http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java deleted file mode 100644 index 745876d..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/WrappedWorkflow.java +++ /dev/null @@ -1,169 +0,0 @@ -/* - */ -package org.taverna.server.master.soap; -/* - * 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 javax.xml.bind.annotation.XmlAccessType.NONE; -import static org.apache.commons.io.IOUtils.closeQuietly; - -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; -import java.io.PipedInputStream; -import java.io.PipedOutputStream; - -import javax.activation.DataHandler; -import javax.activation.DataSource; -import javax.xml.bind.annotation.XmlAccessorType; -import javax.xml.bind.annotation.XmlMimeType; -import javax.xml.bind.annotation.XmlTransient; -import javax.xml.bind.annotation.XmlType; - -import org.taverna.server.master.common.Workflow; - -import org.apache.taverna.scufl2.api.io.ReaderException; -import org.apache.taverna.scufl2.api.io.WorkflowBundleIO; -import org.apache.taverna.scufl2.api.io.WriterException; - -/** - * An MTOM-capable description of how to transfer the contents of a file. - * - * @author Donal Fellows - */ -@XmlType(name = "WorkflowReference") -@XmlAccessorType(NONE) -public class WrappedWorkflow { - @XmlMimeType("application/octet-stream") - // JAXB bug: must be this - public DataHandler workflowData; - Workflow workflow; - - /** - * Initialize the contents of this descriptor from the given file and - * content type. - * - * @param workflow - * The workflow that is to be reported. - */ - public void setWorkflow(Workflow workflow) { - workflowData = new DataHandler(new WorkflowSource(workflow)); - } - - @XmlTransient - public Workflow getWorkflow() throws IOException { - if (workflow != null) - return workflow; - try { - return new Workflow(new WorkflowBundleIO().readBundle( - workflowData.getInputStream(), null)); - } catch (ReaderException e) { - throw new IOException("problem converting to scufl2 bundle", e); - } - } -} - -/** - * A data source that knows how to deliver a workflow. - * - * @author Donal Fellows - */ -class WorkflowSource implements DataSource { - WorkflowSource(Workflow workflow) { - this.wf = workflow; - this.io = new WorkflowBundleIO(); - } - - Workflow wf; - final WorkflowBundleIO io; - - @Override - public String getContentType() { - return wf.getPreferredContentType().getContentType(); - } - - @Override - public String getName() { - switch (wf.getPreferredContentType()) { - case SCUFL2: - return "workflow.scufl2"; - case T2FLOW: - return "workflow.t2flow"; - default: - return "workflow"; - } - } - - @Override - public InputStream getInputStream() throws IOException { - PipedInputStream is = new PipedInputStream(); - final OutputStream os = new PipedOutputStream(is); - new Worker() { - @Override - public void doWork() throws WriterException, IOException { - io.writeBundle(wf.getScufl2Workflow(), os, wf - .getPreferredContentType().getContentType()); - } - - @Override - public void doneWork() { - closeQuietly(os); - } - }; - return is; - } - - @Override - public OutputStream getOutputStream() throws IOException { - final PipedInputStream is = new PipedInputStream(); - OutputStream os = new PipedOutputStream(is); - new Worker() { - @Override - public void doWork() throws IOException, ReaderException { - wf = new Workflow(io.readBundle(is, null)); - } - - @Override - public void doneWork() { - closeQuietly(is); - } - }; - return os; - } - - static abstract class Worker extends Thread { - public Worker() { - setDaemon(true); - start(); - } - - public abstract void doWork() throws Exception; - - public abstract void doneWork(); - - @Override - public void run() { - try { - doWork(); - } catch (Exception e) { - // do nothing. - } finally { - doneWork(); - } - } - } -} \ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java deleted file mode 100644 index 5b2d261..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/ZippedDirectory.java +++ /dev/null @@ -1,102 +0,0 @@ -/* - */ -package org.taverna.server.master.soap; -/* - * 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.taverna.server.master.api.ContentTypes.APPLICATION_ZIP_TYPE; - -import java.io.IOException; -import java.io.InputStream; -import java.io.OutputStream; - -import javax.activation.DataHandler; -import javax.activation.DataSource; -import javax.activation.UnsupportedDataTypeException; -import javax.xml.bind.annotation.XmlElement; -import javax.xml.bind.annotation.XmlMimeType; -import javax.xml.bind.annotation.XmlType; - -import org.taverna.server.master.exceptions.FilesystemAccessException; -import org.taverna.server.master.interfaces.Directory; - -/** - * An MTOM-capable description of how to transfer the zipped contents of a - * directory. - * - * @author Donal Fellows - * @see Directory#getContentsAsZip() - */ -@XmlType(name = "ZippedDirectory") -public class ZippedDirectory { - @XmlElement - public String name; - @XmlMimeType("application/octet-stream") - // JAXB bug: must be this - public DataHandler fileData; - - public ZippedDirectory() { - } - - /** - * Initialise the contents of this descriptor from the given directory. - * - * @param dir - * The directory that is to be reported. - */ - public ZippedDirectory(Directory dir) { - name = dir.getFullName(); - fileData = new DataHandler(new ZipSource(dir)); - } -} - -/** - * A data source that knows how to communicate with the Taverna Server back-end. - * - * @author Donal Fellows - */ -class ZipSource implements DataSource { - ZipSource(Directory d) { - this.d = d; - } - - private final Directory d; - - @Override - public String getContentType() { - return APPLICATION_ZIP_TYPE.toString(); - } - - @Override - public String getName() { - return d.getName(); - } - - @Override - public InputStream getInputStream() throws IOException { - try { - return d.getContentsAsZip(); - } catch (FilesystemAccessException e) { - throw new IOException(e); - } - } - - @Override - public OutputStream getOutputStream() throws IOException { - throw new UnsupportedDataTypeException(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java deleted file mode 100644 index cd753b7..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/soap/package-info.java +++ /dev/null @@ -1,44 +0,0 @@ -/* - */ -/** - * This package contains the SOAP interface to Taverna Server. - * @author Donal Fellows - */ -@XmlSchema(namespace = SERVER_SOAP, elementFormDefault = QUALIFIED, attributeFormDefault = QUALIFIED, xmlns = { - @XmlNs(prefix = "xlink", namespaceURI = XLINK), - @XmlNs(prefix = "ts", namespaceURI = SERVER), - @XmlNs(prefix = "ts-rest", namespaceURI = SERVER_REST), - @XmlNs(prefix = "ts-soap", namespaceURI = SERVER_SOAP), - @XmlNs(prefix = "port", namespaceURI = DATA), - @XmlNs(prefix = "feed", namespaceURI = FEED), - @XmlNs(prefix = "admin", namespaceURI = ADMIN) }) -package org.taverna.server.master.soap; -/* - * 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 javax.xml.bind.annotation.XmlNsForm.QUALIFIED; -import static org.taverna.server.master.common.Namespaces.ADMIN; -import static org.taverna.server.master.common.Namespaces.FEED; -import static org.taverna.server.master.common.Namespaces.SERVER; -import static org.taverna.server.master.common.Namespaces.SERVER_REST; -import static org.taverna.server.master.common.Namespaces.SERVER_SOAP; -import static org.taverna.server.master.common.Namespaces.XLINK; -import static org.taverna.server.port_description.Namespaces.DATA; - -import javax.xml.bind.annotation.XmlNs; -import javax.xml.bind.annotation.XmlSchema; - http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java deleted file mode 100644 index b1f0602..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecord.java +++ /dev/null @@ -1,130 +0,0 @@ -/* - */ -package org.taverna.server.master.usage; -/* - * 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.Date; - -import javax.jdo.annotations.Column; -import javax.jdo.annotations.Index; -import javax.jdo.annotations.PersistenceCapable; -import javax.jdo.annotations.Persistent; -import javax.jdo.annotations.PrimaryKey; -import javax.jdo.annotations.Queries; -import javax.jdo.annotations.Query; -import javax.xml.bind.JAXBException; - -import org.apache.taverna.server.usagerecord.JobUsageRecord; - -/** - * A usage record as recorded in the database. - * - * @author Donal Fellows - */ -@PersistenceCapable(table = "USAGE_RECORD_LOG", schema = "UR", cacheable = "true") -@Queries({ @Query(name = "allByDate", value = "SELECT USAGE_RECORD FROM UR.USAGE_RECORD_LOG ORDER BY CREATE_DATE", resultClass = String.class, unmodifiable = "true", unique = "false", language = "SQL") }) -public class UsageRecord { - /** - * Create an empty usage record database entry. - */ - public UsageRecord() { - } - - /** - * Create a usage record database entry that is populated from the given UR. - * - * @param usageRecord - * The originating usage record. - * @throws JAXBException - * If deserialization of the record fails. - */ - public UsageRecord(String usageRecord) throws JAXBException { - JobUsageRecord jur = JobUsageRecord.unmarshal(usageRecord); - setUsageRecord(usageRecord); - setCreateDate(jur.getRecordIdentity().getCreateTime() - .toGregorianCalendar().getTime()); - setId(jur.getRecordIdentity().getRecordId()); - setUserid(jur.getUserIdentity().get(0).getLocalUserId()); - } - - /** - * Create a usage record database entry that is populated from the given UR. - * - * @param usageRecord - * The originating usage record. - * @throws JAXBException - * If serialization of the record fails. - */ - public UsageRecord(JobUsageRecord usageRecord) throws JAXBException { - setUsageRecord(usageRecord.marshal()); - setCreateDate(usageRecord.getRecordIdentity().getCreateTime() - .toGregorianCalendar().getTime()); - setId(usageRecord.getRecordIdentity().getRecordId()); - setUserid(usageRecord.getUserIdentity().get(0).getLocalUserId()); - } - - @PrimaryKey - @Column(name = "ID", length = 40) - private String id; - - @Persistent - @Index(name = "USERID_IDX") - @Column(name = "USERID", length = 24) - private String userid; - - @Persistent - @Index(name = "CREATE_IDX") - @Column(name = "CREATE_DATE") - private Date createDate; - - @Persistent - @Column(name = "USAGE_RECORD", jdbcType = "CLOB") - private String usageRecord; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getUserid() { - return userid; - } - - public void setUserid(String userid) { - this.userid = userid; - } - - public Date getCreateDate() { - return createDate; - } - - public void setCreateDate(Date createDate) { - this.createDate = createDate; - } - - public String getUsageRecord() { - return usageRecord; - } - - public void setUsageRecord(String usageRecord) { - this.usageRecord = usageRecord; - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java deleted file mode 100644 index 18aeb3b..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java +++ /dev/null @@ -1,178 +0,0 @@ -/* - */ -package org.taverna.server.master.usage; -/* - * 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.logging.LogFactory.getLog; - -import java.io.FileWriter; -import java.io.IOException; -import java.io.PrintWriter; -import java.util.ArrayList; -import java.util.List; - -import javax.annotation.PreDestroy; -import javax.xml.bind.JAXBException; - -import org.apache.commons.logging.Log; -import org.apache.taverna.server.usagerecord.JobUsageRecord; -import org.springframework.beans.factory.annotation.Required; -import org.taverna.server.master.api.ManagementModel; -import org.taverna.server.master.utils.Contextualizer; -import org.taverna.server.master.utils.JDOSupport; - -/** - * A simple state-aware writer of usage records. It just appends them, one by - * one, to the file whose name is stored in the state. - * - * @author Donal Fellows - */ -public class UsageRecordRecorder extends JDOSupport<UsageRecord> { - private Log log = getLog("Taverna.Server.Webapp"); - public UsageRecordRecorder() { - super(UsageRecord.class); - } - - private String logFile = null; - private boolean disableDB = false; - private ManagementModel state; - private Contextualizer contextualizer; - private String logDestination; - private PrintWriter writer; - private Object lock = new Object(); - private UsageRecordRecorder self; - - /** - * @param state - * the state to set - */ - @Required - public void setState(ManagementModel state) { - this.state = state; - } - - @Required - public void setSelf(UsageRecordRecorder self) { - this.self = self; - } - - public void setLogFile(String logFile) { - this.logFile = (logFile == null || logFile.equals("none")) ? null : logFile; - } - - public void setDisableDB(String disable) { - disableDB = "yes".equalsIgnoreCase(disable); - } - - /** - * @param contextualizer - * the system's contextualizer, used to allow making the UR dump - * file be placed relative to the webapp. - */ - @Required - public void setContextualizer(Contextualizer contextualizer) { - this.contextualizer = contextualizer; - } - - /** - * Accept a usage record for recording. - * - * @param usageRecord - * The serialized usage record to record. - */ - public void storeUsageRecord(String usageRecord) { - String logfile = state.getUsageRecordLogFile(); - if (logfile == null) - logfile = this.logFile; - if (logfile != null) { - logfile = contextualizer.contextualize(logfile); - synchronized (lock) { - if (!logfile.equals(logDestination)) { - if (writer != null) { - writer.close(); - writer = null; - } - try { - writer = new PrintWriter(new FileWriter(logfile)); - logDestination = logfile; - } catch (IOException e) { - log.warn("failed to open usage record log file", e); - } - } - if (writer != null) { - writer.println(usageRecord); - writer.flush(); - } - } - } - - if (!disableDB) - saveURtoDB(usageRecord); - } - - /** - * How to save a usage record to the database. - * - * @param usageRecord - * The serialized usage record to save. - */ - protected void saveURtoDB(String usageRecord) { - UsageRecord ur; - try { - ur = new UsageRecord(usageRecord); - } catch (JAXBException e) { - log.warn("failed to deserialize usage record", e); - return; - } - - try { - self.saveURtoDB(ur); - } catch (RuntimeException e) { - log.warn("failed to save UR to database", e); - } - } - - @WithinSingleTransaction - public void saveURtoDB(UsageRecord ur) { - persist(ur); - } - - @WithinSingleTransaction - public List<JobUsageRecord> getUsageRecords() { - List<String> urs = allByDate(); - List<JobUsageRecord> result = new ArrayList<>(); - for (String ur : urs) - try { - result.add(JobUsageRecord.unmarshal(ur)); - } catch (JAXBException e) { - log.warn("failed to unmarshal UR", e); - } - return result; - } - - @SuppressWarnings("unchecked") - private List<String> allByDate() { - return (List<String>) namedQuery("allByDate").execute(); - } - - @PreDestroy - public void close() { - if (writer != null) - writer.close(); - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java deleted file mode 100644 index a7fe733..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/usage/package-info.java +++ /dev/null @@ -1,22 +0,0 @@ -/* - */ -/** - * Resource usage recording mechanism. - */ -package org.taverna.server.master.usage; -/* - * 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. - */ http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java deleted file mode 100644 index 4452935..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimeLogger.java +++ /dev/null @@ -1,100 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.String.format; -import static java.lang.System.nanoTime; -import static java.lang.annotation.ElementType.METHOD; -import static java.lang.annotation.RetentionPolicy.RUNTIME; -import static org.apache.commons.logging.LogFactory.getLog; -import static org.taverna.server.master.TavernaServer.JMX_ROOT; - -import java.lang.annotation.Documented; -import java.lang.annotation.Retention; -import java.lang.annotation.Target; - -import org.apache.commons.logging.Log; -import org.aspectj.lang.ProceedingJoinPoint; -import org.aspectj.lang.annotation.Around; -import org.aspectj.lang.annotation.Aspect; -import org.springframework.jmx.export.annotation.ManagedAttribute; -import org.springframework.jmx.export.annotation.ManagedResource; -import org.taverna.server.master.common.version.Version; - -/** - * This class is responsible for timing all invocations of publicly-exposed - * methods of the webapp. It's connected to the webapp through an AspectJ-style - * pointcut that targets a custom annotation. - * - * @author Donal Fellows - */ -@Aspect -@ManagedResource(objectName = JMX_ROOT + "PerformanceMonitor", description = "The performance monitor for Taverna Server " - + Version.JAVA - + ". Writes to application log using the category 'Taverna.Server.Performance'.") -public class CallTimeLogger { - private long threshold = 4000000; - private Log log = getLog("Taverna.Server.Performance"); - - @ManagedAttribute(description = "Threshold beneath which monitored call times are not logged. In nanoseconds.") - public long getThreshold() { - return threshold; - } - - @ManagedAttribute(description = "Threshold beneath which monitored call times are not logged. In nanoseconds.") - public void setThreshold(long threshold) { - this.threshold = threshold; - } - - /** - * The timer for this aspect. The wrapped invocation will be timed, and a - * log message written if the configured threshold is exceeded. - * - * @param call - * The call being wrapped. - * @return The result of the call. - * @throws Throwable - * If anything goes wrong with the wrapped call. - * @see System#nanoTime() - */ - @Around("@annotation(org.taverna.server.master.utils.CallTimeLogger.PerfLogged)") - public Object time(ProceedingJoinPoint call) throws Throwable { - long fore = nanoTime(); - try { - return call.proceed(); - } finally { - long aft = nanoTime(); - long elapsed = aft - fore; - if (elapsed > threshold) - log.info(format("call to %s took %.3fms", call.toShortString(), - elapsed / 1000000.0)); - } - } - - /** - * Mark methods that should be counted by the invocation counter. - * - * @author Donal Fellows - */ - @Retention(RUNTIME) - @Documented - @Target(METHOD) - public static @interface PerfLogged { - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java deleted file mode 100644 index d8ad78d..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java +++ /dev/null @@ -1,81 +0,0 @@ -/** - * - */ -package org.taverna.server.master.utils; -/* - * 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.String.format; -import static java.lang.System.nanoTime; -import static org.apache.commons.logging.LogFactory.getLog; - -import java.io.IOException; - -import javax.servlet.Filter; -import javax.servlet.FilterChain; -import javax.servlet.FilterConfig; -import javax.servlet.ServletException; -import javax.servlet.ServletRequest; -import javax.servlet.ServletResponse; -import javax.servlet.http.HttpServletRequest; -import javax.servlet.http.HttpServletResponse; - -import org.apache.commons.logging.Log; - -/** - * Logs the time it takes to service HTTP calls into Taverna Server. - * <p> - * This class is currently not used. - * - * @author Donal Fellows - */ -public class CallTimingFilter implements Filter { - private Log log; - private String name; - - @Override - public void init(FilterConfig filterConfig) throws ServletException { - log = getLog("Taverna.Server.Performance"); - name = filterConfig.getInitParameter("name"); - } - - @Override - public void doFilter(ServletRequest request, ServletResponse response, - FilterChain chain) throws IOException, ServletException { - if (request instanceof HttpServletRequest) - doFilter((HttpServletRequest) request, - (HttpServletResponse) response, chain); - else - chain.doFilter(request, response); - } - - public void doFilter(HttpServletRequest request, - HttpServletResponse response, FilterChain chain) - throws IOException, ServletException { - long start = nanoTime(); - chain.doFilter(request, response); - long elapsedTime = nanoTime() - start; - log.info(format("%s call to %s %s took %.3fms", name, - request.getMethod(), request.getRequestURI(), - elapsedTime / 1000000.0)); - } - - @Override - public void destroy() { - log = null; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java deleted file mode 100644 index 1387e05..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java +++ /dev/null @@ -1,60 +0,0 @@ -package org.taverna.server.master.utils; -/* - * 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.net.URI; -import java.util.ArrayList; -import java.util.List; -import java.util.Map.Entry; -import java.util.Properties; - -import javax.annotation.PostConstruct; - -import org.taverna.server.master.common.Capability; - -/** - * Utility for listing the capabilities supported by this Taverna Server - * installation. - * - * @author Donal Fellows - */ -public class CapabilityLister { - public static final String CAPABILITY_RESOURCE_FILE = "/capabilities.properties"; - private Properties properties = new Properties(); - - @PostConstruct - void loadCapabilities() throws IOException { - try (InputStream is = getClass().getResourceAsStream( - CAPABILITY_RESOURCE_FILE)) { - if (is != null) - properties.load(is); - } - } - - public List<Capability> getCapabilities() { - List<Capability> caps = new ArrayList<>(); - for (Entry<Object, Object> entry : properties.entrySet()) { - Capability c = new Capability(); - c.capability = URI.create(entry.getKey().toString()); - c.version = entry.getValue().toString(); - caps.add(c); - } - return caps; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java deleted file mode 100644 index 76ef017..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java +++ /dev/null @@ -1,212 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.Arrays.asList; -import static java.util.Collections.unmodifiableList; - -import java.io.IOException; -import java.net.URI; -import java.security.GeneralSecurityException; -import java.security.KeyManagementException; -import java.security.KeyStore; -import java.security.KeyStoreException; -import java.security.NoSuchAlgorithmException; -import java.security.cert.CertificateException; -import java.security.cert.X509Certificate; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import javax.net.ssl.SSLContext; -import javax.net.ssl.SSLException; -import javax.net.ssl.SSLSocket; -import javax.net.ssl.SSLSocketFactory; -import javax.net.ssl.TrustManager; -import javax.net.ssl.TrustManagerFactory; -import javax.net.ssl.X509TrustManager; -import javax.xml.ws.Holder; - -/** - * Obtains the certificate chain for an arbitrary SSL service. Maintains a - * cache. - * - * @author Donal Fellows - */ -public class CertificateChainFetcher { - public String getProtocol() { - return protocol; - } - - public void setProtocol(String protocol) { - this.protocol = protocol; - } - - public String getKeystoreType() { - return keystoreType; - } - - public void setKeystoreType(String keystoreType) { - this.keystoreType = keystoreType; - } - - public String getAlgorithm() { - return algorithm; - } - - public void setAlgorithm(String algorithm) { - this.algorithm = algorithm; - } - - public int getTimeout() { - return timeout; - } - - public void setTimeout(int timeout) { - this.timeout = timeout; - } - - public void setSecure(boolean secure) { - this.secure = secure; - } - - private boolean secure = true; - private String protocol = "TLS"; - private String keystoreType = KeyStore.getDefaultType(); - private String algorithm = TrustManagerFactory.getDefaultAlgorithm(); - private int timeout = 10000; - - /** - * Get the certificate chain for a service. - * - * @param host - * The host (name or IP address) to contact the service on. - * @param port - * The port to contact the service on. - * @return The certificate chain, or <tt>null</tt> if no credentials are - * available. - * @throws NoSuchAlgorithmException - * If the trust manager cannot be set up because of algorithm - * problems. - * @throws KeyStoreException - * If the trust manager cannot be set up because of problems - * with the keystore type. - * @throws CertificateException - * If a bad certificate is present in the default keystore; - * <i>should be impossible</i>. - * @throws IOException - * If problems happen when trying to contact the service. - * @throws KeyManagementException - * If the SSL context can't have its special context manager - * installed. - */ - private X509Certificate[] getCertificateChainForService(String host, - int port) throws NoSuchAlgorithmException, KeyStoreException, - CertificateException, IOException, KeyManagementException { - KeyStore ks = KeyStore.getInstance(keystoreType); - SSLContext context = SSLContext.getInstance(protocol); - TrustManagerFactory tmf = TrustManagerFactory.getInstance(algorithm); - ks.load(null, null); - tmf.init(ks); - final Holder<X509Certificate[]> chain = new Holder<>(); - final X509TrustManager defaultTrustManager = (X509TrustManager) tmf - .getTrustManagers()[0]; - context.init(null, new TrustManager[] { new X509TrustManager() { - @Override - public void checkClientTrusted(X509Certificate[] clientChain, - String authType) throws CertificateException { - throw new UnsupportedOperationException(); - } - - @Override - public void checkServerTrusted(X509Certificate[] serverChain, - String authType) throws CertificateException { - chain.value = serverChain; - defaultTrustManager.checkServerTrusted(serverChain, authType); - } - - @Override - public X509Certificate[] getAcceptedIssuers() { - throw new UnsupportedOperationException(); - } - } }, null); - SSLSocketFactory factory = context.getSocketFactory(); - try (SSLSocket socket = (SSLSocket) factory.createSocket(host, port)) { - socket.setSoTimeout(timeout); - socket.startHandshake(); - } catch (SSLException e) { - // Ignore - } - return chain.value; - } - - private Map<URI, List<X509Certificate>> cache = new HashMap<>(); - - /** - * Gets the certificate chain for a service identified by URI. - * - * @param uri - * The URI of the (secure) service to identify. - * @return The certificate chain. Will be <tt>null</tt> if the service is - * not secure. - * @throws IOException - * If the service is unreachable or other connection problems - * occur. - * @throws GeneralSecurityException - * If any of a number of security-related problems occur, such - * as an inability to match detailed security protocols. - */ - public List<X509Certificate> getTrustsForURI(URI uri) throws IOException, - GeneralSecurityException { - if (!secure) - return null; - synchronized (this) { - if (!cache.containsKey(uri)) { - int port = uri.getPort(); - if (port == -1) - switch (uri.getScheme()) { - case "http": - port = 80; - break; - case "https": - port = 443; - break; - default: - return null; - } - X509Certificate[] chain = getCertificateChainForService( - uri.getHost(), port); - if (chain != null) - cache.put(uri, unmodifiableList(asList(chain))); - else - cache.put(uri, null); - } - return cache.get(uri); - } - } - - /** - * Flushes the cache. - */ - public void flushCache() { - synchronized (this) { - cache.clear(); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java deleted file mode 100644 index e0ee4d1..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java +++ /dev/null @@ -1,79 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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 javax.servlet.ServletContext; -import javax.ws.rs.core.UriInfo; - -import org.springframework.web.context.ServletContextAware; -import org.taverna.server.master.common.version.Version; - -/** - * Convert a string (URL, etc) to a version that is contextualized to the - * web-application. - * - * @author Donal Fellows - */ -public class Contextualizer implements ServletContextAware { - static final String ROOT_PLACEHOLDER = "%{WEBAPPROOT}"; - static final String VERSION_PLACEHOLDER = "%{VERSION}"; - static final String BASE_PLACEHOLDER = "%{BASEURL}"; - - /** - * Apply the contextualization operation. This consists of replacing the - * string <tt>{@value #ROOT_PLACEHOLDER}</tt> with the real root of the webapp. - * - * @param input - * the string to contextualize - * @return the contextualized string - */ - public String contextualize(String input) { - // Hack to work around bizarre CXF bug - String path = context.getRealPath("/").replace("%2D", "-"); - return input.replace(ROOT_PLACEHOLDER, path).replace( - VERSION_PLACEHOLDER, Version.JAVA); - } - - /** - * Apply the contextualization operation. This consists of replacing the - * string <tt>{@value #ROOT_PLACEHOLDER}</tt> with the real root of the - * webapp. - * - * @param ui - * Where to get information about the URL used to access the - * webapp. - * @param input - * the string to contextualize - * @return the contextualized string - */ - public String contextualize(UriInfo ui, String input) { - // Hack to work around bizarre CXF bug - String baseuri = ui.getBaseUri().toString().replace("%2D", "-"); - if (baseuri.endsWith("/")) - baseuri = baseuri.substring(0, baseuri.length() - 1); - return contextualize(input).replace(BASE_PLACEHOLDER, baseuri); - } - - private ServletContext context; - - @Override - public void setServletContext(ServletContext servletContext) { - context = servletContext; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java deleted file mode 100644 index e4be90b..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java +++ /dev/null @@ -1,84 +0,0 @@ -package org.taverna.server.master.utils; -/* - * 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.EOFException; -import java.io.IOException; -import java.io.Writer; - -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -/** - * Utility class, used to make Derby less broken. - * - * @see <a - * href="http://stackoverflow.com/questions/1004327/getting-rid-of-derby-log";> - * Getting rid of derby.log </a> - * @see <a - * href="http://stackoverflow.com/questions/3339736/set-system-property-with-spring-configuration-file";> - * Set system property with Spring configuration file </a> - */ -public class DerbyUtils { - /** - * A writer that channels things on to the log. - */ - public static final Writer TO_LOG = new DBLog(); - // Hack - public static final Writer DEV_NULL = TO_LOG; -} - -class DBLog extends Writer { - private Log log = LogFactory.getLog("Taverna.Server.Database"); - private StringBuilder sb = new StringBuilder(); - private boolean closed = false; - - @Override - public void write(char[] cbuf, int off, int len) throws IOException { - if (closed) - throw new EOFException(); - if (!log.isInfoEnabled()) - return; - sb.append(cbuf, off, len); - while (!closed) { - int idx = sb.indexOf("\n"), realIdx = idx; - if (idx < 0) - break; - char ch; - while (idx > 0 && ((ch = sb.charAt(idx - 1)) == '\r' || ch == ' ' || ch == '\t')) - idx--; - if (idx > 0) - log.info(sb.substring(0, idx)); - sb.delete(0, realIdx + 1); - } - } - - @Override - public void flush() throws IOException { - if (sb.length() > 0) { - log.info(sb.toString()); - sb = new StringBuilder(); - } - } - - @Override - public void close() throws IOException { - flush(); - closed = true; - sb = null; - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java deleted file mode 100644 index 3c39326..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java +++ /dev/null @@ -1,281 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.List; - -import javax.ws.rs.core.PathSegment; - -import org.taverna.server.master.common.DirEntryReference; -import org.taverna.server.master.exceptions.FilesystemAccessException; -import org.taverna.server.master.exceptions.NoDirectoryEntryException; -import org.taverna.server.master.interfaces.Directory; -import org.taverna.server.master.interfaces.DirectoryEntry; -import org.taverna.server.master.interfaces.File; -import org.taverna.server.master.interfaces.TavernaRun; - -/** - * Utility functions for getting entries from directories. - * - * @author Donal Fellows - */ -public class FilenameUtils { - private static final String TYPE_ERROR = "trying to take subdirectory of file"; - private static final String NO_FILE = "no such directory entry"; - private static final String NOT_A_FILE = "not a file"; - private static final String NOT_A_DIR = "not a directory"; - - /** - * Get a named directory entry from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param name - * The name of the directory entry to look up. - * @return The directory entry whose name is equal to the last part of the - * path; an empty path will retrieve the working directory handle - * itself. - * @throws NoDirectoryEntryException - * If there is no such entry. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable. - */ - public DirectoryEntry getDirEntry(TavernaRun run, String name) - throws FilesystemAccessException, NoDirectoryEntryException { - Directory dir = run.getWorkingDirectory(); - if (name == null || name.isEmpty()) - return dir; - DirectoryEntry found = dir; - boolean mustBeLast = false; - - // Must be nested loops; avoids problems with %-encoded "/" chars - for (String bit : name.split("/")) { - if (mustBeLast) - throw new FilesystemAccessException(TYPE_ERROR); - found = getEntryFromDir(bit, dir); - dir = null; - if (found instanceof Directory) { - dir = (Directory) found; - mustBeLast = false; - } else - mustBeLast = true; - } - return found; - } - - /** - * Get a named directory entry from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param d - * The path segments describing what to look up. - * @return The directory entry whose name is equal to the last part of the - * path; an empty path will retrieve the working directory handle - * itself. - * @throws NoDirectoryEntryException - * If there is no such entry. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable. - */ - public DirectoryEntry getDirEntry(TavernaRun run, List<PathSegment> d) - throws FilesystemAccessException, NoDirectoryEntryException { - Directory dir = run.getWorkingDirectory(); - if (d == null || d.isEmpty()) - return dir; - DirectoryEntry found = dir; - boolean mustBeLast = false; - - // Must be nested loops; avoids problems with %-encoded "/" chars - for (PathSegment segment : d) - for (String bit : segment.getPath().split("/")) { - if (mustBeLast) - throw new FilesystemAccessException(TYPE_ERROR); - found = getEntryFromDir(bit, dir); - dir = null; - if (found instanceof Directory) { - dir = (Directory) found; - mustBeLast = false; - } else - mustBeLast = true; - } - return found; - } - - /** - * Get a named directory entry from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param d - * The directory reference describing what to look up. - * @return The directory entry whose name is equal to the last part of the - * path in the directory reference; an empty path will retrieve the - * working directory handle itself. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable. - * @throws NoDirectoryEntryException - * If there is no such entry. - */ - public DirectoryEntry getDirEntry(TavernaRun run, DirEntryReference d) - throws FilesystemAccessException, NoDirectoryEntryException { - Directory dir = run.getWorkingDirectory(); - if (d == null || d.path == null || d.path.isEmpty()) - return dir; - DirectoryEntry found = dir; - boolean mustBeLast = false; - - for (String bit : d.path.split("/")) { - if (mustBeLast) - throw new FilesystemAccessException(TYPE_ERROR); - found = getEntryFromDir(bit, dir); - dir = null; - if (found instanceof Directory) { - dir = (Directory) found; - mustBeLast = false; - } else - mustBeLast = true; - } - return found; - } - - /** - * Get a named directory entry from a directory. - * - * @param name - * The name of the entry; must be "<tt>/</tt>"-free. - * @param dir - * The directory to look in. - * @return The directory entry whose name is equal to the given name. - * @throws NoDirectoryEntryException - * If there is no such entry. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable. - */ - private DirectoryEntry getEntryFromDir(String name, Directory dir) - throws FilesystemAccessException, NoDirectoryEntryException { - if (dir == null) - throw new FilesystemAccessException(NO_FILE); - for (DirectoryEntry entry : dir.getContents()) - if (entry.getName().equals(name)) - return entry; - throw new NoDirectoryEntryException(NO_FILE); - } - - /** - * Get a named directory from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param d - * The directory reference describing what to look up. - * @return The directory whose name is equal to the last part of the path in - * the directory reference; an empty path will retrieve the working - * directory handle itself. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable, or if the - * name doesn't refer to a directory. - * @throws NoDirectoryEntryException - * If there is no such entry. - */ - public Directory getDirectory(TavernaRun run, DirEntryReference d) - throws FilesystemAccessException, NoDirectoryEntryException { - DirectoryEntry dirEntry = getDirEntry(run, d); - if (dirEntry instanceof Directory) - return (Directory) dirEntry; - throw new FilesystemAccessException(NOT_A_DIR); - } - - /** - * Get a named directory from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param name - * The name of the directory to look up. - * @return The directory. - * @throws FilesystemAccessException - * If the directory isn't specified or isn't readable, or if the - * name doesn't refer to a directory. - * @throws NoDirectoryEntryException - * If there is no such entry. - */ - public Directory getDirectory(TavernaRun run, String name) - throws FilesystemAccessException, NoDirectoryEntryException { - DirectoryEntry dirEntry = getDirEntry(run, name); - if (dirEntry instanceof Directory) - return (Directory) dirEntry; - throw new FilesystemAccessException(NOT_A_DIR); - } - - /** - * Get a named file from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param d - * The directory reference describing what to look up. - * @return The file whose name is equal to the last part of the path in the - * directory reference; an empty path will retrieve the working - * directory handle itself. - * @throws FilesystemAccessException - * If the file isn't specified or isn't readable, or if the name - * doesn't refer to a file. - * @throws NoDirectoryEntryException - * If there is no such entry. - */ - public File getFile(TavernaRun run, DirEntryReference d) - throws FilesystemAccessException, NoDirectoryEntryException { - DirectoryEntry dirEntry = getDirEntry(run, d); - if (dirEntry instanceof File) - return (File) dirEntry; - throw new FilesystemAccessException(NOT_A_FILE); - } - - /** - * Get a named file from a workflow run. - * - * @param run - * The run whose working directory is to be used as the root of - * the search. - * @param name - * The name of the file to look up. - * @return The file whose name is equal to the last part of the path in the - * directory reference; an empty path will retrieve the working - * directory handle itself. - * @throws FilesystemAccessException - * If the file isn't specified or isn't readable, or if the name - * doesn't refer to a file. - * @throws NoDirectoryEntryException - * If there is no such entry. - */ - public File getFile(TavernaRun run, String name) - throws FilesystemAccessException, NoDirectoryEntryException { - DirectoryEntry dirEntry = getDirEntry(run, name); - if (dirEntry instanceof File) - return (File) dirEntry; - throw new FilesystemAccessException(NOT_A_FILE); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java deleted file mode 100644 index 7f5f92a..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java +++ /dev/null @@ -1,34 +0,0 @@ -package org.taverna.server.master.utils; -/* - * 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 org.apache.cxf.jaxrs.provider.ProviderFactory; -import org.apache.cxf.message.Message; -import org.apache.cxf.phase.AbstractPhaseInterceptor; -import org.apache.cxf.phase.Phase; - -public class FlushThreadLocalCacheInterceptor extends - AbstractPhaseInterceptor<Message> { - public FlushThreadLocalCacheInterceptor() { - super(Phase.USER_LOGICAL_ENDING); - } - - @Override - public void handleMessage(Message message) { - ProviderFactory.getInstance(message).clearThreadLocalProxies(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java deleted file mode 100644 index 0600857..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java +++ /dev/null @@ -1,61 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.annotation.ElementType.METHOD; -import static java.lang.annotation.RetentionPolicy.RUNTIME; - -import java.lang.annotation.Documented; -import java.lang.annotation.Retention; -import java.lang.annotation.Target; - -import org.aspectj.lang.annotation.Aspect; -import org.aspectj.lang.annotation.Before; - -/** - * This class is responsible for counting all invocations of publicly-exposed - * methods of the webapp. It's connected to the webapp primarily through an - * AspectJ-style pointcut. - * - * @author Donal Fellows - */ -@Aspect -public class InvocationCounter { - private int count; - - @Before("@annotation(org.taverna.server.master.utils.InvocationCounter.CallCounted)") - public synchronized void count() { - count++; - } - - public synchronized int getCount() { - return count; - } - - /** - * Mark methods that should be counted by the invocation counter. - * - * @author Donal Fellows - */ - @Retention(RUNTIME) - @Documented - @Target(METHOD) - public static @interface CallCounted { - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java deleted file mode 100644 index 7f248ff..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java +++ /dev/null @@ -1,73 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.Integer.MAX_VALUE; -import static javax.crypto.Cipher.getMaxAllowedKeyLength; -import static org.apache.commons.logging.LogFactory.getLog; - -import java.security.GeneralSecurityException; -import java.security.NoSuchAlgorithmException; - -import javax.annotation.PostConstruct; - -import org.apache.commons.logging.Log; - -/** - * Trivial bean that checks for whether the JCE policy files that allow - * unlimited strength security are present, and warns in the log if not. - * - * @author Donal Fellows - */ -public class JCECheck { - /** - * Write a message to the log that says whether an unlimited strength - * {@linkplain #Cipher cipher} is present. This is the official proxy for - * whether the unlimited strength JCE policy files have been installed; if - * absent, the message is logged as a warning, otherwise it is just - * informational. - */ - @PostConstruct - public void checkForUnlimitedJCE() { - Log log = getLog("Taverna.Server.Utils"); - - try { - if (getMaxAllowedKeyLength("AES") < MAX_VALUE) - log.warn("maximum key length very short; unlimited " - + "strength JCE policy files maybe missing"); - else - log.info("unlimited strength JCE policy in place"); - } catch (GeneralSecurityException e) { - log.warn("problem computing key length limits!", e); - } - } - - /** - * @return Whether the unlimited strength JCE policy files are present (or - * rather whether an unlimited strength {@linkplain #Cipher cipher} - * is permitted). - */ - public boolean isUnlimitedStrength() { - try { - return getMaxAllowedKeyLength("AES") == MAX_VALUE; - } catch (NoSuchAlgorithmException e) { - return false; - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java deleted file mode 100644 index 96f6a11..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java +++ /dev/null @@ -1,285 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.annotation.ElementType.METHOD; -import static java.lang.annotation.RetentionPolicy.RUNTIME; -import static org.apache.commons.logging.LogFactory.getLog; - -import java.lang.annotation.Documented; -import java.lang.annotation.Retention; -import java.lang.annotation.Target; -import java.util.WeakHashMap; - -import javax.annotation.Nonnull; -import javax.annotation.Nullable; -import javax.annotation.PreDestroy; -import javax.jdo.JDOException; -import javax.jdo.PersistenceManager; -import javax.jdo.PersistenceManagerFactory; -import javax.jdo.Query; -import javax.jdo.Transaction; - -import org.apache.commons.logging.Log; -import org.aspectj.lang.ProceedingJoinPoint; -import org.aspectj.lang.annotation.Around; -import org.aspectj.lang.annotation.Aspect; -import org.springframework.beans.factory.annotation.Required; - -/** - * Simple support class that wraps up and provides access to the correct parts - * of JDO. - * - * @author Donal Fellows - * - * @param <T> The context class that the subclass will be working with. - */ -public abstract class JDOSupport<T> { - private Class<T> contextClass; - private PersistenceManagerBuilder pmb; - - /** - * Instantiate this class, supplying it a handle to the class that will be - * used to provide context for queries and accesses. - * - * @param contextClass - * Must match the type parameter to the class itself. - */ - protected JDOSupport(@Nonnull Class<T> contextClass) { - this.contextClass = contextClass; - } - - /** - * @param persistenceManagerBuilder - * The JDO engine to use for managing persistence. - */ - @Required - public void setPersistenceManagerBuilder( - PersistenceManagerBuilder persistenceManagerBuilder) { - pmb = persistenceManagerBuilder; - } - - private PersistenceManager pm() { - if (isPersistent()) - return pmb.getPersistenceManager(); - return null; - } - - /** - * Has this class actually been configured with a persistence manager by - * Spring? - * - * @return Whether there is a persistence manager installed. - */ - protected boolean isPersistent() { - return pmb != null; - } - - /** - * Get an instance of a query in JDOQL. - * - * @param filter - * The filter part of the query. - * @return The query, which should be executed to retrieve the results. - */ - @Nonnull - protected Query<T> query(@Nonnull String filter) { - return pm().newQuery(contextClass, filter); - } - - /** - * Get an instance of a named query attached to the context class (as an - * annotation). Note that the result is a <i>raw</i> {@link Query} because - * not all queries return instances of the context class. - * - * @param name - * The name of the query. - * @return The query, which should be executed to retrieve the results. - * @see javax.jdo.annotations.Query - */ - @Nonnull - @SuppressWarnings("rawtypes") - protected Query namedQuery(@Nonnull String name) { - return pm().newNamedQuery(contextClass, name); - } - - /** - * Make an instance of the context class persist in the database. It's - * identity must not already exist. - * - * @param value - * The instance to persist. - * @return The persistence-coupled instance. - */ - @Nullable - protected T persist(@Nullable T value) { - if (value == null) - return null; - return pm().makePersistent(value); - } - - /** - * Make a non-persistent (i.e., will hold its value past the end of the - * transaction) copy of a persistence-coupled instance of the context class. - * - * @param value - * The value to decouple. - * @return The non-persistent copy. - */ - @Nullable - protected T detach(@Nullable T value) { - if (value == null) - return null; - return pm().detachCopy(value); - } - - /** - * Look up an instance of the context class by its identity. - * - * @param id - * The identity of the object. - * @return The instance, which is persistence-coupled. - */ - @Nullable - protected T getById(Object id) { - try { - return pm().getObjectById(contextClass, id); - } catch (Exception e) { - return null; - } - } - - /** - * Delete a persistence-coupled instance of the context class. - * - * @param value - * The value to delete. - */ - protected void delete(@Nullable T value) { - if (value != null) - pm().deletePersistent(value); - } - - /** - * Manages integration of JDO transactions with Spring. - * - * @author Donal Fellows - */ - @Aspect - public static class TransactionAspect { - private Object lock = new Object(); - private Log log = getLog("Taverna.Server.Utils"); - private volatile int txid; - - @Around(value = "@annotation(org.taverna.server.master.utils.JDOSupport.WithinSingleTransaction) && target(support)", argNames = "support") - Object applyTransaction(ProceedingJoinPoint pjp, JDOSupport<?> support) - throws Throwable { - synchronized (lock) { - PersistenceManager pm = support.pm(); - int id = ++txid; - Transaction tx = (pm == null) ? null : pm.currentTransaction(); - if (tx != null && tx.isActive()) - tx = null; - if (tx != null) { - if (log.isDebugEnabled()) - log.debug("starting transaction #" + id); - tx.begin(); - } - try { - Object result = pjp.proceed(); - if (tx != null) { - tx.commit(); - if (log.isDebugEnabled()) - log.debug("committed transaction #" + id); - } - tx = null; - return result; - } catch (Throwable t) { - try { - if (tx != null) { - tx.rollback(); - if (log.isDebugEnabled()) - log.debug("rolled back transaction #" + id); - } - } catch (JDOException e) { - log.warn("rollback failed unexpectedly", e); - } - throw t; - } - } - } - } - - /** - * Mark a method (of a subclass of {@link JDOSupport}) as having a - * transaction wrapped around it. The transactions are managed correctly in - * the multi-threaded case. - * - * @author Donal Fellows - */ - @Target(METHOD) - @Retention(RUNTIME) - @Documented - public @interface WithinSingleTransaction { - } - - /** - * Manages {@linkplain PersistenceManager persistence managers} in a way - * that doesn't cause problems when the web application is unloaded. - * - * @author Donal Fellows - */ - public static class PersistenceManagerBuilder { - private PersistenceManagerFactory pmf; - private WeakHashMap<Thread, PersistenceManager> cache = new WeakHashMap<>(); - - /** - * @param persistenceManagerFactory - * The JDO engine to use for managing persistence. - */ - @Required - public void setPersistenceManagerFactory( - PersistenceManagerFactory persistenceManagerFactory) { - pmf = persistenceManagerFactory; - } - - @Nonnull - public PersistenceManager getPersistenceManager() { - if (cache == null) - return pmf.getPersistenceManager(); - Thread t = Thread.currentThread(); - PersistenceManager pm = cache.get(t); - if (pm == null && pmf != null) { - pm = pmf.getPersistenceManager(); - cache.put(t, pm); - } - return pm; - } - - @PreDestroy - void clearThreadCache() { - WeakHashMap<Thread, PersistenceManager> cache = this.cache; - this.cache = null; - for (PersistenceManager pm : cache.values()) - if (pm != null) - pm.close(); - cache.clear(); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java deleted file mode 100644 index 8bd0506..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java +++ /dev/null @@ -1,154 +0,0 @@ -package org.taverna.server.master.utils; -/* - * 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 java.lang.Thread.sleep; -import static org.apache.commons.logging.LogFactory.getLog; - -import java.sql.DatabaseMetaData; -import java.util.Properties; - -import org.apache.commons.logging.Log; -import org.datanucleus.store.rdbms.adapter.DerbyAdapter; -import org.datanucleus.store.rdbms.identifier.IdentifierFactory; -import org.datanucleus.store.rdbms.key.CandidateKey; -import org.datanucleus.store.rdbms.key.ForeignKey; -import org.datanucleus.store.rdbms.key.Index; -import org.datanucleus.store.rdbms.key.PrimaryKey; -import org.datanucleus.store.rdbms.sql.SQLTable; -import org.datanucleus.store.rdbms.table.Column; -import org.datanucleus.store.rdbms.table.Table; -import org.datanucleus.store.rdbms.table.TableImpl; -import org.datanucleus.store.rdbms.table.ViewImpl; - -/** - * Evil hack to allow logging of the DDL spat out to Derby. - * - * @author Donal Fellows - */ -public class LoggingDerbyAdapter extends DerbyAdapter { - Log log = getLog("Taverna.Server.SQL"); - - private StringBuilder ddl = new StringBuilder(); - private volatile long timeout; - private Thread timer; - - private synchronized void logDDL() { - if (ddl.length() > 0) { - log.info("Data definition language:\n" + ddl); - ddl.setLength(0); - } - timer = null; - } - - private synchronized void doLog(String item) { - ddl.append(item); - if (!item.endsWith("\n")) - ddl.append('\n'); - timeout = currentTimeMillis() + 5000; - if (timer == null) - timer = new OneShotThread("DDL logger timeout", new Runnable() { - @Override - public void run() { - try { - while (timeout > currentTimeMillis()) - sleep(1000); - } catch (InterruptedException e) { - // Ignore - } - logDDL(); - } - }); - } - - /** - * Creates an Apache Derby adapter based on the given metadata which logs - * the DDL it creates. - */ - public LoggingDerbyAdapter(DatabaseMetaData metadata) { - super(metadata); - } - - @Override - public String getCreateTableStatement(TableImpl table, Column[] columns, - Properties props, IdentifierFactory factory) { - String statement = super.getCreateTableStatement(table, columns, props, - factory); - doLog(statement); - return statement; - } - - @Override - public String getCreateIndexStatement(Index index, IdentifierFactory factory) { - String statement = super.getCreateIndexStatement(index, factory); - doLog(statement); - return statement; - } - - @Override - public String getAddCandidateKeyStatement(CandidateKey ck, - IdentifierFactory factory) { - String statement = super.getAddCandidateKeyStatement(ck, factory); - doLog(statement); - return statement; - } - - @Override - public String getAddPrimaryKeyStatement(PrimaryKey pk, - IdentifierFactory factory) { - String statement = super.getAddPrimaryKeyStatement(pk, factory); - doLog(statement); - return statement; - } - - @Override - public String getAddColumnStatement(Table table, Column col) { - String statement = super.getAddColumnStatement(table, col); - doLog(statement); - return statement; - } - - @Override - public String getAddForeignKeyStatement(ForeignKey fk, - IdentifierFactory factory) { - String statement = super.getAddForeignKeyStatement(fk, factory); - doLog(statement); - return statement; - } - - @Override - public String getDeleteTableStatement(SQLTable tbl) { - String statement = super.getDeleteTableStatement(tbl); - doLog(statement); - return statement; - } - - @Override - public String getDropTableStatement(Table table) { - String statement = super.getDropTableStatement(table); - doLog(statement); - return statement; - } - - @Override - public String getDropViewStatement(ViewImpl view) { - String statement = super.getDropViewStatement(view); - doLog(statement); - return statement; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java deleted file mode 100644 index 32cca5a..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java +++ /dev/null @@ -1,26 +0,0 @@ -package org.taverna.server.master.utils; -/* - * 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. - */ - -public class OneShotThread extends Thread { - public OneShotThread(String name, Runnable target) { - super(target, name); - setContextClassLoader(null); - setDaemon(true); - start(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java deleted file mode 100644 index d69612e..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java +++ /dev/null @@ -1,45 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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 javax.ws.rs.OPTIONS; -import javax.ws.rs.core.Response; - -/** - * Utilities that make it easier to write REST services. - * - * @author Donal Fellows - */ -public class RestUtils { - /** - * Generate a response to an HTTP OPTIONS request. - * - * @param methods - * The state-changing methods supported, if any. - * @return the required response - * @see OPTIONS - */ - public static Response opt(String... methods) { - StringBuilder sb = new StringBuilder("GET,"); - for (String m : methods) - sb.append(m).append(","); - sb.append("HEAD,OPTIONS"); - return Response.ok().header("Allow", sb.toString()).entity("").build(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java deleted file mode 100644 index 333febe..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java +++ /dev/null @@ -1,50 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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 org.aspectj.lang.annotation.AfterThrowing; -import org.aspectj.lang.annotation.Aspect; -import org.taverna.server.master.exceptions.GeneralFailureException; - -/** - * Aspect used to convert {@linkplain RuntimeException runtime exceptions} into - * a form that can be nicely conveyed to the outside world as HTTP errors. - * - * @author Donal Fellows - */ -@Aspect -public class RuntimeExceptionWrapper { - /** - * Map an unexpected exception to one that can be correctly reported as a - * problem. - * - * @param exn - * The runtime exception being trapped. - * @throws GeneralFailureException - * The known exception type that it is mapped to. - */ - @AfterThrowing(pointcut = "execution(* org.taverna.server.master.rest..*(..)) && !bean(*Provider.*)", throwing = "exn") - public void wrapRuntimeException(RuntimeException exn) - throws GeneralFailureException { - // Exclude security-related exceptions - if (exn.getClass().getName().startsWith("org.springframework.security.")) - return; - throw new GeneralFailureException(exn); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/00397eff/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java ---------------------------------------------------------------------- diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java deleted file mode 100644 index 25cf64f..0000000 --- a/taverna-server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java +++ /dev/null @@ -1,82 +0,0 @@ -/* - */ -package org.taverna.server.master.utils; -/* - * 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.Serializable; -import java.security.Principal; - -import org.springframework.security.core.Authentication; -import org.springframework.security.core.userdetails.UserDetails; - -/** - * A simple serializable principal that just records the name. - * - * @author Donal Fellows - */ -public class UsernamePrincipal implements Principal, Serializable { - private static final long serialVersionUID = 2703493248562435L; - public UsernamePrincipal(String username) { - this.name = username; - } - - public UsernamePrincipal(Principal other) { - this.name = other.getName(); - } - - public UsernamePrincipal(Authentication auth) { - this(auth.getPrincipal()); - } - - public UsernamePrincipal(Object principal) { - if (principal instanceof Principal) - this.name = ((Principal) principal).getName(); - else if (principal instanceof String) - this.name = (String) principal; - else if (principal instanceof UserDetails) - this.name = ((UserDetails) principal).getUsername(); - else - this.name = principal.toString(); - } - - private String name; - - @Override - public String getName() { - return name; - } - - @Override - public String toString() { - return "Principal<" + name + ">"; - } - - @Override - public boolean equals(Object o) { - if (o instanceof Principal) { - Principal p = (Principal) o; - return name.equals(p.getName()); - } - return false; - } - - @Override - public int hashCode() { - return name.hashCode(); - } -}
