ensembl-hive
2.5
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Module to encapsulate all db access for persistent class AnalysisJob. There should be just one per application and database connection.
Definition at line 22 of file AnalysisJobAdaptor.pm.
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::class_specific_execute | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::default_insertion_method | ( | ) |
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 Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::discard_jobs_for_analysis_id | ( | ) |
Arg [1] : list-ref of int $analysis_id Arg [2] : filter status Description: Resets all $input_status jobs of the matching analyses to DONE. Semaphores are updated accordingly. Caller : beekeeper.pl and guiHive
public Reference Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_all_by_analysis_id_status | ( | ) |
Arg [1] : (optional) listref $list_of_analyses 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_all_unfinished_jobs_with_no_roles | ( | ) |
Undocumented method
public AnalysisJob Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_by_analysis_id_and_input_id | ( | ) |
Arg [1] : Integer $analysis_id Arg [2] : String $input_id Example :
Description: Attempts to find the job by contents, then makes another attempt if the input_id is expected to have overflown into analysis_data Returntype : AnalysisJob object
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 String Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::job_status_cast | ( | ) |
Example :
Description : Returns a job-status expression that the SQL driver understands. This is needed for PostgreSQL Returntype : String Exceptions : none
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::object_class | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::prelock_semaphore_for_update | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_and_age_job | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_claimed_jobs_from_role | ( | ) |
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' (see the $ALL_STATUSES_OF_RUNNING_JOBS variable) 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] : arrayref of Analyses Arg [2] : arrayref of job statuses $input_statuses Description: Resets all the jobs of the selected analyses that have one of the required statuses to 'READY' and their retry_count to 0. Semaphores are updated accordingly. Caller : beekeeper.pl and guiHive
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 Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::semaphore_job_by_id | ( | ) |
Undocumented method
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::store_a_semaphored_group_of_jobs | ( | ) |
Arg [1] : Bio::EnsEMBL::Hive::AnalysisJob $funnel_job Arg [2] : arrayref of Bio::EnsEMBL::Hive::AnalysisJob $fan_jobs Arg [3] : (optional) Bio::EnsEMBL::Hive::AnalysisJob $emitting_job Arg [4] : (optional) boolean $no_leeching Example :
Description: Attempts to store a semaphored group of jobs, returns a list of successfully stored job_ids Returntype : ($funnel_semaphore_id, $funnel_job_id, )
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 Arg [3] : (optional) Int $emitting_job_id 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
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::unblock_jobs_for_analysis_id | ( | ) |
Arg [1] : list-ref of int $analysis_id Description: Sets all the SEMAPHORED jobs of the given analyses to READY and also unblocks their upstream semaphores Caller : beekeeper.pl and guiHive
public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::unsemaphore_job_by_id | ( | ) |
Undocumented method