org.opencb.opencga.client.rest.clients.StudyClient Maven / Gradle / Ivy
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/*
* Copyright 2015-2024 OpenCB
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.opencb.opencga.client.rest.clients;
import org.opencb.commons.datastore.core.ObjectMap;
import org.opencb.opencga.client.config.ClientConfiguration;
import org.opencb.opencga.client.exceptions.ClientException;
import org.opencb.opencga.client.rest.*;
import org.opencb.opencga.core.models.AclEntryList;
import org.opencb.opencga.core.models.audit.AuditRecord;
import org.opencb.opencga.core.models.job.Job;
import org.opencb.opencga.core.models.notes.Note;
import org.opencb.opencga.core.models.notes.NoteCreateParams;
import org.opencb.opencga.core.models.notes.NoteUpdateParams;
import org.opencb.opencga.core.models.study.CustomGroup;
import org.opencb.opencga.core.models.study.Group;
import org.opencb.opencga.core.models.study.GroupCreateParams;
import org.opencb.opencga.core.models.study.GroupUpdateParams;
import org.opencb.opencga.core.models.study.PermissionRule;
import org.opencb.opencga.core.models.study.Study;
import org.opencb.opencga.core.models.study.StudyAclEntryList;
import org.opencb.opencga.core.models.study.StudyAclUpdateParams;
import org.opencb.opencga.core.models.study.StudyCreateParams;
import org.opencb.opencga.core.models.study.StudyUpdateParams;
import org.opencb.opencga.core.models.study.TemplateParams;
import org.opencb.opencga.core.models.study.Variable;
import org.opencb.opencga.core.models.study.VariableSet;
import org.opencb.opencga.core.models.study.VariableSetCreateParams;
import org.opencb.opencga.core.response.RestResponse;
/*
* WARNING: AUTOGENERATED CODE
*
* This code was generated by a tool.
*
* Manual changes to this file may cause unexpected behavior in your application.
* Manual changes to this file will be overwritten if the code is regenerated.
*/
/**
* This class contains methods for the Study webservices.
* PATH: studies
*/
public class StudyClient extends AbstractParentClient {
public StudyClient(String token, ClientConfiguration configuration) {
super(token, configuration);
}
/**
* Update the set of permissions granted for the member.
* @param members Comma separated list of user or group ids.
* @param action Action to be performed [ADD, SET, REMOVE or RESET].
* @param data JSON containing the parameters to modify ACLs. 'template' could be either 'admin', 'analyst' or 'view_only'.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateAcl(String members, String action, StudyAclUpdateParams data) throws ClientException {
ObjectMap params = new ObjectMap();
params.putIfNotNull("action", action);
params.put("body", data);
return execute("studies", null, "acl", members, "update", params, POST, StudyAclEntryList.class);
}
/**
* Create a new study.
* @param data study.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* project: Project [organization@]project where project can be either the ID or the alias.
* includeResult: Flag indicating to include the created or updated document result in the response.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse create(StudyCreateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", null, null, null, "create", params, POST, Study.class);
}
/**
* Search studies.
* @param project Project [organization@]project where project can be either the ID or the alias.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* limit: Number of results to be returned.
* skip: Number of results to skip.
* count: Get the total number of results matching the query. Deactivated by default.
* name: Study name.
* id: Study ID.
* alias: Study alias.
* fqn: Study full qualified name.
* creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
* modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
* internalStatus: Filter by internal status.
* status: Filter by status.
* attributes: Attributes.
* release: Release value.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse search(String project, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("project", project);
return execute("studies", null, null, null, "search", params, GET, Study.class);
}
/**
* Return the acl of the study. If member is provided, it will only return the acl for the member.
* @param studies Comma separated list of Studies [[organization@]project:]study where study and project can be either the ID or UUID
* up to a maximum of 100.
* @param params Map containing any of the following optional parameters.
* member: User or group id.
* silent: Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries
* looked for cannot be shown for whichever reason.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse acl(String studies, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", studies, null, null, "acl", params, GET, AclEntryList.class);
}
/**
* Fetch study information.
* @param studies Comma separated list of Studies [[organization@]project:]study where study and project can be either the ID or UUID
* up to a maximum of 100.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse info(String studies, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", studies, null, null, "info", params, GET, Study.class);
}
/**
* Search audit collection.
* @param study Study ID.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* limit: Number of results to be returned.
* skip: Number of results to skip.
* count: Get the total number of results matching the query. Deactivated by default.
* operationId: Audit operation UUID.
* userId: User ID.
* action: Action performed by the user.
* resource: Resource involved.
* resourceId: Resource ID.
* resourceUuid: resource UUID.
* status: Filter by status.
* date: Date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse searchAudit(String study, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, "audit", null, "search", params, GET, AuditRecord.class);
}
/**
* Return the groups present in the study. For owners and administrators only.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param params Map containing any of the following optional parameters.
* id: Group id. If provided, it will only fetch information for the provided group.
* silent: Boolean to retrieve all possible entries that are queried for, false to raise an exception whenever one of the entries
* looked for cannot be shown for whichever reason.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse groups(String study, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, null, null, "groups", params, GET, CustomGroup.class);
}
/**
* Add or remove a group.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param data JSON containing the parameters.
* @param params Map containing any of the following optional parameters.
* action: Action to be performed: ADD or REMOVE a group.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateGroups(String study, GroupCreateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "groups", null, "update", params, POST, Group.class);
}
/**
* Add, set or remove users from an existing group.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param group Group name.
* @param data JSON containing the parameters.
* @param params Map containing any of the following optional parameters.
* action: Action to be performed: ADD, SET or REMOVE users to/from a group.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateGroupsUsers(String study, String group, GroupUpdateParams data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "groups", group, "users/update", params, POST, Group.class);
}
/**
* Create a new note.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param data JSON containing the Note to be added.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* includeResult: Flag indicating to include the created or updated document result in the response.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse createNotes(String study, NoteCreateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "notes", null, "create", params, POST, Note.class);
}
/**
* Search for notes of scope STUDY.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
* modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
* id: Note unique identifier.
* uuid: Unique 32-character identifier assigned automatically by OpenCGA.
* userId: User that wrote that Note.
* tags: Note tags.
* visibility: Visibility of the Note.
* version: Autoincremental version assigned to the registered entry. By default, updates does not create new versions. To enable
* versioning, users must set the `incVersion` flag from the /update web service when updating the document.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse searchNotes(String study, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, "notes", null, "search", params, GET, Note.class);
}
/**
* Delete note.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param id Note unique identifier.
* @param params Map containing any of the following optional parameters.
* includeResult: Flag indicating to include the created or updated document result in the response.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse deleteNotes(String study, String id, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, "notes", id, "delete", params, DELETE, Note.class);
}
/**
* Update a note.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param id Note unique identifier.
* @param data JSON containing the Note fields to be updated.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* tagsAction: Action to be performed if the array of tags is being updated.
* includeResult: Flag indicating to include the created or updated document result in the response.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateNotes(String study, String id, NoteUpdateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "notes", id, "update", params, POST, Note.class);
}
/**
* Fetch permission rules.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param entity Entity where the permission rules should be applied to.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse permissionRules(String study, String entity) throws ClientException {
ObjectMap params = new ObjectMap();
params.putIfNotNull("entity", entity);
return execute("studies", study, null, null, "permissionRules", params, GET, PermissionRule.class);
}
/**
* Add or remove a permission rule.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param entity Entity where the permission rules should be applied to.
* @param data JSON containing the permission rule to be created or removed.
* @param params Map containing any of the following optional parameters.
* action: Action to be performed: ADD to add a new permission rule; REMOVE to remove all permissions assigned by an existing
* permission rule (even if it overlaps any manual permission); REVERT to remove all permissions assigned by an existing
* permission rule (keep manual overlaps); NONE to remove an existing permission rule without removing any permissions that
* could have been assigned already by the permission rule.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updatePermissionRules(String study, String entity, PermissionRule data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.putIfNotNull("entity", entity);
params.put("body", data);
return execute("studies", study, "permissionRules", null, "update", params, POST, PermissionRule.class);
}
/**
* Execute template.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param data Template loader parameters.
* @param params Map containing any of the following optional parameters.
* jobId: Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided.
* jobDependsOn: Comma separated list of existing job IDs the job will depend on.
* jobDescription: Job description.
* jobTags: Job tags.
* jobScheduledStartTime: Time when the job is scheduled to start.
* jobPriority: Priority of the job.
* jobDryRun: Flag indicating that the job will be executed in dry-run mode. In this mode, OpenCGA will validate that all
* parameters and prerequisites are correctly set for successful execution, but the job will not actually run.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runTemplates(String study, TemplateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "templates", null, "run", params, POST, Job.class);
}
/**
* Resource to upload a zipped template.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param params Map containing any of the following optional parameters.
* file: File to upload.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse uploadTemplates(String study, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, "templates", null, "upload", params, POST, String.class);
}
/**
* Delete template.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param templateId Template id.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse deleteTemplates(String study, String templateId) throws ClientException {
ObjectMap params = new ObjectMap();
return execute("studies", study, "templates", templateId, "delete", params, DELETE, Boolean.class);
}
/**
* Update some study attributes.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param data JSON containing the params to be updated.
* @param params Map containing any of the following optional parameters.
* include: Fields included in the response, whole JSON path must be provided.
* exclude: Fields excluded in the response, whole JSON path must be provided.
* includeResult: Flag indicating to include the created or updated document result in the response.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse update(String study, StudyUpdateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, null, null, "update", params, POST, Study.class);
}
/**
* Fetch variableSets from a study.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param params Map containing any of the following optional parameters.
* id: Id of the variableSet to be retrieved. If no id is passed, it will show all the variableSets of the study.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse variableSets(String study, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("studies", study, null, null, "variableSets", params, GET, VariableSet.class);
}
/**
* Add or remove a variableSet.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param data JSON containing the VariableSet to be created or removed.
* @param params Map containing any of the following optional parameters.
* action: Action to be performed: ADD, REMOVE or FORCE_REMOVE a variableSet.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateVariableSets(String study, VariableSetCreateParams data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "variableSets", null, "update", params, POST, VariableSet.class);
}
/**
* Add or remove variables to a VariableSet.
* @param study Study [[organization@]project:]study where study and project can be either the ID or UUID.
* @param variableSet VariableSet id of the VariableSet to be updated.
* @param data JSON containing the variable to be added or removed. For removing, only the variable id will be needed.
* @param params Map containing any of the following optional parameters.
* action: Action to be performed: ADD or REMOVE a variable.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse updateVariableSetsVariables(String study, String variableSet, Variable data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("studies", study, "variableSets", variableSet, "variables/update", params, POST, VariableSet.class);
}
}