Example usage for java.util ArrayList remove

List of usage examples for java.util ArrayList remove

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Introduction

In this page you can find the example usage for java.util ArrayList remove.

Prototype

public boolean remove(Object o)

Source Link

Document

Removes the first occurrence of the specified element from this list, if it is present.

Usage

From source file:gov.nih.nci.cabig.caaers.api.impl.SAEEvaluationServiceImpl.java

/**
 * To Create or Update Advese Events.//from   w ww . j  av a 2  s  .  c o m
 * Sync Flag is used only incase of SAE Evaluation service, As service can soft-delete the Adverse Events.
 * @param rpSrc
 * @param errors
 * @param syncFlag
 * @return
 */

private AdverseEventReportingPeriod createOrUpdateAdverseEvents(AdverseEventReportingPeriod rpSrc,
        ValidationErrors errors, boolean syncFlag) {

    Study study = fetchStudy(rpSrc.getStudy().getFundingSponsorIdentifierValue());
    if (study == null) {
        logger.error("Study not present in caAERS with the sponsor identifier : "
                + rpSrc.getStudy().getFundingSponsorIdentifierValue());
        errors.addValidationError(
                "WS_AEMS_003", "Study with sponsor identifier "
                        + rpSrc.getStudy().getFundingSponsorIdentifierValue() + " does not exist in caAERS",
                rpSrc.getStudy().getFundingSponsorIdentifierValue());
        return null;
    }
    //async update study removed because the updates would most likely happen after this process is finished.

    //migrate the domain object
    AdverseEventReportingPeriod rpDest = new AdverseEventReportingPeriod();
    DomainObjectImportOutcome<AdverseEventReportingPeriod> rpOutcome = new DomainObjectImportOutcome<AdverseEventReportingPeriod>();
    reportingPeriodMigrator.migrate(rpSrc, rpDest, rpOutcome);
    logger.info("Reporting period migration result :" + String.valueOf(rpOutcome.getMessages()));
    if (rpOutcome.hasErrors()) {
        //translate error and create a response.
        logger.error("Errors while migrating :" + String.valueOf(rpOutcome.getErrorMessages()));
        errors.addValidationErrors(rpOutcome.getValidationErrors().getErrors());
        return null;
    }

    //check if we need the create path or update path.
    String tac = rpDest.getTreatmentAssignment() != null ? rpDest.getTreatmentAssignment().getCode() : null;
    String epochName = rpDest.getEpoch() != null ? rpDest.getEpoch().getName() : null;
    AdverseEventReportingPeriod rpFound = rpDest.getAssignment().findReportingPeriod(rpDest.getExternalId(),
            rpDest.getStartDate(), rpDest.getEndDate(), rpDest.getCycleNumber(), epochName, tac);

    ArrayList<AdverseEventReportingPeriod> reportingPeriodList = new ArrayList<AdverseEventReportingPeriod>(
            rpDest.getAssignment().getActiveReportingPeriods());
    if (rpFound != null) {
        // This is used only incase of SAE Evaluation Service.
        if (syncFlag) {
            syncAdverseEventWithSrc(rpFound, rpSrc);
        }
        int i = findIndexFromReportPeriodList(reportingPeriodList, rpFound);
        if (i >= 0)
            reportingPeriodList.remove(i);
    }

    ValidationErrors dateValidationErrors = validateRepPeriodDates(rpDest, reportingPeriodList,
            rpDest.getAssignment().getStartDateOfFirstCourse(), rpDest.getEpoch());
    logger.info("Reporting period validation result :" + String.valueOf(dateValidationErrors));
    if (dateValidationErrors.hasErrors()) {
        //translate errors and create a response
        logger.error("Errors while migrating :" + String.valueOf(dateValidationErrors));
        errors.addValidationErrors(dateValidationErrors.getErrors());
        return null;
    }

    //validate adverse events
    for (AdverseEvent adverseEvent : rpDest.getAdverseEvents()) {
        if (adverseEvent.getGradedDate() == null)
            adverseEvent.setGradedDate(new Date());
        Set<ConstraintViolation<AdverseEvent>> constraintViolations = validator.validate(adverseEvent,
                AdverseEventGroup.class, Default.class);
        if (!constraintViolations.isEmpty()) {
            //translate errors to response.
            for (ConstraintViolation<AdverseEvent> v : constraintViolations) {
                errors.addValidationError("WS_GEN_006", v.getMessage(), v.getPropertyPath());
            }
            return null;
        }
    }
    // validate Reporting Period.
    AdverseEventReportingPeriod rpTarget = rpFound;
    if (rpTarget == null)
        rpTarget = rpDest;

    Set<ConstraintViolation<AdverseEventReportingPeriod>> constraintViolations = validator.validate(rpTarget,
            CourseCycleGroup.class, Default.class);
    if (!constraintViolations.isEmpty()) {
        //translate errors to response.
        for (ConstraintViolation<AdverseEventReportingPeriod> v : constraintViolations) {
            errors.addValidationError("WS_GEN_006", v.getMessage(), v.getPropertyPath());
        }
        return null;
    }

    if (rpFound == null) {
        //new reporting period
        rpFound = rpDest;
        rpFound.getAssignment().addReportingPeriod(rpFound);
        // Validate the Reporting Period before saving.
        adverseEventValidatior.validate(rpFound, rpFound.getStudy(), errors);
        adverseEventReportingPeriodDao.save(rpFound);
        if (configuration.get(Configuration.ENABLE_WORKFLOW)) {
            Long wfId = adverseEventRoutingAndReviewRepository.enactReportingPeriodWorkflow(rpFound);
            logger.debug("Enacted workflow : " + wfId);
        }
    } else {
        //existing reporting period.
        reportingPeriodSynchronizer.migrate(rpDest, rpFound, rpOutcome);
        // Validate the Reporting Period before saving.
        adverseEventValidatior.validate(rpFound, rpFound.getStudy(), errors);
        if (errors.hasErrors()) {
            logger.error(
                    "Error(s) while validating with Adverse Event " + String.valueOf(errors.getErrorCount()));
            return null;
        }
        adverseEventReportingPeriodDao.save(rpFound);

    }
    return rpFound;
}

From source file:com.hichinaschool.flashcards.libanki.Models.java

public void moveTemplate(JSONObject m, JSONObject template, int idx) {
    try {//from ww  w .j ava 2  s  .c om
        JSONArray ja = m.getJSONArray("tmpls");
        int oldidx = -1;
        ArrayList<JSONObject> l = new ArrayList<JSONObject>();
        HashMap<Integer, Integer> oldidxs = new HashMap<Integer, Integer>();
        for (int i = 0; i < ja.length(); ++i) {
            if (ja.get(i).equals(template)) {
                oldidx = i;
                if (idx == oldidx) {
                    return;
                }
            }
            JSONObject t = ja.getJSONObject(i);
            oldidxs.put(t.hashCode(), t.getInt("ord"));
            l.add(t);
        }
        l.remove(oldidx);
        l.add(idx, template);
        m.put("tmpls", new JSONArray(l));
        _updateTemplOrds(m);
        // generate change map - We use StringBuilder
        StringBuilder sb = new StringBuilder();
        ja = m.getJSONArray("tmpls");
        for (int i = 0; i < ja.length(); ++i) {
            JSONObject t = ja.getJSONObject(i);
            sb.append("when ord = ").append(oldidxs.get(t.hashCode())).append(" then ").append(t.getInt("ord"));
            if (i != ja.length() - 1) {
                sb.append(" ");
            }
        }
        // apply
        save(m);
        mCol.getDb().execute(
                "update cards set ord = (case " + sb.toString()
                        + " end),usn=?,mod=? where nid in (select id from notes where mid = ?)",
                new Object[] { mCol.usn(), Utils.intNow(), m.getLong("id") });
    } catch (JSONException e) {
        throw new RuntimeException(e);
    }
}

From source file:com.hichinaschool.flashcards.libanki.Models.java

public void moveField(JSONObject m, JSONObject field, int idx) {
    mCol.modSchema();//from   w  ww . j  a va  2s . co  m
    try {
        JSONArray ja = m.getJSONArray("flds");
        ArrayList<JSONObject> l = new ArrayList<JSONObject>();
        int oldidx = -1;
        for (int i = 0; i < ja.length(); ++i) {
            l.add(ja.getJSONObject(i));
            if (field.equals(ja.getJSONObject(i))) {
                oldidx = i;
                if (idx == oldidx) {
                    return;
                }
            }
        }
        // remember old sort field
        String sortf = Utils.jsonToString(m.getJSONArray("flds").getJSONObject(m.getInt("sortf")));
        // move
        l.remove(oldidx);
        l.add(idx, field);
        m.put("flds", new JSONArray(l));
        // restore sort field
        ja = m.getJSONArray("flds");
        for (int i = 0; i < ja.length(); ++i) {
            if (Utils.jsonToString(ja.getJSONObject(i)).equals(sortf)) {
                m.put("sortf", i);
                break;
            }
        }
        _updateFieldOrds(m);
        save(m);
        _transformFields(m, new TransformFieldMove(idx, oldidx));
        renameField(m, field, null);
    } catch (JSONException e) {
        throw new RuntimeException(e);
    }

}

From source file:com.krawler.spring.crm.common.crmManagerDAOImpl.java

public KwlReturnObject getMaster(HashMap<String, Object> requestParams) throws ServiceException {
    List ll = null;/* ww  w  .ja  va 2  s  .c  om*/
    int dl = 0;
    try {
        ArrayList filter_params = new ArrayList();
        ArrayList hqlfilter_names = new ArrayList();
        hqlfilter_names.add("NOTINcomboname");
        String hql = "from CrmCombomaster cm";
        ArrayList hqlfilter_params = new ArrayList();
        String filtercombos = Constants.MASTERCONFIG_HIDECOMBO;
        if (!requestParams.containsKey("allowLeadType")) {
            filtercombos += ",'Lead Type'";
        }

        hqlfilter_params.add(filtercombos);
        String hqlfilterQuery = StringUtil.filterQuery(hqlfilter_names, "where");
        int ind = hqlfilterQuery.indexOf("(");
        if (ind > -1) {
            int index = Integer.valueOf(hqlfilterQuery.substring(ind + 1, ind + 2));
            hqlfilterQuery = hqlfilterQuery.replaceAll("(" + index + ")",
                    hqlfilter_params.get(index).toString());
            hqlfilter_params.remove(index);
        }
        hql += hqlfilterQuery;
        if (requestParams.containsKey(Constants.filter_params)) {
            ArrayList filter_params1 = (ArrayList) requestParams.get(Constants.filter_params);
            filter_params.addAll(filter_params1);
            ArrayList filter_names = (ArrayList) requestParams.get("filter_names");
            String filterQuery = StringUtil.filterQuery(filter_names, "and");
            hql += filterQuery;
        }
        hql += " order by comboname";
        ll = executeQuery(hql, filter_params.toArray());
        dl = ll.size();
    } catch (Exception e) {
        throw ServiceException.FAILURE("crmManager.getMaster", e);
    }
    return new KwlReturnObject(true, KWLErrorMsgs.S01, "", ll, dl);
}

From source file:ca.uhn.fhir.jpa.term.TerminologyLoaderSvc.java

private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain,
        Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {

    theChain.add(theConcept.getCode());/* www .  ja va  2s  .c o  m*/
    for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter
            .hasNext();) {
        TermConceptParentChildLink next = childIter.next();
        TermConcept nextChild = next.getChild();
        if (theChain.contains(nextChild.getCode())) {

            StringBuilder b = new StringBuilder();
            b.append("Removing circular reference code ");
            b.append(nextChild.getCode());
            b.append(" from parent ");
            b.append(next.getParent().getCode());
            b.append(". Chain was: ");
            for (String nextInChain : theChain) {
                TermConcept nextCode = theCode2concept.get(nextInChain);
                b.append(nextCode.getCode());
                b.append('[');
                b.append(StringUtils.substring(nextCode.getDisplay(), 0, 20).replace("[", "").replace("]", "")
                        .trim());
                b.append("] ");
            }
            ourLog.info(b.toString(), theConcept.getCode());
            childIter.remove();
            nextChild.getParents().remove(next);

        } else {
            dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
        }
    }
    theChain.remove(theChain.size() - 1);

}

From source file:com.mellanox.r4h.DFSInputStream.java

private ByteBuffer getFirstToComplete(CompletionService<ByteBuffer> hedgedService,
        ArrayList<Future<ByteBuffer>> futures) throws InterruptedException {
    if (futures.isEmpty()) {
        throw new InterruptedException("let's retry");
    }/*ww  w  . jav  a  2  s  . c  o m*/
    Future<ByteBuffer> future = null;
    try {
        future = hedgedService.take();
        ByteBuffer bb = future.get();
        futures.remove(future);
        return bb;
    } catch (ExecutionException e) {
        // already logged in the Callable
        futures.remove(future);
    } catch (CancellationException ce) {
        // already logged in the Callable
        futures.remove(future);
    }

    throw new InterruptedException("let's retry");
}

From source file:com.cttapp.bby.mytlc.layer8apps.CalendarHandler.java

private ArrayList<Shift> checkForDuplicates(ArrayList<Shift> newShifts) {
    Preferences pf = new Preferences(this);
    ArrayList<String> oldShifts = pf.getSavedShifts();

    ContentResolver cr = getContentResolver();

    for (String id : oldShifts) {
        Cursor cursor = cr.query(getEventsUri(), new String[] { "dtstart", "dtend" },
                "CALENDAR_ID = " + calID + " AND _ID = " + id, null, null);

        if (!cursor.moveToFirst()) {
            continue;
        }/*w w  w.j ava2 s . c om*/

        do {
            Calendar now = Calendar.getInstance();

            Calendar startTime = Calendar.getInstance();
            startTime.setTimeInMillis(cursor.getLong(0));

            Calendar endTime = Calendar.getInstance();
            endTime.setTimeInMillis(cursor.getLong(1));

            if (endTime.compareTo(now) == -1) {
                deleteShift(id);
                continue;
            }

            boolean shiftFound = false;

            for (Shift shift : newShifts) {
                if (shift.getStartDate().get(Calendar.HOUR_OF_DAY) == startTime.get(Calendar.HOUR_OF_DAY)
                        && shift.getEndDate().get(Calendar.MINUTE) == shift.getEndDate().get(Calendar.MINUTE)) {
                    newShifts.remove(shift);
                    shiftFound = true;
                    break;
                }
            }

            if (!shiftFound) {
                cr.delete(getEventsUri(), "CALENDAR_ID = " + calID + " AND _ID = " + String.valueOf(id), null);
            }
        } while (cursor.moveToNext());
    }
    return newShifts;
}

From source file:edu.isi.karma.er.helper.SPARQLGeneratorUtil.java

/**
 * @author shri/*from  w ww . j  a va  2  s.c  o  m*/
 * This method will genereate a sparql query to select the list of columns (in the order they are provided)
 * 
 * @param root This object of TriplesMap is the root from which this method begins to fetch columns
 * @param columns This ArrayList<String> has the list of columns to be fetched. These columns are identifyed by their complete URL as defined in the ontology. <br /> 
 * For example: <http://isi.edu/integration/karma/ontologies/model/accelerometer#AccelerometerReading>. Now there may exists many instance of a class in within the same ontology. 
 * */
public String get_query(TriplesMap root, ArrayList<HashMap<String, String>> columns, boolean distinct_query) {

    ArrayList<Object> queue = new ArrayList<>();
    queue.add(root);
    StringBuffer query = new StringBuffer();
    this.var_count = 1;
    this.prefix_list = new HashMap<>();
    this.select_params = new StringBuffer();
    //      ArrayList<String> select_param = new ArrayList<String>();
    HashMap<TriplesMap, String> markedTriples = new HashMap<>();

    ArrayList<String> visited_columns = new ArrayList<>();
    this.ParentMapingInfoList = new HashMap<>();

    // save the column predicate url and the column name to be dislayed
    HashMap<Predicate, String> predicateList = new HashMap<>();
    HashMap<String, String> columnList = new HashMap<>();
    if (columns != null && !columns.isEmpty()) {
        //         for (String k : columns) {
        //            int index = 0;
        //            if(k.indexOf("#") > 0) {
        //               index = k.lastIndexOf('#')+1;
        //            } else if(k.indexOf("/") > 0) {
        //               index = k.lastIndexOf('/')+1;
        //            }
        //            columnList.put(k, k.substring(index, k.length()));
        //         }
        for (HashMap<String, String> col : columns) {
            columnList.put(col.get("name"), col.get("url"));
        }
    }

    // using a BFS approach, we traverse the tree from the root node and add triples/predicates to the queue
    while (!queue.isEmpty()) {
        Object currentObj = queue.remove(0);

        // if this is a tripleMap, then add all its RefObjects to the queue
        // for the predicates, add only the ones that satisfy the criteria of being <...hasValue>
        if (currentObj instanceof TriplesMap) {
            String var = "x" + var_count;
            TriplesMap triple = (TriplesMap) currentObj;
            boolean foundHasValue = false;
            List<PredicateObjectMap> predicates = triple.getPredicateObjectMaps();

            for (PredicateObjectMap p_map : predicates) {

                if (p_map.getObject().hasRefObjectMap()) {
                    RefObjectMap objMap = p_map.getObject().getRefObjectMap();
                    queue.add(objMap.getParentTriplesMap());

                    logger.info(triple.getSubject().getId() + "  ---> "
                            + objMap.getParentTriplesMap().getSubject().getId());

                    // maintain a list of mapping properties between triples
                    ParentMapingInfoList.put(objMap.getParentTriplesMap().getSubject().getId(),
                            new ParentMapingInfo(triple, p_map.getPredicate()));

                } else {
                    queue.add(p_map.getPredicate());
                    predicateList.put(p_map.getPredicate(), var);
                    foundHasValue = true;
                }
            }
            // if this triple is marked to be included in the query,
            // we add it to the markedTriples list and add to the query string
            // for its class type Eg. 
            // Prefix pref1: <.../.../Input>
            // x2 a pref1:
            if (foundHasValue) {
                markedTriples.put(triple, var);
                String rdfsTypes = triple.getSubject().getRdfsType().get(0).toString();
                this.prefix_list.put("pref" + var_count, rdfsTypes);
                query.append(" ?" + var + " a pref" + var_count + ": .");

                // if the parent of this triple is also marked for the query
                // then we add the relation to between triples to the query. Eg.

                //               TriplesMap parentTriple = parent.get(triple.getSubject().getId());
                ParentMapingInfo parentTriple = ParentMapingInfoList.get(triple.getSubject().getId());

                // from the current node, keep poping out till we reach the last node in the 
                // parent map to see if any of the parents are connected
                if (parentTriple != null) {
                    String sq = checkParentMarked(triple, markedTriples, var);
                    if (sq.length() > 1) {
                        query.append(sq);
                    }

                }
                //               if( parentTriple != null && markedTriples.containsKey(parentTriple.parent)) {
                //                  String predicate = parentTriple.predicate.getTemplate().toString();
                ////                  PredicateObjectMap parentPredicate = getPredicateBetweenTriples(triple, parentTriple);
                //                  if(predicate != null) {
                //                     query.append(" ?" + markedTriples.get(parentTriple.parent) + " " + 
                //                        predicate + " ?"+var + " . ");
                //                  } else {
                //                     System.out.println("predicate is null from parent : " + triple.getSubject().getRdfsType().toString());
                //                  }
                //               }

            }
            var_count++;
        }
        // if it is a predicate Object, create a variable in in the query string
        else if (currentObj instanceof Predicate) {
            Predicate predicate = (Predicate) currentObj;
            String k = predicate.getTemplate().toString();
            k = k.replace('<', ' ').replace('>', ' ').trim();
            if (columns != null && !columns.isEmpty()) {
                //               if(columnList.containsKey(k)) {
                if (columnList.containsValue(k)) {
                    Iterator<String> itr = columnList.keySet().iterator();
                    while (itr.hasNext()) {
                        String cName = itr.next();
                        if (columnList.get(cName).equals(k) && !visited_columns.contains(cName)) {
                            // get the column name from the end of this url - either the last '/' or the '#'
                            query.append(" ?" + predicateList.get(predicate)).append(" ")
                                    .append(predicate.getTemplate()).append(" ?").append(cName + " . ");
                            //columnList.remove(cName);
                            visited_columns.add(cName);
                            var_count++;
                            break;
                        }
                    }
                    // get the column name from the end of this url - either the last '/' or the '#'
                    //                  query.append(" ?" + predicateList.get(predicate))
                    //                     .append(" ")
                    //                     .append(predicate.getTemplate())
                    //                     .append(" ?")
                    //                     .append(columnList.get(k) + " . ");
                    //                  var_count++;
                } else {
                    logger.info("ColumnList does not contain : " + k + " " + currentObj);
                }
            } else {
                int index = 0;
                if (k.indexOf("#") > 0) {
                    index = k.lastIndexOf('#') + 1;
                } else if (k.indexOf("/") > 0) {
                    index = k.lastIndexOf('/') + 1;
                }
                query.append(" ?" + predicateList.get(predicate)).append(" ").append(predicate.getTemplate())
                        .append(" ?").append(k.substring(index, k.length())).append(" .");
                var_count++;
            }

        }
        // if this is a RefObject add the Child Triple to the queue
        else if (currentObj instanceof RefObjectMap) {
            RefObjectMap refObj = (RefObjectMap) currentObj;
            TriplesMap t = refObj.getParentTriplesMap();
            queue.add(t);

        }
    }

    // append the list of prefixes
    Iterator<String> itr = this.prefix_list.keySet().iterator();
    StringBuffer sQuery = new StringBuffer();
    while (itr.hasNext()) {
        String key = itr.next();
        sQuery.append(" PREFIX ").append(key).append(": ").append(this.prefix_list.get(key));
    }
    // append the columns to be selected in the order they are specified
    sQuery.append(" select ");
    if (distinct_query) {
        sQuery.append(" distinct ");
    }
    for (HashMap<String, String> s : columns) {
        sQuery.append(" ?" + s.get("name"));
    }
    sQuery.append(" where { ").append(query.toString()).append(" } ");
    logger.info("Generated Query : " + sQuery);
    return sQuery.toString();
}

From source file:org.opendatakit.security.server.SecurityServiceUtil.java

/**
 * Method to enforce an access configuration constraining only registered users, authenticated
 * users and anonymous access./*  www . j  a  v a2 s  .c  o m*/
 * 
 * Add additional checks of the incoming parameters and patch things up if the incoming list of
 * users omits the super-user.
 * 
 * @param users
 * @param anonGrants
 * @param allGroups
 * @param cc
 * @throws DatastoreFailureException
 * @throws AccessDeniedException
 */
public static final void setStandardSiteAccessConfiguration(ArrayList<UserSecurityInfo> users,
        ArrayList<GrantedAuthorityName> allGroups, CallingContext cc)
        throws DatastoreFailureException, AccessDeniedException {

    // remove anonymousUser from the set of users and collect its
    // permissions (anonGrantStrings) which will be placed in
    // the granted authority hierarchy table.
    List<String> anonGrantStrings = new ArrayList<String>();
    {
        UserSecurityInfo anonUser = null;
        for (UserSecurityInfo i : users) {
            if (i.getType() == UserType.ANONYMOUS) {
                anonUser = i;
                // clean up grants for anonymousUser --
                // ignore anonAuth (the grant under which we will place things)
                // and forbid Site Admin
                for (GrantedAuthorityName a : i.getAssignedUserGroups()) {
                    if (anonAuth.getAuthority().equals(a.name()))
                        continue; // avoid circularity...
                    // only allow ROLE_ATTACHMENT_VIEWER and GROUP_ assignments.
                    if (!a.name().startsWith(GrantedAuthorityName.GROUP_PREFIX)) {
                        continue;
                    }
                    // do not allow Site Admin assignments for Anonymous --
                    // or Tables super-user or Tables Administrator.
                    // those all give access to the full set of users on the system
                    // and giving that information to Anonymous is a security
                    // risk.
                    if (GrantedAuthorityName.GROUP_SITE_ADMINS.equals(a)
                            || GrantedAuthorityName.GROUP_ADMINISTER_TABLES.equals(a)
                            || GrantedAuthorityName.GROUP_SUPER_USER_TABLES.equals(a)) {
                        continue;
                    }
                    anonGrantStrings.add(a.name());
                }
                break;
            }
        }
        if (anonUser != null) {
            users.remove(anonUser);
        }
    }

    // scan through the users and remove any entries under assigned user groups
    // that do not begin with GROUP_.
    //
    // Additionally, if the user is an e-mail, remove the GROUP_DATA_COLLECTORS
    // permission since ODK Collect does not support oauth2 authentication.
    {
        TreeSet<GrantedAuthorityName> toRemove = new TreeSet<GrantedAuthorityName>();
        for (UserSecurityInfo i : users) {
            // only working with registered users
            if (i.getType() != UserType.REGISTERED) {
                continue;
            }
            // get the list of assigned groups
            // -- this is not a copy -- we can directly manipulate this.
            TreeSet<GrantedAuthorityName> assignedGroups = i.getAssignedUserGroups();

            // scan the set of assigned groups and remove any that don't begin with GROUP_
            toRemove.clear();
            for (GrantedAuthorityName name : assignedGroups) {
                if (!name.name().startsWith(GrantedAuthorityName.GROUP_PREFIX)) {
                    toRemove.add(name);
                }
            }
            if (!toRemove.isEmpty()) {
                assignedGroups.removeAll(toRemove);
            }
            // for e-mail accounts, remove the Data Collector permission since ODK Collect
            // does not support an oauth2 authentication mechanism.
            if (i.getEmail() != null) {
                assignedGroups.remove(GrantedAuthorityName.GROUP_DATA_COLLECTORS);
            }
        }
    }

    // find the entry(entries) for the designated super-user(s)
    String superUserUsername = cc.getUserService().getSuperUserUsername();
    int expectedSize = ((superUserUsername != null) ? 1 : 0);
    ArrayList<UserSecurityInfo> superUsers = new ArrayList<UserSecurityInfo>();
    for (UserSecurityInfo i : users) {
        if (i.getType() == UserType.REGISTERED) {
            if (i.getUsername() != null && superUserUsername != null
                    && i.getUsername().equals(superUserUsername)) {
                superUsers.add(i);
            }
        }
    }

    if (superUsers.size() != expectedSize) {
        // we are missing one or both super-users.
        // remove any we have and recreate them from scratch.
        users.removeAll(superUsers);
        superUsers.clear();

        // Synthesize a UserSecurityInfo object for the super-user(s)
        // and add it(them) to the list.

        try {
            List<RegisteredUsersTable> tList = RegisteredUsersTable.assertSuperUsers(cc);

            for (RegisteredUsersTable t : tList) {
                UserSecurityInfo i = new UserSecurityInfo(t.getUsername(), t.getFullName(), t.getEmail(),
                        UserSecurityInfo.UserType.REGISTERED);
                superUsers.add(i);
                users.add(i);
            }

        } catch (ODKDatastoreException e) {
            e.printStackTrace();
            throw new DatastoreFailureException("Incomplete update");
        }
    }

    // reset super-user privileges to have (just) site admin privileges
    // even if caller attempts to change, add, or remove them.
    for (UserSecurityInfo i : superUsers) {
        TreeSet<GrantedAuthorityName> grants = new TreeSet<GrantedAuthorityName>();
        grants.add(GrantedAuthorityName.GROUP_SITE_ADMINS);
        grants.add(GrantedAuthorityName.ROLE_SITE_ACCESS_ADMIN);
        // override whatever the user gave us.
        i.setAssignedUserGroups(grants);
    }

    try {
        // enforce our fixed set of groups and their inclusion hierarchy.
        // this is generally a no-op during normal operations.
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(siteAuth,
                SecurityServiceUtil.siteAdministratorGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(administerTablesAuth,
                SecurityServiceUtil.administerTablesGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(superUserTablesAuth,
                SecurityServiceUtil.superUserTablesGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(synchronizeTablesAuth,
                SecurityServiceUtil.synchronizeTablesGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(dataOwnerAuth,
                SecurityServiceUtil.dataOwnerGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(dataViewerAuth,
                SecurityServiceUtil.dataViewerGrants, cc);
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(dataCollectorAuth,
                SecurityServiceUtil.dataCollectorGrants, cc);

        // place the anonymous user's permissions in the granted authority table.
        GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(anonAuth, anonGrantStrings, cc);

        // get all granted authority names
        TreeSet<String> authorities = GrantedAuthorityHierarchyTable
                .getAllPermissionsAssignableGrantedAuthorities(cc.getDatastore(), cc.getCurrentUser());
        // remove the groups that have structure (i.e., those defined above).
        authorities.remove(siteAuth.getAuthority());
        authorities.remove(administerTablesAuth.getAuthority());
        authorities.remove(superUserTablesAuth.getAuthority());
        authorities.remove(synchronizeTablesAuth.getAuthority());
        authorities.remove(dataOwnerAuth.getAuthority());
        authorities.remove(dataViewerAuth.getAuthority());
        authorities.remove(dataCollectorAuth.getAuthority());
        authorities.remove(anonAuth.getAuthority());

        // delete all hierarchy structures under anything else.
        // i.e., if somehow USER_IS_REGISTERED had been granted GROUP_FORM_MANAGER
        // then this loop would leave USER_IS_REGISTERED without any grants.
        // (it repairs the database to conform to our privilege hierarchy expectations).
        List<String> empty = Collections.emptyList();
        for (String s : authorities) {
            GrantedAuthorityHierarchyTable.assertGrantedAuthorityHierarchy(new SimpleGrantedAuthority(s), empty,
                    cc);
        }

        // declare all the users (and remove users that are not in this set)
        Map<UserSecurityInfo, String> pkMap = setUsers(users, cc);

        // now, for each GROUP_..., update the user granted authority
        // table with the users that have that GROUP_... assignment.
        setUsersOfGrantedAuthority(pkMap, siteAuth, cc);
        setUsersOfGrantedAuthority(pkMap, administerTablesAuth, cc);
        setUsersOfGrantedAuthority(pkMap, superUserTablesAuth, cc);
        setUsersOfGrantedAuthority(pkMap, synchronizeTablesAuth, cc);
        setUsersOfGrantedAuthority(pkMap, dataOwnerAuth, cc);
        setUsersOfGrantedAuthority(pkMap, dataViewerAuth, cc);
        setUsersOfGrantedAuthority(pkMap, dataCollectorAuth, cc);
        // all super-users would already have their site admin role and
        // we leave that unchanged. The key is to ensure that the
        // super users are in the users list so they don't get
        // accidentally removed and that they have siteAuth group
        // membership. I.e., we don't need to manage ROLE_SITE_ACCESS_ADMIN
        // here. it is done elsewhere.

    } catch (ODKDatastoreException e) {
        e.printStackTrace();
        throw new DatastoreFailureException("Incomplete update");
    } finally {
        Datastore ds = cc.getDatastore();
        User user = cc.getCurrentUser();
        try {
            SecurityRevisionsTable.setLastRegisteredUsersRevisionDate(ds, user);
        } catch (ODKDatastoreException e) {
            // if it fails, use RELOAD_INTERVAL to force reload.
            e.printStackTrace();
        }
        try {
            SecurityRevisionsTable.setLastRoleHierarchyRevisionDate(ds, user);
        } catch (ODKDatastoreException e) {
            // if it fails, use RELOAD_INTERVAL to force reload.
            e.printStackTrace();
        }
    }
}

From source file:europarl.PhraseTranslation.java

private void postProcessData(ArrayList<PhraseTranslation> translations, Bag<String> words_list) {
    //it can remove useless attributes (in a COHERENT way: both from words_list and from translations)
    //it can remove instances (so it can even remove whole classes)
    log.debug("Start preprocessing");
    HashSet<String> to_remove = new HashSet<String>();

    //BEGIN removing too many classes
    Bag<String> classes = new Bag<String>();
    for (PhraseTranslation phraseTranslation : translations) {
        classes.add(phraseTranslation.getTranslatedWord());
    }/*from  w  w w. java 2  s.com*/
    if (log.isDebugEnabled())
        for (String translation : classes)
            if (classes.getCount(translation) > 2)
                System.out.println("Class " + translation + " : " + classes.getCount(translation));

    ArrayList<Integer> class_occurrencies = new ArrayList<Integer>(classes.values());
    java.util.Collections.sort(class_occurrencies);
    System.out.println("CLASS OCC " + class_occurrencies);
    ArrayList<PhraseTranslation> tr_to_remove = new ArrayList<PhraseTranslation>();
    for (String cl : classes) {
        if (classes.getCount(cl) < class_occurrencies
                .get(class_occurrencies.size() - Cfg.cfg.getInt("target_classes", 4))) {
            for (PhraseTranslation phraseTranslation : translations) {
                if (phraseTranslation.getTranslatedWord().equals(cl))
                    tr_to_remove.add(phraseTranslation);
            }
        }
    }
    for (PhraseTranslation phraseTranslation : tr_to_remove) {
        for (String word : phraseTranslation.getPhraseWords()) {
            words_list.countdown(word);
        }
        translations.remove(phraseTranslation);
    }
    System.out.println(translations.size());

    //END removing too many classes

    //BEGIN removing "useless" words, ie words with less than K occurrences
    for (String word : words_list) {
        assert 2 == Cfg.cfg.getInt("minimum_word_occurrencies");
        if (words_list.getCount(word) <= Cfg.cfg.getInt("minimum_word_occurrencies")
                || words_list.getCount(word) >= translations.size() * 50 / 100) {
            log.debug(word + "occurs only" + words_list.getCount(word) + " times");
            to_remove.add(word);
        }
    }
    for (String word : to_remove) {
        words_list.remove(word);
        for (PhraseTranslation trans : translations)
            trans.removeWord(word);
    }
    log.info("Useless words: " + to_remove.size() + ". Now: " + words_list.size());
    to_remove.clear();
    //END removing "useless" words

}