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Emmanuel QUEVILLON
BIGSdb
Commits
36d91845
Commit
36d91845
authored
Dec 21, 2014
by
Keith Jolley
Browse files
Offline scripts: Add support for view selection.
parent
acefb76f
Changes
3
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Inline
Side-by-side
lib/BIGSdb/Offline/Script.pm
View file @
36d91845
...
...
@@ -93,9 +93,19 @@ sub initiate {
}
}
$self
->
set_system_overrides
;
$self
->
{'
dataConnector
'}
->
initiate
(
$self
->
{'
system
'},
$self
->
{'
config
'}
);
$self
->
db_connect
;
$self
->
setup_datastore
if
$self
->
{'
db
'};
if
(
$self
->
{'
db
'}){
$self
->
setup_datastore
;
if
(
defined
$self
->
{'
options
'}
->
{'
v
'}
)
{
my
$view_exists
=
$self
->
{'
datastore
'}
->
run_query
(
"
SELECT EXISTS(SELECT * FROM information_schema.tables WHERE table_name=?)
",
$self
->
{'
options
'}
->
{'
v
'}
);
die
"
Invalid view selected.
\n
"
if
!
$view_exists
;
$self
->
{'
system
'}
->
{'
view
'}
=
$self
->
{'
options
'}
->
{'
v
'};
}
}
return
;
}
...
...
scripts/automation/autotag.pl
View file @
36d91845
...
...
@@ -62,7 +62,8 @@ GetOptions(
'
o|order
'
=>
\
$opts
{'
o
'},
'
q|quiet
'
=>
\
$opts
{'
q
'},
'
r|random
'
=>
\
$opts
{'
r
'},
'
T|already_tagged
'
=>
\
$opts
{'
T
'}
'
T|already_tagged
'
=>
\
$opts
{'
T
'},
'
v|view=s
'
=>
\
$opts
{'
v
'}
)
or
die
("
Error in command line arguments
\n
");
if
(
$opts
{'
h
'}
)
{
...
...
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
${bold}-T,
--
already_tagged$norm
Scan
even
when
sequence
tagged
(
no
designation
)
.
$
{
bold
}
-
v
,
--
view$norm
$
{
under
}
VIEW$norm
Isolate
database
view
(
overrides
value
set
in
config
.
xml
)
.
$
{
bold
}
-
w
,
--
word_size$norm
$
{
under
}
SIZE$norm
BLASTN
word
size
.
...
...
scripts/automation/scannew.pl
View file @
36d91845
...
...
@@ -63,7 +63,8 @@ GetOptions(
'
n|new_only
'
=>
\
$opts
{'
n
'},
'
o|order
'
=>
\
$opts
{'
o
'},
'
r|random
'
=>
\
$opts
{'
r
'},
'
T|already_tagged
'
=>
\
$opts
{'
T
'}
'
T|already_tagged
'
=>
\
$opts
{'
T
'},
'
v|view=s
'
=>
\
$opts
{'
v
'}
)
or
die
("
Error in command line arguments
\n
");
if
(
$opts
{'
h
'}
)
{
...
...
@@ -235,6 +236,9 @@ ${bold}--threads$norm ${under}THREADS$norm
${bold}-T,
--
already_tagged$norm
Scan
even
when
sequence
tagged
(
no
designation
)
.
$
{
bold
}
-
v
,
--
view$norm
$
{
under
}
VIEW$norm
Isolate
database
view
(
overrides
value
set
in
config
.
xml
)
.
$
{
bold
}
-
w
,
--
word_size$norm
$
{
under
}
SIZE$norm
BLASTN
word
size
.
...
...
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