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Emmanuel QUEVILLON
BIGSdb
Commits
094d33bc
Commit
094d33bc
authored
May 27, 2016
by
Keith Jolley
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Add status field to classification schemes.
parent
8e1effe0
Changes
6
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6 changed files
with
21 additions
and
13 deletions
+21
-13
lib/BIGSdb/IsolateInfoPage.pm
lib/BIGSdb/IsolateInfoPage.pm
+4
-4
lib/BIGSdb/TableAttributes.pm
lib/BIGSdb/TableAttributes.pm
+13
-9
sql/isolatedb.sql
sql/isolatedb.sql
+1
-0
sql/seqdef.sql
sql/seqdef.sql
+1
-0
sql/upgrade/isolatedb_v1.14.sql
sql/upgrade/isolatedb_v1.14.sql
+1
-0
sql/upgrade/seqdefdb_v1.14.sql
sql/upgrade/seqdefdb_v1.14.sql
+1
-0
No files found.
lib/BIGSdb/IsolateInfoPage.pm
View file @
094d33bc
...
...
@@ -527,19 +527,19 @@ sub _get_classification_group_data {
:
q()
;
my
$plural
=
$cscheme
->
{'
inclusion_threshold
'}
==
1
?
q()
:
q(es)
;
$buffer
.=
qq(<tr class="td$td"><td>$cscheme->{'name'}$tooltip</td><td>$scheme_info->{'description'}</td>)
.
qq(<td>Single-linkage</td><td>$cscheme->{'inclusion_threshold'}</td><td>$cg_buffer</td></tr>)
;
.
qq(<td>Single-linkage</td><td>$cscheme->{'inclusion_threshold'}</td><td>$cscheme->{'status'}</td><td>)
.
qq($cg_buffer</td></tr>)
;
$td
=
$td
==
1
?
2
:
1
;
}
}
if
(
$buffer
)
{
$buffer
=
q(<h2>Similar isolates (determined by classification schemes)</h2>)
.
q(<p>Please note that group numbers are subject to change and are not a stable part )
.
q(of the nomenclature.</p>)
.
q(<p>Experimental schemes are subject to change and are not a stable part of the nomenclature.</p>)
.
q(<div class="scrollable">)
.
q(<div class="resultstable" style="float:left"><table class="resultstable"><tr>)
.
q(<th>Classification scheme</th><th>Underlying scheme</th><th>Clustering method</th>)
.
qq(<th>Mismatch threshold</th><th>Group</th></tr>$buffer</table></div></div>)
;
.
qq(<th>Mismatch threshold</th><th>
Status</th><th>
Group</th></tr>$buffer</table></div></div>)
;
}
return
$buffer
;
}
...
...
lib/BIGSdb/TableAttributes.pm
View file @
094d33bc
...
...
@@ -1961,7 +1961,8 @@ sub get_classification_schemes_table_attributes {
}
];
if
(
$self
->
{'
system
'}
->
{'
dbtype
'}
eq
'
isolates
'
)
{
push
@$attributes
,
(
push
@$attributes
,
(
{
name
=>
'
seqdef_cscheme_id
',
type
=>
'
int
',
...
...
@@ -1969,17 +1970,20 @@ sub get_classification_schemes_table_attributes {
tooltip
=>
'
seqdef_cscheme_id - The id used in the isolate database will be used if this is not defined.
'
},
{
name
=>
'
display_order
',
type
=>
'
int
'
}
);
{
name
=>
'
display_order
',
type
=>
'
int
'
}
);
}
push
@$attributes
,
(
push
@$attributes
,
(
{
name
=>
'
status
',
type
=>
'
text
',
required
=>
'
yes
',
optlist
=>
'
experimental;stable
',
default
=>
'
experimental
'
},
{
name
=>
'
curator
',
type
=>
'
int
',
required
=>
'
yes
',
dropdown_query
=>
'
yes
'
},
{
name
=>
'
datestamp
',
type
=>
'
date
',
required
=>
'
yes
'
}
);
);
return
$attributes
;
}
...
...
sql/isolatedb.sql
View file @
094d33bc
...
...
@@ -1252,6 +1252,7 @@ inclusion_threshold int NOT NULL,
use_relative_threshold
boolean
NOT
NULL
,
seqdef_cscheme_id
int
,
display_order
int
,
status
text
NOT
NULL
,
curator
int
NOT
NULL
,
datestamp
date
NOT
NULL
,
PRIMARY
KEY
(
id
),
...
...
sql/seqdef.sql
View file @
094d33bc
...
...
@@ -1254,6 +1254,7 @@ name text NOT NULL,
description
text
,
inclusion_threshold
int
NOT
NULL
,
use_relative_threshold
boolean
NOT
NULL
,
status
text
NOT
NULL
,
curator
int
NOT
NULL
,
datestamp
date
NOT
NULL
,
PRIMARY
KEY
(
id
),
...
...
sql/upgrade/isolatedb_v1.14.sql
View file @
094d33bc
...
...
@@ -243,6 +243,7 @@ inclusion_threshold int NOT NULL,
use_relative_threshold
boolean
NOT
NULL
,
seqdef_cscheme_id
int
,
display_order
int
,
status
text
NOT
NULL
,
curator
int
NOT
NULL
,
datestamp
date
NOT
NULL
,
PRIMARY
KEY
(
id
),
...
...
sql/upgrade/seqdefdb_v1.14.sql
View file @
094d33bc
...
...
@@ -284,6 +284,7 @@ name text NOT NULL,
description
text
,
inclusion_threshold
int
NOT
NULL
,
use_relative_threshold
boolean
NOT
NULL
,
status
text
NOT
NULL
,
curator
int
NOT
NULL
,
datestamp
date
NOT
NULL
,
PRIMARY
KEY
(
id
),
...
...
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