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ensembl-hive: modules/Bio/EnsEMBL/Hive/PipeConfig/LongMultSt_pyconf.pm File Reference
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+
+
+ ensembl-hive
+ 2.3
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/doxygen/_statement_handle_8pm.html b/docs/doxygen/_statement_handle_8pm.html
index 07b9e6b4eb7cbdfdb1d84b7d0b8cb81301212ac5..34a84bde7babfab016670c07d5af62417286bafe 100644
--- a/docs/doxygen/_statement_handle_8pm.html
+++ b/docs/doxygen/_statement_handle_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_stopwatch_8pm.html b/docs/doxygen/_stopwatch_8pm.html
index d15baf043eee8a79b6b78cf6eef4a9966a0201f7..941b2b4e71a2fc237774f4d013cfc5f6831ce14b 100644
--- a/docs/doxygen/_stopwatch_8pm.html
+++ b/docs/doxygen/_stopwatch_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_storable_8pm.html b/docs/doxygen/_storable_8pm.html
index 242d2f7c457a432fb3e365a270dd189dd43e6915..3b83df803c34e1c1e4b3b48d3f5f781b86bdcd6d 100644
--- a/docs/doxygen/_storable_8pm.html
+++ b/docs/doxygen/_storable_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_system_cmd_8pm.html b/docs/doxygen/_system_cmd_8pm.html
index e13fcd0a4a5bf4f30533c71bb8a3ad1e49270d0e..5b423d95d5117dcec890690c3e0545e2ead271e1 100644
--- a/docs/doxygen/_system_cmd_8pm.html
+++ b/docs/doxygen/_system_cmd_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_table_dumper_zipper__conf_8pm.html b/docs/doxygen/_table_dumper_zipper__conf_8pm.html
index 063cbd2b037acdd4c8f428cb5524ea87f20f934f..7947dc0837ab81996f2580e2a23f8a6137dd893f 100644
--- a/docs/doxygen/_table_dumper_zipper__conf_8pm.html
+++ b/docs/doxygen/_table_dumper_zipper__conf_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_test_8pm.html b/docs/doxygen/_test_8pm.html
new file mode 100644
index 0000000000000000000000000000000000000000..98058452209f92be18c0602a8882627457960327
--- /dev/null
+++ b/docs/doxygen/_test_8pm.html
@@ -0,0 +1,141 @@
+
+
+
+
+
+
+
ensembl-hive: modules/Bio/EnsEMBL/Hive/Utils/Test.pm File Reference
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ensembl-hive
+ 2.3
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/doxygen/_top_up__conf_8pm.html b/docs/doxygen/_top_up__conf_8pm.html
index 9f69282d4ffd7d2f1db4660f72477f4453470d12..97062e69cbf5101885866f210b1b507ff7320927 100644
--- a/docs/doxygen/_top_up__conf_8pm.html
+++ b/docs/doxygen/_top_up__conf_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_u_r_l_8pm.html b/docs/doxygen/_u_r_l_8pm.html
index f733149934f2e6ad422c2b89d606359b4d48589f..95c5b2c7b523d761a7b8b203d931a0d33691a068 100644
--- a/docs/doxygen/_u_r_l_8pm.html
+++ b/docs/doxygen/_u_r_l_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_u_r_l_factory_8pm.html b/docs/doxygen/_u_r_l_factory_8pm.html
index bf6eb06e9790c1ae02c35be73fa6a9317d83e164..5d141d1e9a4c104d0c67b170127e0e4cea436f20 100644
--- a/docs/doxygen/_u_r_l_factory_8pm.html
+++ b/docs/doxygen/_u_r_l_factory_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_utils_8pm.html b/docs/doxygen/_utils_8pm.html
index e5f3f93623b258bdb1075e8591ef999245d9089e..e9966897fb04c080b71e63824b722c6f6a3082aa 100644
--- a/docs/doxygen/_utils_8pm.html
+++ b/docs/doxygen/_utils_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_valley_8pm.html b/docs/doxygen/_valley_8pm.html
index 6a4a163793b5b3d03ff81740e7d1f8306129de38..7336fa7e868bb80852bd42fc02e3cfbe2c62f10b 100644
--- a/docs/doxygen/_valley_8pm.html
+++ b/docs/doxygen/_valley_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_version_8pm.html b/docs/doxygen/_version_8pm.html
index d582138d07a579d1ec2cd8c14c5a8bea8b8f6c0a..9fa9179e41e592d39d7ec85aa0647dfaa6936d68 100644
--- a/docs/doxygen/_version_8pm.html
+++ b/docs/doxygen/_version_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/_worker_8pm.html b/docs/doxygen/_worker_8pm.html
index 532baa93cf8d1cc13f2461846367a36535d888c2..bbf297866f5371ccc80c908cd4f5515df01d4132 100644
--- a/docs/doxygen/_worker_8pm.html
+++ b/docs/doxygen/_worker_8pm.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
diff --git a/docs/doxygen/all__tests_8pl.html b/docs/doxygen/all__tests_8pl.html
new file mode 100644
index 0000000000000000000000000000000000000000..c3875581dac0b4515591a6dd3c8f64b5f35c1481
--- /dev/null
+++ b/docs/doxygen/all__tests_8pl.html
@@ -0,0 +1,298 @@
+
+
+
+
+
+
+
ensembl-hive: scripts/all_tests.pl File Reference
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ensembl-hive
+ 2.3
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ public clean
+ (
+ )
+
+
+
+
Undocumented method
+
+
click to view
+
+
+
# Unset environment variable indicating final cleanup should be
+
# performed
+
delete $ENV{'RUNTESTS_HARNESS' };
+
+
+
my @clean_tests = grep { $_ =~ /CLEAN\.t$/ } @new_tests;
+
eval { $harness->runtests(@clean_tests); };
+
warn $@ if $@;
+
}
+
return ;
+
}
+
+
+
+
+
+
+
+
+ public Listref get_all_tests
+ (
+ )
+
+
+
+
+ Description: Returns a list of testfiles in the directories specified by
+ the argument. The relative path is given as well as
+ with the testnames returned. Only files ending with .t are
+ returned. Subdirectories are recursively entered and the test
+ files returned within them are returned as well.
+ Returntype : listref of strings.
+ Exceptions : none
+ Caller : general
+
click to view
+
+
+
my @files;
+
my @out;
+
+
#If we had files use them
+
if ( $input_files_directories && @{$input_files_directories} ) {
+
@files = @{$input_files_directories};
+
}
+
#Otherwise use current directory
+
else {
+
push(@files, File::Spec->curdir());
+
}
+
+
my $is_test = sub {
+
my ($suspect_file) = @_;
+
return 0 unless $suspect_file =~ /\.t$/;
+
if (! -f $suspect_file) {
+
warn "Cannot find file '$suspect_file'" ;
+
}
+
elsif(! -r $suspect_file) {
+
warn "Cannot read file '$suspect_file'" ;
+
}
+
return 1;
+
};
+
+
while (my $file = shift @files) {
+
#If it was a directory use it as a point to search from
+
if (-d $file) {
+
my $dir = $file;
+
#find cd's to the dir in question so use relative for tests
+
+
if ( $_ ne '.' && $_ ne '..' && $_ ne 'CVS' ) {
+
if ($is_test->($_)) {
+
push(@out, $File::Find::name);
+
}
+
}
+
}, $dir);
+
}
+
#Otherwise add it if it was a test
+
else {
+
push(@out, $file) if $is_test->($file);
+
}
+
}
+
+
return @out;
+
}
+
+
+
+
+
+
+
+
+ public usage
+ (
+ )
+
+
+
+
Undocumented method
+
+
click to view
+
+
+
print <<EOT;
+
Usage:
+
\t$0 [-c] [-v] [<test files or directories> ...]
+
\t$0 -l [<test files or directories> ...]
+
\t$0 -h
+
+
\t-l|--list|--tests|--list-tests\n\t\tlist available tests
+
\t-c|--
clean |--clear\n\t\trun tests and
clean up in each directory
+
\t\tvisited (
default is not to
clean up)
+
\t--skip <test_name>[,<test_name>...]\n\t\tskip listed tests
+
\t-v|--verbose\n\t\tbe verbose
+
\t-h|--help\n\t\tdisplay this help text
+
+
If no directory or test file is given on the command line, the script
+
will assume the current directory.
+
EOT
+
}
+
Undocumented method
+
+
click to view
+
+
+
print <<EOT;
+
Usage:
+
\t$0 [-date <day_of_the_patch>] [-driver <name_of_first_driver>] [-driver <name_of_second_driver>] ...
+
\t$0 -h
+
+
\t-date\n\t\tdate in ISO format, e.g. 2015-02-14. Defaults to the current date
+
\t-driver (can be repeated)\n\t\tdriver for which create a patch. Defaults to MySQL, SQLite, and Postgre
+
\t-h|--help\n\t\tdisplay this help text
+
+
EOT
+
}
+
+
+
+
+
+
+
+
+
diff --git a/docs/doxygen/all__tests_8pl.js b/docs/doxygen/all__tests_8pl.js
new file mode 100644
index 0000000000000000000000000000000000000000..b8c6a65aefbd9ac24c8bf3102010dfcd15621f47
--- /dev/null
+++ b/docs/doxygen/all__tests_8pl.js
@@ -0,0 +1,6 @@
+var all__tests_8pl =
+[
+ [ "clean", "all__tests_8pl.html#a422ef8d1a748ca4ffbcd453fbf22ba8b", null ],
+ [ "get_all_tests", "all__tests_8pl.html#afec6f985b18aa1e7edb785fb6c35aada", null ],
+ [ "usage", "all__tests_8pl.html#a9449f3118943816afb79e9c3394972ca", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/annotated.html b/docs/doxygen/annotated.html
index 973a21e3a5bc41cb291a6a5b15d23ab9b72820b5..21b84cb470b17f31e470cd18f58a9922ffede5b2 100644
--- a/docs/doxygen/annotated.html
+++ b/docs/doxygen/annotated.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
@@ -114,97 +113,107 @@ $(document).ready(function(){initNavTree('annotated.html','');});
Bio EnsEMBL Hive
-
DBSQL
-
AccumulatorAdaptor
-
AnalysisAdaptor
-
AnalysisCtrlRuleAdaptor
-
AnalysisDataAdaptor
-
AnalysisJobAdaptor
-
AnalysisStatsAdaptor
-
BaseAdaptor
-
CoreDBConnection
-
DataflowRuleAdaptor
-
DBAdaptor
-
DBConnection
-
LogMessageAdaptor
-
MetaAdaptor
-
NakedTableAdaptor
-
ObjectAdaptor
-
PipelineWideParametersAdaptor
-
ResourceClassAdaptor
-
ResourceDescriptionAdaptor
-
RoleAdaptor
-
SqlSchemaAdaptor
-
StatementHandle
-
Meadow
-
LOCAL
-
LSF
-
PipeConfig
-
AnyCommands_conf
-
ApplyToDatabases_conf
-
CompressFiles_conf
-
EnsemblGeneric_conf
-
FailureTest_conf
-
FastaSplitter_conf
-
HiveGeneric_conf
-
LongMult_conf
-
LongMultSt_conf
-
LongMultWf_conf
-
MemlimitTest_conf
-
RunListOfCommandsOnFarm_conf
-
TableDumperZipper_conf
-
TopUp_conf
-
RunnableDB
-
LongMult
-
AddTogether
-
DigitFactory
-
PartMultiply
-
DatabaseDumper
-
Dummy
-
FailureTest
-
FastaFactory
-
JobFactory
-
MySQLTransfer
-
NotifyByEmail
-
SqlCmd
-
SqlHealthcheck
-
SystemCmd
-
Utils
-
Collection
-
Config
-
Graph
-
GraphViz
-
RedirectStack
-
Stopwatch
-
URL
-
Accumulator
-
Analysis
-
AnalysisCtrlRule
-
AnalysisJob
-
AnalysisStats
-
Cacheable
-
Configurable
-
DataflowRule
-
DependentOptions
-
Limiter
-
Meadow
-
MetaParameters
-
NakedTable
-
Params
-
Pipeline
-
PipelineWideParameters
-
Process
-
Queen
-
ResourceClass
-
ResourceDescription
-
Role
-
Scheduler
-
Storable
-
URLFactory
-
Utils
-
Valley
-
Version
-
Worker
+
DBSQL
+
AccumulatorAdaptor
+
AnalysisAdaptor
+
AnalysisCtrlRuleAdaptor
+
AnalysisDataAdaptor
+
AnalysisJobAdaptor
+
AnalysisStatsAdaptor
+
BaseAdaptor
+
CoreDBConnection
+
DataflowRuleAdaptor
+
DBAdaptor
+
DBConnection
+
LogMessageAdaptor
+
MetaAdaptor
+
NakedTableAdaptor
+
ObjectAdaptor
+
PipelineWideParametersAdaptor
+
ResourceClassAdaptor
+
ResourceDescriptionAdaptor
+
RoleAdaptor
+
SqlSchemaAdaptor
+
StatementHandle
+
Meadow
+
LOCAL
+
LSF
+
PipeConfig
+
AnyCommands_conf
+
ApplyToDatabases_conf
+
CompressFiles_conf
+
EnsemblGeneric_conf
+
FailureTest_conf
+
FastaSplitter_conf
+
HiveGeneric_conf
+
LongMult_conf
+
LongMultForeign_conf
+
LongMultSt_conf
+
LongMultSt_pyconf
+
LongMultWf_conf
+
MemlimitTest_conf
+
OverloadTest_conf
+
RunListOfCommandsOnFarm_conf
+
TableDumperZipper_conf
+
TopUp_conf
+
RunnableDB
+
LongMult
+
AddTogether
+
DigitFactory
+
PartMultiply
+
DatabaseDumper
+
DbCmd
+
Dummy
+
FailureTest
+
FastaFactory
+
JobFactory
+
MySQLTransfer
+
NotifyByEmail
+
SqlCmd
+
SqlHealthcheck
+
SystemCmd
+
Scripts
+
InitPipeline
+
RunWorker
+
StandaloneJob
+
Utils
+
Collection
+
Config
+
Graph
+
GraphViz
+
RedirectStack
+
Stopwatch
+
Test
+
URL
+
Accumulator
+
Analysis
+
AnalysisCtrlRule
+
AnalysisJob
+
AnalysisStats
+
Cacheable
+
Configurable
+
DataflowRule
+
DependentOptions
+
GuestProcess
+
Limiter
+
Meadow
+
MetaParameters
+
NakedTable
+
Params
+
Pipeline
+
PipelineWideParameters
+
Process
+
Queen
+
ResourceClass
+
ResourceDescription
+
Role
+
Scheduler
+
Storable
+
URLFactory
+
Utils
+
Valley
+
Version
+
Worker Hive MiniPecanMulti_conf MiniPecanSingle2_conf
diff --git a/docs/doxygen/beekeeper_8pl.html b/docs/doxygen/beekeeper_8pl.html
index 3e420309d2b084efabcdf8d3729aada0d7554cb0..27cb4ea66a93879e5ed13f47e3b36fafc99c4f78 100644
--- a/docs/doxygen/beekeeper_8pl.html
+++ b/docs/doxygen/beekeeper_8pl.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
@@ -325,7 +324,9 @@ Functions
script_usage(1);
}
-
$self->{' safe_url'} = $self->{' dba'}->dbc->url(' WORKER_PASSWORD');
+
if( $self->{' url'} ) { # protect the URL that we pass to Workers by hiding the password in %ENV:
+
$self->{' url'} = "' ". $self->{'dba'}->dbc->url('EHIVE_PASS') ." '";
+
}
my $queen = $self->{' dba'}->get_Queen;
@@ -411,7 +412,7 @@ Functions
}
if( $self->{'logic_name'} ) { # FIXME: for now, logic_name will override analysis_pattern quietly
-
# warn " -logic_name is now deprecated, please use -analyses_pattern that extends the functionality of -logic_name .\n";
+
warn " -logic_name is now deprecated, please use -analyses_pattern that extends the functionality of -logic_name .\n";
$self->{'analyses_pattern'} = $self->{'logic_name'};
}
@@ -435,48 +436,51 @@ Functions
}
if($reset_all_jobs || $reset_failed_jobs) {
-
$self->{'dba'}->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id( $list_of_analyses, $reset_all_jobs );
-
$self->{'dba'}->get_Queen->synchronize_hive( $list_of_analyses );
-
}
-
-
if($all_dead) { $queen->register_all_workers_dead(); }
-
if($check_for_dead) { $queen->check_for_dead_workers($valley, 1); }
-
if($balance_semaphores) { $self->{'dba'}->get_AnalysisJobAdaptor->balance_semaphores( $list_of_analyses ); }
-
-
if ($max_loops) { # positive $max_loop means limited, negative means unlimited
-
-
run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $self->{'analyses_pattern'}, $run_job_id, $force);
-
-
} else {
-
# the output of several methods will look differently depending on $analysis being [un]defined
-
-
if($sync) {
-
$queen->synchronize_hive( $list_of_analyses );
-
}
-
print $queen->print_status_and_return_reasons_to_exit( $list_of_analyses, !$self->{'no_analysis_stats'} );
-
-
if($show_worker_stats) {
-
print " \n===== List of live Workers according to the Queen: ======\n";
-
foreach my $worker (@{ $queen->fetch_overdue_workers(0) }) {
-
print $worker->toString(1)." \n";
-
}
-
}
-
$self->{'dba'}->get_RoleAdaptor->print_active_role_counts;
-
-
Bio::EnsEMBL::Hive::Scheduler::schedule_workers_resync_if_necessary($queen, $valley, $list_of_analyses); # show what would be submitted, but do not actually submit
-
-
if($show_failed_jobs) {
-
print(" ===== failed jobs\n");
-
my $failed_job_list = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status( $self->{'logic_name'} and $list_of_analyses , 'FAILED');
-
-
foreach my $job (@{$failed_job_list}) {
-
print $job->toString. " \n";
-
}
-
}
-
}
-
-
exit(0);
-
}
+
if ($reset_all_jobs and not $self->{'analyses_pattern'}) {
+
die " Beekeeper : do you really want to reset *all* the jobs ? If yes, add \"-analyses_pattern '%'\" to the command line\n" ;
+
}
+
$self->{'dba' }->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id( $list_of_analyses, $reset_all_jobs );
+
$self->{'dba' }->get_Queen->synchronize_hive( $list_of_analyses );
+
}
+
+
if ($all_dead) { $queen->register_all_workers_dead(); }
+
if ($check_for_dead) { $queen->check_for_dead_workers($valley, 1); }
+
if ($balance_semaphores) { $self->{'dba' }->get_AnalysisJobAdaptor->balance_semaphores( $list_of_analyses ); }
+
+
if ($max_loops) { # positive $max_loop means limited, negative means unlimited
+
+
run_autonomously ($self, $max_loops, $keep_alive, $queen, $valley, $list_of_analyses, $self->{
'analyses_pattern' }, $run_job_id, $force);
+
+
} else {
+
# the output of several methods will look differently depending on $analysis being [un]defined
+
+
if ($sync) {
+
$queen->synchronize_hive( $list_of_analyses );
+
}
+
print $queen->print_status_and_return_reasons_to_exit( $list_of_analyses, !$self->{'no_analysis_stats' } );
+
+
if ($show_worker_stats) {
+
print "\n===== List of live Workers according to the Queen: ======\n" ;
+
foreach my $worker (@{ $queen->fetch_overdue_workers(0) }) {
+
print $worker->toString(1)."\n" ;
+
}
+
}
+
$self->{'dba' }->get_RoleAdaptor->print_active_role_counts;
+
+
+
+
if ($show_failed_jobs) {
+
print("===== failed jobs\n" );
+
my $failed_job_list = $self->{'dba' }->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status( $self->{'logic_name' } and $list_of_analyses , 'FAILED' );
+
+
foreach my $job (@{$failed_job_list}) {
+
print $job->toString. "\n" ;
+
}
+
}
+
}
+
+
exit(0);
+
}
Undocumented method
Code:
@@ -484,7 +488,7 @@ Functions
click to view
-
my ($reg_conf, $reg_type, $reg_alias, $executable, $url, @prepend, @append, $sqlcmd, $to_params, $verbose, $help, $report_versions);
+
my ($reg_conf, $reg_type, $reg_alias, $executable, $url, @prepend, @append, $sqlcmd, $verbose, $help, $report_versions);
GetOptions(
# connect to the database:
@@ -497,14 +501,13 @@ Functions
'prepend=s@' => \@prepend,
'append|extra=s@' => \@append,
'sqlcmd=s' => \$sqlcmd,
-
'to_params!' => \$to_params, # is being phased out and so no longer documented
'verbose!' => \$verbose,
'help!' => \$help,
'v|versions!' => \$report_versions,
);
-
my $dbc_hash;
+
my $dbc;
if ($help) {
@@ -542,35 +545,28 @@ Functions
$dba = $dbas->[0];
}
-
my $dbc = $dba->dbc();
+
$dbc = $dba->dbc();
-
$dbc_hash = {
-
'driver' => $dbc->driver,
-
'host' => $dbc->host,
-
'port' => $dbc->port,
-
'user' => $dbc->username,
-
'pass' => $dbc->password,
-
'dbname' => $dbc->dbname,
-
};
} elsif($url) {
-
-
|| die "Could not parse URL '$url'" ;
+
} else {
script_usage(1);
}
-
my @cmd = @{
dbc_hash_to_cmd ( $dbc_hash, $executable, \@prepend, \@append, $sqlcmd, $to_params ) };
-
-
my $flat_cmd = join(' ' , map { ($_=~/^-?\w+$/) ? $_ : "\"$_\"" } @cmd);
-
-
if ($to_params) {
-
print "$flat_cmd\n" ;
-
} else {
-
warn "\nRunning command:\n\t$flat_cmd\n\n" if ($verbose);
-
-
exec(@cmd);
-
}
-
}
+
if (@append) {
+
warn qq{In db_cmd.pl, final arguments don't have to be declared with --append any more. All the remaining arguments are considered to be appended.\n};
+
}
+
+
my @cmd = @{ $dbc->to_cmd( $executable, \@prepend, [@append, @ARGV], $sqlcmd ) };
+
+
if( $verbose ) {
+
my $flat_cmd = join(' ', map { ($_=~/^-?\w+$/) ? $_ : "\"$_\"" } @cmd);
+
+
warn "\nThe actual command I am running is:\n\t$flat_cmd\n\n";
+
}
+
+
exec(@cmd);
+
}
Undocumented method
Code:
@@ -796,13 +792,13 @@ Functions
my %layers = ();
{
my $sql = $key eq 'analysis'
-
? 'SELECT born, died, worker_id, resource_class_id, analysis_id FROM worker LEFT JOIN role USING (worker_id)'
-
: 'SELECT born, died, worker_id, resource_class_id FROM worker' ;
+
? 'SELECT when_born, when_died, worker_id, resource_class_id, analysis_id FROM worker LEFT JOIN role USING (worker_id)'
+
: 'SELECT when_born, when_died, worker_id, resource_class_id FROM worker' ;
my @tmp_dates = @{$dbh->selectall_arrayref($sql)};
warn scalar(@tmp_dates), " rows\n" if $verbose;
foreach my $db_entry (@tmp_dates) {
-
my ($born, $died, $worker_id, $resource_class_id, $analysis_id) = @$db_entry;
+
my ($when_born, $when_died, $worker_id, $resource_class_id, $analysis_id) = @$db_entry;
# In case $resource_class_id is undef
@@ -811,24 +807,24 @@ Functions
$key_value = -1 if not defined $key_value;
if ($mode eq 'workers' ) {
-
add_event (\%events, $key_value, $born, $died, 1);
+
add_event (\%events, $key_value, $when_born, $when_died, 1);
} elsif ($mode eq 'memory' ) {
my $offset = ($mem_resources{$resource_class_id} || $default_memory) / 1024.;
-
add_event (\%events, $key_value, $born, $died, $offset);
+
add_event (\%events, $key_value, $when_born, $when_died, $offset);
$offset = ($used_res{$worker_id}->[0]) / 1024. if exists $used_res{$worker_id} and $used_res{$worker_id}->[0];
-
add_event (\%layers, $key_value, $born, $died, $offset);
+
add_event (\%layers, $key_value, $when_born, $when_died, $offset);
} elsif ($mode eq 'cores' ) {
my $offset = ($cpu_resources{$resource_class_id} || $default_cores);
-
add_event (\%events, $key_value, $born, $died, $offset);
+
add_event (\%events, $key_value, $when_born, $when_died, $offset);
$offset = $used_res{$worker_id}->[1] if exists $used_res{$worker_id} and $used_res{$worker_id}->[1];
-
add_event (\%layers, $key_value, $born, $died, $offset);
+
add_event (\%layers, $key_value, $when_born, $when_died, $offset);
} else {
if (exists $used_res{$worker_id} and $used_res{$worker_id}->[2]) {
my $pending_sec = $used_res{$worker_id}->[2];
-
add_event (\%events, $key_value, -$pending_sec, $born, 1);
-
add_event (\%layers, $key_value, -$pending_sec, $born, $pending_sec/60);
+
add_event (\%events, $key_value, -$pending_sec, $when_born, 1);
+
add_event (\%layers, $key_value, -$pending_sec, $when_born, $pending_sec/60);
}
}
}
@@ -969,7 +965,7 @@ Functions
my $sql = qq{
DELETE j FROM job j
WHERE j.status='DONE'
-
AND j.completed < $threshold_datetime_expression
+
AND j.when_completed < $threshold_datetime_expression
};
my $dbc = $hive_dba->dbc();
@@ -997,22 +993,7 @@ Functions
my $file_or_module = shift @ARGV or script_usage(0);
-
my $pipeconfig_package_name = load_file_or_module( $file_or_module );
-
-
my $pipeconfig_object = $pipeconfig_package_name->new();
-
$pipeconfig_object->process_options( 1 );
-
-
$pipeconfig_object->run_pipeline_create_commands();
-
-
-
-
$hive_dba->load_collections();
-
-
$pipeconfig_object->add_objects_from_config();
-
-
$hive_dba->save_collections();
-
-
print $pipeconfig_object->useful_commands_legend();
+
}
Undocumented method
@@ -1172,33 +1153,6 @@ Functions
script_usage(1);
}
-
my $queen = $hive_dba->get_Queen();
-
-
-
-
my $worker = $queen->create_new_worker(
-
# Worker identity:
-
-meadow_type => $meadow_type,
-
-meadow_name => $meadow_name,
-
-process_id => $process_id,
-
-exec_host => $exec_host,
-
-resource_class_id => $resource_class_id,
-
-resource_class_name => $resource_class_name,
-
-
# Worker control parameters:
-
-job_limit => $job_limit,
-
-life_span => $life_span,
-
-no_cleanup => $no_cleanup,
-
-no_write => $no_write,
-
-worker_log_dir => $worker_log_dir,
-
-hive_log_dir => $hive_log_dir,
-
-retry_throwing_jobs => $retry_throwing_jobs,
-
-can_respecialize => $can_respecialize,
-
-
# Other parameters:
-
-debug => $debug,
-
);
-
if ( $logic_name ) {
warn "-logic_name is now deprecated, please use -analyses_pattern that extends the functionality of -logic_name and -analysis_id .\n" ;
$analyses_pattern = $logic_name;
@@ -1207,11 +1161,28 @@ Functions
$analyses_pattern = $analysis_id;
}
-
$worker->run( {
-
-analyses_pattern => $analyses_pattern,
-
-job_id => $job_id,
-
-force => $force,
-
} );
+
my %specialization_options = (
+
resource_class_id => $resource_class_id,
+
resource_class_name => $resource_class_name,
+
can_respecialize => $can_respecialize,
+
analyses_pattern => $analyses_pattern,
+
job_id => $job_id,
+
force => $force,
+
);
+
my %life_options = (
+
job_limit => $job_limit,
+
life_span => $life_span,
+
retry_throwing_jobs => $retry_throwing_jobs,
+
);
+
my %execution_options = (
+
no_cleanup => $no_cleanup,
+
no_write => $no_write,
+
worker_log_dir => $worker_log_dir,
+
hive_log_dir => $hive_log_dir,
+
debug => $debug,
+
);
+
+
}
Undocumented method
@@ -1295,7 +1266,7 @@ Functions
click to view
-
my ($reg_conf, $help, $debug, $no_write, $no_cleanup, $flow_into, $input_id);
+
my ($reg_conf, $help, $debug, $no_write, $no_cleanup, $flow_into, $input_id, $language);
my $module_or_file = shift @ARGV or script_usage();
@@ -1307,68 +1278,56 @@ Functions
'no_cleanup' => \$no_cleanup,
'flow_into|flow=s' => \$flow_into,
'input_id=s' => \$input_id,
+
'language=s' => \$language,
);
if ($help or !$module_or_file) {
script_usage(0);
}
-
my $runnable_module = load_file_or_module( $module_or_file );
-
if ($reg_conf) {
require Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_all($reg_conf);
}
-
my $runnable_object = $runnable_module->new();
-
$runnable_object->debug($debug) if ($debug);
-
$runnable_object->execute_writes(not $no_write);
-
-
-
unless($input_id) {
my ($param_hash, $param_list) = parse_cmdline_options();
$input_id = stringify($param_hash);
}
-
$job->input_id( $input_id );
-
warn "\nRunning '$runnable_module' with input_id='$input_id' :\n" ;
+
warn "\nRunning '$module_or_file' with input_id='$input_id' :\n" ;
+
+
my %flags = (
+
no_write => $no_write,
+
no_cleanup => $no_cleanup,
+
debug => $debug,
+
);
+
+
exit(1) unless $job_successful;
+
}
+
Undocumented method
+
+
Code:
+
+
click to view
+
+
+
my $url;
+
+
GetOptions(
+
'url=s' => \$url,
+
);
-
$job->param_init( $runnable_object->strict_hash_format(), $runnable_object->param_defaults(), $job->input_id() );
+
if ($url) {
+
+
|| die "Could not parse URL '$url'" ;
-
$flow_into = $flow_into ? destringify($flow_into) : []; # empty dataflow for branch 1 by default
-
$flow_into = { 1 => $flow_into } unless(ref($flow_into) eq 'HASH' ); # force non-hash into a hash
-
foreach my $branch_code (keys %$flow_into) {
-
my $heirs = $flow_into->{$branch_code};
+
my $sql = "UPDATE hive_meta SET meta_value=63 WHERE meta_key='hive_sql_schema_version' AND meta_value='62'" ;
+
my $sth = $dbc->do( $sql );
-
$heirs = [ $heirs ] unless(ref($heirs)); # force scalar into an arrayref first
-
$heirs = { map { ($_ => undef) } @$heirs } if (ref($heirs) eq 'ARRAY' ); # now force it into a hash if it wasn't
-
-
my @dataflow_rules = ();
-
-
while(my ($heir_url, $input_id_template_list) = each %$heirs) {
-
-
$input_id_template_list = [ $input_id_template_list ] unless(ref($input_id_template_list) eq ' ARRAY'); # allow for more than one template per analysis
-
-
foreach my $input_id_template (@$input_id_template_list) {
-
-
push @dataflow_rules, Bio::EnsEMBL::Hive::DataflowRule->new(
-
' to_analysis_url' => $heir_url,
-
' input_id_template' => $input_id_template,
-
);
-
}
-
}
-
-
$job->dataflow_rules( $branch_code, \@dataflow_rules );
-
}
-
-
-
$runnable_object->input_job($job);
-
$runnable_object->life_cycle();
-
-
exit(1) if($job->died_somewhere());
-
-
$runnable_object->cleanup_worker_temp_directory() unless($no_cleanup);
-
}
+
} else {
+
die "Please provide -url parameter to this patch script" ;
+
}
+
}
my $resourceless_worker_cmd =
generate_worker_cmd ($self, $analyses_pattern, $run_job_id, $force);
- my $rc_id2name = $self->{'dba' }->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();
- my %meadow_type_rc_name2resource_param_list = ();
- foreach my $rd (@{ $self->{'dba' }->get_ResourceDescriptionAdaptor->fetch_all() }) {
- $meadow_type_rc_name2resource_param_list{ $rd->meadow_type() }{ $rc_id2name->{$rd->resource_class_id} } = [ $rd->submission_cmd_args, $rd->worker_cmd_args ];
- }
-
my $beekeeper_pid = $$;
my $iteration=0;
@@ -1434,6 +1387,13 @@ Functions
make_path( $submit_log_subdir );
}
+ # make sure the Resources are loaded fresh every time we need them:
+'dba' }->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();
+ my %meadow_type_rc_name2resource_param_list = ();
+ foreach my $rd (@{ $self->{'dba' }->get_ResourceDescriptionAdaptor->fetch_all() }) {
+ $meadow_type_rc_name2resource_param_list{ $rd->meadow_type() }{ $rc_id2name->{$rd->resource_class_id} } = [ $rd->submission_cmd_args, $rd->worker_cmd_args ];
+ }
+
foreach my $meadow_type (keys %$workers_to_submit_by_meadow_type_rc_name) {
my $this_meadow = $valley->available_meadow_hash->{$meadow_type};
@@ -1461,6 +1421,10 @@ Functions
$self->{'dba' }->dbc->disconnect_if_idle;
printf("Beekeeper : going to sleep for %.2f minute(s). Expect next iteration at %s\n" , $self->{'sleep_minutes' }, scalar localtime(time+$self->{'sleep_minutes' }*60));
sleep($self->{'sleep_minutes' }*60);
+
+ unless($run_job_id) { # refresh the data from analysis_base table
+ $list_of_analyses = $self->{'dba' }->get_AnalysisAdaptor->fetch_all_by_pattern( $analyses_pattern );
+ }
}
}
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive.html
index d4400935eba5447661642222fada25006faa189e..88c70b5ef766a8771aa2eaabcfd94aca04ef9ae7 100644
--- a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive.html
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+ All Classes Namespaces Files Functions
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html
index 8d07a6878356949c190ea5a661bff27f269e8281..83212dc32a1e93b5f2967b8ceb728d2d2277c498 100644
--- a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html
@@ -30,7 +30,7 @@
ensembl-hive
- 2.2
+ 2.3
@@ -45,7 +45,6 @@ var searchBox = new SearchBox("searchBox", "search",false,'Search');
+
All Classes Namespaces Files Functions
+
+ 
Code:
+
