protected InterMineBag createEmployeeList() throws Exception {
ObjectStoreWriter osw = null;
try {
Profile superUser = im.getProfileManager().getSuperuserProfile();
osw = ObjectStoreWriterFactory.getObjectStoreWriter("osw.unittest");
Employee e1 = new Employee();
e1.setName("Employee1");
Employee e2 = new Employee();
e2.setName("Employee2");
Department d1 = new Department();
d1.setName("department");
Company company = new CompanyShadow();
company.setName("company");
Contractor contractor = new Contractor();
contractor.setName("contractor");
osw.store(contractor);
company.addContractors(contractor);
osw.store(company);
d1.setCompany(company);
osw.store(d1);
e1.setDepartment(d1);
e2.setDepartment(d1);
osw.store(e1);
osw.store(e2);
InterMineBag list = superUser.createBag("employeeList", "Employee", "", im.getClassKeys());
Collection<Integer> ids = new ArrayList<Integer>();
ids.add(e1.getId());
ids.add(e2.getId());
list.addIdsToBag(ids, "Employee");
return list;
} finally {
osw.close();
}
}
public void tearDown() throws Exception {
LOG.info("in tear down");
ObjectStoreWriter osw = ObjectStoreWriterFactory.getObjectStoreWriter("osw.unittest");
if (osw.isInTransaction()) {
osw.abortTransaction();
}
Query q = new Query();
QueryClass qc = new QueryClass(InterMineObject.class);
q.addFrom(qc);
q.addToSelect(qc);
SingletonResults res = osw.getObjectStore().executeSingleton(q);
LOG.info("created results");
Iterator resIter = res.iterator();
osw.beginTransaction();
while (resIter.hasNext()) {
InterMineObject o = (InterMineObject) resIter.next();
LOG.info("deleting: " + o.getId());
osw.delete(o);
}
osw.commitTransaction();
LOG.info("committed transaction");
osw.close();
LOG.info("closed objectstore");
}
@AfterClass
public static void shutdown() {
int deleted = 0;
if (osw != null) {
try {
osw.beginTransaction();
PathQuery pq = new PathQuery(osw.getModel());
pq.addView("Types.id");
pq.addConstraint(Constraints.eq("Types.name", "histo*"));
Query q = MainHelper.makeQuery(pq, new HashMap(), new HashMap(), null, new HashMap());
Results res = osw.execute(q, 50000, true, false, true);
for (Object row : res) {
Types thing = (Types) ((List) row).get(0);
osw.delete(thing);
deleted++;
}
osw.commitTransaction();
} catch (ObjectStoreException e) {
LOG.warn(e);
}
try {
osw.close();
} catch (ObjectStoreException e) {
LOG.warn(e);
}
}
System.out.printf("\n[CLEAN UP] Deleted %d things\n", deleted);
}
protected InterMineBag createCompanyList() throws Exception {
ObjectStoreWriter osw = null;
try {
osw = ObjectStoreWriterFactory.getObjectStoreWriter("osw.unittest");
Profile superUser = im.getProfileManager().getSuperuserProfile();
Company c1 = new CompanyShadow();
c1.setName("CompanyA");
Company c2 = new CompanyShadow();
c2.setName("CompanyB");
osw.store(c1);
osw.store(c2);
InterMineBag list = superUser.createBag("companyList", "Company", "", im.getClassKeys());
Collection<Integer> ids = new ArrayList<Integer>();
ids.add(c1.getId());
ids.add(c2.getId());
list.addIdsToBag(ids, "Company");
return list;
} finally {
osw.close();
}
}
/**
* Run the task
*
* @throws BuildException if a problem occurs
*/
@Override
public void execute() {
if (clsName == null) {
throw new BuildException("clsName attribute is not set");
}
if (getOsName() == null) {
throw new BuildException("osName attribute is not set");
}
if (getModelName() == null) {
throw new BuildException("modelName attribute is not set");
}
if (dbAlias == null) {
throw new BuildException("dbAlias attribute is not set");
}
try {
ObjectStoreWriter osw = ObjectStoreWriterFactory.getObjectStoreWriter(getOsName());
ObjectStoreItemWriter writer = new ObjectStoreItemWriter(osw);
Database database = DatabaseFactory.getDatabase(dbAlias);
Class<?> c = Class.forName(clsName);
if (!DBConverter.class.isAssignableFrom(c)) {
throw new IllegalArgumentException(
"Class (" + clsName + ") is not a subclass of " + DBConverter.class.getName());
}
Constructor<?> m =
c.getConstructor(new Class[] {Database.class, Model.class, ItemWriter.class});
Model model = Model.getInstanceByName(getModelName());
DBConverter converter = (DBConverter) m.newInstance(new Object[] {database, model, writer});
configureDynamicAttributes(converter);
converter.process();
converter.close();
converter.getItemWriter().close();
osw.close();
} catch (Exception e) {
throw new BuildException("problem while running converter reading from db: " + dbAlias, e);
}
}
/**
* Run the task
*
* @throws org.apache.tools.ant.BuildException if a problem occurs
*/
public void execute() {
ObjectStoreWriter osw = null;
try {
osw = ObjectStoreWriterFactory.getObjectStoreWriter(osName);
Class c = Class.forName(clsName);
if (!PostProcessor.class.isAssignableFrom(c)) {
throw new IllegalArgumentException(
"Class ("
+ clsName
+ ") is not a subclass"
+ "of org.intermine.postprocess.PostProcessor!");
}
Constructor m = c.getConstructor(new Class[] {ObjectStoreWriter.class});
PostProcessor pp = (PostProcessor) m.newInstance(new Object[] {osw});
configureDynamicAttributes(pp);
pp.postProcess();
} catch (Exception e) {
throw new BuildException(e);
} finally {
try {
if (osw != null) {
osw.close();
}
} catch (Exception e) {
throw new BuildException(e);
}
}
}
/**
* Run the task.
*
* @throws BuildException if a problem occurs
*/
public void execute() {
if (dataDir == null) {
throw new BuildException("dataDir must be specified");
}
File dir = new File(dataDir);
String directoryName = dir.getName();
if (!dir.isDirectory()) {
throw new BuildException("dataDir is not a directory:" + directoryName);
}
if (dir.listFiles().length == 0) {
throw new BuildException("dataDir contains no files:" + directoryName);
}
if (clsName == null) {
throw new BuildException("clsName attribute is not set");
}
if (getOsName() == null) {
throw new BuildException("osName attribute is not set");
}
if (getModelName() == null) {
throw new BuildException("modelName attribute is not set");
}
// Needed so that STAX can find its implementation classes
ClassLoader cl = Thread.currentThread().getContextClassLoader();
Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
ObjectStoreWriter osw = null;
ItemWriter writer = null;
try {
Model model = Model.getInstanceByName(getModelName());
osw = ObjectStoreWriterFactory.getObjectStoreWriter(getOsName());
writer = new ObjectStoreItemWriter(osw);
Class c = Class.forName(clsName);
if (!DirectoryConverter.class.isAssignableFrom(c)) {
throw new IllegalArgumentException(
"Class ("
+ clsName
+ ") is not a subclass"
+ "of org.intermine.dataconversion.Directory.");
}
Constructor m = c.getConstructor(new Class[] {ItemWriter.class, Model.class});
DirectoryConverter converter =
(DirectoryConverter) m.newInstance(new Object[] {writer, model});
try {
configureDynamicAttributes(converter);
File file = new File(dataDir);
if (file.isDirectory()) {
converter.process(file);
} else {
throw new IllegalArgumentException(dataDir + " is not a directory");
}
} finally {
converter.close();
}
} catch (Exception e) {
throw new BuildException(e);
} finally {
Thread.currentThread().setContextClassLoader(cl);
try {
if (writer != null) {
writer.close();
}
if (writer != null) {
osw.close();
}
} catch (Exception e) {
throw new BuildException(e);
}
}
try {
doSQL(osw.getObjectStore());
} catch (Exception e) {
throw new BuildException(e);
}
}
