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ensembl-gh-mirror
ensembl-hive
Commits
b2d80235
Commit
b2d80235
authored
Apr 24, 2017
by
Leo Gordon
Browse files
added the option to also generate parallel A-diagrams for the walkthrough
parent
25ab8993
Changes
1
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1 changed file
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32 additions
and
8 deletions
+32
-8
t/03.scripts/visualize_jobs.t
t/03.scripts/visualize_jobs.t
+32
-8
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t/03.scripts/visualize_jobs.t
View file @
b2d80235
...
...
@@ -25,16 +25,17 @@ use Test::File::Contents; # import file_contents_eq_or_diff()
use
Test::
More
;
use
Bio::EnsEMBL::Hive::Utils::
Config
;
# for Bio::EnsEMBL::Hive::Utils::Config->default_system_config
use
Bio::EnsEMBL::Hive::Utils::
Test
qw(init_pipeline runWorker beekeeper visualize_jobs run_sql_on_db get_test_url_or_die)
;
use
Bio::EnsEMBL::Hive::Utils::
Test
qw(init_pipeline runWorker beekeeper visualize_jobs
generate_graph
run_sql_on_db get_test_url_or_die)
;
# eHive needs this to initialize the pipeline (and run db_cmd.pl)
$ENV
{'
EHIVE_ROOT_DIR
'}
||=
File::Basename::
dirname
(
File::Basename::
dirname
(
File::Basename::
dirname
(
Cwd::
realpath
(
$
0
)
)
)
);
my
(
$generate_files
,
$generate_format
)
=
(
0
,
'
dot
');
my
(
$generate_files
,
$generate_format
,
$gg
)
=
(
0
,
'
dot
'
,
0
);
GetOptions
(
# Example: "visualize_jobs.t -generate -format png" would yield a visualized walk-through
'
generate!
'
=>
\
$generate_files
,
'
format=s
'
=>
\
$generate_format
,
'
gg!
'
=>
\
$gg
,
);
my
$vj_url
=
get_test_url_or_die
(
-
tag
=>
'
vj
',
-
no_user_prefix
=>
1
);
...
...
@@ -86,24 +87,47 @@ foreach my $conf (keys %$conf_2_plan) {
}
visualize_jobs
(
$vj_url
,
[
-
accu_values
,
# -config_file => Bio::EnsEMBL::Hive::Utils::Config->default_system_config, ## FIXME: not supported yet
(
$generate_format
eq
'
dot
')
?
(
-
output
=>
'
/dev/null
',
-
format
=>
'
canon
',
-
dot_input
=>
$generated_diagram_filename
,
# -config_file => Bio::EnsEMBL::Hive::Utils::Config->default_system_config, ## FIXME: not supported yet
)
:
(
-
format
=>
$generate_format
,
-
output
=>
$generated_diagram_filename
,
)
],
"
Generated a
PNG
J-diagram for pipeline '
$pipeline_name
', step
$step_number
, with accu values
"
);
)
,
],
"
Generated a
'
$generate_format
'
J-diagram for pipeline '
$pipeline_name
', step
$step_number
, with accu values
"
);
my
$ref_filename
=
sprintf
("
%s/%s_jobs_%02d.%s
",
$ref_directory
,
$pipeline_name
,
$step_number
,
$generate_format
);
my
$ref_
jdiag_
filename
=
sprintf
("
%s/%s_jobs_%02d.%s
",
$ref_directory
,
$pipeline_name
,
$step_number
,
$generate_format
);
if
(
$generate_files
)
{
system
('
cp
',
'
-f
',
$generated_diagram_filename
,
$ref_filename
);
system
('
cp
',
'
-f
',
$generated_diagram_filename
,
$ref_
jdiag_
filename
);
}
else
{
files_eq_or_diff
(
$generated_diagram_filename
,
$ref_filename
);
files_eq_or_diff
(
$generated_diagram_filename
,
$ref_jdiag_filename
);
}
if
(
$gg
)
{
generate_graph
(
$vj_url
,
[
(
$generate_format
eq
'
dot
')
?
(
-
output
=>
'
/dev/null
',
-
format
=>
'
canon
',
-
dot_input
=>
$generated_diagram_filename
,
-
config_file
=>
Bio::EnsEMBL::Hive::Utils::
Config
->
default_system_config
,
# to ensure JSON Config-independent reproducibility
)
:
(
-
format
=>
$generate_format
,
-
output
=>
$generated_diagram_filename
,
),
],
"
Generated a '
$generate_format
' A-diagram for pipeline '
$pipeline_name
', step
$step_number
, with accu values
"
);
my
$ref_adiag_filename
=
sprintf
("
%s/%s_analyses_%02d.%s
",
$ref_directory
,
$pipeline_name
,
$step_number
,
$generate_format
);
if
(
$generate_files
)
{
system
('
cp
',
'
-f
',
$generated_diagram_filename
,
$ref_adiag_filename
);
}
else
{
files_eq_or_diff
(
$generated_diagram_filename
,
$ref_adiag_filename
);
}
}
}
}
...
...
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