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ensembl-gh-mirror
ensembl-hive
Commits
381d510f
Commit
381d510f
authored
Mar 18, 2014
by
Leo Gordon
Browse files
using display_name() to distinguish between own and foreign nodes with the same name
parent
5fe24972
Changes
3
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3 changed files
with
31 additions
and
15 deletions
+31
-15
modules/Bio/EnsEMBL/Hive/Analysis.pm
modules/Bio/EnsEMBL/Hive/Analysis.pm
+8
-0
modules/Bio/EnsEMBL/Hive/NakedTable.pm
modules/Bio/EnsEMBL/Hive/NakedTable.pm
+13
-9
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
+10
-6
No files found.
modules/Bio/EnsEMBL/Hive/Analysis.pm
View file @
381d510f
...
...
@@ -178,6 +178,14 @@ sub url {
}
sub
display_name
{
my
(
$self
,
$ref_dba
)
=
@_
;
return
(
$self
->
adaptor
and
$self
->
adaptor
->
db
ne
(
$ref_dba
//
'')
)
?
$self
->
adaptor
->
db
->
dbc
->
dbname
.
'
/
'
.
$self
->
logic_name
:
$self
->
logic_name
;
}
=head2 stats
Arg [1] : none
...
...
modules/Bio/EnsEMBL/Hive/NakedTable.pm
View file @
381d510f
...
...
@@ -57,15 +57,19 @@ sub insertion_method {
sub
url
{
my
$self
=
shift
@_
;
my
$ref_dba
=
shift
@_
;
# if reference dba is the same as 'our' dba, a shorter url can be generated
if
(
my
$adaptor
=
$self
->
adaptor
)
{
my
$conn_prefix
=
(
$adaptor
->
db
==
$ref_dba
)
?
'
:///
'
:
$adaptor
->
db
->
dbc
->
url
();
return
$conn_prefix
.
'
/
'
.
$self
->
table_name
()
.
'
?insertion_method=
'
.
$self
->
insertion_method
();
}
else
{
return
;
}
my
(
$self
,
$ref_dba
)
=
@_
;
# if reference dba is the same as 'our' dba, a shorter url is generated
my
$adaptor
=
$self
->
adaptor
;
return
(
(
$adaptor
and
$adaptor
->
db
ne
(
$ref_dba
//
'')
)
?
$adaptor
->
db
->
dbc
->
url
:
'
:///
'
)
.
'
/
'
.
$self
->
table_name
.
'
?insertion_method=
'
.
$self
->
insertion_method
;
}
sub
display_name
{
my
(
$self
,
$ref_dba
)
=
@_
;
# if reference dba is the same as 'our' dba, a shorter display_name is generated
my
$adaptor
=
$self
->
adaptor
;
return
(
(
$adaptor
and
$adaptor
->
db
ne
(
$ref_dba
//
'')
)
?
$adaptor
->
db
->
dbc
->
dbname
.
'
/
'
:
'')
.
$self
->
table_name
;
}
...
...
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
View file @
381d510f
...
...
@@ -127,15 +127,19 @@ sub hive_dba {
sub
_analysis_node_name
{
my
(
$analysis
)
=
@_
;
return
'
analysis_
'
.
$analysis
->
logic_name
;
my
$analysis_node_name
=
'
analysis_
'
.
$analysis
->
display_name
;
$analysis_node_name
=~
s/\W/__/g
;
return
$analysis_node_name
;
}
sub
_table_node_name
{
my
(
$self
,
$df_rule
)
=
@_
;
return
'
table_
'
.
$df_rule
->
to_analysis
->
table
_name
.
my
$table_node_name
=
'
table_
'
.
$df_rule
->
to_analysis
->
display
_name
.
(
$self
->
config_get
('
DuplicateTables
')
?
'
_
'
.
$df_rule
->
from_analysis
->
logic_name
:
'');
$table_node_name
=~
s/\W/__/g
;
return
$table_node_name
;
}
...
...
@@ -442,7 +446,7 @@ sub _add_dataflow_rules {
}
elsif
(
UNIVERSAL::
isa
(
$target_object
,
'
Bio::EnsEMBL::Hive::NakedTable
'))
{
$target_node_name
=
$self
->
_table_node_name
(
$df_rule
);
$self
->
_add_table_node
(
$target_node_name
,
$target_object
->
table_name
);
$self
->
_add_table_node
(
$target_node_name
,
$target_object
);
}
elsif
(
UNIVERSAL::
isa
(
$target_object
,
'
Bio::EnsEMBL::Hive::Accumulator
'))
{
...
...
@@ -510,7 +514,7 @@ sub _add_dataflow_rules {
sub
_add_table_node
{
my
(
$self
,
$table_node_name
,
$
table_nam
e
)
=
@_
;
my
(
$self
,
$table_node_name
,
$
naked_tabl
e
)
=
@_
;
my
$node_fontname
=
$self
->
config_get
('
Node
',
'
Table
',
'
Font
');
my
(
@column_names
,
$columns
,
$table_data
,
$data_limit
,
$hit_limit
);
...
...
@@ -518,7 +522,7 @@ sub _add_table_node {
my
$hive_dba
=
$self
->
hive_dba
;
if
(
$data_limit
=
$self
->
config_get
('
DisplayData
')
and
my
$naked_table_adaptor
=
$hive_dba
&&
$hive_dba
->
get_NakedTableAdaptor
)
{
$naked_table_adaptor
->
table_name
(
$table_name
);
$naked_table_adaptor
->
table_name
(
$
naked_table
->
table_name
);
@column_names
=
sort
keys
%
{
$naked_table_adaptor
->
column_set
};
$columns
=
scalar
(
@column_names
);
...
...
@@ -530,7 +534,7 @@ sub _add_table_node {
}
}
my
$table_label
=
'
<<table border="0" cellborder="0" cellspacing="0" cellpadding="1"><tr><td colspan="
'
.
(
$columns
||
1
)
.
'
">
'
.
$table_name
.
'
</td></tr>
';
my
$table_label
=
'
<<table border="0" cellborder="0" cellspacing="0" cellpadding="1"><tr><td colspan="
'
.
(
$columns
||
1
)
.
'
">
'
.
$naked_table
->
display_name
(
$hive_dba
)
.
'
</td></tr>
';
if
(
$self
->
config_get
('
DisplayData
')
)
{
$table_label
.=
'
<tr><td colspan="
'
.
$columns
.
'
"> </td></tr>
';
...
...
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