model);
+ }
+ return ontologyModels.get(ontologyURI);
+ }
+ }
+
+ @Override
+ public List<PortProfile> getInputPortProfiles() {
+ List<PortProfile> portProfiles = new ArrayList<>();
+ try {
+ for (Port port : getProfileDocument().getComponent().getInputPort())
+ portProfiles.add(new PortProfileImpl(this, port));
+ } catch (ComponentException e) {
+ }
+ if (!isBase())
+ portProfiles.addAll(base.getProfile().getInputPortProfiles());
+ return portProfiles;
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getInputSemanticAnnotationProfiles()
+ throws ComponentException {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ List<PortProfile> portProfiles = getInputPortProfiles();
+ portProfiles.addAll(parent().getInputPortProfiles());
+ for (PortProfile portProfile : portProfiles)
+ saProfiles.addAll(portProfile.getSemanticAnnotations());
+ if (!isBase())
+ saProfiles.addAll(base.getProfile()
+ .getInputSemanticAnnotationProfiles());
+ return getUniqueSemanticAnnotationProfiles(saProfiles);
+ }
+
+ @Override
+ public List<PortProfile> getOutputPortProfiles() {
+ List<PortProfile> portProfiles = new ArrayList<>();
+ try {
+ for (Port port : getProfileDocument().getComponent()
+ .getOutputPort())
+ portProfiles.add(new PortProfileImpl(this, port));
+ } catch (ComponentException e) {
+ }
+ if (!isBase())
+ portProfiles.addAll(base.getProfile().getOutputPortProfiles());
+ return portProfiles;
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getOutputSemanticAnnotationProfiles()
+ throws ComponentException {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ List<PortProfile> portProfiles = getOutputPortProfiles();
+ portProfiles.addAll(parent().getOutputPortProfiles());
+ for (PortProfile portProfile : portProfiles)
+ saProfiles.addAll(portProfile.getSemanticAnnotations());
+ if (!isBase())
+ saProfiles.addAll(base.getProfile()
+ .getOutputSemanticAnnotationProfiles());
+ return getUniqueSemanticAnnotationProfiles(saProfiles);
+ }
+
+ @Override
+ public List<io.github.taverna_extras.component.api.profile.ActivityProfile> getActivityProfiles() {
+ List<io.github.taverna_extras.component.api.profile.ActivityProfile> activityProfiles = new ArrayList<>();
+ try {
+ for (Activity activity : getProfileDocument().getComponent()
+ .getActivity())
+ activityProfiles.add(new ActivityProfileImpl(this, activity));
+ } catch (ComponentException e) {
+ }
+ return activityProfiles;
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getActivitySemanticAnnotationProfiles()
+ throws ComponentException {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ List<ActivityProfile> activityProfiles = getActivityProfiles();
+ activityProfiles.addAll(parent().getActivityProfiles());
+ for (ActivityProfile activityProfile : activityProfiles)
+ saProfiles.addAll(activityProfile.getSemanticAnnotations());
+ if (!isBase())
+ saProfiles.addAll(base.getProfile()
+ .getActivitySemanticAnnotationProfiles());
+ return getUniqueSemanticAnnotationProfiles(saProfiles);
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getSemanticAnnotations()
+ throws ComponentException {
+ List<SemanticAnnotationProfile> saProfiles = getComponentProfiles();
+ saProfiles.addAll(parent().getSemanticAnnotations());
+ if (!isBase())
+ saProfiles.addAll(base.getProfile().getSemanticAnnotations());
+ return saProfiles;
+ }
+
+ private List<SemanticAnnotationProfile> getComponentProfiles() {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ try {
+ for (SemanticAnnotation semanticAnnotation : getProfileDocument()
+ .getComponent().getSemanticAnnotation())
+ saProfiles.add(new SemanticAnnotationProfileImpl(this,
+ semanticAnnotation));
+ } catch (ComponentException e) {
+ }
+ return saProfiles;
+ }
+
+ private List<SemanticAnnotationProfile> getUniqueSemanticAnnotationProfiles(
+ List<SemanticAnnotationProfile> semanticAnnotationProfiles) {
+ List<SemanticAnnotationProfile> uniqueSemanticAnnotations = new ArrayList<>();
+ Set<OntProperty> predicates = new HashSet<>();
+ for (SemanticAnnotationProfile semanticAnnotationProfile : semanticAnnotationProfiles) {
+ OntProperty prop = semanticAnnotationProfile.getPredicate();
+ if (prop != null && !predicates.contains(prop)) {
+ predicates.add(prop);
+ uniqueSemanticAnnotations.add(semanticAnnotationProfile);
+ }
+ }
+ return uniqueSemanticAnnotations;
+ }
+
+ @Override
+ public ExceptionHandling getExceptionHandling() {
+ try {
+ if (exceptionHandling == null
+ && getProfileDocument().getComponent()
+ .getExceptionHandling() != null)
+ exceptionHandling = new ExceptionHandling(getProfileDocument()
+ .getComponent().getExceptionHandling());
+ } catch (ComponentException e) {
+ }
+ return exceptionHandling;
+ }
+
+ @Override
+ public String toString() {
+ return "ComponentProfile" + "\n Name : " + getName()
+ + "\n Description : " + getDescription()
+ + "\n InputPortProfiles : " + getInputPortProfiles()
+ + "\n OutputPortProfiles : " + getOutputPortProfiles();
+ }
+
+ @Override
+ public int hashCode() {
+ return 31 + ((getId() == null) ? 0 : getId().hashCode());
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ComponentProfileImpl other = (ComponentProfileImpl) obj;
+ if (!loaded || !other.loaded)
+ return false;
+ if (getId() == null)
+ return other.getId() == null;
+ return getId().equals(other.getId());
+ }
+
+ public OntClass getClass(String className) {
+ try {
+ for (Ontology ontology : getProfileDocument().getOntology()) {
+ OntModel ontModel = getOntology(ontology.getId());
+ if (ontModel != null) {
+ OntClass result = ontModel.getOntClass(className);
+ if (result != null)
+ return result;
+ }
+ }
+ } catch (ComponentException e) {
+ }
+ return null;
+ }
+
+ @Override
+ public void delete() throws ComponentException {
+ throw new ComponentException("Deletion not supported.");
+ }
+}
+
+/**
+ * A simple do-nothing implementation of a profile. Used when there's no other
+ * option for what a <i>real</i> profile extends.
+ *
+ * @author Donal Fellows
+ */
+final class EmptyProfile implements
+ io.github.taverna_extras.component.api.profile.Profile {
+ @Override
+ public String getName() {
+ return "";
+ }
+
+ @Override
+ public String getDescription() {
+ return "";
+ }
+
+ @Override
+ public Registry getComponentRegistry() {
+ return null;
+ }
+
+ @Override
+ public String getXML() throws ComponentException {
+ throw new ComponentException("No document.");
+ }
+
+ @Override
+ public Profile getProfileDocument() {
+ return new Profile();
+ }
+
+ @Override
+ public String getId() {
+ return "";
+ }
+
+ @Override
+ public String getOntologyLocation(String ontologyId) {
+ return "";
+ }
+
+ @Override
+ public Map<String, String> getPrefixMap() {
+ return emptyMap();
+ }
+
+ @Override
+ public OntModel getOntology(String ontologyId) {
+ return null;
+ }
+
+ @Override
+ public List<PortProfile> getInputPortProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getInputSemanticAnnotationProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<PortProfile> getOutputPortProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getOutputSemanticAnnotationProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<io.github.taverna_extras.component.api.profile.ActivityProfile> getActivityProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getActivitySemanticAnnotationProfiles() {
+ return emptyList();
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getSemanticAnnotations() {
+ return emptyList();
+ }
+
+ @Override
+ public ExceptionHandling getExceptionHandling() {
+ return null;
+ }
+
+ @Override
+ public void delete() throws ComponentException {
+ throw new ComponentException("Deletion forbidden.");
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/PortProfileImpl.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/PortProfileImpl.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/PortProfileImpl.java
new file mode 100644
index 0000000..53a1190
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/PortProfileImpl.java
@@ -0,0 +1,58 @@
+package io.github.taverna_extras.component.profile;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import java.util.ArrayList;
+import java.util.List;
+
+import io.github.taverna_extras.component.api.profile.PortProfile;
+import io.github.taverna_extras.component.api.profile.SemanticAnnotationProfile;
+
+import io.github.taverna_extras.component.api.profile.doc.Port;
+import io.github.taverna_extras.component.api.profile.doc.SemanticAnnotation;
+
+/**
+ * Specifies the semantic annotations that a port must have.
+ *
+ * @author David Withers
+ */
+public class PortProfileImpl implements PortProfile {
+ private final ComponentProfileImpl componentProfile;
+ private final Port port;
+
+ public PortProfileImpl(ComponentProfileImpl componentProfile, Port port) {
+ this.componentProfile = componentProfile;
+ this.port = port;
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getSemanticAnnotations() {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ for (SemanticAnnotation annotation : port.getSemanticAnnotation())
+ saProfiles.add(new SemanticAnnotationProfileImpl(componentProfile,
+ annotation));
+ return saProfiles;
+ }
+
+ @Override
+ public String toString() {
+ return "PortProfile \n SemanticAnnotations : "
+ + getSemanticAnnotations();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/SemanticAnnotationProfileImpl.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/SemanticAnnotationProfileImpl.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/SemanticAnnotationProfileImpl.java
new file mode 100644
index 0000000..a3b5afa
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/SemanticAnnotationProfileImpl.java
@@ -0,0 +1,175 @@
+package io.github.taverna_extras.component.profile;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import static java.io.File.createTempFile;
+import static org.apache.commons.io.FileUtils.writeStringToFile;
+import static org.apache.log4j.Logger.getLogger;
+
+import java.io.IOException;
+import java.io.StringWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.profile.SemanticAnnotationProfile;
+
+import io.github.taverna_extras.component.api.profile.doc.SemanticAnnotation;
+
+import org.apache.jena.ontology.Individual;
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntProperty;
+import org.apache.jena.ontology.OntResource;
+
+/**
+ * Definition of a semantic annotation for a component element.
+ *
+ * @author David Withers
+ */
+public class SemanticAnnotationProfileImpl implements SemanticAnnotationProfile {
+ private static final Logger log = getLogger(SemanticAnnotationProfileImpl.class);
+ private final ComponentProfileImpl componentProfile;
+ private final SemanticAnnotation semanticAnnotation;
+
+ public SemanticAnnotationProfileImpl(ComponentProfileImpl componentProfile,
+ SemanticAnnotation semanticAnnotation) {
+ this.componentProfile = componentProfile;
+ this.semanticAnnotation = semanticAnnotation;
+ }
+
+ /**
+ * Returns the ontology that defines semantic annotation.
+ *
+ * @return the ontology that defines semantic annotation
+ */
+ @Override
+ public OntModel getOntology() {
+ String ontology = semanticAnnotation.getOntology();
+ if (ontology == null)
+ return null;
+ return componentProfile.getOntology(ontology);
+ }
+
+ /**
+ * Returns the predicate for the semantic annotation.
+ *
+ * @return the predicate for the semantic annotation
+ */
+ @Override
+ public OntProperty getPredicate() {
+ OntModel ontology = getOntology();
+ if (ontology == null)
+ return null;
+ String predicate = semanticAnnotation.getPredicate();
+ if (predicate == null)
+ return null;
+ if (predicate.contains("foaf")) {
+ StringWriter sw = new StringWriter();
+ ontology.writeAll(sw, null, "RDF/XML");
+ try {
+ writeStringToFile(createTempFile("foaf", null), sw.toString());
+ } catch (IOException e) {
+ log.info("failed to write foaf ontology to temporary file", e);
+ }
+ }
+
+ return ontology.getOntProperty(predicate);
+ }
+
+ @Override
+ public String getPredicateString() {
+ return semanticAnnotation.getPredicate();
+ }
+
+ @Override
+ public String getClassString() {
+ return semanticAnnotation.getClazz();
+ }
+
+ /**
+ * Returns the individual that the semantic annotation must use.
+ *
+ * May be null if no explicit individual is required.
+ *
+ * @return the individual that the semantic annotation must use
+ */
+ @Override
+ public Individual getIndividual() {
+ String individual = semanticAnnotation.getValue();
+ if (individual == null || individual.isEmpty())
+ return null;
+ return getOntology().getIndividual(individual);
+ }
+
+ /**
+ * Returns the individuals in the range of the predicate defined in the
+ * ontology.
+ *
+ * @return the individuals in the range of the predicate defined in the
+ * ontology
+ */
+ @Override
+ public List<Individual> getIndividuals() {
+ OntModel ontology = getOntology();
+ OntProperty prop = getPredicate();
+ if (ontology == null || prop == null)
+ return new ArrayList<>();
+ OntResource range = prop.getRange();
+ if (range == null)
+ return new ArrayList<>();
+ return ontology.listIndividuals(range).toList();
+ }
+
+ @Override
+ public Integer getMinOccurs() {
+ return semanticAnnotation.getMinOccurs().intValue();
+ }
+
+ @Override
+ public Integer getMaxOccurs() {
+ try {
+ return Integer.valueOf(semanticAnnotation.getMaxOccurs());
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ }
+
+ @Override
+ public String toString() {
+ return "SemanticAnnotation " + "\n Predicate : " + getPredicate()
+ + "\n Individual : " + getIndividual() + "\n Individuals : "
+ + getIndividuals();
+ }
+
+ @Override
+ public OntClass getRangeClass() {
+ String clazz = this.getClassString();
+ if (clazz != null)
+ return componentProfile.getClass(clazz);
+
+ OntProperty prop = getPredicate();
+ if (prop == null)
+ return null;
+ OntResource range = prop.getRange();
+ if (range != null && range.isClass())
+ return range.asClass();
+ return null;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ClientVersion.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ClientVersion.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ClientVersion.java
new file mode 100644
index 0000000..c9fda59
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ClientVersion.java
@@ -0,0 +1,51 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.Properties;
+
+public class ClientVersion {
+ private static final String DEFAULT_VERSION = "1.1.0";
+ public static final String VERSION;
+
+ private ClientVersion() {
+ }
+
+ static {
+ InputStream is = ClientVersion.class
+ .getResourceAsStream("version.properties");
+ String version = DEFAULT_VERSION;
+ if (is != null)
+ try {
+ Properties p = new Properties();
+ p.load(is);
+ version = p.getProperty("project.version", DEFAULT_VERSION);
+ } catch (IOException e) {
+ } finally {
+ try {
+ is.close();
+ } catch (IOException e) {
+ }
+ }
+ VERSION = version;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/Component.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/Component.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/Component.java
new file mode 100644
index 0000000..afdf2b8
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/Component.java
@@ -0,0 +1,161 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+
+import static java.util.Collections.synchronizedSortedMap;
+
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Version;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+/**
+ * A Component is a building block for creating Taverna workflows. Components
+ * and must comply with the ComponentProfile of their ComponentFamily.
+ *
+ * @author David Withers
+ */
+public abstract class Component implements
+ io.github.taverna_extras.component.api.Component {
+ private String name;
+ private String description;
+ private URL url;
+ /**
+ * Mapping from version numbers to version implementations.
+ */
+ protected SortedMap<Integer, Version> versionMap = new TreeMap<>();
+
+ protected Component(URL url) {
+ this.url = url;
+ }
+
+ protected Component(String url) {
+ try {
+ this.url = new URL(url);
+ } catch (MalformedURLException e) {
+ // nothing
+ }
+ }
+
+ protected Component(File fileDir) {
+ try {
+ this.url = fileDir.toURI().toURL();
+ } catch (MalformedURLException e) {
+ // nothing
+ }
+ }
+
+ @Override
+ public final synchronized String getName() {
+ if (name == null)
+ name = internalGetName();
+ return name;
+ }
+
+ /**
+ * The real implementation of the name fetching. Caching already handled.
+ *
+ * @return The name of the component.
+ */
+ protected abstract String internalGetName();
+
+ @Override
+ public final synchronized String getDescription() {
+ if (description == null)
+ description = internalGetDescription();
+ return description;
+ }
+
+ /**
+ * The real implementation of the description fetching. Caching already
+ * handled.
+ *
+ * @return The description of the component.
+ */
+ protected abstract String internalGetDescription();
+
+ @Override
+ public final SortedMap<Integer, Version> getComponentVersionMap() {
+ synchronized (versionMap) {
+ checkComponentVersionMap();
+ return synchronizedSortedMap(versionMap);
+ }
+ }
+
+ private void checkComponentVersionMap() {
+ if (versionMap.isEmpty())
+ populateComponentVersionMap();
+ }
+
+ /**
+ * Create the contents of the {@link #versionMap} field.
+ */
+ protected abstract void populateComponentVersionMap();
+
+ @Override
+ public final Version getComponentVersion(Integer version)
+ throws ComponentException {
+ synchronized (versionMap) {
+ checkComponentVersionMap();
+ return versionMap.get(version);
+ }
+ }
+
+ @Override
+ public final Version addVersionBasedOn(WorkflowBundle bundle,
+ String revisionComment) throws ComponentException {
+ Version result = internalAddVersionBasedOn(bundle, revisionComment);
+ synchronized (versionMap) {
+ checkComponentVersionMap();
+ versionMap.put(result.getVersionNumber(), result);
+ }
+ return result;
+ }
+
+ /**
+ * Manufacture a new version of a component. Does not add to the overall
+ * version map.
+ *
+ * @param bundle
+ * The definition of the component.
+ * @param revisionComment
+ * The description of the version.
+ * @return The new version of the component.
+ * @throws RegistryException
+ */
+ protected abstract Version internalAddVersionBasedOn(WorkflowBundle bundle,
+ String revisionComment) throws ComponentException;
+
+ @Override
+ public final URL getComponentURL() {
+ return url;
+ }
+
+ @Override
+ public void delete() throws ComponentException {
+ getFamily().removeComponent(this);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentFamily.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentFamily.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentFamily.java
new file mode 100644
index 0000000..ce8a782
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentFamily.java
@@ -0,0 +1,161 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import io.github.taverna_extras.component.api.Component;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Registry;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.profile.Profile;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+/**
+ * A ComponentFamily is a collection of Components that share the same
+ * ComponentProfile.
+ *
+ * @author David Withers
+ */
+public abstract class ComponentFamily implements
+ io.github.taverna_extras.component.api.Family {
+ private Registry parentRegistry;
+ private String name;
+ private String description;
+ private Profile componentProfile;
+ private ComponentUtil util;
+
+ protected Map<String, Component> componentCache = new HashMap<>();
+
+ public ComponentFamily(Registry componentRegistry, ComponentUtil util) {
+ this.parentRegistry = componentRegistry;
+ this.util = util;
+ }
+
+ @Override
+ public Registry getComponentRegistry() {
+ return parentRegistry;
+ }
+
+ @Override
+ public final synchronized String getName() {
+ if (name == null) {
+ name = internalGetName();
+ }
+ return name;
+ }
+
+ protected abstract String internalGetName();
+
+ @Override
+ public final synchronized String getDescription() {
+ if (description == null) {
+ description = internalGetDescription();
+ }
+ return description;
+ }
+
+ protected abstract String internalGetDescription();
+
+ @Override
+ public final synchronized Profile getComponentProfile()
+ throws ComponentException {
+ if (componentProfile == null)
+ componentProfile = internalGetComponentProfile();
+ if (componentProfile == null) {
+ Profile baseProfile = util.getBaseProfile();
+ if (baseProfile != null) {
+ return baseProfile;
+ }
+ }
+ return componentProfile;
+ }
+
+ protected abstract Profile internalGetComponentProfile()
+ throws ComponentException;
+
+ @Override
+ public final List<Component> getComponents() throws ComponentException {
+ checkComponentCache();
+ return new ArrayList<>(componentCache.values());
+ }
+
+ private void checkComponentCache() throws ComponentException {
+ synchronized (componentCache) {
+ if (componentCache.isEmpty())
+ populateComponentCache();
+ }
+ }
+
+ protected abstract void populateComponentCache() throws ComponentException;
+
+ @Override
+ public final Component getComponent(String componentName)
+ throws ComponentException {
+ checkComponentCache();
+ return componentCache.get(componentName);
+ }
+
+ @Override
+ public final Version createComponentBasedOn(String componentName,
+ String description, WorkflowBundle bundle) throws ComponentException {
+ if (componentName == null)
+ throw new ComponentException("Component name must not be null");
+ if (bundle == null)
+ throw new ComponentException("workflow must not be null");
+ checkComponentCache();
+ if (componentCache.containsKey(componentName))
+ throw new ComponentException("Component name already used");
+ Version version = internalCreateComponentBasedOn(componentName,
+ description, bundle);
+ synchronized (componentCache) {
+ Component c = version.getComponent();
+ componentCache.put(componentName, c);
+ }
+ return version;
+ }
+
+ protected abstract Version internalCreateComponentBasedOn(
+ String componentName, String description, WorkflowBundle bundle)
+ throws ComponentException;
+
+ @Override
+ public final void removeComponent(Component component)
+ throws ComponentException {
+ if (component != null) {
+ checkComponentCache();
+ synchronized (componentCache) {
+ componentCache.remove(component.getName());
+ }
+ internalRemoveComponent(component);
+ }
+ }
+
+ protected abstract void internalRemoveComponent(Component component)
+ throws ComponentException;
+
+ @Override
+ public void delete() throws ComponentException {
+ getComponentRegistry().removeComponentFamily(this);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentImplementationCache.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentImplementationCache.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentImplementationCache.java
new file mode 100644
index 0000000..91846a3
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentImplementationCache.java
@@ -0,0 +1,75 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import static java.lang.System.currentTimeMillis;
+import static org.apache.log4j.Logger.getLogger;
+
+import java.util.Map;
+import java.util.WeakHashMap;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Version;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+public class ComponentImplementationCache {
+ private class Entry {
+ WorkflowBundle implementation;
+ long timestamp;
+ }
+ private final long VALIDITY = 15 * 60 * 1000;
+ private final Logger logger = getLogger(ComponentImplementationCache.class);
+ private final Map<Version.ID, Entry> cache = new WeakHashMap<>();
+ private ComponentUtil utils;
+
+ public void setComponentUtil(ComponentUtil utils) {
+ this.utils = utils;
+ }
+
+ public WorkflowBundle getImplementation(Version.ID id) throws ComponentException {
+ long now = currentTimeMillis();
+ synchronized (id) {
+ Entry entry = cache.get(id);
+ if (entry != null && entry.timestamp >= now)
+ return entry.implementation;
+ logger.info("before calculate component version for " + id);
+ Version componentVersion;
+ try {
+ componentVersion = utils.getVersion(id);
+ } catch (RuntimeException e) {
+ if (entry != null)
+ return entry.implementation;
+ throw new ComponentException(e.getMessage(), e);
+ }
+ logger.info("calculated component version for " + id + " as "
+ + componentVersion.getVersionNumber() + "; retrieving dataflow");
+ WorkflowBundle implementation = componentVersion.getImplementation();
+ //DataflowValidationReport report = implementation.checkValidity();
+ //logger.info("component version " + id + " incomplete:"
+ // + report.isWorkflowIncomplete() + " valid:"
+ // + report.isValid());
+ entry = new Entry();
+ entry.implementation = implementation;
+ entry.timestamp = now + VALIDITY;
+ return cache.put(id, entry).implementation;
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentRegistry.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentRegistry.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentRegistry.java
new file mode 100644
index 0000000..325da27
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentRegistry.java
@@ -0,0 +1,242 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+import java.io.File;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Family;
+import io.github.taverna_extras.component.api.License;
+import io.github.taverna_extras.component.api.SharingPolicy;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.profile.Profile;
+
+/**
+ * A ComponentRegistry contains ComponentFamilies and ComponentProfiles.
+ *
+ * @author David Withers
+ */
+public abstract class ComponentRegistry implements
+ io.github.taverna_extras.component.api.Registry {
+ protected Map<String, Family> familyCache = new HashMap<>();
+ protected List<Profile> profileCache = new ArrayList<>();
+ protected List<SharingPolicy> permissionCache = new ArrayList<>();
+ protected List<License> licenseCache = new ArrayList<>();
+
+ private URL registryBase;
+
+ protected ComponentRegistry(URL registryBase) throws ComponentException {
+ this.registryBase = registryBase;
+ }
+
+ protected ComponentRegistry(File fileDir) throws ComponentException {
+ try {
+ this.registryBase = fileDir.toURI().toURL();
+ } catch (MalformedURLException e) {
+ throw new ComponentException(e);
+ }
+ }
+
+ @Override
+ public final List<Family> getComponentFamilies() throws ComponentException {
+ checkFamilyCache();
+ return new ArrayList<Family>(familyCache.values());
+ }
+
+ private void checkFamilyCache() throws ComponentException {
+ synchronized (familyCache) {
+ if (familyCache.isEmpty())
+ populateFamilyCache();
+ }
+ }
+
+ protected abstract void populateFamilyCache() throws ComponentException;
+
+ @Override
+ public final Family getComponentFamily(String familyName)
+ throws ComponentException {
+ checkFamilyCache();
+ return familyCache.get(familyName);
+ }
+
+ @Override
+ public final Family createComponentFamily(String familyName,
+ Profile componentProfile, String description, License license,
+ SharingPolicy sharingPolicy) throws ComponentException {
+ if (familyName == null)
+ throw new ComponentException(
+ "Component family name must not be null");
+ if (componentProfile == null)
+ throw new ComponentException("Component profile must not be null");
+ if (getComponentFamily(familyName) != null)
+ throw new ComponentException("Component family already exists");
+
+ Family result = internalCreateComponentFamily(familyName,
+ componentProfile, description, license, sharingPolicy);
+ checkFamilyCache();
+ synchronized (familyCache) {
+ familyCache.put(familyName, result);
+ }
+ return result;
+ }
+
+ protected abstract Family internalCreateComponentFamily(String familyName,
+ Profile componentProfile, String description, License license,
+ SharingPolicy sharingPolicy) throws ComponentException;
+
+ @Override
+ public final void removeComponentFamily(Family componentFamily)
+ throws ComponentException {
+ if (componentFamily != null) {
+ checkFamilyCache();
+ synchronized (familyCache) {
+ familyCache.remove(componentFamily.getName());
+ }
+ internalRemoveComponentFamily(componentFamily);
+ }
+ }
+
+ protected abstract void internalRemoveComponentFamily(Family componentFamily)
+ throws ComponentException;
+
+ @Override
+ public final URL getRegistryBase() {
+ return registryBase;
+ }
+
+ @Override
+ public final String getRegistryBaseString() {
+ String urlString = getRegistryBase().toString();
+ if (urlString.endsWith("/"))
+ urlString = urlString.substring(0, urlString.length() - 1);
+ return urlString;
+ }
+
+ private void checkProfileCache() throws ComponentException {
+ synchronized (profileCache) {
+ if (profileCache.isEmpty())
+ populateProfileCache();
+ }
+ }
+
+ protected abstract void populateProfileCache() throws ComponentException;
+
+ @Override
+ public final List<Profile> getComponentProfiles() throws ComponentException {
+ checkProfileCache();
+ return profileCache;
+ }
+
+ @Override
+ public final Profile getComponentProfile(String id)
+ throws ComponentException {
+ // TODO use a map instead of a *linear search*...
+ for (Profile p : getComponentProfiles())
+ if (p.getId().equals(id))
+ return p;
+ return null;
+ }
+
+ @Override
+ public final Profile addComponentProfile(Profile componentProfile,
+ License license, SharingPolicy sharingPolicy)
+ throws ComponentException {
+ if (componentProfile == null) {
+ throw new ComponentException("componentProfile is null");
+ }
+ Profile result = null;
+ checkProfileCache();
+ for (Profile p : getComponentProfiles())
+ if (p.getId().equals(componentProfile.getId())) {
+ result = p;
+ break;
+ }
+
+ if (result == null) {
+ result = internalAddComponentProfile(componentProfile, license,
+ sharingPolicy);
+ synchronized (profileCache) {
+ profileCache.add(result);
+ }
+ }
+ return result;
+ }
+
+ protected abstract Profile internalAddComponentProfile(
+ Profile componentProfile, License license,
+ SharingPolicy sharingPolicy) throws ComponentException;
+
+ private void checkPermissionCache() {
+ synchronized (permissionCache) {
+ if (permissionCache.isEmpty())
+ populatePermissionCache();
+ }
+ }
+
+ protected abstract void populatePermissionCache();
+
+ @Override
+ public final List<SharingPolicy> getPermissions() throws ComponentException {
+ checkPermissionCache();
+ return permissionCache;
+ }
+
+ private void checkLicenseCache() {
+ synchronized (licenseCache) {
+ if (licenseCache.isEmpty())
+ populateLicenseCache();
+ }
+ }
+
+ protected abstract void populateLicenseCache();
+
+ @Override
+ public final List<License> getLicenses() throws ComponentException {
+ checkLicenseCache();
+ return licenseCache;
+ }
+
+ protected License getLicenseByAbbreviation(String licenseString)
+ throws ComponentException {
+ checkLicenseCache();
+ for (License l : getLicenses())
+ if (l.getAbbreviation().equals(licenseString))
+ return l;
+ return null;
+ }
+
+ @Override
+ public abstract License getPreferredLicense() throws ComponentException;
+
+ @Override
+ public abstract Set<Version.ID> searchForComponents(String prefixString,
+ String text) throws ComponentException;
+
+ @Override
+ public String toString() {
+ String[] names = getClass().getName().split("\\.");
+ return names[names.length-1] + ": " + registryBase;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentUtil.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentUtil.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentUtil.java
new file mode 100644
index 0000000..cc31f05
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentUtil.java
@@ -0,0 +1,130 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import java.net.URL;
+import java.util.HashMap;
+import java.util.Map;
+
+import io.github.taverna_extras.component.api.Component;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.ComponentFactory;
+import io.github.taverna_extras.component.api.Family;
+import io.github.taverna_extras.component.api.Registry;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.profile.Profile;
+import io.github.taverna_extras.component.profile.BaseProfileLocator;
+import io.github.taverna_extras.component.profile.ComponentProfileImpl;
+import io.github.taverna_extras.component.registry.local.LocalComponentRegistryFactory;
+import io.github.taverna_extras.component.registry.standard.NewComponentRegistryFactory;
+import org.springframework.beans.factory.annotation.Required;
+
+/**
+ * @author alanrw
+ * @author dkf
+ */
+public class ComponentUtil implements ComponentFactory {
+ private NewComponentRegistryFactory netLocator;
+ private BaseProfileLocator base;
+ private LocalComponentRegistryFactory fileLocator;
+
+ private final Map<String, Registry> cache = new HashMap<>();
+
+ @Required
+ public void setNetworkLocator(NewComponentRegistryFactory locator) {
+ this.netLocator = locator;
+ }
+
+ @Required
+ public void setFileLocator(LocalComponentRegistryFactory fileLocator) {
+ this.fileLocator = fileLocator;
+ }
+
+ @Required
+ public void setBaseLocator(BaseProfileLocator base) {
+ this.base = base;
+ }
+
+ @Override
+ public Registry getRegistry(URL registryBase) throws ComponentException {
+ Registry registry = cache.get(registryBase.toString());
+ if (registry != null)
+ return registry;
+
+ if (registryBase.getProtocol().startsWith("http")) {
+ if (!netLocator.verifyBase(registryBase))
+ throw new ComponentException(
+ "Unable to establish credentials for " + registryBase);
+ registry = netLocator.getComponentRegistry(registryBase);
+ } else
+ registry = fileLocator.getComponentRegistry(registryBase);
+ cache.put(registryBase.toString(), registry);
+ return registry;
+ }
+
+ @Override
+ public Family getFamily(URL registryBase, String familyName)
+ throws ComponentException {
+ return getRegistry(registryBase).getComponentFamily(familyName);
+ }
+
+ @Override
+ public Component getComponent(URL registryBase, String familyName,
+ String componentName) throws ComponentException {
+ return getRegistry(registryBase).getComponentFamily(familyName)
+ .getComponent(componentName);
+ }
+
+ @Override
+ public Version getVersion(URL registryBase, String familyName,
+ String componentName, Integer componentVersion)
+ throws ComponentException {
+ return getRegistry(registryBase).getComponentFamily(familyName)
+ .getComponent(componentName)
+ .getComponentVersion(componentVersion);
+ }
+
+ @Override
+ public Version getVersion(Version.ID ident) throws ComponentException {
+ return getVersion(ident.getRegistryBase(), ident.getFamilyName(),
+ ident.getComponentName(), ident.getComponentVersion());
+ }
+
+ @Override
+ public Component getComponent(Version.ID ident) throws ComponentException {
+ return getComponent(ident.getRegistryBase(), ident.getFamilyName(),
+ ident.getComponentName());
+ }
+
+ @Override
+ public Profile getProfile(URL url) throws ComponentException {
+ Profile p = new ComponentProfileImpl(url, base);
+ p.getProfileDocument(); // force immediate loading
+ return p;
+ }
+
+ @Override
+ public Profile getBaseProfile() throws ComponentException {
+ return base.getProfile();
+ }
+
+ public BaseProfileLocator getBaseProfileLocator() {
+ return base;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersion.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersion.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersion.java
new file mode 100644
index 0000000..ab95218
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersion.java
@@ -0,0 +1,77 @@
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import io.github.taverna_extras.component.api.Component;
+import io.github.taverna_extras.component.api.ComponentException;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+public abstract class ComponentVersion implements
+ io.github.taverna_extras.component.api.Version {
+ private Integer versionNumber;
+ private String description;
+ private Component component;
+
+ protected ComponentVersion(Component component) {
+ this.component = component;
+ }
+
+ @Override
+ public final synchronized Integer getVersionNumber() {
+ if (versionNumber == null)
+ versionNumber = internalGetVersionNumber();
+ return versionNumber;
+ }
+
+ protected abstract Integer internalGetVersionNumber();
+
+ @Override
+ public final synchronized String getDescription() {
+ if (description == null)
+ description = internalGetDescription();
+
+ return description;
+ }
+
+ protected abstract String internalGetDescription();
+
+ @Override
+ public final synchronized WorkflowBundle getImplementation()
+ throws ComponentException {
+ // Cached in dataflow cache
+ return internalGetImplementation();
+ }
+
+ protected abstract WorkflowBundle internalGetImplementation()
+ throws ComponentException;
+
+ @Override
+ public final Component getComponent() {
+ return component;
+ }
+
+ @Override
+ public ID getID() {
+ Component c = getComponent();
+ return new ComponentVersionIdentification(c.getRegistry()
+ .getRegistryBase(), c.getFamily().getName(), c.getName(),
+ getVersionNumber());
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersionIdentification.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersionIdentification.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersionIdentification.java
new file mode 100644
index 0000000..4cecab5
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/ComponentVersionIdentification.java
@@ -0,0 +1,212 @@
+
+package io.github.taverna_extras.component.registry;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import java.net.URL;
+
+import io.github.taverna_extras.component.api.Family;
+import io.github.taverna_extras.component.api.Registry;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.Version.ID;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ComponentVersionIdentification implements
+ io.github.taverna_extras.component.api.Version.ID {
+ private static final long serialVersionUID = 1768548650702925916L;
+ private URL registryBase;
+ private String familyName;
+ private String componentName;
+ private Integer componentVersion;
+
+ public ComponentVersionIdentification(URL registryBase, String familyName,
+ String componentName, Integer componentVersion) {
+ super();
+ this.registryBase = registryBase;
+ this.familyName = familyName;
+ this.componentName = componentName;
+ this.componentVersion = componentVersion;
+ }
+
+ public ComponentVersionIdentification(Registry registry, Family family,
+ io.github.taverna_extras.component.api.Component component, Integer version) {
+ this(registry.getRegistryBase(), family.getName(), component.getName(), version);
+ }
+
+ public ComponentVersionIdentification(Version.ID toBeCopied) {
+ this.registryBase = toBeCopied.getRegistryBase();
+ this.familyName = toBeCopied.getFamilyName();
+ this.componentName = toBeCopied.getComponentName();
+ this.componentVersion = toBeCopied.getComponentVersion();
+ }
+
+ /**
+ * @return the registryBase
+ */
+ @Override
+ public URL getRegistryBase() {
+ return registryBase;
+ }
+
+ /**
+ * @return the familyName
+ */
+ @Override
+ public String getFamilyName() {
+ return familyName;
+ }
+
+ /**
+ * @return the componentName
+ */
+ @Override
+ public String getComponentName() {
+ return componentName;
+ }
+
+ /**
+ * @return the componentVersion
+ */
+ @Override
+ public Integer getComponentVersion() {
+ return componentVersion;
+ }
+
+ /**
+ * @param componentVersion
+ * the componentVersion to set
+ */
+ public void setComponentVersion(Integer componentVersion) {
+ this.componentVersion = componentVersion;
+ }
+
+ /**
+ * @param registryBase
+ * the registryBase to set
+ */
+ public void setRegistryBase(URL registryBase) {
+ this.registryBase = registryBase;
+ }
+
+ /**
+ * @param familyName
+ * the familyName to set
+ */
+ public void setFamilyName(String familyName) {
+ this.familyName = familyName;
+ }
+
+ /**
+ * @param componentName
+ * the componentName to set
+ */
+ public void setComponentName(String componentName) {
+ this.componentName = componentName;
+ }
+
+ @Override
+ public int hashCode() {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result
+ + ((componentName == null) ? 0 : componentName.hashCode());
+ result = prime
+ * result
+ + ((componentVersion == null) ? 0 : componentVersion.hashCode());
+ result = prime * result
+ + ((familyName == null) ? 0 : familyName.hashCode());
+ result = prime * result
+ + ((registryBase == null) ? 0 : registryBase.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ComponentVersionIdentification other = (ComponentVersionIdentification) obj;
+ if (componentName == null) {
+ if (other.componentName != null)
+ return false;
+ } else if (!componentName.equals(other.componentName))
+ return false;
+ if (componentVersion == null) {
+ if (other.componentVersion != null)
+ return false;
+ } else if (!componentVersion.equals(other.componentVersion))
+ return false;
+ if (familyName == null) {
+ if (other.familyName != null)
+ return false;
+ } else if (!familyName.equals(other.familyName))
+ return false;
+ if (registryBase == null) {
+ if (other.registryBase != null)
+ return false;
+ } else if (!registryBase.toString().equals(other.registryBase.toString()))
+ return false;
+ return true;
+ }
+
+ @Override
+ public String toString() {
+ return getComponentName() + " V. " + getComponentVersion()
+ + " in family " + getFamilyName() + " on "
+ + getRegistryBase().toExternalForm();
+ }
+
+ @Override
+ public boolean mostlyEqualTo(ID id) {
+ if (this == id)
+ return true;
+ if (id == null)
+ return false;
+ if (getClass() != id.getClass())
+ return false;
+ ComponentVersionIdentification other = (ComponentVersionIdentification) id;
+ if (componentName == null) {
+ if (other.componentName != null)
+ return false;
+ } else if (!componentName.equals(other.componentName))
+ return false;
+ if (familyName == null) {
+ if (other.familyName != null)
+ return false;
+ } else if (!familyName.equals(other.familyName))
+ return false;
+ if (registryBase == null) {
+ if (other.registryBase != null)
+ return false;
+ } else if (!registryBase.toString().equals(other.registryBase.toString()))
+ return false;
+ return true;
+ }
+
+ @Override
+ public boolean mostlyEqualTo(io.github.taverna_extras.component.api.Component c) {
+ return mostlyEqualTo(new ComponentVersionIdentification(c.getRegistry(), c.getFamily(), c, 0));
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponent.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponent.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponent.java
new file mode 100644
index 0000000..697f57f
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponent.java
@@ -0,0 +1,149 @@
+package io.github.taverna_extras.component.registry.local;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+
+import static org.apache.commons.io.FileUtils.readFileToString;
+import static org.apache.commons.io.FileUtils.writeStringToFile;
+import static org.apache.log4j.Logger.getLogger;
+import static io.github.taverna_extras.component.registry.local.LocalComponentRegistry.ENC;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.NoSuchElementException;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Family;
+import io.github.taverna_extras.component.api.Registry;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.registry.Component;
+import io.github.taverna_extras.component.utils.SystemUtils;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+/**
+ * @author alanrw
+ *
+ */
+class LocalComponent extends Component {
+ static final String COMPONENT_FILENAME = "dataflow.t2flow";
+ private final File componentDir;
+ private final LocalComponentRegistry registry;
+ private final LocalComponentFamily family;
+ private static Logger logger = getLogger(LocalComponent.class);
+ private SystemUtils system;
+
+ public LocalComponent(File componentDir, LocalComponentRegistry registry,
+ LocalComponentFamily family, SystemUtils system) {
+ super(componentDir);
+ this.system = system;
+ this.componentDir = componentDir;
+ this.registry = registry;
+ this.family = family;
+ }
+
+ @Override
+ protected final Version internalAddVersionBasedOn(WorkflowBundle bundle,
+ String revisionComment) throws ComponentException {
+ Integer nextVersionNumber = 1;
+ try {
+ nextVersionNumber = getComponentVersionMap().lastKey() + 1;
+ } catch (NoSuchElementException e) {
+ // This is OK
+ }
+ File newVersionDir = new File(componentDir,
+ nextVersionNumber.toString());
+ newVersionDir.mkdirs();
+ LocalComponentVersion newComponentVersion = new LocalComponentVersion(
+ this, newVersionDir, system);
+ try {
+ system.saveBundle(bundle, new File(newVersionDir,
+ COMPONENT_FILENAME));
+ } catch (Exception e) {
+ throw new ComponentException("Unable to save component version", e);
+ }
+ File revisionCommentFile = new File(newVersionDir, "description");
+ try {
+ writeStringToFile(revisionCommentFile, revisionComment, ENC);
+ } catch (IOException e) {
+ throw new ComponentException("Could not write out description", e);
+ }
+
+ return newComponentVersion;
+ }
+
+ @Override
+ protected final String internalGetName() {
+ return componentDir.getName();
+ }
+
+ @Override
+ protected final void populateComponentVersionMap() {
+ for (File subFile : componentDir.listFiles())
+ try {
+ if (subFile.isDirectory())
+ versionMap.put(Integer.valueOf(subFile.getName()),
+ new LocalComponentVersion(this, subFile, system));
+ } catch (NumberFormatException e) {
+ // Ignore
+ }
+ }
+
+ @Override
+ public int hashCode() {
+ return 31 + ((componentDir == null) ? 0 : componentDir.hashCode());
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ LocalComponent other = (LocalComponent) obj;
+ if (componentDir == null)
+ return (other.componentDir == null);
+ return componentDir.equals(other.componentDir);
+ }
+
+ @Override
+ protected final String internalGetDescription() {
+ File descriptionFile = new File(componentDir, "description");
+ try {
+ if (descriptionFile.isFile())
+ return readFileToString(descriptionFile);
+ } catch (IOException e) {
+ logger.error("failed to get description from " + descriptionFile, e);
+ }
+ return "";
+ }
+
+ @Override
+ public Registry getRegistry() {
+ return registry;
+ }
+
+ @Override
+ public Family getFamily() {
+ return family;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponentFamily.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponentFamily.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponentFamily.java
new file mode 100644
index 0000000..b9a692c
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/registry/local/LocalComponentFamily.java
@@ -0,0 +1,155 @@
+package io.github.taverna_extras.component.registry.local;
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+import static org.apache.commons.io.FileUtils.deleteDirectory;
+import static org.apache.commons.io.FileUtils.readFileToString;
+import static org.apache.commons.io.FileUtils.writeStringToFile;
+import static org.apache.log4j.Logger.getLogger;
+import static io.github.taverna_extras.component.registry.local.LocalComponentRegistry.ENC;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.Component;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.profile.Profile;
+import io.github.taverna_extras.component.registry.ComponentFamily;
+import io.github.taverna_extras.component.registry.ComponentUtil;
+import io.github.taverna_extras.component.utils.SystemUtils;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
+/**
+ * @author alanrw
+ *
+ */
+class LocalComponentFamily extends ComponentFamily {
+ private static Logger logger = getLogger(LocalComponentFamily.class);
+ private static final String PROFILE = "profile";
+
+ private final File componentFamilyDir;
+ private SystemUtils system;
+
+ public LocalComponentFamily(LocalComponentRegistry parentRegistry,
+ File componentFamilyDir, ComponentUtil util, SystemUtils system) {
+ super(parentRegistry, util);
+ this.componentFamilyDir = componentFamilyDir;
+ this.system = system;
+ }
+
+ @Override
+ protected final Profile internalGetComponentProfile()
+ throws ComponentException {
+ LocalComponentRegistry parentRegistry = (LocalComponentRegistry) getComponentRegistry();
+ File profileFile = new File(componentFamilyDir, PROFILE);
+ String profileName;
+ try {
+ profileName = readFileToString(profileFile, ENC);
+ } catch (IOException e) {
+ throw new ComponentException("Unable to read profile name", e);
+ }
+ for (Profile p : parentRegistry.getComponentProfiles())
+ if (p.getName().equals(profileName))
+ return p;
+ return null;
+ }
+
+ @Override
+ protected void populateComponentCache() throws ComponentException {
+ for (File subFile : componentFamilyDir.listFiles()) {
+ if (!subFile.isDirectory())
+ continue;
+ LocalComponent newComponent = new LocalComponent(subFile,
+ (LocalComponentRegistry) getComponentRegistry(), this,
+ system);
+ componentCache.put(newComponent.getName(), newComponent);
+ }
+ }
+
+ @Override
+ protected final String internalGetName() {
+ return componentFamilyDir.getName();
+ }
+
+ @Override
+ protected final Version internalCreateComponentBasedOn(
+ String componentName, String description, WorkflowBundle bundle)
+ throws ComponentException {
+ File newSubFile = new File(componentFamilyDir, componentName);
+ if (newSubFile.exists())
+ throw new ComponentException("Component already exists");
+ newSubFile.mkdirs();
+ File descriptionFile = new File(newSubFile, "description");
+ try {
+ writeStringToFile(descriptionFile, description, ENC);
+ } catch (IOException e) {
+ throw new ComponentException("Could not write out description", e);
+ }
+ LocalComponent newComponent = new LocalComponent(newSubFile,
+ (LocalComponentRegistry) getComponentRegistry(), this, system);
+
+ return newComponent.addVersionBasedOn(bundle, "Initial version");
+ }
+
+ @Override
+ public int hashCode() {
+ return 31 + ((componentFamilyDir == null) ? 0 : componentFamilyDir
+ .hashCode());
+ }
+
+ @Override
+ public boolean equals(Object obj) {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ LocalComponentFamily other = (LocalComponentFamily) obj;
+ if (componentFamilyDir == null)
+ return (other.componentFamilyDir == null);
+ return componentFamilyDir.equals(other.componentFamilyDir);
+ }
+
+ @Override
+ protected final String internalGetDescription() {
+ File descriptionFile = new File(componentFamilyDir, "description");
+ try {
+ if (descriptionFile.isFile())
+ return readFileToString(descriptionFile);
+ } catch (IOException e) {
+ logger.error("failed to get description from " + descriptionFile, e);
+ }
+ return "";
+ }
+
+ @Override
+ protected final void internalRemoveComponent(Component component)
+ throws ComponentException {
+ File componentDir = new File(componentFamilyDir, component.getName());
+ try {
+ deleteDirectory(componentDir);
+ } catch (IOException e) {
+ throw new ComponentException("Unable to delete component", e);
+ }
+ }
+}