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Genesys PGR
Genesys Backend
Commits
e55711f4
Commit
e55711f4
authored
Feb 04, 2014
by
Matija Obreza
Browse files
Source formatting
parent
61c0b948
Changes
34
Hide whitespace changes
Inline
Side-by-side
src/main/java/net/tanesha/recaptcha/ReCaptchaImpl.java
View file @
e55711f4
...
...
@@ -26,38 +26,42 @@ public class ReCaptchaImpl implements ReCaptcha {
public
static
final
String
PROPERTY_THEME
=
"theme"
;
public
static
final
String
PROPERTY_TABINDEX
=
"tabindex"
;
public
static
final
String
HTTP_SERVER
=
"http://www.google.com/recaptcha/api"
;
public
static
final
String
HTTPS_SERVER
=
"https://www.google.com/recaptcha/api"
;
// HTTPS Verify url
public
static
final
String
VERIFY_URL
=
"https://www.google.com/recaptcha/api/verify"
;
private
String
privateKey
;
private
String
publicKey
;
private
String
recaptchaServer
=
HTTP_SERVER
;
private
boolean
includeNoscript
=
false
;
private
HttpLoader
httpLoader
=
new
SimpleHttpLoader
();
public
void
setPrivateKey
(
String
privateKey
)
{
this
.
privateKey
=
privateKey
;
}
public
void
setPublicKey
(
String
publicKey
)
{
this
.
publicKey
=
publicKey
;
}
public
void
setRecaptchaServer
(
String
recaptchaServer
)
{
this
.
recaptchaServer
=
recaptchaServer
;
}
public
void
setIncludeNoscript
(
boolean
includeNoscript
)
{
this
.
includeNoscript
=
includeNoscript
;
}
public
void
setHttpLoader
(
HttpLoader
httpLoader
)
{
this
.
httpLoader
=
httpLoader
;
this
.
httpLoader
=
httpLoader
;
}
public
ReCaptchaResponse
checkAnswer
(
String
remoteAddr
,
String
challenge
,
String
response
)
{
String
postParameters
=
"privatekey="
+
URLEncoder
.
encode
(
privateKey
)
+
"&remoteip="
+
URLEncoder
.
encode
(
remoteAddr
)
+
"&challenge="
+
URLEncoder
.
encode
(
challenge
)
+
"&response="
+
URLEncoder
.
encode
(
response
);
String
postParameters
=
"privatekey="
+
URLEncoder
.
encode
(
privateKey
)
+
"&remoteip="
+
URLEncoder
.
encode
(
remoteAddr
)
+
"&challenge="
+
URLEncoder
.
encode
(
challenge
)
+
"&response="
+
URLEncoder
.
encode
(
response
);
String
message
=
httpLoader
.
httpPost
(
VERIFY_URL
,
postParameters
);
...
...
@@ -77,7 +81,7 @@ public class ReCaptchaImpl implements ReCaptcha {
else
errorMessage
=
"recaptcha4j-missing-error-message"
;
}
return
new
ReCaptchaResponse
(
valid
,
errorMessage
);
}
...
...
@@ -90,17 +94,16 @@ public class ReCaptchaImpl implements ReCaptcha {
message
+=
"<script type=\"text/javascript\" src=\""
+
recaptchaServer
+
"/challenge?k="
+
publicKey
+
errorPart
+
"\"></script>\r\n"
;
if
(
includeNoscript
)
{
String
noscript
=
"<noscript>\r\n"
+
" <iframe src=\""
+
recaptchaServer
+
"/noscript?k="
+
publicKey
+
errorPart
+
"\" height=\"300\" width=\"500\" frameborder=\"0\"></iframe><br>\r\n"
+
" <textarea name=\"recaptcha_challenge_field\" rows=\"3\" cols=\"40\"></textarea>\r\n"
+
" <input type=\"hidden\" name=\"recaptcha_response_field\" value=\"manual_challenge\">\r\n"
+
"</noscript>"
;
String
noscript
=
"<noscript>\r\n"
+
" <iframe src=\""
+
recaptchaServer
+
"/noscript?k="
+
publicKey
+
errorPart
+
"\" height=\"300\" width=\"500\" frameborder=\"0\"></iframe><br>\r\n"
+
" <textarea name=\"recaptcha_challenge_field\" rows=\"3\" cols=\"40\"></textarea>\r\n"
+
" <input type=\"hidden\" name=\"recaptcha_response_field\" value=\"manual_challenge\">\r\n"
+
"</noscript>"
;
message
+=
noscript
;
}
return
message
;
}
public
String
createRecaptchaHtml
(
String
errorMessage
,
String
theme
,
Integer
tabindex
)
{
Properties
options
=
new
Properties
();
...
...
@@ -127,19 +130,17 @@ public class ReCaptchaImpl implements ReCaptcha {
return
""
;
}
String
jsOptions
=
"<script type=\"text/javascript\">\r\n"
+
"var RecaptchaOptions = {"
;
for
(
Enumeration
e
=
properties
.
keys
();
e
.
hasMoreElements
();
)
{
String
jsOptions
=
"<script type=\"text/javascript\">\r\n"
+
"var RecaptchaOptions = {"
;
for
(
Enumeration
e
=
properties
.
keys
();
e
.
hasMoreElements
();)
{
String
property
=
(
String
)
e
.
nextElement
();
jsOptions
+=
property
+
":'"
+
properties
.
getProperty
(
property
)
+
"'"
;
jsOptions
+=
property
+
":'"
+
properties
.
getProperty
(
property
)
+
"'"
;
if
(
e
.
hasMoreElements
())
{
jsOptions
+=
","
;
}
}
jsOptions
+=
"};\r\n</script>\r\n"
;
...
...
src/main/java/org/genesys2/server/lucene/genesys/FaoInstituteBridge.java
View file @
e55711f4
...
...
@@ -49,7 +49,7 @@ public class FaoInstituteBridge implements FieldBridge {
if
(
institute
.
getAccessionCount
()
>
0
)
field
.
setBoost
(
2
*
luceneOptions
.
getBoost
());
document
.
add
(
field
);
}
...
...
src/main/java/org/genesys2/server/model/UserRole.java
View file @
e55711f4
...
...
@@ -18,7 +18,7 @@ package org.genesys2.server.model;
public
enum
UserRole
{
USER
(
"User"
),
ADMINISTRATOR
(
"Administrator"
),
ORGANIZATION_ADMINISTRATOR
(
"Organization Administrator"
),
NETWORK_ADMINISTRATOR
(
"Network Administrator"
),
VALIDATEDUSER
(
"Validated user"
),
VETTEDUSER
(
"Vetted user"
);
"Validated user"
),
VETTEDUSER
(
"Vetted user"
);
String
label
;
...
...
src/main/java/org/genesys2/server/model/genesys/AccessionTrait.java
View file @
e55711f4
...
...
@@ -26,7 +26,7 @@ import javax.persistence.UniqueConstraint;
import
org.genesys2.server.model.BusinessModel
;
@Entity
@Table
(
name
=
"accessiontrait"
,
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UQ_accessiontrait_all"
,
columnNames
=
{
"metadataId"
,
"accessionId"
,
"methodId"
})
})
@Table
(
name
=
"accessiontrait"
,
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UQ_accessiontrait_all"
,
columnNames
=
{
"metadataId"
,
"accessionId"
,
"methodId"
})
})
public
class
AccessionTrait
extends
BusinessModel
{
private
static
final
long
serialVersionUID
=
-
240056837800843686L
;
...
...
src/main/java/org/genesys2/server/model/genesys/Metadata.java
View file @
e55711f4
...
...
@@ -173,7 +173,6 @@ public class Metadata extends VersionedAuditedModel implements AclAwareModel, Ge
this
.
uuid
=
uuid
;
}
@Override
public
String
toString
()
{
return
MessageFormat
.
format
(
"Metadata id={0,number,#} inst={2} title={1}"
,
id
,
title
,
instituteCode
);
...
...
src/main/java/org/genesys2/server/model/genesys/MetadataAccession.java
View file @
e55711f4
...
...
@@ -25,7 +25,7 @@ import javax.persistence.UniqueConstraint;
import
org.genesys2.server.model.BusinessModel
;
@Entity
@Table
(
name
=
"metadataaccession"
,
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UI_metadataaccession_all"
,
columnNames
=
{
"metadataId"
,
"accessionId"
})
})
@Table
(
name
=
"metadataaccession"
,
uniqueConstraints
=
{
@UniqueConstraint
(
name
=
"UI_metadataaccession_all"
,
columnNames
=
{
"metadataId"
,
"accessionId"
})
})
public
class
MetadataAccession
extends
BusinessModel
{
private
static
final
long
serialVersionUID
=
-
240056837800843686L
;
...
...
src/main/java/org/genesys2/server/model/impl/User.java
View file @
e55711f4
...
...
@@ -217,7 +217,7 @@ public class User extends BusinessModel {
// We don't support password expiration
return
false
;
}
public
boolean
hasRole
(
String
roleName
)
{
for
(
UserRole
userRole
:
getRoles
())
{
if
(
userRole
.
getName
().
equalsIgnoreCase
(
roleName
))
{
...
...
src/main/java/org/genesys2/server/persistence/domain/AccessionTraitRepository.java
View file @
e55711f4
...
...
@@ -41,7 +41,6 @@ public interface AccessionTraitRepository extends JpaRepository<AccessionTrait,
List
<
AccessionTrait
>
findByMetadataIdAndAccession
(
Long
id
,
Accession
accession
);
@Query
(
"select count(id) from AccessionTrait at where at.metadataId = ?1 and at.accession = ?2"
)
long
countByMetadataAndAccessionId
(
long
metadataId
,
Accession
accession
);
...
...
src/main/java/org/genesys2/server/persistence/domain/GenesysLowlevelRepositoryImpl.java
View file @
e55711f4
...
...
@@ -277,7 +277,7 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
}
},
rowCallbackHandler
);
}
@Override
public
void
listMetadataAccessions
(
final
long
id
,
RowCallbackHandler
rowCallbackHandler
)
{
jdbcTemplate
.
query
(
new
PreparedStatementCreator
()
{
...
...
@@ -292,14 +292,13 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
}
},
rowCallbackHandler
);
}
@Override
public
void
listAccessionsAccenames
(
RowCallbackHandler
rowCallbackHandler
)
{
jdbcTemplate
.
query
(
new
PreparedStatementCreator
()
{
@Override
public
PreparedStatement
createPreparedStatement
(
Connection
con
)
throws
SQLException
{
PreparedStatement
stmt
=
con
.
prepareStatement
(
"select accessionId, names, otherIds from accessionname"
);
PreparedStatement
stmt
=
con
.
prepareStatement
(
"select accessionId, names, otherIds from accessionname"
);
// Set mysql JConnector to stream results
stmt
.
setFetchSize
(
Integer
.
MIN_VALUE
);
return
stmt
;
...
...
src/main/java/org/genesys2/server/persistence/domain/TraitValueRepositoryImpl.java
View file @
e55711f4
...
...
@@ -341,16 +341,17 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
return
this
.
jdbcTemplate
.
queryForObject
(
String
.
format
(
"SELECT COUNT(*) FROM `%s` WHERE metadataId=? AND accessionId=?"
,
methodId
),
Integer
.
class
,
metadataId
,
accessionId
);
}
@Override
public
Map
<
String
,
Long
>
getStatistics
(
Method
method
)
{
final
HashMap
<
String
,
Long
>
stats
=
new
HashMap
<
String
,
Long
>();
this
.
jdbcTemplate
.
query
(
MessageFormat
.
format
(
"SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`"
,
method
.
getFieldName
(),
method
.
getId
()),
new
RowCallbackHandler
()
{
@Override
public
void
processRow
(
ResultSet
rs
)
throws
SQLException
{
stats
.
put
(
rs
.
getString
(
1
),
rs
.
getLong
(
2
));
}
});
final
HashMap
<
String
,
Long
>
stats
=
new
HashMap
<
String
,
Long
>();
this
.
jdbcTemplate
.
query
(
MessageFormat
.
format
(
"SELECT `{0}`, COUNT(*) FROM `{1,number,#}` GROUP BY `{0}`"
,
method
.
getFieldName
(),
method
.
getId
()),
new
RowCallbackHandler
()
{
@Override
public
void
processRow
(
ResultSet
rs
)
throws
SQLException
{
stats
.
put
(
rs
.
getString
(
1
),
rs
.
getLong
(
2
));
}
});
return
stats
;
}
}
src/main/java/org/genesys2/server/service/AclService.java
View file @
e55711f4
...
...
@@ -16,6 +16,9 @@
package
org.genesys2.server.service
;
import
java.util.List
;
import
java.util.Map
;
import
org.genesys2.server.model.AclAwareModel
;
import
org.genesys2.server.model.acl.AclEntry
;
import
org.genesys2.server.model.acl.AclObjectIdentity
;
...
...
@@ -23,48 +26,45 @@ import org.genesys2.server.model.acl.AclSid;
import
org.genesys2.server.security.AuthUserDetails
;
import
org.springframework.security.acls.model.Permission
;
import
java.util.List
;
import
java.util.Map
;
public
interface
AclService
{
void
addCreatorPermissions
(
AclAwareModel
target
);
void
addCreatorPermissions
(
AclAwareModel
target
);
/**
/**
* List ObjectIdentities of specified class for user with specified
* permission
*
* @param clazz
* @param authUser
* @return
*/
List
<
Long
>
listIdentitiesForSid
(
Class
<?
extends
AclAwareModel
>
clazz
,
AuthUserDetails
authUser
,
Permission
permission
);
*
* @param clazz
* @param authUser
* @return
*/
List
<
Long
>
listIdentitiesForSid
(
Class
<?
extends
AclAwareModel
>
clazz
,
AuthUserDetails
authUser
,
Permission
permission
);
AclObjectIdentity
getObjectIdentity
(
long
id
);
AclObjectIdentity
getObjectIdentity
(
long
id
);
AclObjectIdentity
getObjectIdentity
(
String
clazz
,
long
id
);
AclObjectIdentity
getObjectIdentity
(
String
clazz
,
long
id
);
AclObjectIdentity
ensureObjectIdentity
(
String
clazz
,
long
id
);
AclObjectIdentity
ensureObjectIdentity
(
String
clazz
,
long
id
);
AclObjectIdentity
getObjectIdentity
(
AclAwareModel
entity
);
AclObjectIdentity
getObjectIdentity
(
AclAwareModel
entity
);
List
<
AclEntry
>
getAclEntries
(
AclObjectIdentity
objectIdentity
);
List
<
AclEntry
>
getAclEntries
(
AclObjectIdentity
objectIdentity
);
List
<
AclEntry
>
getAclEntries
(
AclAwareModel
entity
);
List
<
AclEntry
>
getAclEntries
(
AclAwareModel
entity
);
Permission
[]
getAvailablePermissions
(
String
className
);
Permission
[]
getAvailablePermissions
(
String
className
);
List
<
AclSid
>
getSids
(
AclAwareModel
entity
);
List
<
AclSid
>
getSids
(
AclAwareModel
entity
);
List
<
AclSid
>
getSids
(
long
id
,
String
className
);
List
<
AclSid
>
getSids
(
long
id
,
String
className
);
Map
<
String
,
Map
<
Integer
,
Boolean
>>
getPermissions
(
AclAwareModel
entity
);
Map
<
String
,
Map
<
Integer
,
Boolean
>>
getPermissions
(
long
id
,
String
className
);
boolean
addPermissions
(
long
objectIdIdentity
,
String
className
,
String
uuid
,
boolean
principal
,
Map
<
Integer
,
Boolean
>
permissions
);
boolean
addPermissions
(
long
objectIdIdentity
,
String
className
,
String
uuid
,
boolean
principal
,
Map
<
Integer
,
Boolean
>
permissions
);
void
updatePermission
(
AclObjectIdentity
entity
,
String
sid
,
Map
<
Integer
,
Boolean
>
permissionMap
);
void
updatePermission
(
AclObjectIdentity
entity
,
String
sid
,
Map
<
Integer
,
Boolean
>
permissionMap
);
List
<
AclSid
>
getAllSids
();
List
<
AclSid
>
getAllSids
();
}
src/main/java/org/genesys2/server/service/EMailVerificationService.java
View file @
e55711f4
...
...
@@ -25,8 +25,7 @@ public interface EMailVerificationService {
void
sendPasswordResetEmail
(
User
user
);
void
cancelValidation
(
String
tokenUuid
);
boolean
validateEMail
(
String
tokenUuid
,
String
key
);
boolean
changePassword
(
String
tokenUuid
,
String
key
,
String
password
);
...
...
src/main/java/org/genesys2/server/service/GenesysFilterService.java
View file @
e55711f4
...
...
@@ -28,7 +28,8 @@ import com.fasterxml.jackson.databind.JsonNode;
public
interface
GenesysFilterService
{
String
[]
DEFAULT_FILTERS
=
{
"crop"
,
"genus"
,
"taxon"
,
"origin"
,
"lat"
,
"lon"
,
"organization"
,
"institute"
,
"accenumb"
,
"inSvalbard"
,
"mls"
,
"inTrust"
,
"available"
};
String
[]
DEFAULT_FILTERS
=
{
"crop"
,
"genus"
,
"taxon"
,
"origin"
,
"lat"
,
"lon"
,
"organization"
,
"institute"
,
"accenumb"
,
"inSvalbard"
,
"mls"
,
"inTrust"
,
"available"
};
Page
<
Accession
>
listAccessions
(
JsonNode
jsonTree
,
Pageable
pageable
);
...
...
src/main/java/org/genesys2/server/service/OAuth2ClientDetailsService.java
View file @
e55711f4
...
...
@@ -16,17 +16,17 @@
package
org.genesys2.server.service
;
import
java.util.Collection
;
import
org.genesys2.server.model.oauth.OAuthAccessToken
;
import
org.springframework.security.oauth2.provider.ClientDetailsService
;
import
org.springframework.security.oauth2.provider.ClientRegistrationService
;
import
java.util.Collection
;
public
interface
OAuth2ClientDetailsService
extends
ClientDetailsService
,
ClientRegistrationService
{
boolean
exists
(
String
clientId
);
Collection
<
OAuthAccessToken
>
findTokensByClientId
(
String
clientId
);
Collection
<
OAuthAccessToken
>
findTokensByClientId
(
String
clientId
);
Collection
<
OAuthAccessToken
>
findTokensByUserUuid
(
String
uuid
);
Collection
<
OAuthAccessToken
>
findTokensByUserUuid
(
String
uuid
);
}
src/main/java/org/genesys2/server/service/RequestService.java
View file @
e55711f4
...
...
@@ -20,9 +20,8 @@ import java.util.Set;
import
org.genesys2.server.service.impl.EasySMTAConnector.EasySMTAUserData
;
public
interface
RequestService
{
void
sendRequest
(
EasySMTAUserData
pid
,
Set
<
Long
>
accessionIds
);
}
src/main/java/org/genesys2/server/service/SearchService.java
View file @
e55711f4
...
...
@@ -24,7 +24,7 @@ import org.springframework.data.domain.Pageable;
public
interface
SearchService
{
Page
<?>
search
(
String
searchQuery
,
String
[]
fields
,
Pageable
pageable
,
Class
<?>
...
targetClass
)
throws
SearchException
;
Page
<?>
search
(
String
searchQuery
,
String
[]
fields
,
Pageable
pageable
,
Class
<?>...
targetClass
)
throws
SearchException
;
<
T
>
List
<
T
>
autocomplete
(
String
searchQuery
,
Class
<
T
>
clazz
);
...
...
src/main/java/org/genesys2/server/service/TeamService.java
View file @
e55711f4
...
...
@@ -16,6 +16,8 @@
package
org.genesys2.server.service
;
import
java.util.List
;
import
org.genesys2.server.model.impl.FaoInstitute
;
import
org.genesys2.server.model.impl.Team
;
import
org.genesys2.server.model.impl.User
;
...
...
@@ -24,8 +26,6 @@ import org.springframework.data.domain.Pageable;
import
org.springframework.security.access.prepost.PostAuthorize
;
import
org.springframework.security.access.prepost.PreAuthorize
;
import
java.util.List
;
public
interface
TeamService
{
/**
...
...
@@ -100,6 +100,6 @@ public interface TeamService {
@PreAuthorize
(
"hasRole('ADMINISTRATOR') or hasPermission(#team, 'READ')"
)
List
<
User
>
getMembers
(
Team
team
);
@PreAuthorize
(
"hasRole('ADMINISTRATOR') or hasPermission(#team, 'WRITE')"
)
void
updateTeamInformation
(
String
teamUuid
,
String
teamName
);
@PreAuthorize
(
"hasRole('ADMINISTRATOR') or hasPermission(#team, 'WRITE')"
)
void
updateTeamInformation
(
String
teamUuid
,
String
teamName
);
}
src/main/java/org/genesys2/server/service/UserService.java
View file @
e55711f4
...
...
@@ -33,7 +33,7 @@ public interface UserService {
@PreAuthorize
(
"hasRole('ADMINISTRATOR') || hasPermission(#user, 'WRITE')"
)
void
updateUser
(
User
user
)
throws
UserException
;
//
@PreAuthorize("hasRole('ADMINISTRATOR') || principal.user.id == #userId")
//
@PreAuthorize("hasRole('ADMINISTRATOR') || principal.user.id == #userId")
void
updatePassword
(
long
userId
,
String
rawPassword
)
throws
UserException
;
@PreAuthorize
(
"hasRole('ADMINISTRATOR') || hasPermission(#user, 'WRITE')"
)
...
...
@@ -72,5 +72,5 @@ public interface UserService {
void
userEmailValidated
(
String
uuid
);
void
addVettedUserRole
(
String
uuid
);
void
addVettedUserRole
(
String
uuid
);
}
src/main/java/org/genesys2/server/service/impl/AclServiceImpl.java
View file @
e55711f4
...
...
@@ -16,7 +16,12 @@
package
org.genesys2.server.service.impl
;
import
java.util.HashMap
;
import
java.util.List
;
import
java.util.Map
;
import
net.sf.ehcache.CacheManager
;
import
org.genesys2.server.aspect.AsAdminAspect
;
import
org.genesys2.server.model.AclAwareModel
;
import
org.genesys2.server.model.acl.AclClass
;
...
...
@@ -40,10 +45,6 @@ import org.springframework.security.acls.model.Permission;
import
org.springframework.stereotype.Service
;
import
org.springframework.transaction.annotation.Transactional
;
import
java.util.HashMap
;
import
java.util.List
;
import
java.util.Map
;
/**
* TODO Add support for cleaning up after objects are removed
*/
...
...
src/main/java/org/genesys2/server/service/impl/ContentServiceImpl.java
View file @
e55711f4
...
...
@@ -64,8 +64,7 @@ public class ContentServiceImpl implements ContentService {
@Autowired
private
VelocityEngine
velocityEngine
;
@Override
public
Locale
getDefaultLocale
()
{
return
Locale
.
getDefault
();
...
...
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