Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
ensembl-gh-mirror
ensembl-hive
Commits
110ce127
Commit
110ce127
authored
Jun 06, 2012
by
Leo Gordon
Browse files
reorganized the "Graph" part of the config file
parent
07c188fe
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
40 additions
and
45 deletions
+40
-45
hive_config.json
hive_config.json
+22
-25
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
+18
-20
No files found.
hive_config.json
View file @
110ce127
...
...
@@ -25,32 +25,29 @@
},
},
"Graph"
:
{
#
configure
diagram-generation
options
here:
"Colours"
:
{
"Status"
:
{
"BLOCKED"
:
"grey"
,
"LOADING"
:
"yellow"
,
"SYNCHING"
:
"yellow"
,
"READY"
:
"yellow"
,
"WORKING"
:
"yellow"
,
"ALL_CLAIMED"
:
"yellow"
,
"DONE"
:
"green"
,
"FAILED"
:
"red"
,
"OTHER"
:
"white"
,
"TABLE"
:
"black"
,
},
"Flows"
:
{
"data"
:
"blue"
,
"control"
:
"red"
,
"semablock"
:
"red"
,
},
"SemaphoreBoxes"
:
{
"ColourScheme"
:
"blues9"
,
#
Examples:
"blues9"
or
"bugn7"
or
"orrd8"
or
"purples7"
or
"ylorbr9"
"ColourOffset"
:
1
,
},
"Node"
:
{
"Font"
:
"Times-Roman"
,
"Colour"
:
"white"
,
"READY"
:
{
"Colour"
:
"yellow"
},
#
immediately
claimable
"WORKING"
:
{
"Colour"
:
"yellow"
},
#
immediately
claimable
"LOADING"
:
{
"Colour"
:
"orange"
},
#
need
a
sync
to
claim
"ALL_CLAIMED"
:
{
"Colour"
:
"orange"
},
#
need
a
sync
to
claim
"SYNCHING"
:
{
"Colour"
:
"orange"
},
#
need
a
sync
to
complete
to
claim
"BLOCKED"
:
{
"Colour"
:
"grey"
},
#
need
a
sync
that
may
or
may
not
unblock
"DONE"
:
{
"Colour"
:
"green"
},
"FAILED"
:
{
"Colour"
:
"red"
},
"Table"
:
{
"Colour"
:
"black"
,
"Font"
:
"Courier"
},
"Details"
:
{
"Font"
:
"Helvetica"
},
},
"Edge"
:
{
"Font"
:
"Helvetica"
,
"Data"
:
{
"Colour"
:
"blue"
},
"Control"
:
{
"Colour"
:
"red"
},
"Semablock"
:
{
"Colour"
:
"red"
},
},
"
Fonts"
:
{
"
nod
e"
:
"
Helvetica"
,
"
edge
"
:
"Helvetica"
,
"
Box"
:
{
"
ColourSchem
e"
:
"
blues9"
,
#
Examples:
"blues9"
or
"bugn7"
or
"orrd8"
or
"purples7"
or
"ylorbr9"
"
ColourOffset
"
:
1
,
},
"DisplayDetails"
:
1
,
"DisplayStretched"
:
0
,
...
...
modules/Bio/EnsEMBL/Hive/Utils/Graph.pm
View file @
110ce127
...
...
@@ -28,7 +28,7 @@ $Author: lg4 $
=head1 VERSION
$Revision: 1.1
6
$
$Revision: 1.1
7
$
=cut
...
...
@@ -197,8 +197,8 @@ sub build {
if
(
$self
->
config
->
get
('
Graph
',
'
DisplaySemaphoreBoxes
')
)
{
$self
->
graph
->
subgraphs
(
\
%subgraph_allocation
);
$self
->
graph
->
colour_scheme
(
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Semaphore
Box
es
',
'
ColourScheme
')
);
$self
->
graph
->
colour_offset
(
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Semaphore
Box
es
',
'
ColourOffset
')
);
$self
->
graph
->
colour_scheme
(
$self
->
config
->
get
('
Graph
',
'
Box
',
'
ColourScheme
')
);
$self
->
graph
->
colour_offset
(
$self
->
config
->
get
('
Graph
',
'
Box
',
'
ColourOffset
')
);
}
return
$self
->
graph
();
...
...
@@ -251,12 +251,12 @@ sub _allocate_to_subgraph {
sub
_add_hive_details
{
my
(
$self
)
=
@_
;
my
$node_fontname
=
$self
->
config
->
get
('
Graph
',
'
Font
s
',
'
edge
');
my
$node_fontname
=
$self
->
config
->
get
('
Graph
',
'
Node
',
'
Detail
s
',
'
Font
');
if
(
$self
->
config
->
get
('
Graph
',
'
DisplayDetails
')
)
{
my
$dbc
=
$self
->
dba
()
->
dbc
();
my
$label
=
sprintf
('
%s@%s
',
$dbc
->
dbname
,
$dbc
->
host
||
'
-
');
$self
->
graph
()
->
add_node
(
'
d
etails
',
$self
->
graph
()
->
add_node
(
'
D
etails
',
label
=>
$label
,
fontname
=>
$node_fontname
,
shape
=>
'
plaintext
',
...
...
@@ -273,9 +273,8 @@ sub _add_analysis_node {
my
$can_be_empty
=
$a
->
stats
()
->
can
('
can_be_empty
')
&&
$a
->
stats
()
->
can_be_empty
();
my
$shape
=
(
$can_be_empty
)
?
'
doubleoctagon
'
:
'
ellipse
'
;
my
$status_colour
=
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Status
',
$a
->
stats
->
status
)
||
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Status
',
'
OTHER
');
my
$node_fontname
=
$self
->
config
->
get
('
Graph
',
'
Fonts
',
'
edge
');
my
$status_colour
=
$self
->
config
->
get
('
Graph
',
'
Node
',
$a
->
stats
->
status
,
'
Colour
');
my
$node_fontname
=
$self
->
config
->
get
('
Graph
',
'
Node
',
$a
->
stats
->
status
,
'
Font
');
$graph
->
add_node
(
_analysis_node_name
(
$a
->
dbID
()
),
label
=>
$a
->
logic_name
()
.
'
(
'
.
$a
->
dbID
()
.
'
)\n
'
.
$a
->
stats
()
->
done_job_count
()
.
'
+
'
.
$a
->
stats
()
->
remaining_job_count
()
.
'
=
'
.
$a
->
stats
()
->
total_job_count
(),
...
...
@@ -290,8 +289,7 @@ sub _add_analysis_node {
sub
_control_rules
{
my
(
$self
,
$all_ctrl_rules
)
=
@_
;
my
$control_colour
=
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Flows
',
'
control
');
my
$edge_fontname
=
$self
->
config
->
get
('
Graph
',
'
Fonts
',
'
edge
');
my
$control_colour
=
$self
->
config
->
get
('
Graph
',
'
Edge
',
'
Control
',
'
Colour
');
my
$graph
=
$self
->
graph
();
#The control rules are always from and to an analysis so no need to search for odd cases here
...
...
@@ -299,7 +297,6 @@ sub _control_rules {
my
(
$from
,
$to
)
=
(
_analysis_node_name
(
$rule
->
condition_analysis
()
->
dbID
()
),
_analysis_node_name
(
$rule
->
ctrled_analysis
()
->
dbID
()
)
);
$graph
->
add_edge
(
$from
=>
$to
,
color
=>
$control_colour
,
fontname
=>
$edge_fontname
,
arrowhead
=>
'
tee
',
);
}
...
...
@@ -310,9 +307,9 @@ sub _dataflow_rules {
my
(
$self
,
$all_dataflow_rules
)
=
@_
;
my
$graph
=
$self
->
graph
();
my
$dataflow_colour
=
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Flows
',
'
data
');
my
$semablock_colour
=
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Flows
',
'
s
emablock
');
my
$edge_fontname
=
$self
->
config
->
get
('
Graph
',
'
Fonts
',
'
edge
');
my
$dataflow_colour
=
$self
->
config
->
get
('
Graph
',
'
Edge
',
'
Data
',
'
Colour
');
my
$semablock_colour
=
$self
->
config
->
get
('
Graph
',
'
Edge
',
'
S
emablock
'
,
'
Colour
'
);
my
$
df_
edge_fontname
=
$self
->
config
->
get
('
Graph
',
'
Edge
',
'
Data
',
'
Font
');
my
%needs_a_midpoint
=
();
my
%aid2aid_nonsem
=
();
# simply a directed graph between numerical analysis_ids, except for semaphored rules
...
...
@@ -361,7 +358,7 @@ sub _dataflow_rules {
color
=>
$dataflow_colour
,
arrowhead
=>
'
none
',
label
=>
'
#
'
.
$branch_code
,
fontname
=>
$edge_fontname
,
fontname
=>
$
df_
edge_fontname
,
);
$graph
->
add_edge
(
$midpoint_name
=>
$to_node
,
# second half of the two-part arrow
color
=>
$dataflow_colour
,
...
...
@@ -369,7 +366,6 @@ sub _dataflow_rules {
if
(
$funnel_dataflow_rule_id
)
{
$graph
->
add_edge
(
$midpoint_name
=>
_midpoint_name
(
$funnel_dataflow_rule_id
),
# semaphore inter-rule link
color
=>
$semablock_colour
,
fontname
=>
$edge_fontname
,
style
=>
'
dashed
',
arrowhead
=>
'
tee
',
dir
=>
'
both
',
...
...
@@ -381,7 +377,7 @@ sub _dataflow_rules {
$graph
->
add_edge
(
$from_node
=>
$to_node
,
color
=>
$dataflow_colour
,
label
=>
'
#
'
.
$branch_code
,
fontname
=>
$edge_fontname
,
fontname
=>
$
df_
edge_fontname
,
);
}
# /if($needs_a_midpoint{$rule_id})
}
# /foreach my $rule (@$all_dataflow_rules)
...
...
@@ -391,12 +387,14 @@ sub _dataflow_rules {
sub
_add_table_node
{
my
(
$self
,
$table
)
=
@_
;
my
$node_fontname
=
$self
->
config
->
get
('
Graph
',
'
Node
',
'
Table
',
'
Font
');
$self
->
graph
()
->
add_node
(
$table
,
label
=>
$table
.
'
\n
',
fontname
=>
'
serif
',
shape
=>
'
tab
',
fontname
=>
$
self
->
config
->
get
('
Graph
',
'
Fonts
',
'
node
')
,
color
=>
$self
->
config
->
get
('
Graph
',
'
Colours
',
'
Status
',
'
TABLE
'),
fontname
=>
$
node_fontname
,
color
=>
$self
->
config
->
get
('
Graph
',
'
Node
',
'
Table
',
'
Colour
'),
);
}
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment