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    • org.opencb.opencga.client.rest.clients.JobClient Maven / Gradle / Ivy

    /*
* 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 java.lang.Object;
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.file.FileContent;
import org.opencb.opencga.core.models.job.Job;
import org.opencb.opencga.core.models.job.JobAclEntryList;
import org.opencb.opencga.core.models.job.JobAclUpdateParams;
import org.opencb.opencga.core.models.job.JobCreateParams;
import org.opencb.opencga.core.models.job.JobRetryParams;
import org.opencb.opencga.core.models.job.JobTop;
import org.opencb.opencga.core.models.job.JobUpdateParams;
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 Job webservices.
 *    PATH: jobs
 */
public class JobClient extends AbstractParentClient {

    public JobClient(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 add ACLs.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse updateAcl(String members, String action, JobAclUpdateParams data) throws ClientException {
        ObjectMap params = new ObjectMap();
        params.putIfNotNull("action", action);
        params.put("body", data);
        return execute("jobs", null, "acl", members, "update", params, POST, JobAclEntryList.class);
    }

    /**
     * Register an executed job with POST method.
     * @param data job.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse create(JobCreateParams data, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        params.put("body", data);
        return execute("jobs", null, null, null, "create", params, POST, Job.class);
    }

    /**
     * Job distinct method.
     * @param field Comma separated list of fields for which to obtain the distinct values.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one.
     *       id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e.
     *            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
     *       uuid: Comma separated list of job UUIDs up to a maximum of 100.
     *       toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g.
     *            '~value' for case sensitive, '~/value/i' for case insensitive search.
     *       toolType: Tool type executed by the job [OPERATION, ANALYSIS].
     *       userId: User that created the job.
     *       priority: Priority of the job.
     *       status: Filter by status.
     *       internalStatus: Filter by internal status.
     *       creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
     *       modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
     *       visited: Visited status of job.
     *       tags: Job tags.
     *       input: Comma separated list of file IDs used as input.
     *       output: Comma separated list of file IDs used as output.
     *       acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example:
     *            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS
     *            permissions. Only study owners or administrators can query by this field. .
     *       release: Release when it was created.
     *       deleted: Boolean to retrieve deleted entries.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse distinct(String field, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        params.putIfNotNull("field", field);
        return execute("jobs", null, null, null, "distinct", params, GET, Object.class);
    }

    /**
     * Relaunch a failed job.
     * @param data job.
     * @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.
     *       jobDescription: Job description.
     *       jobDependsOn: Comma separated list of existing job IDs the job will depend on.
     *       jobTags: Job tags.
     *       jobScheduledStartTime: Time when the job is scheduled to start.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse retry(JobRetryParams data, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        params.put("body", data);
        return execute("jobs", null, null, null, "retry", params, POST, Job.class);
    }

    /**
     * Job search method.
     * @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.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       otherStudies: Flag indicating the entries being queried can belong to any related study, not just the primary one.
     *       id: Comma separated list of job IDs up to a maximum of 100. Also admits basic regular expressions using the operator '~', i.e.
     *            '~{perl-regex}' e.g. '~value' for case sensitive, '~/value/i' for case insensitive search.
     *       uuid: Comma separated list of job UUIDs up to a maximum of 100.
     *       toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g.
     *            '~value' for case sensitive, '~/value/i' for case insensitive search.
     *       toolType: Tool type executed by the job [OPERATION, ANALYSIS].
     *       userId: User that created the job.
     *       priority: Priority of the job.
     *       status: Filter by status.
     *       internalStatus: Filter by internal status.
     *       creationDate: Creation date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
     *       modificationDate: Modification date. Format: yyyyMMddHHmmss. Examples: >2018, 2017-2018, <201805.
     *       visited: Visited status of job.
     *       tags: Job tags.
     *       input: Comma separated list of file IDs used as input.
     *       output: Comma separated list of file IDs used as output.
     *       acl: Filter entries for which a user has the provided permissions. Format: acl={user}:{permissions}. Example:
     *            acl=john:WRITE,WRITE_ANNOTATIONS will return all entries for which user john has both WRITE and WRITE_ANNOTATIONS
     *            permissions. Only study owners or administrators can query by this field. .
     *       release: Release when it was created.
     *       deleted: Boolean to retrieve deleted entries.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse search(ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", null, null, null, "search", params, GET, Job.class);
    }

    /**
     * Provide a summary of the running jobs.
     * @param params Map containing any of the following optional parameters.
     *       limit: Maximum number of jobs to be returned.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       internalStatus: Filter by internal status.
     *       priority: Priority of the job.
     *       userId: User that created the job.
     *       toolId: Tool ID executed by the job. Also admits basic regular expressions using the operator '~', i.e. '~{perl-regex}' e.g.
     *            '~value' for case sensitive, '~/value/i' for case insensitive search.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse top(ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", null, null, null, "top", params, GET, JobTop.class);
    }

    /**
     * Return the acl of the job. If member is provided, it will only return the acl for the member.
     * @param jobs Comma separated list of job IDs or UUIDs 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 jobs, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", jobs, null, null, "acl", params, GET, JobAclEntryList.class);
    }

    /**
     * Delete existing jobs.
     * @param jobs Comma separated list of job ids.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse delete(String jobs, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", jobs, null, null, "delete", params, DELETE, Job.class);
    }

    /**
     * Get job information.
     * @param jobs Comma separated list of job IDs or UUIDs 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.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       deleted: Boolean to retrieve deleted jobs.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse info(String jobs, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", jobs, null, null, "info", params, GET, Job.class);
    }

    /**
     * Update some job attributes.
     * @param jobs Comma separated list of job IDs or UUIDs up to a maximum of 100.
     * @param data body.
     * @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.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       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 jobs, JobUpdateParams data, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        params.put("body", data);
        return execute("jobs", jobs, null, null, "update", params, POST, Job.class);
    }

    /**
     * Send a signal to kill a pending or running job.
     * @param job Job ID or UUID.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse kill(String job, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", job, null, null, "kill", params, POST, Job.class);
    }

    /**
     * Show the first lines of a log file (up to a limit).
     * @param job Job ID or UUID.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       offset: Starting byte from which the file will be read.
     *       lines: Maximum number of lines to be returned up to a maximum of 1000.
     *       type: Log file to be shown (stdout or stderr).
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse headLog(String job, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", job, "log", null, "head", params, GET, FileContent.class);
    }

    /**
     * Show the last lines of a log file (up to a limit).
     * @param job Job ID or UUID.
     * @param params Map containing any of the following optional parameters.
     *       study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
     *       lines: Maximum number of lines to be returned up to a maximum of 1000.
     *       type: Log file to be shown (stdout or stderr).
     * @return a RestResponse object.
     * @throws ClientException ClientException if there is any server error.
     */
    public RestResponse tailLog(String job, ObjectMap params) throws ClientException {
        params = params != null ? params : new ObjectMap();
        return execute("jobs", job, "log", null, "tail", params, GET, FileContent.class);
    }
}
    
    
    
    

    




    
    
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