ensembl-hive
2.1
|
Module to encapsulate all db access for persistent class AnalysisJob. There should be just one per application and database connection.
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::balance_semaphores | ( | ) |
Description: Reset all semaphore_counts to the numbers of unDONE semaphoring jobs.
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::check_in_job | ( | ) |
Arg [1] : $analysis_id Example :
Description: updates the job.status in the database Returntype : Exceptions : Caller : general
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::decrease_semaphore_count_for_jobid | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::default_overflow_limit | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::default_table_name | ( | ) |
Undocumented method
public Reference Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_all_by_analysis_id_status | ( | ) |
Arg [1] : (optional) int $analysis_id Arg [2] : (optional) string $status Arg [3] : (optional) int $retry_at_least Example :
Description: Returns a list of all jobs filtered by given analysis_id (if specified) and given status (if specified). Returntype : reference to list of Bio::EnsEMBL::Hive::AnalysisJob objects
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_all_incomplete_jobs_by_role_id | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_by_url_query | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_input_ids_for_job_ids | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_job_counts_hashed_by_status | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_some_by_analysis_id_limit | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::gc_dataflow | ( | ) |
Description: perform automatic dataflow from a dead job that overused resources if a corresponding dataflow rule was provided Should only be called once during garbage collection phase, when the job is definitely 'abandoned' and not being worked on.
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::grab_jobs_for_role | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::Role object $role Arg [2] : int $how_many_this_role Example: my $jobs = $job_adaptor->grab_jobs_for_role( $role, $how_many ); Description: For the specified Role, it will search available jobs, and using the how_many_this_batch parameter, claim/fetch that number of jobs, and then return them. Returntype : reference to array of Bio::EnsEMBL::Hive::AnalysisJob objects Caller : Bio::EnsEMBL::Hive::Worker::run
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::increase_semaphore_count_for_jobid | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::object_class | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_and_age_job | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_undone_jobs_from_role | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::Role object Arg [2] : optional message to be recorded in 'job_message' table Example :
Description: If a Worker has died some of its jobs need to be reset back to 'READY' so they can be rerun. Jobs in state CLAIMED as simply reset back to READY. If jobs was 'in progress' (PRE_CLEANUP, FETCH_INPUT, RUN, WRITE_OUTPUT, POST_CLEANUP) the retry_count is increased and the status set back to READY. If the retry_count >= $max_retry_count (3 by default) the job is set to 'FAILED' and not rerun again. Exceptions : $role must be defined Caller : Bio::EnsEMBL::Hive::Queen
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::reset_jobs_for_analysis_id | ( | ) |
Arg [1] : int $analysis_id Arg [2] : bool $all (false by default) Description: Resets either all FAILED jobs of an analysis (default) or ALL jobs of an analysis to 'READY' and their retry_count to 0. Caller : beekeeper.pl
public Bio::EnsEMBL::Hive::AnalysisJob Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::reset_or_grab_job_by_dbID | ( | ) |
Arg [1] : int $job_id Arg [2] : int $role_id (optional) Description: resets a job to to 'READY' (if no $role_id given) or directly to 'CLAIMED' so it can be run again, and fetches it. NB: Will also reset a previously 'SEMAPHORED' job to READY. The retry_count will be set to 1 for previously run jobs (partially or wholly) to trigger PRE_CLEANUP for them, but will not change retry_count if a job has never *really* started. Returntype : Bio::EnsEMBL::Hive::AnalysisJob or undef
public Reference Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::store_jobs_and_adjust_counters | ( | ) |
Arg [1] : arrayref of Bio::EnsEMBL::Hive::AnalysisJob $jobs_to_store Arg [2] : (optional) boolean $push_new_semaphore Example :
Description: Attempts to store a list of jobs, returns an arrayref of successfully stored job_ids Returntype : Reference to list of job_dbIDs
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::store_out_files | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::AnalysisJob $job Example :
Description: update locations of log files, if present Returntype : Exceptions : Caller : Bio::EnsEMBL::Hive::Worker