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Genesys PGR
Genesys Backend
Commits
2a977f6e
Commit
2a977f6e
authored
Apr 15, 2016
by
Matija Obreza
Browse files
opencsv upgraded
parent
6e0bedfd
Changes
7
Hide whitespace changes
Inline
Side-by-side
pom.xml
View file @
2a977f6e
...
...
@@ -325,11 +325,6 @@
<scope>
runtime
</scope>
</dependency>
<dependency>
<groupId>
net.sf.opencsv
</groupId>
<artifactId>
opencsv
</artifactId>
<version>
2.3
</version>
</dependency>
<dependency>
<groupId>
org.sitemesh
</groupId>
<artifactId>
sitemesh
</artifactId>
...
...
@@ -502,6 +497,11 @@
<artifactId>
jsoup
</artifactId>
<version>
1.8.2
</version>
</dependency>
<dependency>
<groupId>
com.opencsv
</groupId>
<artifactId>
opencsv
</artifactId>
<version>
3.7
</version>
</dependency>
</dependencies>
<build>
...
...
src/main/java/org/genesys2/server/service/impl/CSVResultSetHelper.java
View file @
2a977f6e
...
...
@@ -2,22 +2,18 @@ package org.genesys2.server.service.impl;
import
java.io.IOException
;
import
java.io.Reader
;
import
java.math.BigDecimal
;
import
java.sql.Clob
;
import
java.sql.ResultSet
;
import
java.sql.ResultSetMetaData
;
import
java.sql.SQLException
;
import
java.sql.Time
;
import
java.sql.Timestamp
;
import
java.sql.Types
;
import
java.text.SimpleDateFormat
;
import
java.util.ArrayList
;
import
java.util.List
;
import
java.util.UUID
;
import
org.genesys2.util.NumberUtils
;
import
au.com.bytecode
.opencsv.ResultSetHelperService
;
import
com
.opencsv.ResultSetHelperService
;
/**
* This class extends {@link ResultSetHelperService} by adding support for UUID.
...
...
@@ -34,56 +30,43 @@ public class CSVResultSetHelper extends ResultSetHelperService {
private
static
final
int
LONGNVARCHAR
=
-
16
;
private
static
final
int
NCLOB
=
2011
;
/// Copied straight from superclass
/**
* Get all the column values from the result set.
*
* @param rs
* - the ResultSet containing the values.
* @param trim
* - values should have white spaces trimmed.
* @param dateFormatString
* - format String for dates.
* @param timeFormatString
* - format String for timestamps.
* @return - String array containing all the column values.
* @throws SQLException
* - thrown by the result set.
* @throws IOException
* - thrown by the result set.
*/
@Override
public
String
[]
getColumnValues
(
ResultSet
rs
)
throws
SQLException
,
IOException
{
public
String
[]
getColumnValues
(
ResultSet
rs
,
boolean
trim
,
String
dateFormatString
,
String
timeFormatString
)
throws
SQLException
,
IOException
{
List
<
String
>
values
=
new
ArrayList
<
String
>();
ResultSetMetaData
metadata
=
rs
.
getMetaData
();
for
(
int
i
=
0
;
i
<
metadata
.
getColumnCount
();
i
++)
{
values
.
add
(
getColumnValue
(
rs
,
metadata
.
getColumnType
(
i
+
1
),
i
+
1
));
values
.
add
(
getColumnValue
(
rs
,
metadata
.
getColumnType
(
i
+
1
),
i
+
1
,
trim
,
dateFormatString
,
timeFormatString
));
}
String
[]
valueArray
=
new
String
[
values
.
size
()];
return
values
.
toArray
(
valueArray
);
}
private
String
handleObject
(
Object
obj
)
{
return
obj
==
null
?
""
:
String
.
valueOf
(
obj
);
}
private
String
handleBigDecimal
(
BigDecimal
decimal
)
{
return
decimal
==
null
?
""
:
decimal
.
toString
();
}
private
String
handleLong
(
ResultSet
rs
,
int
columnIndex
)
throws
SQLException
{
long
lv
=
rs
.
getLong
(
columnIndex
);
return
rs
.
wasNull
()
?
""
:
Long
.
toString
(
lv
);
}
private
String
handleInteger
(
ResultSet
rs
,
int
columnIndex
)
throws
SQLException
{
int
i
=
rs
.
getInt
(
columnIndex
);
return
rs
.
wasNull
()
?
""
:
Integer
.
toString
(
i
);
}
private
String
handleDate
(
ResultSet
rs
,
int
columnIndex
)
throws
SQLException
{
java
.
sql
.
Date
date
=
rs
.
getDate
(
columnIndex
);
String
value
=
null
;
if
(
date
!=
null
)
{
SimpleDateFormat
dateFormat
=
new
SimpleDateFormat
(
"dd-MMM-yyyy"
);
value
=
dateFormat
.
format
(
date
);
}
return
value
;
}
private
String
handleBinary
(
ResultSet
rs
,
int
colIndex
)
throws
SQLException
{
byte
[]
bs
=
rs
.
getBytes
(
colIndex
);
if
(
bs
==
null
)
{
return
null
;
}
if
(
bs
.
length
==
16
)
{
// UUID?
UUID
uuid
=
NumberUtils
.
toUUID
(
bs
);
...
...
@@ -94,16 +77,19 @@ public class CSVResultSetHelper extends ResultSetHelperService {
}
}
private
String
handleTime
(
Time
time
)
{
return
time
==
null
?
null
:
time
.
toString
();
}
private
String
handleTimestamp
(
Timestamp
timestamp
)
{
SimpleDateFormat
timeFormat
=
new
SimpleDateFormat
(
"dd-MMM-yyyy HH:mm:ss"
);
return
timestamp
==
null
?
null
:
timeFormat
.
format
(
timestamp
);
private
static
String
read
(
Clob
c
)
throws
SQLException
,
IOException
{
StringBuilder
sb
=
new
StringBuilder
((
int
)
c
.
length
());
Reader
r
=
c
.
getCharacterStream
();
char
[]
cbuf
=
new
char
[
CLOBBUFFERSIZE
];
int
n
;
while
((
n
=
r
.
read
(
cbuf
,
0
,
cbuf
.
length
))
!=
-
1
)
{
sb
.
append
(
cbuf
,
0
,
n
);
}
return
sb
.
toString
();
}
private
String
getColumnValue
(
ResultSet
rs
,
int
colType
,
int
colIndex
)
throws
SQLException
,
IOException
{
private
String
getColumnValue
(
ResultSet
rs
,
int
colType
,
int
colIndex
,
boolean
trim
,
String
dateFormatString
,
String
timestampFormatString
)
throws
SQLException
,
IOException
{
String
value
=
""
;
...
...
@@ -127,25 +113,29 @@ public class CSVResultSetHelper extends ResultSetHelperService {
value
=
handleLong
(
rs
,
colIndex
);
break
;
case
Types
.
DECIMAL
:
case
Types
.
DOUBLE
:
case
Types
.
FLOAT
:
case
Types
.
REAL
:
case
Types
.
NUMERIC
:
value
=
handleBigDecimal
(
rs
.
getBigDecimal
(
colIndex
));
break
;
case
Types
.
DOUBLE
:
value
=
handleDouble
(
rs
.
getDouble
(
colIndex
));
break
;
case
Types
.
FLOAT
:
value
=
handleFloat
(
rs
.
getFloat
(
colIndex
));
break
;
case
Types
.
INTEGER
:
case
Types
.
TINYINT
:
case
Types
.
SMALLINT
:
value
=
handleInteger
(
rs
,
colIndex
);
break
;
case
Types
.
DATE
:
value
=
handleDate
(
rs
,
colIndex
);
value
=
handleDate
(
rs
,
colIndex
,
dateFormatString
);
break
;
case
Types
.
TIME
:
value
=
handleTime
(
rs
.
getTime
(
colIndex
));
break
;
case
Types
.
TIMESTAMP
:
value
=
handleTimestamp
(
rs
.
getTimestamp
(
colIndex
));
value
=
handleTimestamp
(
rs
.
getTimestamp
(
colIndex
)
,
timestampFormatString
);
break
;
case
NVARCHAR:
// todo : use rs.getNString
case
NCHAR:
// todo : use rs.getNString
...
...
@@ -153,13 +143,17 @@ public class CSVResultSetHelper extends ResultSetHelperService {
case
Types
.
LONGVARCHAR
:
case
Types
.
VARCHAR
:
case
Types
.
CHAR
:
value
=
rs
.
getString
(
colIndex
);
String
columnValue
=
rs
.
getString
(
colIndex
);
if
(
trim
&&
columnValue
!=
null
)
{
value
=
columnValue
.
trim
();
}
else
{
value
=
columnValue
;
}
break
;
case
Types
.
BINARY
:
value
=
handleBinary
(
rs
,
colIndex
);
break
;
default
:
// System.err.println("SQLType not handled " + colType);
value
=
""
;
}
...
...
@@ -168,17 +162,5 @@ public class CSVResultSetHelper extends ResultSetHelperService {
}
return
value
;
}
private
static
String
read
(
Clob
c
)
throws
SQLException
,
IOException
{
StringBuilder
sb
=
new
StringBuilder
((
int
)
c
.
length
());
Reader
r
=
c
.
getCharacterStream
();
char
[]
cbuf
=
new
char
[
CLOBBUFFERSIZE
];
int
n
;
while
((
n
=
r
.
read
(
cbuf
,
0
,
cbuf
.
length
))
!=
-
1
)
{
sb
.
append
(
cbuf
,
0
,
n
);
}
return
sb
.
toString
();
}
}
src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @
2a977f6e
...
...
@@ -119,9 +119,9 @@ import org.springframework.security.acls.domain.BasePermission;
import
org.springframework.stereotype.Service
;
import
org.springframework.transaction.annotation.Transactional
;
import
au.com.bytecode
.opencsv.CSVWriter
;
import
au.com.bytecode
.opencsv.ResultSetHelper
;
import
au.com.bytecode
.opencsv.ResultSetHelperService
;
import
com
.opencsv.CSVWriter
;
import
com
.opencsv.ResultSetHelper
;
import
com
.opencsv.ResultSetHelperService
;
@Service
@Transactional
(
readOnly
=
true
)
...
...
src/main/java/org/genesys2/server/service/worker/GeoNamesCountrySource.java
View file @
2a977f6e
...
...
@@ -37,7 +37,7 @@ import org.apache.http.impl.client.HttpClientBuilder;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.stereotype.Component
;
import
au.com.bytecode
.opencsv.CSVReader
;
import
com
.opencsv.CSVReader
;
/**
* Fetch and parse country information from
...
...
src/main/java/org/genesys2/server/service/worker/ITPGRFAStatusUpdater.java
View file @
2a977f6e
...
...
@@ -43,7 +43,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import
org.springframework.core.task.TaskExecutor
;
import
org.springframework.stereotype.Component
;
import
au.com.bytecode
.opencsv.CSVReader
;
import
com
.opencsv.CSVReader
;
/**
* Update country ITPGRFA status by fetching data from
...
...
src/main/java/org/genesys2/server/service/worker/InstituteUpdater.java
View file @
2a977f6e
...
...
@@ -46,7 +46,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import
org.springframework.core.task.TaskExecutor
;
import
org.springframework.stereotype.Component
;
import
au.com.bytecode
.opencsv.CSVReader
;
import
com
.opencsv.CSVReader
;
@Component
public
class
InstituteUpdater
{
...
...
@@ -225,12 +225,6 @@ public class InstituteUpdater {
LOG
.
info
(
"Updating FaoInstitutes: "
+
toSave
.
size
());
instituteService
.
update
(
toSave
);
}
// try {
// Thread.sleep(2000);
// } catch (final InterruptedException e) {
// LOG.warn(e.getMessage());
// }
}
private
FaoInstitute
insertData
(
String
[]
line
)
{
...
...
@@ -267,7 +261,9 @@ public class InstituteUpdater {
}
faoInstitute
.
setAcronym
(
acronym
);
faoInstitute
.
setFullName
(
fullName
);
LOG
.
info
(
"Updating: "
+
instCode
+
" "
+
fullName
);
if
(
LOG
.
isTraceEnabled
())
{
LOG
.
trace
(
"Updating: code="
+
instCode
+
" fullname='"
+
fullName
+
"' acronym="
+
acronym
);
}
faoInstitute
.
setPgrActivity
(
pgrActivity
);
faoInstitute
.
setMaintainsCollection
(
maintColl
);
faoInstitute
.
setEmail
(
email
);
...
...
src/main/java/org/genesys2/server/service/worker/SGSVUpdate.java
View file @
2a977f6e
...
...
@@ -38,8 +38,6 @@ import org.genesys2.server.model.genesys.Accession;
import
org.genesys2.server.model.genesys.SvalbardData
;
import
org.genesys2.server.persistence.domain.SvalbardRepository
;
import
org.genesys2.server.service.GenesysService
;
import
org.genesys2.server.service.GeoService
;
import
org.genesys2.server.service.TaxonomyService
;
import
org.hibernate.exception.ConstraintViolationException
;
import
org.springframework.beans.factory.annotation.Autowired
;
import
org.springframework.core.task.TaskExecutor
;
...
...
@@ -47,7 +45,7 @@ import org.springframework.orm.hibernate3.HibernateOptimisticLockingFailureExcep
import
org.springframework.security.access.prepost.PreAuthorize
;
import
org.springframework.stereotype.Component
;
import
au.com.bytecode
.opencsv.CSVReader
;
import
com
.opencsv.CSVReader
;
@Component
public
class
SGSVUpdate
{
...
...
@@ -71,12 +69,6 @@ public class SGSVUpdate {
@Autowired
private
GenesysService
genesysService
;
@Autowired
private
TaxonomyService
taxonomyService
;
@Autowired
private
GeoService
geoService
;
@Autowired
private
SvalbardRepository
svalbardRepository
;
...
...
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