private void completeEvidenceDocument() throws IOException {
String tempText =
"<table><tr><td class=\"subHeading\">Evidence:</td><td class=\"info\">"
+ this.theEvidence.getName()
+ "</td></tr>\n";
// add the type of evidence
tempText +=
"<tr><td class=\"subHeading\">Type:</td><td class=\"info\">"
+ this.theEvidence.getType()
+ "</td></tr>\n";
// add the evidence description
tempText +=
"<tr><td class=\"subHeading\">Description:</td><td class=\"info\">"
+ this.theEvidence.getDescription()
+ "</td></tr>\n";
// add the sources relating to the given piece of evidence
tempText += "<tr><td class=\"subHeading\">References:</td><td class=\"info\" colspan=\"3\">\n";
for (Source s : this.theEvidence.getSources(allTheSources)) {
tempText +=
"\t<li><a href=\"../source/" + s.getName() + ".html\">" + s.getName() + "</a></li>\n";
}
tempText += "</td></tr>\n";
// tempText +="</body></html>";
tempText +=
"</table></div>\n<div id=\"footer\">\n\t© "
+ getYear()
+ " <a href=\"http://www.eecs.qmul.ac.uk/research/view/risk-and-information-management\"> Risk and Information Management (RIM) Research Group, Queen Mary, University of London</a>\n</div>\n</body>\n</html>";
appendCurrentDocument(tempText, "evidence");
}
/**
* Determines if the subset of information in a SourceRef is equal to particular Source object.
* Note that only the final segment of the href field of the SourceRef is compared to the Source
* object, as the Source object does not contain its own URI. Thus if the SourceRef was from a
* different server than the Source object, this test would return true even though the SourceRef
* points to a different copy of this Source object.
*
* @param source The Source to be compared.
* @return True if all the fields in the SourceRef correspond to the same fields in the Source
*/
public boolean equalsSource(Source source) {
String hrefSourceName = this.getHref().substring(this.getHref().lastIndexOf('/') + 1);
return (this.getName().equals(source.getName())
&& (this.getOwner().equals(source.getOwner()))
&& (this.isPublic() == source.isPublic())
&& (this.isVirtual() == source.isVirtual())
&& (this.getCoordinates().equals(source.getCoordinates()))
&& (this.getLocation().equals(source.getLocation()))
&& (this.getDescription().equals(source.getDescription()))
&& (source.getName().equals(hrefSourceName)));
}
/**
* Return the Properties that enumerate the keys for this Source
*
* @param source the Source
* @return the relevant Properties
*/
protected static Properties getKeyProperties(Source source) {
Properties keys = null;
synchronized (sourceKeys) {
keys = sourceKeys.get(source);
if (keys == null) {
String sourceNameKeysFileName = source.getName() + "_keys.properties";
keys = PropertiesUtil.loadProperties(sourceNameKeysFileName);
String sourceTypeKeysFileName = source.getType() + "_keys.properties";
if (keys == null) {
keys = PropertiesUtil.loadProperties(sourceTypeKeysFileName);
}
if (keys == null) {
throw new RuntimeException(
"can't find keys for source: "
+ source
+ " after trying to find: "
+ sourceNameKeysFileName
+ " and: "
+ sourceTypeKeysFileName);
}
sourceKeys.put(source, keys);
}
}
return keys;
}
protected void say(Source source, String str) {
Server server = source.getServer();
if (source.talkable()) {
source.messageReceived(server.getNick(), str);
server.say(source.getName(), str);
} else {
source.report(getText(IRCTextProvider.INTERPRETOR_NOT_ON_CHANNEL));
}
}
/**
* Creates a SourceRef object from a Source object using the provided URI for the SourceRef
* pointing to the full Source resource. Needs to be kept up to date with any changes to the
* schema, which is bogus.
*
* @param source The Source to build the SourceRef from.
* @param uri The URI where the Source is located.
*/
public SourceRef(Source source, String uri) {
this(
source.getName(),
source.getOwner(),
source.isPublic(),
source.isVirtual(),
source.getCoordinates(),
source.getLocation(),
source.getDescription(),
uri);
}
public Object getValueAt(int row, int col) {
Source s = sources.get(row);
switch (col) {
case 0:
return s.getName();
case 1:
return s.getPosition();
case 2:
return s.getEmail();
}
return null;
}
private Source getSource(String serverName, String type, String name) {
Enumeration<Server> e = _servers.keys();
while (e.hasMoreElements()) {
Server s = (Server) e.nextElement();
String sname = s.getServerName();
if (sname.equals(serverName) || serverName.length() == 0) {
Enumeration<Source> f = s.getSources();
while (f.hasMoreElements()) {
Source src = (Source) f.nextElement();
if (src.getType().equals(type) && src.getName().equals(name)) return src;
}
}
}
return null;
}
private String associateFile(Source source, String propertyName) throws Exception {
if (source.hasProperty(propertyName)) {
source.deleteProperty(propertyName);
}
File stats = source.createFileProperty(propertyName);
DataSource ds = dsf.getDataSource(source.getName());
ds.open();
long rc = ds.getRowCount();
ds.close();
FileOutputStream fis = new FileOutputStream(stats);
String rcStr = Long.toString(rc);
fis.write(rcStr.getBytes());
fis.close();
return rcStr;
}
@Override
public int compareTo(Source other) {
return getName().compareTo(other.getName());
}
protected AndromedaFile parseAllFiles(IParser p) throws Exception {
AndromedaFile af = null;
// Assemble file lists
List<Source> natives =
FileCollector.getFilesFromList(options.nativeLibFolder, options.nativeList);
List<Source> langFiles = getLanguageFiles();
List<Source> triggers = null;
int numFiles = files.size();
if (options.mapIn != null) {
if (numFiles > 0) {
Program.log.caption(
"+++ Compiling map "
+ options.mapIn.getName()
+ " and "
+ numFiles
+ " additional script files +++");
} else {
Program.log.caption("+++ Compiling map " + options.mapIn.getName() + " +++");
}
System.out.print("Extracting code from map file...");
map = new MoPaQ(options.mapIn);
triggers = new TriggerExtractor().extractTriggers(map);
System.out.println(" DONE (" + getTime() + " ms)");
} else {
if (options.triggersIn != null) {
triggers = new TriggerExtractor().extractTriggers(options.triggersIn);
}
Program.log.caption("+++ Compiling " + numFiles + " script files +++");
if (numFiles > 0) {
} else {
Program.log.caption("+++ Compiling map " + options.mapIn.getName() + " +++");
}
}
// Natives
if (parseNatives)
for (Source f : natives) {
System.out.print("Parsing native library [" + f.getName() + "]...");
af = p.parse(f, af, AndromedaFileInfo.TYPE_NATIVE);
System.out.println(" DONE (" + getTime() + " ms)");
}
// Language files
for (Source f : langFiles) {
System.out.print("Parsing andromeda system library [" + f.getName() + "]...");
af = p.parse(f, af, AndromedaFileInfo.TYPE_LANGUAGE);
System.out.println(" DONE (" + getTime() + " ms)");
}
// Normal files
for (Source f : files) {
System.out.print("Parsing " + f.getTypeName() + " [" + f.getName() + "]...");
af = p.parse(f, af, AndromedaFileInfo.TYPE_MAIN);
System.out.println(" DONE (" + getTime() + " ms)");
}
// Triggers in the input map if one was specified
if (triggers != null) {
for (Source f : triggers) {
System.out.print("Parsing " + f.getTypeName() + " [" + f.getName() + "]...");
af = p.parse(f, af, AndromedaFileInfo.TYPE_MAIN);
System.out.println(" DONE (" + getTime() + " ms)");
}
}
return af;
}
@Override
public String getName() {
return base.getName();
}
/**
* Creates a SourceRef object from a Source object. The Server argument is required to build the
* URI in the SourceRef pointing to the full Source resource.
*
* @param source The Source to build the SourceRef from.
* @param server The Server where the Source is located.
*/
public SourceRef(Source source, Server server) {
this(source, server.getHostName() + Server.SOURCES_URI + "/" + source.getName());
}
/**
* Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor. The Set contains
* all the primary keys that exist on a particular class that are used by the source, without
* performing any recursion. The Model.getClassDescriptorsForClass() method is recommended if you
* wish for all the primary keys of the class' parents as well.
*
* @param cld the ClassDescriptor
* @param source the Source
* @param os the ObjectStore that these PrimaryKeys are used in, for creating indexes
* @return a Set of PrimaryKeys
*/
public static Set<PrimaryKey> getPrimaryKeys(ClassDescriptor cld, Source source, ObjectStore os) {
GetPrimaryKeyCacheKey key = new GetPrimaryKeyCacheKey(cld, source);
synchronized (getPrimaryKeyCache) {
Set<PrimaryKey> keySet = getPrimaryKeyCache.get(key);
if (keySet == null) {
keySet = new LinkedHashSet<PrimaryKey>();
Properties keys = getKeyProperties(source);
if (keys != null) {
if (!verifiedSources.contains(source)) {
String packageNameWithDot =
cld.getName().substring(0, cld.getName().lastIndexOf('.') + 1);
LOG.info(
"Verifying primary key config for source "
+ source
+ ", packageName = "
+ packageNameWithDot);
for (Map.Entry<Object, Object> entry : keys.entrySet()) {
String cldName = (String) entry.getKey();
String keyList = (String) entry.getValue();
if (!cldName.contains(".")) {
ClassDescriptor iCld =
cld.getModel().getClassDescriptorByName(packageNameWithDot + cldName);
if (iCld != null) {
Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(iCld);
String[] tokens = keyList.split(",");
for (int i = 0; i < tokens.length; i++) {
String token = tokens[i].trim();
if (map.get(token) == null) {
throw new IllegalArgumentException(
"Primary key "
+ token
+ " for class "
+ cldName
+ " required by datasource "
+ source.getName()
+ " in "
+ source.getName()
+ "_keys.properties is not defined in "
+ cld.getModel().getName()
+ "_keyDefs.properties");
}
}
} else {
LOG.warn(
"Ignoring entry for "
+ cldName
+ " in file "
+ cld.getModel().getName()
+ "_keyDefs.properties - not in model!");
}
}
}
verifiedSources.add(source);
}
Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(cld);
String cldName = TypeUtil.unqualifiedName(cld.getName());
String keyList = (String) keys.get(cldName);
if (keyList != null) {
String[] tokens = keyList.split(",");
for (int i = 0; i < tokens.length; i++) {
String token = tokens[i].trim();
if (map.get(token) == null) {
throw new IllegalArgumentException(
"Primary key "
+ token
+ " for class "
+ cld.getName()
+ " required by data source "
+ source.getName()
+ " in "
+ source.getName()
+ "_keys.properties is not defined in "
+ cld.getModel().getName()
+ "_keyDefs.properties");
} else {
keySet.add(map.get(token));
}
}
}
for (Map.Entry<Object, Object> entry : keys.entrySet()) {
String propKey = (String) entry.getKey();
String fieldList = (String) entry.getValue();
int posOfDot = propKey.indexOf('.');
if (posOfDot > 0) {
String propCldName = propKey.substring(0, posOfDot);
if (cldName.equals(propCldName)) {
String keyName = propKey.substring(posOfDot + 1);
PrimaryKey pk = new PrimaryKey(keyName, fieldList, cld);
if (!keySet.contains(pk)) {
keySet.add(pk);
if (os instanceof ObjectStoreInterMineImpl) {
ObjectStoreInterMineImpl osimi = (ObjectStoreInterMineImpl) os;
DatabaseSchema schema = osimi.getSchema();
ClassDescriptor tableMaster = schema.getTableMaster(cld);
String tableName = DatabaseUtil.getTableName(tableMaster);
List<String> fields = new ArrayList<String>();
for (String field : pk.getFieldNames()) {
String colName = DatabaseUtil.generateSqlCompatibleName(field);
if (tableMaster.getReferenceDescriptorByName(field, true) != null) {
colName += "id";
}
fields.add(colName);
}
String sql =
"CREATE INDEX "
+ tableName
+ "__"
+ keyName
+ " ON "
+ tableName
+ " ("
+ StringUtil.join(fields, ", ")
+ ")";
System.out.println("Creating index: " + sql);
LOG.info("Creating index: " + sql);
Connection conn = null;
try {
conn = osimi.getConnection();
conn.createStatement().execute(sql);
} catch (SQLException e) {
LOG.warn("Index creation failed", e);
} finally {
if (conn != null) {
osimi.releaseConnection(conn);
}
}
}
}
}
}
}
} else {
throw new IllegalArgumentException(
"Unable to find keys for source "
+ source.getName()
+ " in file "
+ source.getName()
+ "_keys.properties");
}
getPrimaryKeyCache.put(key, keySet);
}
return keySet;
}
}
private static String makeKey(Source source, String shortcutId) {
return source.getName() + "#" + shortcutId;
}
public String getName() {
return mSource.getName();
}
