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Genesys PGR
Uploader
Commits
db7edf6f
Commit
db7edf6f
authored
Jul 02, 2018
by
Matija Obreza
Browse files
Set "Include null" to true by default
- Except CROPNAME and booleans
parent
9f7eb593
Changes
6
Hide whitespace changes
Inline
Side-by-side
anno-gui/src/main/java/org/genesys2/anno/gui/DataSourceSheet.java
View file @
db7edf6f
...
@@ -203,6 +203,7 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
...
@@ -203,6 +203,7 @@ public class DataSourceSheet extends AbstractModelObject implements IDataSourceS
column
.
setRdfTerm
(
columnDef
.
getRdfTerm
());
column
.
setRdfTerm
(
columnDef
.
getRdfTerm
());
column
.
setMultiple
(
columnDef
.
hasAllowMultiple
());
column
.
setMultiple
(
columnDef
.
hasAllowMultiple
());
column
.
setDescription
(
columnDef
.
getTitle
());
column
.
setDescription
(
columnDef
.
getTitle
());
column
.
setIncludeNull
(
columnDef
.
hasIncludeNull
());
}
}
}
}
}
}
...
...
anno-gui/src/main/java/org/genesys2/anno/gui/DwcaBuilder.java
View file @
db7edf6f
...
@@ -154,6 +154,7 @@ public class DwcaBuilder extends AbstractModelObject {
...
@@ -154,6 +154,7 @@ public class DwcaBuilder extends AbstractModelObject {
column
.
put
(
"pattern"
,
sourceColumn
.
getPattern
());
column
.
put
(
"pattern"
,
sourceColumn
.
getPattern
());
column
.
put
(
"separator"
,
sourceColumn
.
getSeparator
());
column
.
put
(
"separator"
,
sourceColumn
.
getSeparator
());
column
.
put
(
"groupPattern"
,
sourceColumn
.
getGroupPattern
());
column
.
put
(
"groupPattern"
,
sourceColumn
.
getGroupPattern
());
column
.
put
(
"includeNull"
,
sourceColumn
.
isIncludeNull
());
columns
.
put
(
column
);
columns
.
put
(
column
);
}
}
}
}
...
@@ -273,6 +274,8 @@ public class DwcaBuilder extends AbstractModelObject {
...
@@ -273,6 +274,8 @@ public class DwcaBuilder extends AbstractModelObject {
sourceColumn
.
setDataType
(
ColumnDataType
.
valueOf
(
column
.
getString
(
"dataType"
)));
sourceColumn
.
setDataType
(
ColumnDataType
.
valueOf
(
column
.
getString
(
"dataType"
)));
if
(
column
.
has
(
"multiple"
))
if
(
column
.
has
(
"multiple"
))
sourceColumn
.
setMultiple
(
column
.
getBoolean
(
"multiple"
));
sourceColumn
.
setMultiple
(
column
.
getBoolean
(
"multiple"
));
if
(
column
.
has
(
"includeNull"
))
sourceColumn
.
setIncludeNull
(
column
.
getBoolean
(
"includeNull"
));
if
(
loadedColumns
.
contains
(
sourceColumn
))
{
if
(
loadedColumns
.
contains
(
sourceColumn
))
{
columnList
.
add
(
sourceColumn
);
columnList
.
add
(
sourceColumn
);
...
...
anno-gui/src/main/java/org/genesys2/anno/gui/PushDialog.java
View file @
db7edf6f
...
@@ -28,11 +28,6 @@ import java.util.concurrent.ThreadPoolExecutor;
...
@@ -28,11 +28,6 @@ import java.util.concurrent.ThreadPoolExecutor;
import
java.util.concurrent.TimeUnit
;
import
java.util.concurrent.TimeUnit
;
import
java.util.function.Consumer
;
import
java.util.function.Consumer
;
import
com.fasterxml.jackson.core.JsonProcessingException
;
import
com.fasterxml.jackson.databind.JsonNode
;
import
com.fasterxml.jackson.databind.ObjectMapper
;
import
com.fasterxml.jackson.databind.node.ObjectNode
;
import
org.apache.commons.lang3.ArrayUtils
;
import
org.apache.commons.lang3.ArrayUtils
;
import
org.apache.log4j.Level
;
import
org.apache.log4j.Level
;
import
org.apache.log4j.LogManager
;
import
org.apache.log4j.LogManager
;
...
@@ -66,6 +61,11 @@ import org.genesys2.client.oauth.PleaseRetryException;
...
@@ -66,6 +61,11 @@ import org.genesys2.client.oauth.PleaseRetryException;
import
org.genesys2.client.oauth.api.accession.Api1Constants
;
import
org.genesys2.client.oauth.api.accession.Api1Constants
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
com.fasterxml.jackson.core.JsonProcessingException
;
import
com.fasterxml.jackson.databind.JsonNode
;
import
com.fasterxml.jackson.databind.ObjectMapper
;
import
com.fasterxml.jackson.databind.node.ObjectNode
;
import
swing2swt.layout.BorderLayout
;
import
swing2swt.layout.BorderLayout
;
public
class
PushDialog
extends
Dialog
{
public
class
PushDialog
extends
Dialog
{
...
@@ -89,7 +89,7 @@ public class PushDialog extends Dialog {
...
@@ -89,7 +89,7 @@ public class PushDialog extends Dialog {
protected
DataSourceLoader
dataSourceLoader
;
protected
DataSourceLoader
dataSourceLoader
;
BlockingQueue
<
Runnable
>
linkedBlockingDeque
=
new
LinkedBlockingDeque
<
Runnable
>(
4
);
BlockingQueue
<
Runnable
>
linkedBlockingDeque
=
new
LinkedBlockingDeque
<
Runnable
>(
4
);
private
ThreadPoolExecutor
executorService
=
new
ThreadPoolExecutor
(
1
,
2
,
30
,
TimeUnit
.
SECONDS
,
linkedBlockingDeque
,
new
ThreadPoolExecutor
.
CallerRunsPolicy
());
private
ThreadPoolExecutor
executorService
=
new
ThreadPoolExecutor
(
1
,
4
,
30
,
TimeUnit
.
SECONDS
,
linkedBlockingDeque
,
new
ThreadPoolExecutor
.
CallerRunsPolicy
());
protected
Object
result
;
protected
Object
result
;
protected
Shell
shell
;
protected
Shell
shell
;
...
@@ -482,8 +482,6 @@ public class PushDialog extends Dialog {
...
@@ -482,8 +482,6 @@ public class PushDialog extends Dialog {
if
(
_log
.
isDebugEnabled
())
if
(
_log
.
isDebugEnabled
())
_log
.
debug
(
serverResponse
);
_log
.
debug
(
serverResponse
);
_log
.
info
(
"Push done."
);
try
{
try
{
JsonNode
ri
=
objectMapper
.
readTree
(
serverResponse
);
JsonNode
ri
=
objectMapper
.
readTree
(
serverResponse
);
ri
.
forEach
(
new
Consumer
<
JsonNode
>()
{
ri
.
forEach
(
new
Consumer
<
JsonNode
>()
{
...
@@ -497,6 +495,8 @@ public class PushDialog extends Dialog {
...
@@ -497,6 +495,8 @@ public class PushDialog extends Dialog {
}
}
});
});
_log
.
info
(
"Push done."
);
}
catch
(
IOException
e
)
{
}
catch
(
IOException
e
)
{
// TODO Auto-generated catch block
// TODO Auto-generated catch block
e
.
printStackTrace
();
e
.
printStackTrace
();
...
...
anno-gui/src/main/java/org/genesys2/anno/model/Column.java
View file @
db7edf6f
...
@@ -28,17 +28,18 @@ public class Column extends AbstractModelObject {
...
@@ -28,17 +28,18 @@ public class Column extends AbstractModelObject {
private
String
separator
=
";"
;
private
String
separator
=
";"
;
private
String
pattern
;
private
String
pattern
;
private
String
groupPattern
;
private
String
groupPattern
;
private
boolean
includeNull
=
fals
e
;
private
boolean
includeNull
=
tru
e
;
public
Column
()
{
public
Column
()
{
}
}
public
Column
(
String
preferredName
,
ColumnDataType
dataType
,
boolean
multiple
,
boolean
unique
,
String
rdfTerm
)
{
public
Column
(
String
preferredName
,
ColumnDataType
dataType
,
boolean
multiple
,
boolean
unique
,
String
rdfTerm
,
boolean
includeNull
)
{
this
.
preferredName
=
preferredName
;
this
.
preferredName
=
preferredName
;
this
.
dataType
=
dataType
;
this
.
dataType
=
dataType
;
this
.
multiple
=
multiple
;
this
.
multiple
=
multiple
;
this
.
unique
=
unique
;
this
.
unique
=
unique
;
this
.
rdfTerm
=
rdfTerm
;
this
.
rdfTerm
=
rdfTerm
;
this
.
includeNull
=
includeNull
;
}
}
public
String
getPreferredName
()
{
public
String
getPreferredName
()
{
...
...
anno-gui/src/main/java/org/genesys2/anno/model/ColumnDef.java
View file @
db7edf6f
...
@@ -28,6 +28,7 @@ public class ColumnDef extends AbstractModelObject {
...
@@ -28,6 +28,7 @@ public class ColumnDef extends AbstractModelObject {
private
Set
<
ColumnValidator
>
validators
=
new
HashSet
<
ColumnValidator
>();
private
Set
<
ColumnValidator
>
validators
=
new
HashSet
<
ColumnValidator
>();
private
String
title
;
private
String
title
;
private
boolean
allowMultiple
=
false
;
private
boolean
allowMultiple
=
false
;
private
boolean
includeNull
=
true
;
public
ColumnDef
()
{
public
ColumnDef
()
{
}
}
...
@@ -96,4 +97,13 @@ public class ColumnDef extends AbstractModelObject {
...
@@ -96,4 +97,13 @@ public class ColumnDef extends AbstractModelObject {
this
.
allowMultiple
=
allowMultiple
;
this
.
allowMultiple
=
allowMultiple
;
return
this
;
return
this
;
}
}
public
boolean
hasIncludeNull
()
{
return
this
.
includeNull
;
}
public
ColumnDef
setIncludeNull
(
boolean
includeNull
)
{
this
.
includeNull
=
includeNull
;
return
this
;
}
}
}
anno-gui/src/main/java/org/genesys2/anno/predefined/MCPD.java
View file @
db7edf6f
...
@@ -74,7 +74,7 @@ public class MCPD {
...
@@ -74,7 +74,7 @@ public class MCPD {
columnDef
=
new
ColumnDef
(
"SUBTAUTHOR"
,
"Subtaxon authority"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
SUBTAUTHOR
);
columnDef
=
new
ColumnDef
(
"SUBTAUTHOR"
,
"Subtaxon authority"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
SUBTAUTHOR
);
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"CROPNAME"
,
"Common crop name"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
CROPNAME
);
columnDef
=
new
ColumnDef
(
"CROPNAME"
,
"Common crop name"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
CROPNAME
)
.
setIncludeNull
(
false
)
;
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"ACCENAME"
,
"Accession name"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
ACCENAME
).
setAllowMultiple
(
true
);
columnDef
=
new
ColumnDef
(
"ACCENAME"
,
"Accession name"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
ACCENAME
).
setAllowMultiple
(
true
);
...
@@ -158,20 +158,20 @@ public class MCPD {
...
@@ -158,20 +158,20 @@ public class MCPD {
columnDef
=
new
ColumnDef
(
"STORAGE"
,
"Type of germplasm storage"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
STORAGE
).
setAllowMultiple
(
true
);
columnDef
=
new
ColumnDef
(
"STORAGE"
,
"Type of germplasm storage"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
STORAGE
).
setAllowMultiple
(
true
);
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"MLSSTAT"
,
"MLS status of the accession"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
MLSSTAT
);
columnDef
=
new
ColumnDef
(
"MLSSTAT"
,
"MLS status of the accession"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
MLSSTAT
)
.
setIncludeNull
(
false
)
;
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"REMARKS"
,
"Remarks"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
REMARKS
).
setAllowMultiple
(
true
);
columnDef
=
new
ColumnDef
(
"REMARKS"
,
"Remarks"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
REMARKS
).
setAllowMultiple
(
true
);
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
// Genesys specific
// Genesys specific
columnDef
=
new
ColumnDef
(
"INTRUST"
,
"FAO in Trust"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
FAOINTRUST
);
columnDef
=
new
ColumnDef
(
"INTRUST"
,
"FAO in Trust"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
FAOINTRUST
)
.
setIncludeNull
(
false
)
;
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"AVAILABLE"
,
"Accession is available for distribution"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
AVAILABLE
);
columnDef
=
new
ColumnDef
(
"AVAILABLE"
,
"Accession is available for distribution"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
AVAILABLE
)
.
setIncludeNull
(
false
)
;
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"HISTORIC"
,
"Historic entry"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
HISTORIC
);
columnDef
=
new
ColumnDef
(
"HISTORIC"
,
"Historic entry"
,
ColumnDataType
.
BOOLEAN
,
false
,
RdfMCPD
.
HISTORIC
)
.
setIncludeNull
(
false
)
;
columns
.
add
(
columnDef
);
columns
.
add
(
columnDef
);
columnDef
=
new
ColumnDef
(
"ACCEURL"
,
"Accession URL"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
ACCEURL
);
columnDef
=
new
ColumnDef
(
"ACCEURL"
,
"Accession URL"
,
ColumnDataType
.
TEXT
,
false
,
RdfMCPD
.
ACCEURL
);
...
...
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