Example usage for com.mongodb.client.model Filters eq

Introduction

In this page you can find the example usage for com.mongodb.client.model Filters eq.

Prototype

public static <TItem> Bson eq(final String fieldName, @Nullable final TItem value) 

Source Link

Document

Creates a filter that matches all documents where the value of the field name equals the specified value.

Usage

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

@Override
public QueryResult<VariableSet> removeFieldFromVariableSet(long variableSetId, String name)
        throws CatalogDBException {
    long startTime = startQuery();

    try {/*from  w  w  w. j av a2 s . co m*/
        checkVariableInVariableSet(variableSetId, name);
    } catch (CatalogDBException e) {
        checkVariableSetExists(variableSetId);
        throw e;
    }
    Bson bsonQuery = Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId);
    Bson update = Updates.pull(QueryParams.VARIABLE_SET.key() + ".$." + VariableSetParams.VARIABLE.key(),
            Filters.eq("name", name));
    QueryResult<UpdateResult> queryResult = studyCollection.update(bsonQuery, update, null);
    if (queryResult.first().getModifiedCount() != 1) {
        throw new CatalogDBException("Remove field from Variable Set. Could not remove the field " + name
                + " from the variableSet id " + variableSetId);
    }

    // Remove all the annotations from that field
    dbAdaptorFactory.getCatalogSampleDBAdaptor().removeAnnotationField(variableSetId, name);
    dbAdaptorFactory.getCatalogCohortDBAdaptor().removeAnnotationField(variableSetId, name);

    return endQuery("Remove field from Variable Set", startTime, getVariableSet(variableSetId, null));
}

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From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

/**
 * The method will return the variable object given variableSetId and the variableId.
 * @param variableSetId Id of the variableSet.
 * @param variableId Id of the variable inside the variableSet.
 * @return the variable object./*w  w w .j  a va 2s . c o m*/
 */
private Variable getVariable(long variableSetId, String variableId) throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.elemMatch(QueryParams.VARIABLE_SET.key(),
            Filters.eq(VariableSetParams.ID.key(), variableSetId))));
    aggregation.add(Aggregates.project(Projections.include(QueryParams.VARIABLE_SET.key())));
    aggregation.add(Aggregates.unwind("$" + QueryParams.VARIABLE_SET.key()));
    aggregation.add(Aggregates.match(Filters.eq(QueryParams.VARIABLE_SET_ID.key(), variableSetId)));
    aggregation.add(
            Aggregates.unwind("$" + QueryParams.VARIABLE_SET.key() + "." + VariableSetParams.VARIABLE.key()));
    aggregation.add(Aggregates.match(Filters
            .eq(QueryParams.VARIABLE_SET.key() + "." + VariableSetParams.VARIABLE_NAME.key(), variableId)));

    QueryResult<Document> queryResult = studyCollection.aggregate(aggregation, new QueryOptions());

    Document variableSetDocument = (Document) queryResult.first().get(QueryParams.VARIABLE_SET.key());
    VariableSet variableSet = variableSetConverter.convertToDataModelType(variableSetDocument);
    Iterator<Variable> iterator = variableSet.getVariables().iterator();
    if (iterator.hasNext()) {
        return iterator.next();
    } else {
        // This error should never be raised.
        throw new CatalogDBException(
                "VariableSet {id: " + variableSetId + "} - Could not obtain variable object.");
    }
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

/**
 * Checks if the variable given is present in the variableSet.
 * @param variableSetId Identifier of the variableSet where it will be checked.
 * @param variableId VariableId that will be checked.
 * @throws CatalogDBException when the variableId is not present in the variableSet.
 */// w  w w.j ava  2  s  . co  m
private void checkVariableInVariableSet(long variableSetId, String variableId) throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.elemMatch(QueryParams.VARIABLE_SET.key(),
            Filters.and(Filters.eq(VariableSetParams.ID.key(), variableSetId),
                    Filters.eq(VariableSetParams.VARIABLE_NAME.key(), variableId)))));

    if (studyCollection.aggregate(aggregation, new QueryOptions()).getNumResults() == 0) {
        throw new CatalogDBException("VariableSet {id: " + variableSetId + "}. The variable {id: " + variableId
                + "} does not exist.");
    }
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

/**
 * Checks if the variable given is not present in the variableSet.
 * @param variableSetId Identifier of the variableSet where it will be checked.
 * @param variableId VariableId that will be checked.
 * @throws CatalogDBException when the variableId is present in the variableSet.
 *///from w w  w  . jav  a 2s  .c o  m
private void checkVariableNotInVariableSet(long variableSetId, String variableId) throws CatalogDBException {
    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.elemMatch(QueryParams.VARIABLE_SET.key(),
            Filters.and(Filters.eq(VariableSetParams.ID.key(), variableSetId),
                    Filters.ne(VariableSetParams.VARIABLE_NAME.key(), variableId)))));

    if (studyCollection.aggregate(aggregation, new QueryOptions()).getNumResults() == 0) {
        throw new CatalogDBException("VariableSet {id: " + variableSetId + "}. The variable {id: " + variableId
                + "} already exists.");
    }
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

@Override
public QueryResult<VariableSet> getVariableSet(long variableSetId, QueryOptions options)
        throws CatalogDBException {
    long startTime = startQuery();

    Query query = new Query(QueryParams.VARIABLE_SET_ID.key(), variableSetId);
    Bson projection = Projections.elemMatch("variableSets", Filters.eq("id", variableSetId));
    if (options == null) {
        options = new QueryOptions();
    }// www  .  j a v a2  s .com
    QueryOptions qOptions = new QueryOptions(options);
    qOptions.put(MongoDBCollection.ELEM_MATCH, projection);
    QueryResult<Study> studyQueryResult = get(query, qOptions);

    if (studyQueryResult.getResult().isEmpty() || studyQueryResult.first().getVariableSets().isEmpty()) {
        throw new CatalogDBException("VariableSet {id: " + variableSetId + "} does not exist.");
    }

    /*
            Bson query = Filters.eq("variableSets.id", variableSetId);
            Bson projection = Projections.elemMatch("variableSets", Filters.eq("id", variableSetId));
            QueryOptions filteredOptions = filterOptions(options, FILTER_ROUTE_STUDIES);
            
            QueryResult<Document> queryResult = studyCollection.find(query, projection, filteredOptions);
            List<Study> studies = parseStudies(queryResult);
            if (studies.isEmpty() || studies.get(0).getVariableSets().isEmpty()) {
    throw new CatalogDBException("VariableSet {id: " + variableSetId + "} does not exist");
            }
    */
    return endQuery("", startTime, studyQueryResult.first().getVariableSets());
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

@Override
public QueryResult<VariableSet> getAllVariableSets(long studyId, QueryOptions options)
        throws CatalogDBException {

    long startTime = startQuery();

    List<Bson> mongoQueryList = new LinkedList<>();

    for (Map.Entry<String, Object> entry : options.entrySet()) {
        String key = entry.getKey().split("\\.")[0];
        try {/*w w  w  . j  av a2 s. c  o  m*/
            if (isDataStoreOption(key) || isOtherKnownOption(key)) {
                continue; //Exclude DataStore options
            }
            CatalogStudyDBAdaptor.VariableSetParams option = CatalogStudyDBAdaptor.VariableSetParams
                    .getParam(key) != null ? CatalogStudyDBAdaptor.VariableSetParams.getParam(key)
                            : CatalogStudyDBAdaptor.VariableSetParams.getParam(entry.getKey());
            switch (option) {
            case STUDY_ID:
                addCompQueryFilter(option, option.name(), PRIVATE_ID, options, mongoQueryList);
                break;
            default:
                String optionsKey = "variableSets." + entry.getKey().replaceFirst(option.name(), option.key());
                addCompQueryFilter(option, entry.getKey(), optionsKey, options, mongoQueryList);
                break;
            }
        } catch (IllegalArgumentException e) {
            throw new CatalogDBException(e);
        }
    }

    /*
    QueryResult<DBObject> queryResult = studyCollection.aggregate(Arrays.<DBObject>asList(
        new BasicDBObject("$match", new BasicDBObject(PRIVATE_ID, studyId)),
        new BasicDBObject("$project", new BasicDBObject("variableSets", 1)),
        new BasicDBObject("$unwind", "$variableSets"),
        new BasicDBObject("$match", new BasicDBObject("$and", mongoQueryList))
    ), filterOptions(options, FILTER_ROUTE_STUDIES));
    */

    List<Bson> aggregation = new ArrayList<>();
    aggregation.add(Aggregates.match(Filters.eq(PRIVATE_ID, studyId)));
    aggregation.add(Aggregates.project(Projections.include("variableSets")));
    aggregation.add(Aggregates.unwind("$variableSets"));
    if (mongoQueryList.size() > 0) {
        aggregation.add(Aggregates.match(Filters.and(mongoQueryList)));
    }

    QueryResult<Document> queryResult = studyCollection.aggregate(aggregation,
            filterOptions(options, FILTER_ROUTE_STUDIES));

    List<VariableSet> variableSets = parseObjects(queryResult, Study.class).stream()
            .map(study -> study.getVariableSets().get(0)).collect(Collectors.toList());

    return endQuery("", startTime, variableSets);
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

@Override
public QueryResult<VariableSet> deleteVariableSet(long variableSetId, QueryOptions queryOptions)
        throws CatalogDBException {
    long startTime = startQuery();

    checkVariableSetInUse(variableSetId);
    long studyId = getStudyIdByVariableSetId(variableSetId);
    QueryResult<VariableSet> variableSet = getVariableSet(variableSetId, queryOptions);
    Bson query = Filters.eq(PRIVATE_ID, studyId);
    Bson operation = Updates.pull("variableSets", Filters.eq("id", variableSetId));
    QueryResult<UpdateResult> update = studyCollection.update(query, operation, null);

    if (update.first().getModifiedCount() == 0) {
        throw CatalogDBException.idNotFound("VariableSet", variableSetId);
    }//w w  w. j a  v a  2 s .  c  o m
    return endQuery("Delete VariableSet", startTime, variableSet);
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.CatalogMongoStudyDBAdaptor.java

License:Apache License

@Override
public long getStudyIdByVariableSetId(long variableSetId) throws CatalogDBException {
    //        DBObject query = new BasicDBObject("variableSets.id", variableSetId);
    Bson query = Filters.eq("variableSets.id", variableSetId);
    Bson projection = Projections.include("id");

    //        QueryResult<DBObject> queryResult = studyCollection.find(query, new BasicDBObject("id", true), null);
    QueryResult<Document> queryResult = studyCollection.find(query, projection, null);

    if (!queryResult.getResult().isEmpty()) {
        Object id = queryResult.getResult().get(0).get("id");
        return id instanceof Number ? ((Number) id).intValue() : (int) Double.parseDouble(id.toString());
    } else {/*www .  ja v  a 2s  .  com*/
        throw CatalogDBException.idNotFound("VariableSet", variableSetId);
    }
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.IndividualMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<AnnotationSet> annotate(long individualId, AnnotationSet annotationSet, boolean overwrite)
        throws CatalogDBException {
    long startTime = startQuery();

    QueryResult<Long> count = individualCollection.count(
            new Document("annotationSets.name", annotationSet.getName()).append(PRIVATE_ID, individualId));

    if (overwrite) {
        if (count.first() == 0) {
            throw CatalogDBException.idNotFound("AnnotationSet", annotationSet.getName());
        }//  w  w  w  .  j  a  va2 s .  c om
    } else {
        if (count.first() > 0) {
            throw CatalogDBException.alreadyExists("AnnotationSet", "name", annotationSet.getName());
        }
    }

    Document document = getMongoDBDocument(annotationSet, "AnnotationSet");

    Bson query;
    Bson individualQuery = Filters.eq(PRIVATE_ID, individualId);
    if (overwrite) {
        //            query.put("annotationSets.id", annotationSet.getId());
        query = Filters.and(individualQuery, Filters.eq("annotationSets.name", annotationSet.getName()));
    } else {
        //            query.put("annotationSets.id", new BasicDBObject("$ne", annotationSet.getId()));
        query = Filters.and(individualQuery,
                Filters.eq("annotationSets.name", new Document("$ne", annotationSet.getName())));
    }

    Bson update;
    if (overwrite) {
        update = new Document("$set", new Document("annotationSets.$", document));
    } else {
        update = new Document("$push", new Document("annotationSets", document));
    }

    QueryResult<UpdateResult> queryResult = individualCollection.update(query, update, null);

    if (queryResult.first().getModifiedCount() != 1) {
        throw CatalogDBException.alreadyExists("AnnotationSet", "name", annotationSet.getName());
    }

    return endQuery("", startTime, Collections.singletonList(annotationSet));
}

---

From source file:org.opencb.opencga.catalog.db.mongodb.IndividualMongoDBAdaptor.java

License:Apache License

@Override
public QueryResult<AnnotationSet> deleteAnnotation(long individualId, String annotationId)
        throws CatalogDBException {

    long startTime = startQuery();

    Individual individual = get(individualId,
            new QueryOptions("include", "projects.studies.individuals.annotationSets")).first();
    AnnotationSet annotationSet = null;/*from w  w  w.j a  va2s  .co  m*/
    for (AnnotationSet as : individual.getAnnotationSets()) {
        if (as.getName().equals(annotationId)) {
            annotationSet = as;
            break;
        }
    }

    if (annotationSet == null) {
        throw CatalogDBException.idNotFound("AnnotationSet", annotationId);
    }

    //        DBObject query = new BasicDBObject(PRIVATE_ID, individualId);
    //        DBObject update = new BasicDBObject("$pull", new BasicDBObject("annotationSets", new BasicDBObject("id", annotationId)));
    //        QueryResult<WriteResult> resultQueryResult = individualCollection.update(query, update, null);
    //        if (resultQueryResult.first().getN() < 1) {
    //            throw CatalogDBException.idNotFound("AnnotationSet", annotationId);
    //        }

    Bson eq = Filters.eq(PRIVATE_ID, individualId);
    Bson pull = Updates.pull("annotationSets", new Document("name", annotationId));
    QueryResult<UpdateResult> update = individualCollection.update(eq, pull, null);
    if (update.first().getModifiedCount() < 1) {
        throw CatalogDBException.idNotFound("AnnotationSet", annotationId);
    }

    return endQuery("Delete annotation", startTime, Collections.singletonList(annotationSet));
}

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