/**
* Adds objects to the a bag for the matches against a set of identifiers.
*
* @param ids A collection of identifiers
* @param bag The bag to add the objects to
* @param type The type of this bag
* @param extraFieldValue An extra value for disambiguation.
* @param unmatchedIds An accumulator to store the failed matches.
* @param acceptableIssues the list of issues that are OK to ignore.
* @throws ClassNotFoundException if the type is not a valid class.
* @throws InterMineException If something goes wrong building the bag.
* @throws ObjectStoreException If there is a problem on the database level.
*/
protected void addIdsToList(
final Collection<? extends String> ids,
final InterMineBag bag,
final String type,
final String extraFieldValue,
final Set<String> unmatchedIds,
final Collection<String> acceptableIssues)
throws ClassNotFoundException, InterMineException, ObjectStoreException {
final BagQueryResult result =
runner.searchForBag(
type,
new ArrayList<String>(ids),
extraFieldValue,
acceptableIssues.contains(BagQueryResult.WILDCARD));
bag.addIdsToBag(result.getMatches().keySet(), type);
for (final String issueType : result.getIssues().keySet()) {
if (acceptableIssues.contains(issueType)) {
bag.addIdsToBag(result.getIssueIds(issueType), type);
} else {
unmatchedIds.addAll(result.getInputIdentifiersForIssue(issueType));
}
}
unmatchedIds.addAll(result.getUnresolvedIdentifiers());
}
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();
}
}
private ActionForward createBagAndGoToBagDetails(
ActionMapping mapping, InterMineBag imBag, List<Integer> bagList)
throws ObjectStoreException {
imBag.addIdsToBag(bagList, imBag.getType());
return new ForwardParameters(mapping.findForward("bagDetails"))
.addParameter("bagName", imBag.getName())
.forward();
}
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();
}
}