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Ensembl/ensembl-hive

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Showing 446 of 446 total issues

FIXME found
Open

            # FIXME: if GarabageCollector (beekeeper -dead) gets to these processes first, it will register them as DEAD/UNKNOWN.
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Queen.pm by fixme

XXX found
Open

              "branch_name_or_code": XXX,
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/GuestProcess.pm by fixme

FIXME found
Open

                        # FIXME: should not recurse
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/HivePipeline.pm by fixme

XXX found
Open

        3. -url $ehive_url job_id XXX. The reference to an existing job from which the parameters will be pulled. It is
Severity: Minor
Found in scripts/standaloneJob.pl by fixme

XXX found
Open

           "debug": XXX
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/GuestProcess.pm by fixme

FIXME found
Open

    # FIXME: An UPSERT would be better here, but it is only promised in PostgreSQL starting from 9.5, which is not officially out yet.
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Queen.pm by fixme

FIXME found
Open

    my $remaining_job_count = shift @_ || 0;    # FIXME: a better estimate would be $self->claimed_job_count when it is introduced
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/AnalysisStats.pm by fixme

XXX found
Open

             "retry_count": XXX
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/GuestProcess.pm by fixme

FIXME found
Open

    my $remaining_job_count = shift @_ || 0;    # FIXME: a better estimate would be $self->claimed_job_count when it is introduced
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/AnalysisStats.pm by fixme

FIXME found
Open

    # FIXME: An UPSERT would be better here, but it is only promised in PostgreSQL starting from 9.5, which is not officially out yet.
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm by fixme

FIXME found
Open

        # FIXME: would it be possible to retain role_id for READY jobs in order to temporarily keep track of the previous (failed) worker?
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm by fixme

XXX found
Open

              "message": "XXX",
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/GuestProcess.pm by fixme

FIXME found
Open

        #FIXME It should be normalised by the length of the time interval
Severity: Minor
Found in scripts/generate_timeline.pl by fixme

TODO found
Open

    TODO: implement a "expected_value" test
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/RunnableDB/SqlHealthcheck.pm by fixme

TODO found
Open

        warn "[Job $job_id] $msg\n";    # TODO: integrate the STDERR diagnostic output with LogMessageAdaptor calls in general
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm by fixme

FIXME found
Open

        # FIXME: if we want to incorporate Meadow->pipeline_name() filtering here,
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Meadow/LOCAL.pm by fixme

FIXME found
Open

    if(ref($from) eq 'HASH') {      # FIXME: currently we don't merge ARRAY references (the only example we currently have is REMARK), only the HASH references
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Utils/Config.pm by fixme

FIXME found
Open

    } elsif($driver eq 'pgsql') {   # FIXME! temporary hack
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/DBSQL/BaseAdaptor.pm by fixme

FIXME found
Open

            die "Job with dbID='$job_id' is already in progress, cannot run";   # FIXME: try GC first, then complain
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Queen.pm by fixme

FIXME found
Open

                # FIXME: a faster way would be to unclaim( splice(@$jobs, -$jobs_to_unclaim) );  # unclaim the last $jobs_to_unclaim elements
Severity: Minor
Found in modules/Bio/EnsEMBL/Hive/Worker.pm by fixme
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