org.opencb.opencga.client.rest.clients.VariantOperationClient 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 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.config.storage.CellBaseConfiguration;
import org.opencb.opencga.core.config.storage.SampleIndexConfiguration;
import org.opencb.opencga.core.models.job.Job;
import org.opencb.opencga.core.models.operations.variant.JulieParams;
import org.opencb.opencga.core.models.operations.variant.VariantAggregateFamilyParams;
import org.opencb.opencga.core.models.operations.variant.VariantAggregateParams;
import org.opencb.opencga.core.models.operations.variant.VariantAnnotationIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantAnnotationSaveParams;
import org.opencb.opencga.core.models.operations.variant.VariantConfigureParams;
import org.opencb.opencga.core.models.operations.variant.VariantFamilyIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantFileDeleteParams;
import org.opencb.opencga.core.models.operations.variant.VariantFileIndexJobLauncherParams;
import org.opencb.opencga.core.models.operations.variant.VariantIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantPruneParams;
import org.opencb.opencga.core.models.operations.variant.VariantSampleDeleteParams;
import org.opencb.opencga.core.models.operations.variant.VariantScoreIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantSecondaryAnnotationIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantSecondarySampleIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantStatsDeleteParams;
import org.opencb.opencga.core.models.operations.variant.VariantStatsIndexParams;
import org.opencb.opencga.core.models.operations.variant.VariantStorageMetadataRepairToolParams;
import org.opencb.opencga.core.models.operations.variant.VariantStorageMetadataSynchronizeParams;
import org.opencb.opencga.core.models.operations.variant.VariantStudyDeleteParams;
import org.opencb.opencga.core.models.study.VariantSetupResult;
import org.opencb.opencga.core.models.variant.VariantSetupParams;
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 VariantOperation webservices.
* PATH: operation
*/
public class VariantOperationClient extends AbstractParentClient {
public VariantOperationClient(String token, ClientConfiguration configuration) {
super(token, configuration);
}
/**
* Update Cellbase configuration.
* @param data New cellbase configuration.
* @param params Map containing any of the following optional parameters.
* project: Project [organization@]project where project can be either the ID or the alias.
* annotationUpdate: Create and load variant annotations into the database.
* annotationSaveId: Save a copy of the current variant annotation at the database.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse configureCellbase(CellBaseConfiguration data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "cellbase", null, "configure", params, POST, Job.class);
}
/**
* Find variants where not all the samples are present, and fill the empty values, excluding HOM-REF (0/0) values.
* @param data Variant aggregate params.
* @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.
* 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.
* 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 aggregateVariant(VariantAggregateParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "aggregate", params, POST, Job.class);
}
/**
* Deletes a saved copy of variant annotation.
* @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.
* 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.
* project: Project [organization@]project where project can be either the ID or the alias.
* annotationId: Annotation identifier.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse deleteVariantAnnotation(ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("operation", null, "variant/annotation", null, "delete", params, DELETE, Job.class);
}
/**
* Create and load variant annotations into the database.
* @param data Variant annotation index params.
* @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.
* 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.
* project: Project [organization@]project where project can be either the ID or the alias.
* 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 indexVariantAnnotation(VariantAnnotationIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/annotation", null, "index", params, POST, Job.class);
}
/**
* Save a copy of the current variant annotation at the database.
* @param data Variant annotation save params.
* @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.
* 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.
* project: Project [organization@]project where project can be either the ID or the alias.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse saveVariantAnnotation(VariantAnnotationSaveParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/annotation", null, "save", params, POST, Job.class);
}
/**
* Update Variant Storage Engine configuration. Can be updated at Project or Study level.
* @param data Configuration params to update.
* @param params Map containing any of the following optional parameters.
* project: Project [organization@]project where project can be either the ID or the alias.
* 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 configureVariant(VariantConfigureParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "configure", params, POST, ObjectMap.class);
}
/**
* Remove variant files from the variant storage.
* @param data Variant delete file params.
* @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.
* 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.
* 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 deleteVariant(VariantFileDeleteParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "delete", params, POST, Job.class);
}
/**
* Find variants where not all the samples are present, and fill the empty values.
* @param data Variant aggregate family params.
* @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.
* 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.
* 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 aggregateVariantFamily(VariantAggregateFamilyParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/family", null, "aggregate", params, POST, Job.class);
}
/**
* DEPRECATED: integrated in index (DEPRECATED Build the family index).
* @param data Variant family index params.
* @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.
* 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.
* 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 indexVariantFamily(VariantFamilyIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/family", null, "index", params, POST, Job.class);
}
/**
* Index variant files into the variant storage.
* @param data Variant index params.
* @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.
* 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.
* 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 indexVariant(VariantIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "index", params, POST, Job.class);
}
/**
* Detect non-indexed VCF files in the study, and submit a job for indexing them.
* @param data .
* @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.
* 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.
* 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 launcherVariantIndex(VariantFileIndexJobLauncherParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/index", null, "launcher", params, POST, Job.class);
}
/**
* Transform VariantStats into PopulationFrequency values and updates the VariantAnnotation.
* @param data Julie tool params. Specify list of cohorts from multiple studies with {study}:{cohort}.
* @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.
* 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.
* project: project.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse runVariantJulie(JulieParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/julie", null, "run", params, POST, Job.class);
}
/**
* Execute some repairs on Variant Storage Metadata. Advanced users only.
* @param data Variant storage metadata repair params.
* @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.
* 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 repairVariantMetadata(VariantStorageMetadataRepairToolParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/metadata", null, "repair", params, POST, Job.class);
}
/**
* Synchronize catalog with variant storage metadata.
* @param data Variant storage metadata synchronize params.
* @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.
* 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.
* 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 synchronizeVariantMetadata(VariantStorageMetadataSynchronizeParams data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/metadata", null, "synchronize", params, POST, Job.class);
}
/**
* Prune orphan variants from studies in a project.
* @param data Variant prune params. Use dry-run to just generate a report with the orphan variants.
* @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.
* 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 pruneVariant(VariantPruneParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "prune", params, POST, Job.class);
}
/**
* Remove variant samples from the variant storage.
* @param data Variant delete sample params.
* @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.
* 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.
* 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 deleteVariantSample(VariantSampleDeleteParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/sample", null, "delete", params, POST, Job.class);
}
/**
* DEPRECATED You should use the new sample index method instead.
* @param data Variant sample index params.
* @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.
* 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.
* 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 indexVariantSample(VariantSecondarySampleIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/sample", null, "index", params, POST, Job.class);
}
/**
* DEPRECATED You should use the new sample index configure method.
* @param data New SampleIndexConfiguration.
* @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.
* skipRebuild: Skip sample index re-build.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse variantSampleIndexConfigure(SampleIndexConfiguration data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/sample/index", null, "configure", params, POST, Job.class);
}
/**
* Remove a variant score in the database.
* @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.
* 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.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* name: Unique name of the score within the study.
* resume: Resume a previously failed remove.
* force: Force remove of partially indexed scores.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse deleteVariantScore(ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("operation", null, "variant/score", null, "delete", params, DELETE, Job.class);
}
/**
* Index a variant score in the database.
* @param data Variant score index params. scoreName: Unique name of the score within the study. cohort1: Cohort used to compute the
* score. Use the cohort 'ALL' if all samples from the study where used to compute the score. cohort2: Second cohort used to
* compute the score, typically to compare against the first cohort. If only one cohort was used to compute the score, leave empty.
* inputColumns: Indicate which columns to load from the input file. Provide the column position (starting in 0) for the column
* with the score with 'SCORE=n'. Optionally, the PValue column with 'PVALUE=n'. The, to indicate the variant associated with the
* score, provide either the columns ['CHROM', 'POS', 'REF', 'ALT'], or the column 'VAR' containing a variant representation with
* format 'chr:start:ref:alt'. e.g. 'CHROM=0,POS=1,REF=3,ALT=4,SCORE=5,PVALUE=6' or 'VAR=0,SCORE=1,PVALUE=2'. resume: Resume a
* previously failed indexation.
* @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.
* 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.
* 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 indexVariantScore(VariantScoreIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/score", null, "index", params, POST, Job.class);
}
/**
* Creates a secondary index using a search engine. If samples are provided, sample data will be added to the secondary index. (New!).
* @param data Variant secondary annotation index params.
* @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.
* 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.
* project: Project [organization@]project where project can be either the ID or the alias.
* 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 variantSecondaryAnnotationIndex(VariantSecondaryAnnotationIndexParams data, ObjectMap params)
throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/secondary/annotation", null, "index", params, POST, Job.class);
}
/**
* Build and annotate the sample index. (New!) .
* @param data Variant sample index params.
* @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.
* 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.
* 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 variantSecondarySampleIndex(VariantSecondarySampleIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/secondary/sample", null, "index", params, POST, Job.class);
}
/**
* Update SampleIndex configuration (New!).
* @param data New SampleIndexConfiguration.
* @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.
* skipRebuild: Skip sample index re-build.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse configureVariantSecondarySampleIndex(SampleIndexConfiguration data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/secondary/sample/index", null, "configure", params, POST, Job.class);
}
/**
* DEPRECATED you should use the new annotation index method instead.
* @param data Variant secondary annotation index params.
* @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.
* 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.
* project: Project [organization@]project where project can be either the ID or the alias.
* 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 secondaryIndexVariant(VariantSecondaryAnnotationIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "secondaryIndex", params, POST, Job.class);
}
/**
* Remove a secondary index from the search engine for a specific set of samples.
* @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.
* 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.
* study: Study [[organization@]project:]study where study and project can be either the ID or UUID.
* samples: Samples to remove. Needs to provide all the samples in the secondary index.
* @return a RestResponse object.
* @throws ClientException ClientException if there is any server error.
*/
public RestResponse deleteVariantSecondaryIndex(ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
return execute("operation", null, "variant/secondaryIndex", null, "delete", params, DELETE, Job.class);
}
/**
* Execute Variant Setup to allow using the variant engine. This setup is necessary before starting any variant operation.
* @param data Variant setup params.
* @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 setupVariant(VariantSetupParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant", null, "setup", params, POST, VariantSetupResult.class);
}
/**
* Deletes the VariantStats of a cohort/s from the database.
* @param data Variant stats delete params.
* @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.
* 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.
* 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 deleteVariantStats(VariantStatsDeleteParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/stats", null, "delete", params, POST, Job.class);
}
/**
* Compute variant stats for any cohort and any set of variants and index the result in the variant storage database.
* @param data Variant stats params.
* @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.
* 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.
* 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 indexVariantStats(VariantStatsIndexParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/stats", null, "index", params, POST, Job.class);
}
/**
* Remove whole study from the variant storage.
* @param data Variant delete study params.
* @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.
* 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.
* 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 deleteVariantStudy(VariantStudyDeleteParams data, ObjectMap params) throws ClientException {
params = params != null ? params : new ObjectMap();
params.put("body", data);
return execute("operation", null, "variant/study", null, "delete", params, POST, Job.class);
}
}
© 2015 - 2025 Weber Informatics LLC | Privacy Policy