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catalog: start organization implementation, #TASK-4389
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opencga-catalog/src/main/java/org/opencb/opencga/catalog/db/api/OrganizationDBAdaptor.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,235 @@ | ||
| package org.opencb.opencga.catalog.db.api; | ||
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|
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| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.commons.datastore.core.QueryParam; | ||
| import org.opencb.opencga.catalog.exceptions.CatalogDBException; | ||
| import org.opencb.opencga.core.models.organizations.Organization; | ||
|
|
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| import java.util.HashMap; | ||
| import java.util.Map; | ||
|
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| import static org.opencb.commons.datastore.core.QueryParam.Type.*; | ||
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| public interface OrganizationDBAdaptor extends Iterable<Organization> { | ||
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| enum QueryParams implements QueryParam { | ||
| UID("uid", LONG, ""), | ||
| ID("id", STRING, ""), | ||
| UUID("uuid", STRING, ""), | ||
| NAME("name", STRING, ""), | ||
| DOMAIN("domain", STRING, ""), | ||
| OWNER("owner", STRING, ""), | ||
| ADMINS("admins", TEXT_ARRAY, ""), | ||
| CREATION_DATE("creationDate", DATE, ""), | ||
| MODIFICATION_DATE("modificationDate", DATE, ""), | ||
| PROJECTS("projects", OBJECT, ""), | ||
| AUTHENTICATION_ORIGINS("authenticationOrigins", OBJECT, ""), | ||
| ATTRIBUTES("attributes", OBJECT, ""); | ||
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|
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| private static Map<String, QueryParams> map = new HashMap<>(); | ||
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| static { | ||
| for (QueryParams params : QueryParams.values()) { | ||
| map.put(params.key(), params); | ||
| } | ||
| } | ||
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| private final String key; | ||
| private Type type; | ||
| private String description; | ||
|
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| QueryParams(String key, Type type, String description) { | ||
| this.key = key; | ||
| this.type = type; | ||
| this.description = description; | ||
| } | ||
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| @Override | ||
| public String key() { | ||
| return key; | ||
| } | ||
|
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| @Override | ||
| public Type type() { | ||
| return type; | ||
| } | ||
|
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| @Override | ||
| public String description() { | ||
| return description; | ||
| } | ||
|
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| public static Map<String, QueryParams> getMap() { | ||
| return map; | ||
| } | ||
|
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| public static QueryParams getParam(String key) { | ||
| return map.get(key); | ||
| } | ||
| } | ||
|
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| // default boolean exists(long projectId) throws CatalogDBException { | ||
| // return count(new Query(QueryParams.UID.key(), projectId)).getNumMatches() > 0; | ||
| // } | ||
| // | ||
| // default void checkId(long projectId) throws CatalogDBException { | ||
| // if (projectId < 0) { | ||
| // throw CatalogDBException.newInstance("Project id '{}' is not valid: ", projectId); | ||
| // } | ||
| // | ||
| // if (!exists(projectId)) { | ||
| // throw CatalogDBException.newInstance("Project id '{}' does not exist", projectId); | ||
| // } | ||
| // } | ||
| // | ||
| // OpenCGAResult nativeInsert(Map<String, Object> project, String userId) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult insert(Project project, String userId, QueryOptions options) | ||
| // throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult<Project> get(String userId, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult<Project> get(long project, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult incrementCurrentRelease(long projectId) throws CatalogDBException; | ||
| // | ||
| // long getId(String userId, String projectAlias) throws CatalogDBException; | ||
| // | ||
| // String getOwnerId(long projectId) throws CatalogDBException; | ||
| // | ||
| // | ||
| // default OpenCGAResult<Long> count() throws CatalogDBException { | ||
| // return count(new Query()); | ||
| // } | ||
| // | ||
| // OpenCGAResult<Long> count(Query query) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult<Long> count(Query query, String user, StudyPermissions.Permissions studyPermission) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // default OpenCGAResult distinct(String field) throws CatalogDBException { | ||
| // return distinct(new Query(), field); | ||
| // } | ||
| // | ||
| // OpenCGAResult distinct(Query query, String field) throws CatalogDBException; | ||
| // | ||
| // | ||
| // default OpenCGAResult stats() { | ||
| // return stats(new Query()); | ||
| // } | ||
| // | ||
| // OpenCGAResult stats(Query query); | ||
| // | ||
| // | ||
| // OpenCGAResult<Project> get(Query query, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult<Project> get(Query query, QueryOptions options, String user) throws CatalogDBException, CatalogParameterException; | ||
| // | ||
| // default List<OpenCGAResult<Project>> get(List<Query> queries, QueryOptions options) throws CatalogDBException { | ||
| // Objects.requireNonNull(queries); | ||
| // List<OpenCGAResult<Project>> queryResults = new ArrayList<>(queries.size()); | ||
| // for (Query query : queries) { | ||
| // queryResults.add(get(query, options)); | ||
| // } | ||
| // return queryResults; | ||
| // } | ||
| // | ||
| // OpenCGAResult nativeGet(Query query, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult nativeGet(Query query, QueryOptions options, String user) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // default List<OpenCGAResult> nativeGet(List<Query> queries, QueryOptions options) throws CatalogDBException { | ||
| // Objects.requireNonNull(queries); | ||
| // List<OpenCGAResult> queryResults = new ArrayList<>(queries.size()); | ||
| // for (Query query : queries) { | ||
| // queryResults.add(nativeGet(query, options)); | ||
| // } | ||
| // return queryResults; | ||
| // } | ||
| // | ||
| // OpenCGAResult<Project> update(long id, ObjectMap parameters, QueryOptions queryOptions) | ||
| // throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult<Long> update(Query query, ObjectMap parameters, QueryOptions queryOptions) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult delete(Project project) throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult delete(Query query) throws CatalogDBException; | ||
| // | ||
| // default OpenCGAResult<Project> delete(long id, QueryOptions queryOptions) throws CatalogDBException { | ||
| // throw new NotImplementedException(""); | ||
| // } | ||
| // | ||
| // @Deprecated | ||
| // default OpenCGAResult<Long> delete(Query query, QueryOptions queryOptions) throws CatalogDBException { | ||
| // throw new NotImplementedException(""); | ||
| // } | ||
| // | ||
| // @Deprecated | ||
| // default OpenCGAResult<Project> remove(long id, QueryOptions queryOptions) throws CatalogDBException { | ||
| // throw new NotImplementedException(""); | ||
| // } | ||
| // | ||
| // @Deprecated | ||
| // default OpenCGAResult<Long> remove(Query query, QueryOptions queryOptions) throws CatalogDBException { | ||
| // throw new NotImplementedException(""); | ||
| // } | ||
| // | ||
| // OpenCGAResult<Project> restore(long id, QueryOptions queryOptions) | ||
| // throws CatalogDBException, CatalogParameterException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult<Long> restore(Query query, QueryOptions queryOptions) throws CatalogDBException; | ||
| // | ||
| // | ||
| //// OpenCGAResult<Long> updateStatus(Query query, Status status) throws CatalogDBException; | ||
| // | ||
| // | ||
| @Override | ||
| default DBIterator<Organization> iterator() { | ||
| try { | ||
| return iterator(new Query(), new QueryOptions()); | ||
| } catch (CatalogDBException e) { | ||
| throw new RuntimeException(e); | ||
| } | ||
| } | ||
|
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| DBIterator<Organization> iterator(Query query, QueryOptions options) throws CatalogDBException; | ||
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| // default DBIterator nativeIterator() throws CatalogDBException { | ||
| // return nativeIterator(new Query(), new QueryOptions()); | ||
| // } | ||
| // | ||
| // DBIterator nativeIterator(Query query, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // DBIterator<Project> iterator(Query query, QueryOptions options, String user) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // DBIterator nativeIterator(Query query, QueryOptions options, String user) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult rank(Query query, String field, int numResults, boolean asc) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult groupBy(Query query, String field, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult groupBy(Query query, List<String> fields, QueryOptions options) throws CatalogDBException; | ||
| // | ||
| // OpenCGAResult groupBy(Query query, String field, QueryOptions options, String user) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // OpenCGAResult groupBy(Query query, List<String> fields, QueryOptions options, String user) | ||
| // throws CatalogDBException, CatalogAuthorizationException; | ||
| // | ||
| // @Override | ||
| // default void forEach(Consumer action) { | ||
| // try { | ||
| // forEach(new Query(), action, new QueryOptions()); | ||
| // } catch (CatalogDBException e) { | ||
| // throw new RuntimeException(e); | ||
| // } | ||
| // } | ||
| // | ||
| // void forEach(Query query, Consumer<? super Object> action, QueryOptions options) throws CatalogDBException; | ||
|
|
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| } |
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46 changes: 46 additions & 0 deletions
46
...talog/src/main/java/org/opencb/opencga/catalog/db/mongodb/OrganizationMongoDBAdaptor.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| package org.opencb.opencga.catalog.db.mongodb; | ||
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| import com.mongodb.client.ClientSession; | ||
| import org.bson.Document; | ||
| import org.opencb.commons.datastore.core.Query; | ||
| import org.opencb.commons.datastore.core.QueryOptions; | ||
| import org.opencb.commons.datastore.mongodb.MongoDBCollection; | ||
| import org.opencb.commons.datastore.mongodb.MongoDBIterator; | ||
| import org.opencb.opencga.catalog.db.api.DBIterator; | ||
| import org.opencb.opencga.catalog.db.api.OrganizationDBAdaptor; | ||
| import org.opencb.opencga.catalog.db.mongodb.converters.OrganizationConverter; | ||
| import org.opencb.opencga.catalog.db.mongodb.iterators.ProjectCatalogMongoDBIterator; | ||
| import org.opencb.opencga.catalog.exceptions.CatalogDBException; | ||
| import org.opencb.opencga.core.config.Configuration; | ||
| import org.opencb.opencga.core.models.organizations.Organization; | ||
| import org.slf4j.LoggerFactory; | ||
|
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| public class OrganizationMongoDBAdaptor extends MongoDBAdaptor implements OrganizationDBAdaptor { | ||
|
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| private final MongoDBCollection organizationCollection; | ||
| private final MongoDBCollection deletedOrganizationCollection; | ||
| private OrganizationConverter organizationConverter; | ||
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| public OrganizationMongoDBAdaptor(MongoDBCollection organizationCollection, MongoDBCollection deletedOrganizationCollection, | ||
| Configuration configuration, MongoDBAdaptorFactory dbAdaptorFactory) { | ||
| super(configuration, LoggerFactory.getLogger(ProjectMongoDBAdaptor.class)); | ||
| this.dbAdaptorFactory = dbAdaptorFactory; | ||
| this.organizationCollection = organizationCollection; | ||
| this.deletedOrganizationCollection = deletedOrganizationCollection; | ||
| this.organizationConverter = new OrganizationConverter(); | ||
| } | ||
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| @Override | ||
| public DBIterator<Organization> iterator(Query query, QueryOptions options) throws CatalogDBException { | ||
| return iterator(null, query, options); | ||
| } | ||
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| public DBIterator<Organization> iterator(ClientSession clientSession, Query query, QueryOptions options) throws CatalogDBException { | ||
| MongoDBIterator<Document> mongoCursor = getMongoCursor(clientSession, query, options); | ||
| return new ProjectCatalogMongoDBIterator<>(mongoCursor, clientSession, organizationConverter, dbAdaptorFactory, options, null); | ||
| } | ||
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| private MongoDBIterator<Document> getMongoCursor(ClientSession clientSession, Query query, QueryOptions options) { | ||
| return null; | ||
| } | ||
| } |
21 changes: 21 additions & 0 deletions
21
...src/main/java/org/opencb/opencga/catalog/db/mongodb/converters/OrganizationConverter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| package org.opencb.opencga.catalog.db.mongodb.converters; | ||
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| import org.apache.avro.generic.GenericRecord; | ||
| import org.bson.Document; | ||
| import org.opencb.opencga.core.models.common.mixins.GenericRecordAvroJsonMixin; | ||
| import org.opencb.opencga.core.models.organizations.Organization; | ||
|
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| public class OrganizationConverter extends OpenCgaMongoConverter<Organization> { | ||
|
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| public OrganizationConverter() { | ||
| super(Organization.class); | ||
| getObjectMapper().addMixIn(GenericRecord.class, GenericRecordAvroJsonMixin.class); | ||
| } | ||
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| @Override | ||
| public Document convertToStorageType(Organization object) { | ||
| Document document = super.convertToStorageType(object); | ||
| document.put("uid", document.getInteger("uid").longValue()); | ||
| return document; | ||
| } | ||
| } |
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