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minerva
core
Commits
a1c66bb2
Commit
a1c66bb2
authored
Sep 15, 2021
by
Piotr Gawron
Browse files
fields must be private
parent
02e95e8b
Changes
394
Hide whitespace changes
Inline
Side-by-side
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java
View file @
a1c66bb2
...
...
@@ -20,7 +20,7 @@ public class CdPluginFunctions {
@Rule
public
UnitTestFailedWatcher
unitTestFailedWatcher
=
new
UnitTestFailedWatcher
();
String
rdfString
=
"<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
private
String
rdfString
=
"<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+
"<rdf:Description rdf:about=\"#s3\">\n"
+
"<bqmodel:is>\n"
+
"<rdf:Bag>\n"
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyActionTest.java
View file @
a1c66bb2
...
...
@@ -13,9 +13,9 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
import
lcsb.mapviewer.common.SystemClipboard
;
public
class
CopyActionTest
extends
CdPluginFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
SystemClipboard
cp
=
new
SystemClipboard
();
private
SystemClipboard
cp
=
new
SystemClipboard
();
@Test
public
void
testCopyFromSpecies
()
{
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractActionTest.java
View file @
a1c66bb2
...
...
@@ -19,7 +19,7 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import
lcsb.mapviewer.model.map.MiriamType
;
public
class
CopyPasteAbstractActionTest
extends
CdPluginFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Before
public
void
setUp
()
throws
Exception
{
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePluginTest.java
View file @
a1c66bb2
...
...
@@ -15,7 +15,7 @@ import lcsb.mapviewer.common.SystemClipboard;
public
class
CopyPastePluginTest
extends
CdPluginFunctions
{
SystemClipboard
cp
=
new
SystemClipboard
();
private
SystemClipboard
cp
=
new
SystemClipboard
();
@Test
public
void
testConstructor
()
{
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/copypaste/PasteActionTest.java
View file @
a1c66bb2
...
...
@@ -17,7 +17,7 @@ import lcsb.mapviewer.common.SystemClipboard;
public
class
PasteActionTest
extends
CdPluginFunctions
{
SystemClipboard
cp
=
new
SystemClipboard
();
private
SystemClipboard
cp
=
new
SystemClipboard
();
@Test
public
void
testPerformAnnotationOnSpecies
()
{
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoFrameTest.java
View file @
a1c66bb2
...
...
@@ -14,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import
lcsb.mapviewer.cdplugin.CdPluginFunctions
;
public
class
InfoFrameTest
extends
CdPluginFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Test
public
void
testSetEmptySpeciesList
()
{
...
...
CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/info/InfoPluginTest.java
View file @
a1c66bb2
...
...
@@ -14,7 +14,7 @@ import lcsb.mapviewer.cdplugin.CdPluginFunctions;
public
class
InfoPluginTest
extends
CdPluginFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Test
public
void
testConstructor
()
{
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnector.java
View file @
a1c66bb2
...
...
@@ -43,7 +43,7 @@ public final class MiriamConnector extends CachableInterface implements IExterna
*/
private
Logger
logger
=
LogManager
.
getLogger
();
XmlAnnotationParser
xap
=
new
XmlAnnotationParser
();
private
XmlAnnotationParser
xap
=
new
XmlAnnotationParser
();
/**
* Default class constructor. Prevent initialization.
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
View file @
a1c66bb2
...
...
@@ -9,16 +9,16 @@ import lcsb.mapviewer.model.map.species.field.Structure;
*
*/
public
class
PdbBestMappingEntry
{
p
ublic
String
chainId
;
p
ublic
String
experimentalMethod
;
p
ublic
String
pdbId
;
p
ublic
int
start
;
p
ublic
int
end
;
p
ublic
int
unpEnd
;
p
ublic
double
coverage
;
p
ublic
int
unpStart
;
p
ublic
double
resolution
;
p
ublic
int
taxId
;
p
rivate
String
chainId
;
p
rivate
String
experimentalMethod
;
p
rivate
String
pdbId
;
p
rivate
int
start
;
p
rivate
int
end
;
p
rivate
int
unpEnd
;
p
rivate
double
coverage
;
p
rivate
int
unpStart
;
p
rivate
double
resolution
;
p
rivate
int
taxId
;
public
Structure
convertToStructure
()
{
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/ChemicalParser.java
View file @
a1c66bb2
...
...
@@ -44,7 +44,7 @@ public class ChemicalParser {
private
ChemicalEntityDtoConverter
chemicalEntityDtoConverter
;
ObjectMapper
objectMapper
=
new
ObjectMapper
().
configure
(
DeserializationFeature
.
FAIL_ON_UNKNOWN_PROPERTIES
,
private
ObjectMapper
objectMapper
=
new
ObjectMapper
().
configure
(
DeserializationFeature
.
FAIL_ON_UNKNOWN_PROPERTIES
,
false
);
@Autowired
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DrugBankParser.java
View file @
a1c66bb2
...
...
@@ -46,7 +46,7 @@ public class DrugBankParser extends DrugAnnotation implements IExternalService {
private
ChemicalEntityDtoConverter
chemicalEntityDtoConverter
;
ObjectMapper
objectMapper
=
new
ObjectMapper
().
configure
(
DeserializationFeature
.
FAIL_ON_UNKNOWN_PROPERTIES
,
private
ObjectMapper
objectMapper
=
new
ObjectMapper
().
configure
(
DeserializationFeature
.
FAIL_ON_UNKNOWN_PROPERTIES
,
false
);
@Autowired
...
...
annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/dto/DapiDatabase.java
View file @
a1c66bb2
package
lcsb.mapviewer.annotation.services.dapi.dto
;
public
class
DapiDatabase
{
p
ublic
String
name
;
p
rivate
String
name
;
public
DapiDatabase
(
final
String
name
)
{
this
.
name
=
name
;
}
public
String
getName
()
{
return
name
;
}
}
annotation/src/test/java/lcsb/mapviewer/annotation/cache/ApplicationLevelCacheTest.java
View file @
a1c66bb2
...
...
@@ -18,9 +18,9 @@ import lcsb.mapviewer.model.cache.CacheType;
public
class
ApplicationLevelCacheTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
boolean
status
;
private
boolean
status
;
@Before
public
void
setUp
()
throws
Exception
{
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/BigFileCacheTest.java
View file @
a1c66bb2
...
...
@@ -42,15 +42,15 @@ import lcsb.mapviewer.persist.dao.cache.BigFileEntryDao;
public
class
BigFileCacheTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
String
ftpUrl
=
"ftp://ftp.informatik.rwth-aachen.de/README"
;
String
ftpUrlPartContent
=
"Welcome"
;
private
String
ftpUrl
=
"ftp://ftp.informatik.rwth-aachen.de/README"
;
private
String
ftpUrlPartContent
=
"Welcome"
;
String
httpUrl
=
"https://www.google.pl/humans.txt"
;
private
String
httpUrl
=
"https://www.google.pl/humans.txt"
;
@Autowired
BigFileCache
bigFileCache
;
private
BigFileCache
bigFileCache
;
@Before
public
void
setUp
()
throws
Exception
{
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/CachableInterfaceTest.java
View file @
a1c66bb2
...
...
@@ -22,7 +22,7 @@ import lcsb.mapviewer.model.cache.CacheType;
import
lcsb.mapviewer.persist.dao.cache.CacheTypeDao
;
public
class
CachableInterfaceTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Autowired
private
List
<
CachableInterface
>
interfaces
;
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheTest.java
View file @
a1c66bb2
...
...
@@ -19,12 +19,12 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import
lcsb.mapviewer.model.cache.CacheType
;
public
class
GeneralCacheTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
GeneralCache
cache
=
new
GeneralCache
(
null
);
private
GeneralCache
cache
=
new
GeneralCache
(
null
);
@Autowired
PermanentDatabaseLevelCacheInterface
databaseLevelCache
;
private
PermanentDatabaseLevelCacheInterface
databaseLevelCache
;
@AfterClass
public
static
void
tearDownAfterClass
()
throws
Exception
{
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/GeneralCacheWithExclusionTest.java
View file @
a1c66bb2
...
...
@@ -16,7 +16,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import
lcsb.mapviewer.model.cache.CacheType
;
public
class
GeneralCacheWithExclusionTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@AfterClass
public
static
void
tearDownAfterClass
()
throws
Exception
{
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/MockCacheInterface.java
View file @
a1c66bb2
...
...
@@ -9,8 +9,8 @@ package lcsb.mapviewer.annotation.cache;
*/
public
final
class
MockCacheInterface
extends
CachableInterface
{
p
ublic
static
RuntimeException
exceptionToThrow
=
null
;
p
ublic
static
Error
errorToThrow
;
p
rotected
static
RuntimeException
exceptionToThrow
=
null
;
p
rotected
static
Error
errorToThrow
;
/**
* Defsault constructor.
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/cache/PermanentDatabaseLevelCacheTest.java
View file @
a1c66bb2
...
...
@@ -33,7 +33,7 @@ import lcsb.mapviewer.persist.dao.cache.CacheQueryDao;
@Rollback
(
true
)
public
class
PermanentDatabaseLevelCacheTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Autowired
private
PermanentDatabaseLevelCacheInterface
permanentDatabaseLevelCache
;
...
...
annotation/src/test/java/lcsb/mapviewer/annotation/services/ChEMBLParserTest.java
View file @
a1c66bb2
...
...
@@ -43,7 +43,7 @@ import lcsb.mapviewer.model.map.MiriamRelationType;
import
lcsb.mapviewer.model.map.MiriamType
;
public
class
ChEMBLParserTest
extends
AnnotationTestFunctions
{
Logger
logger
=
LogManager
.
getLogger
();
private
static
Logger
logger
=
LogManager
.
getLogger
();
@Autowired
private
GeneralCacheInterface
cache
;
...
...
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