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11 package org.astrogrid.applications.apps;
12
13 import org.astrogrid.applications.AbstractApplication;
14 import org.astrogrid.applications.Application;
15 import org.astrogrid.applications.CeaException;
16 import org.astrogrid.applications.DefaultIDs;
17 import org.astrogrid.applications.Status;
18 import org.astrogrid.applications.apps.tables.TableConverter;
19 import org.astrogrid.applications.beans.v1.parameters.ParameterValue;
20 import org.astrogrid.applications.beans.v1.parameters.types.ParameterTypes;
21 import org.astrogrid.applications.description.ApplicationInterface;
22 import org.astrogrid.applications.description.ParameterDescription;
23 import org.astrogrid.applications.description.base.AbstractApplicationDescription;
24 import org.astrogrid.applications.description.base.ApplicationDescriptionEnvironment;
25 import org.astrogrid.applications.description.base.BaseApplicationInterface;
26 import org.astrogrid.applications.description.base.BaseParameterDescription;
27 import org.astrogrid.applications.description.exception.ParameterDescriptionNotFoundException;
28 import org.astrogrid.applications.parameter.DefaultParameterAdapter;
29 import org.astrogrid.applications.parameter.ParameterAdapter;
30 import org.astrogrid.applications.parameter.StreamParameterAdapter;
31 import org.astrogrid.applications.parameter.protocol.ExternalValue;
32 import org.astrogrid.applications.parameter.protocol.ProtocolLibrary;
33 import org.astrogrid.community.User;
34 import org.astrogrid.component.descriptor.ComponentDescriptor;
35 import org.astrogrid.workflow.beans.v1.Tool;
36
37 import org.apache.commons.logging.Log;
38 import org.apache.commons.logging.LogFactory;
39
40 import uk.ac.starlink.table.StarTableFactory;
41
42 import java.io.InputStream;
43 import java.util.HashMap;
44 import java.util.Iterator;
45 import java.util.Map;
46
47 import javax.mail.Message;
48 import javax.mail.MessagingException;
49 import javax.mail.Session;
50 import javax.mail.Transport;
51 import javax.mail.internet.InternetAddress;
52 import javax.mail.internet.MimeMessage;
53 import javax.naming.Context;
54 import javax.naming.InitialContext;
55 import javax.naming.NamingException;
56
57 import junit.framework.Test;
58 import junit.framework.TestCase;
59 import junit.framework.TestSuite;
60
61 /*** Description of a generic table Manipulation application.
62 * <P>
63 * this application can
64 * <ul>
65 * <li> Transform tables from one representation to another - e.g. CSV to VOTable
66 * <li> Manipulation of table columns within a single table
67 * <li> limited cross matching facility
68 * </ul>
69 * <p> it is based on the Starlink STIL package for generic table manipulations.
70 * @author Paul Harrison (pah@jb.man.ac.uk)
71 *
72 */
73 public class TableManipulatorApplicationDescription extends AbstractApplicationDescription implements ComponentDescriptor {
74 private static final String INPUTTABLENAME = "INTABLE";
75 private static final String INPUT2TABLENAME = "INTABLE2";
76 private static final String OUTPUTTABLENAME = "OUTTABLE";
77 private static final String CONVERT = "convert";
78 private static final String OUTPUTFORMATNAME = "FORMAT";
79
80
81
82 /*** Construct a new Description
83 * @param env
84 */
85 public TableManipulatorApplicationDescription(ApplicationDescriptionEnvironment env) {
86 super(env);
87 this.setMetaData();
88 }
89
90 /*** set up metadata for this instance */
91 private final void setMetaData() {
92 StringBuffer thename = new StringBuffer(env.getAuthIDResolver().getAuthorityID());
93 thename.append("/TableManipulator");
94 setName(thename.toString());
95 BaseParameterDescription inputTable = new BaseParameterDescription();
96 inputTable.setName(INPUTTABLENAME);
97 inputTable.setDisplayName("Input table");
98 inputTable.setDisplayDescription("The table to be manipulated");
99 inputTable.setType(ParameterTypes.BINARY);
100 this.addParameterDescription(inputTable);
101
102 BaseParameterDescription inputTable2 = new BaseParameterDescription();
103 inputTable2.setName(INPUT2TABLENAME);
104 inputTable2.setDisplayName("2nd Input table");
105 inputTable2.setDisplayDescription("The table");
106 inputTable2.setType(ParameterTypes.BINARY);
107 this.addParameterDescription(inputTable);
108 BaseParameterDescription outputTable = new BaseParameterDescription();
109 outputTable.setName(OUTPUTTABLENAME);
110 outputTable.setDisplayName("Output table");
111 outputTable.setDisplayDescription("The output table");
112 outputTable.setType(ParameterTypes.BINARY);
113 this.addParameterDescription(inputTable);
114 BaseParameterDescription outputFormat = new BaseParameterDescription();
115 outputFormat.setName(OUTPUTFORMATNAME);
116 outputFormat.setDisplayName("format");
117 outputFormat.setDisplayDescription("the format to output the table in");
118 outputFormat.setType(ParameterTypes.TEXT);
119 this.addParameterDescription(outputFormat);
120
121 BaseApplicationInterface convertInterface = new BaseApplicationInterface(CONVERT,this);
122 try {
123 convertInterface.addInputParameter(inputTable.getName());
124 convertInterface.addInputParameter(outputFormat.getName());
125 convertInterface.addOutputParameter(outputTable.getName());
126 } catch (ParameterDescriptionNotFoundException e) {
127 logger.fatal("Programming error",e);
128 throw new RuntimeException("Programming error",e);
129 }
130 this.addInterface(convertInterface);
131 }
132
133 /***
134 * Commons Logger for this class
135 */
136 private static final Log logger = LogFactory.getLog(TableManipulatorApplicationDescription.class);
137
138
139
140 /***
141 * @see org.astrogrid.component.descriptor.ComponentDescriptor#getDescription()
142 */
143 public String getDescription() {
144 return "Table Maipulation application\n" + this.toString();
145 }
146
147 /*** installation test verifies mailer session object is present in jndi.
148 * @see org.astrogrid.component.descriptor.ComponentDescriptor#getInstallationTest()
149 */
150 public Test getInstallationTest() {
151 return null;
152 }
153
154 /***
155 * @see org.astrogrid.applications.description.ApplicationDescription#initializeApplication(java.lang.String, org.astrogrid.community.User, org.astrogrid.workflow.beans.v1.Tool)
156 */
157 public Application initializeApplication(String callerAssignedID, User user, Tool tool) throws Exception {
158 String newID = env.getIdGen().getNewID();
159 final DefaultIDs ids = new DefaultIDs(callerAssignedID,newID,user);
160 ApplicationInterface iface = this.getInterface(tool.getInterface());
161 return new TableManipulatorApplication(ids,tool,iface,env.getProtocolLib());
162 }
163
164 /***The actual table manipulator application.
165 * @TODO perhaps this needs to be in its own file.
166 * @author Paul Harrison (pah@jb.man.ac.uk) 09-Nov-2004
167 * @version $Name: $
168 * @since iteration6
169 */
170 public static class TableManipulatorApplication extends AbstractApplication {
171
172 /*** Construct a new SendMailApplication
173 * @param ids
174 * @param tool
175 * @param applicationInterface
176 * @param lib
177 */
178 public TableManipulatorApplication(IDs ids, Tool tool, ApplicationInterface applicationInterface, ProtocolLibrary lib) {
179 super(ids, tool, applicationInterface, lib);
180 }
181
182 protected ParameterAdapter instantiateAdapter(ParameterValue pval,
183 ParameterDescription descr, ExternalValue indirectVal) {
184 if (pval.getName().equals(OUTPUTFORMATNAME)) {
185 return new DefaultParameterAdapter(pval, descr, indirectVal);
186 }
187 else {
188 return new StreamParameterAdapter(pval, descr, indirectVal);
189 }
190 }
191 public Runnable createExecutionTask() throws CeaException {
192
193 createAdapters();
194 setStatus(Status.INITIALIZED);
195 return new Runnable() {
196 public void run() {
197 final Map args = new HashMap();
198 try {
199 for (Iterator i = inputParameterAdapters(); i.hasNext();) {
200 ParameterAdapter a = (ParameterAdapter)i.next();
201 args.put(a.getWrappedParameter().getName(),a.process());
202 }
203 setStatus(Status.RUNNING);
204
205 if(getApplicationInterface().getName().equals(CONVERT)){
206 TableConverter tableconverter = new TableConverter((InputStream)args.get(INPUTTABLENAME), (String)args.get(OUTPUTFORMATNAME));
207 }
208
209 } catch (Throwable t) {
210 reportError("Something went wrong",t);
211 }
212 }
213 };
214
215
216 }
217 }
218
219 }
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