Consistently capitalize Worker, Job, etc, when they refer to eHive co…

…mponents
Ensembl · Apr 8, 2018 · ac8bf38 · ac8bf38
1 parent 5987f09
commit ac8bf38
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Showing 11 changed files with 107 additions and 107 deletions.
diff --git a/docs/advanced_usage/mpi.rst b/docs/advanced_usage/mpi.rst
@@ -51,7 +51,7 @@ Resource Class in your pipeline.
          }
        }
 
-2. You need to add the analysis to your PipeConfig:
+2. You need to add the Analysis to your PipeConfig:
 
    ::
 
@@ -159,7 +159,7 @@ define the correct Resource Class and command lines in eHive.
       times. The memory requested is allocated for each _ptile_ (so
       64/4*16GB=256GB in total in the example).
 
-2. You need to add the analysis to your PipeConfig:
+2. You need to add the Analysis to your PipeConfig:
 
    ::
 

diff --git a/scripts/beekeeper.pl b/scripts/beekeeper.pl
@@ -263,7 +263,7 @@ sub main {
     if($reset_job_id) { $queen->reset_job_by_dbID_and_sync($reset_job_id); }
 
     if($job_id_for_output) {
-        printf("===== job output\n");
+        printf("===== Job output\n");
         my $job = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_by_dbID($job_id_for_output);
         print $job->toString. "\n";
     }
@@ -341,7 +341,7 @@ sub main {
     my $has_task = ($reset_all_jobs || $reset_failed_jobs || $reset_done_jobs || $unblock_semaphored_jobs || $forgive_failed_jobs || $discard_ready_jobs);
     if($reset_all_jobs || $reset_failed_jobs || $reset_done_jobs) {
         if (($reset_all_jobs || $reset_done_jobs) and not $self->{'analyses_pattern'}) {
-            log_and_die($self, "Beekeeper : do you really want to reset *all* the jobs ? If yes, add \"-analyses_pattern '%'\" to the command line\n");
+            log_and_die($self, "Beekeeper : do you really want to reset *all* the Jobs ? If yes, add \"-analyses_pattern '%'\" to the command line\n");
         }
         my $statuses_to_reset = $reset_failed_jobs ? [ 'FAILED' ] : ($reset_done_jobs ? [ 'DONE', 'PASSED_ON' ] : [ 'DONE', 'FAILED', 'PASSED_ON' ]);
         $self->{'dba'}->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id( $list_of_analyses, $statuses_to_reset );
@@ -390,7 +390,7 @@ sub main {
         Bio::EnsEMBL::Hive::Scheduler::schedule_workers_resync_if_necessary($queen, $valley, $list_of_analyses);   # show what would be submitted, but do not actually submit
 
         if($show_failed_jobs) {
-            print("===== failed jobs\n");
+            print("===== failed Jobs\n");
             my $failed_job_list = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status( $list_of_analyses , 'FAILED');
 
             foreach my $job (@{$failed_job_list}) {
@@ -469,7 +469,7 @@ sub register_beekeeper {
 
     $self->{'dba'}->get_BeekeeperAdaptor->store($beekeeper);
     unless ($self->{'beekeeper_id'} = $beekeeper->dbID) {
-        die "There was a problem registering this beekeeper with the eHive database.";
+        die "There was a problem registering this Beekeeper with the eHive database.";
     }
     return $beekeeper;
 }
@@ -502,8 +502,8 @@ sub run_autonomously {
 
         if (($loop_until eq 'JOB_FAILURE') &&
             (scalar(@job_fail_statuses)) > 0) {
-            print "Beekeeper : last loop because at least one job failed and loop-until mode is '$loop_until'\n";
-            print "Beekeeper : details from analyses with failed jobs:\n";
+            print "Beekeeper : last loop because at least one Job failed and loop-until mode is '$loop_until'\n";
+            print "Beekeeper : details from analyses with failed Jobs:\n";
             print join("\n", map {$_->{'message'}} @job_fail_statuses) . "\n";
             $found_reason_to_exit = 1;
             last BKLOOP;
@@ -521,7 +521,7 @@ sub run_autonomously {
                 # loop_until_mode is either job_failure or analysis_failure, and both of these exit on analysis failure
                 unless ($found_reason_to_exit) {
                     print "Beekeeper : last loop because at least one analysis failed and loop-until mode is '$loop_until'\n";
-                    print "Beekeeper : details from analyses with failed jobs:\n";
+                    print "Beekeeper : details from analyses with failed Jobs:\n";
                     print join("\n", map {$_->{'message'}} @analysis_fail_statuses) . "\n";
                     $found_reason_to_exit = 1;
                     last BKLOOP;
@@ -627,7 +627,7 @@ sub run_autonomously {
                 $self->{'beekeeper'}->adaptor->bury_other_beekeepers($self->{'beekeeper'});
                 if ($self->{'beekeeper'}->check_if_blocked()) {
                     print "Beekeeper : We have been blocked !\n".
-                          "This can happen if a job has explicitly required beekeeper to stop (have a look at log_message).\n".
+                          "This can happen if a Job has explicitly required the Beekeeper to stop (have a look at log_message).\n".
                           "It may also happen if someone has set is_blocked=1 in the beekeeper table for beekeeper_id=".$self->{'beekeeper_id'}.".\n";
                 } else {
                     last;
@@ -707,11 +707,11 @@ =head1 NAME
 =head1 DESCRIPTION
 
 The Beekeeper is in charge of interfacing between the eHive database a compute resource or 'compute farm'.
-Its job is to synchronise both, to assess the compute requirements of the pipeline
+Its Job is to synchronise both, to assess the compute requirements of the pipeline
 and to send the requested number of workers to open machines via the runWorker.pl script.
 
 It is also responsible for identifying workers which died
-unexpectedly so that dead workers can be released and unfinished jobs reclaimed.
+unexpectedly so that dead workers can be released and unfinished Jobs reclaimed.
 
 =head1 USAGE EXAMPLES
 
@@ -730,10 +730,10 @@ =head1 USAGE EXAMPLES
         # Restrict the normal execution to one iteration only - can be used for testing a newly set up pipeline
     beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -run
 
-        # Reset failed 'buggy_analysis' jobs to 'READY' state, so that they can be run again
+        # Reset failed 'buggy_analysis' Jobs to 'READY' state, so that they can be run again
     beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -analyses_pattern buggy_analysis -reset_failed_jobs
 
-        # Do a cleanup: find and bury dead workers, reclaim their jobs
+        # Do a cleanup: find and bury dead workers, reclaim their Jobs
     beekeeper.pl -url mysql://username:secret@hostname:port/long_mult_test -dead
 
 =head1 OPTIONS
@@ -784,21 +784,21 @@ =head2 Looping control
 
 =item --loop_until
 
-sets the level of event that will cause the beekeeper to stop looping:
+sets the level of event that will cause the Beekeeper to stop looping:
 
 =over
 
 =item JOB_FAILURE
 
-stop looping if any job fails
+stop looping if any Job fails
 
 =item ANALYSIS_FAILURE
 
-stop looping if any analysis has job failures exceeding its fault tolerance
+stop looping if any Analysis has Job failures exceeding its fault tolerance
 
 =item NO_WORK
 
-ignore job and analysis failures, keep looping until there is no work
+ignore Job and Analysis failures, keep looping until there is no work
 
 =item FOREVER
 
@@ -812,7 +812,7 @@ =head2 Looping control
 
 =item --max_loops <num>
 
-perform max this # of loops in autonomous mode. The beekeeper will stop when
+perform max this # of loops in autonomous mode. The Beekeeper will stop when
 it has performed max_loops loops, even in FOREVER mode
 
 =item --job_id <job_id>
@@ -861,11 +861,11 @@ =head2 Worker control
 
 =item --analyses_pattern <string>
 
-restrict the sync operation, printing of stats or looping of the beekeeper to the specified subset of analyses
+restrict the sync operation, printing of stats or looping of the Beekeeper to the specified subset of analyses
 
 =item --can_respecialize <0|1>
 
-allow workers to re-specialise into another analysis (within resource_class) after their previous analysis was exhausted
+allow workers to re-specialise into another Analysis (within resource_class) after their previous Analysis was exhausted
 
 =item --force
 
@@ -881,11 +881,11 @@ =head2 Worker control
 
 =item --job_limit <num>
 
-#jobs to run before Worker can die naturally
+Number of Jobs to run before Worker can die naturally
 
 =item --retry_throwing_jobs <0|1>
 
-if a job dies *knowingly*, should we retry it by default?
+if a Job dies *knowingly*, should we retry it by default?
 
 =item --hive_log_dir <path>
 
@@ -919,63 +919,63 @@ =head2 Other commands/options
 
 =item --dead
 
-detect all unaccounted dead workers and reset their jobs for resubmission
+detect all unaccounted dead workers and reset their Jobs for resubmission
 
 =item --sync
 
 re-synchronise the ehive
 
 =item --unkwn
 
-detect all workers in UNKWN state and reset their jobs for resubmission (careful, they *may* reincarnate!)
+detect all workers in UNKWN state and reset their Jobs for resubmission (careful, they *may* reincarnate!)
 
 =item --alldead
 
 tell the database all workers are dead (no checks are performed in this mode, so be very careful!)
 
 =item --balance_semaphores
 
-set all semaphore_counts to the numbers of unDONE fan jobs (emergency use only)
+set all Semaphore counters to the numbers of unDONE fan Jobs (emergency use only)
 
 =item --worker_stats
 
 show status of each running Worker
 
 =item --failed_jobs
 
-show all failed jobs
+show all failed Jobs
 
 =item --job_output <job_id>
 
-print details for one job
+print details for one Job
 
 =item --reset_job_id <num>
 
-reset a job back to READY so it can be rerun
+reset a Job back to READY so it can be rerun
 
 =item --reset_failed_jobs
 
-reset FAILED jobs of analyses matching -analyses_pattern back to READY so they can be rerun
+reset FAILED Jobs of analyses matching -analyses_pattern back to READY so they can be rerun
 
 =item --reset_done_jobs
 
-reset DONE and PASSED_ON jobs of analyses matching -analyses_pattern back to READY so they can be rerun
+reset DONE and PASSED_ON Jobs of analyses matching -analyses_pattern back to READY so they can be rerun
 
 =item --reset_all_jobs
 
-reset FAILED, DONE and PASSED_ON jobs of analyses matching -analyses_pattern back to READY so they can be rerun
+reset FAILED, DONE and PASSED_ON Jobs of analyses matching -analyses_pattern back to READY so they can be rerun
 
 =item --forgive_failed_jobs
 
-mark FAILED jobs of analyses matching -analyses_pattern as DONE, and update their semaphores. NOTE: This does not make them dataflow
+mark FAILED Jobs of analyses matching -analyses_pattern as DONE, and update their Semaphores. NOTE: This does not make them dataflow
 
 =item --discard_ready_jobs
 
-mark READY jobs of analyses matching -analyses_pattern as DONE, and update their semaphores. NOTE: This does not make them dataflow
+mark READY Jobs of analyses matching -analyses_pattern as DONE, and update their Semaphores. NOTE: This does not make them dataflow
 
 =item --unblock_semaphored_jobs
 
-set SEMAPHORED jobs of analyses matching -analyses_pattern to READY so they can start
+set SEMAPHORED Jobs of analyses matching -analyses_pattern to READY so they can start
 
 =back
 

diff --git a/scripts/dev/simple_init.py b/scripts/dev/simple_init.py
@@ -18,7 +18,7 @@
 ## Minimalistic init system required for Docker containers
 ##
 
-# Docker doesn't come with an "init" process, meaning that when beekeeper
+# Docker doesn't come with an "init" process, meaning that when the Beekeeper
 # submits LOCAL Workers and exits (beekeeper -run), the Workers will be
 # killed by docker.
 

diff --git a/scripts/generate_graph.pl b/scripts/generate_graph.pl
@@ -138,7 +138,7 @@ =head1 DESCRIPTION
 This program will generate a graphical representation of your eHive pipeline.
 This includes visualising the flow of data from the different analyses, blocking
 rules and table writers. The graph is also coloured to indicate the stage
-an analysis is at. The colours and fonts used can be configured via
+an Analysis is at. The colours and fonts used can be configured via
 hive_config.json configuration file.
 
 =head1 OPTIONS

diff --git a/scripts/generate_timeline.pl b/scripts/generate_timeline.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 
-# Gets the activity of each analysis along time, in a CSV file or in an image (see list of formats supported by GNUplot)
+# Gets the activity of each Analysis along time, in a CSV file or in an image (see list of formats supported by GNUplot)
 
 use strict;
 use warnings;
@@ -103,7 +103,7 @@ sub main {
 
     my %allowed_keys = (
         analysis => 'Analysis',
-        resource_class => 'Resource class',
+        resource_class => 'Resource Class',
     );
     if ($key) {
         die "Unknown key '$key'. Allowed keys are: ".join(", ", keys %allowed_keys) unless exists $allowed_keys{$key};
@@ -515,17 +515,17 @@ =head1 DESCRIPTION
 Based on the command-line parameters "start_date" and "end_date", or on the start time of the first
 Worker and end time of the last Worker (as recorded in pipeline database), it pulls the relevant data out
 of the C<worker> table for accurate timing.
-By default, the output is in CSV format, to allow extra analysis to be carried.
+By default, the output is in CSV format, to allow extra Analysis to be carried.
 
 You can optionally ask the script to generate an image with Gnuplot.
 
 
 =head1 USAGE EXAMPLES
 
-        # Just run it the usual way: only the top 20 analysis will be reported in CSV format
+        # Just run it the usual way: only the top 20 Analysis will be reported in CSV format
     generate_timeline.pl -url mysql://username:secret@hostname:port/database > timeline.csv
 
-        # The same, but getting the analysis that fill 99.5% of the global activity in a PNG file
+        # The same, but getting the Analysis that fill 99.5% of the global activity in a PNG file
     generate_timeline.pl -url mysql://username:secret@hostname:port/database -top .995 -output timeline_top995.png
 
         # Assuming you are only interested in a precise interval (in a PNG file)
@@ -586,7 +586,7 @@ =head2 Timeline configuration
 
 =item --top <float>
 
-maximum number (> 1) or fraction (< 1) of analysis to report (default: 20)
+maximum number (> 1) or fraction (< 1) of Analysis to report (default: 20)
 
 =item --output <string>
 

diff --git a/scripts/hoover_pipeline.pl b/scripts/hoover_pipeline.pl
@@ -128,21 +128,21 @@ =head1 SYNOPSIS
 
 =head1 DESCRIPTION
 
-hoover_pipeline.pl is a script used to remove old "DONE" jobs from a continuously running pipeline database
+hoover_pipeline.pl is a script used to remove old "DONE" Jobs from a continuously running pipeline database
 
 =head1 USAGE EXAMPLES
 
-        # delete all jobs that have been "DONE" for at least a week (default threshold) :
+        # delete all Jobs that have been "DONE" for at least a week (default threshold) :
 
     hoover_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult"
 
 
-        # delete all jobs that have been "DONE" for at least a given number of days
+        # delete all Jobs that have been "DONE" for at least a given number of days
 
     hoover_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult" -days_ago 3
 
 
-        # delete all jobs "DONE" before a specific datetime:
+        # delete all Jobs "DONE" before a specific datetime:
 
     hoover_pipeline.pl -url "mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_long_mult" -before_datetime "2013-02-14 15:42:50"
 
@@ -172,11 +172,11 @@ =head1 OPTIONS
 
 =item --before_datetime <string>
 
-delete jobs "DONE" before a specific time
+delete Jobs "DONE" before a specific time
 
 =item --days_ago <num>
 
-delete jobs that have been "DONE" for at least <num> days
+delete Jobs that have been "DONE" for at least <num> days
 
 =item -h, --help