From: Jim Procter Date: Thu, 23 Oct 2014 22:08:56 +0000 (+0100) Subject: Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch X-Git-Tag: Release_2_8_2b1^2~38 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9493ac8f3b6a02d3cf9747ed6c0d6cf407d284e8;hp=e23bc8f3dd3449ecc15ae868cd5e11b9c6350637;p=jalview.git Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch Conflicts: .classpath RELEASE src/castor.properties --- diff --git a/.classpath b/.classpath index a7270ff..bd96609 100644 --- a/.classpath +++ b/.classpath @@ -3,7 +3,7 @@ - + @@ -14,7 +14,6 @@ - @@ -45,12 +44,13 @@ - + + diff --git a/RELEASE b/RELEASE index 64bbd09..11598ab 100644 --- a/RELEASE +++ b/RELEASE @@ -1,2 +1,2 @@ -jalview.release=Release_2_8_2_Branch -jalview.version=2.8.2 +jalview.release=Release_2_8_2_Branch +jalview.version=2.8.2 diff --git a/lib/xercesImpl.jar b/lib/xercesImpl.jar index 6497101..0aaa990 100755 Binary files a/lib/xercesImpl.jar and b/lib/xercesImpl.jar differ diff --git a/lib/xml-apis.jar b/lib/xml-apis.jar index a3fd9a1..4673346 100755 Binary files a/lib/xml-apis.jar and b/lib/xml-apis.jar differ diff --git a/src/castor.properties b/src/castor.properties index 593fd58..c691302 100644 --- a/src/castor.properties +++ b/src/castor.properties @@ -16,239 +16,239 @@ # You should have received a copy of the GNU General Public License along with Jalview. If not, see . # The Jalview Authors are detailed in the 'AUTHORS' file. ############################################################################### -# THE CASTOR PROPERTIES FILE -# This file specifies values for Castor run-time which may be configured -# by the user. -# $Id$ - -# This section defines Backwards compatibility switches. -# -# Hashtable/Map default mapping. -# For backward compatibility with 0.9.5.2 and earlier. -# -#org.exolab.castor.xml.saveMapKeys=false - -# Defines the default XML parser to be used by Castor. -# The parser must implement org.xml.sax.Parser. -# -org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser - -# Defines the (default) XML serializer factory to use by Castor, which must -# implement org.exolab.castor.xml.SerializerFactory; default is -# org.exolab.castor.xml.XercesXMLSerializerFactory -# -# When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory -# which will use the Xerces instance as shipped with the JDK itself; this avoids -# having to download another Xerces instance and installing it. -org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory -#org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory - -# Defines the NodeType for use with Java primitive types (int, long, boolean, -# etc). This value is only used by the Introspector. Valid values are either -# "attribute" or "element". By default, all primitives are marshaled as -# attributes. Uncomment the following line to change the NodeType to element. -# -#org.exolab.castor.xml.introspector.primitive.nodetype=element - -# Defines the Naming "style" or conventions to use when creating XML names -# from Java class or field names. -# Valid values are as follows: -# ----------------------------------------------------------------- -# lower (default) | All names are lowercase with hyphens -# | separating words. -# | -# | Example: personInfo = person-info -# ----------------------------------------------------------------- -# mixed | All names are mixed case, with Uppercase -# | character as the first letter of a new word. -# | -# | Example: personInfo = personInfo -# | Example: FooBar = fooBar -# ----------------------------------------------------------------- -# {Any ClassName} | Any Class which implements -# | org.exolab.castor.xml.XMLNaming -# ----------------------------------------------------------------- -# -# By default, all names are treated as the "lower" option. To preserve the -# Java mixed-case conventions, uncomment the following line. -# -#org.exolab.castor.xml.naming=mixed - -############################### -# REGULAR EXPRESSION EVALUATORS -# -# Defines the Regular Expression Evaluator to be used by Castor. -# The evaluator must implement org.exolab.castor.util.RegExpEvaluator. -# -# Uncomment the following to basically suppress Regular expressions evaluation: -#org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator -# -# An implementation which uses the Jakarta RegExp library: -#org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator -# -# An implementation which uses the Jakarta ORO library: -org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator - -# True if all documents should be indented on output by default. -# Defaults to false. -# -#org.exolab.castor.indent=true - -# True if xml documents should be validated by the SAX Parser -# Defaults to false. -# -org.exolab.castor.parser.validation=false - -# True for parser to support Namespaces. -# Defaults to false. -# -org.exolab.castor.parser.namespaces=false - -# True if all documents should be validated by the marshaling framework -# Defaults to true. -# -org.exolab.castor.marshalling.validation=true - -# Comma separated list of SAX 2 features that should be enabled for the -# default parser. -# -#org.exolab.castor.sax.features= - -# Comma separated list of SAX 2 features that should be disabled for the -# default parser. -# -#org.exolab.castor.sax.features-to-disable - -# True if debugging output should be generated. -# Defaults to false. -# -org.exolab.castor.debug=false - -# List of collection handlers for Java 1.1 and Java 1.2 run-times: -# -org.exolab.castor.mapping.collections=\ - org.exolab.castor.mapping.loader.J1CollectionHandlers,\ - org.exolab.castor.mapping.loader.J2CollectionHandlers - -# List of persistence factories for the supported database servers: -# -org.exolab.castor.jdo.engines=\ - org.exolab.castor.jdo.drivers.OracleFactory,\ - org.exolab.castor.jdo.drivers.PostgreSQLFactory,\ - org.exolab.castor.jdo.drivers.SybaseFactory,\ - org.exolab.castor.jdo.drivers.SQLServerFactory,\ - org.exolab.castor.jdo.drivers.DB2Factory,\ - org.exolab.castor.jdo.drivers.InformixFactory,\ - org.exolab.castor.jdo.drivers.HsqlFactory,\ - org.exolab.castor.jdo.drivers.InstantDBFactory,\ - org.exolab.castor.jdo.drivers.InterbaseFactory,\ - org.exolab.castor.jdo.drivers.MySQLFactory,\ - org.exolab.castor.jdo.drivers.SapDbFactory,\ - org.exolab.castor.jdo.drivers.GenericFactory,\ - org.exolab.castor.jdo.drivers.DerbyFactory,\ - org.castor.jdo.drivers.PointbaseFactory,\ - org.castor.jdo.drivers.ProgressFactory - -# List of key generator factories: -# -org.exolab.castor.jdo.keyGeneratorFactories=\ - org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\ - org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\ - org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\ - org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\ - org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory - -# Collection handlers for the source code generator: -# -org.exolab.castor.builder.type.j2=\ - org.exolab.castor.builder.FieldInfoFactoryJ2 -org.exolab.castor.builder.type.j1=\ - org.exolab.castor.builder.FieldInfoFactory -org.exolab.castor.builder.type.odmg=\ - org.exolab.castor.builder.FieldInfoFactoryODMG30 - -# Configures the default time zone to apply to dates/times fetched from -# database fields (if not already part of the data). Specify same format as -# in java.util.TimeZone.getTimeZone, or the empty string to use the computer's -# local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for -# detailed information about time zones. -# -org.exolab.castor.jdo.defaultTimeZone= -#org.exolab.castor.jdo.defaultTimeZone=GMT-8:00 - -# List of TxSynchronizeable implementations: -# -#org.exolab.castor.persist.TxSynchronizable= - -# Sets the buffer size in bytes for fetching LOBs (this is dependent upon -# the JDBC driver implementation). The value below == 5k. -# -org.exolab.castor.jdo.lobBufferSize=5120 - -# True if database configuration should be initalization -# when loading it (default: true). -# -#org.exolab.castor.jdo.DatabaseInitializeAtLoad=true - -# True if proxy classes should be used for JDBC connections and -# prepared statements. -# Defaults to true. -# -org.exolab.castor.persist.useProxies=false - -# MappingLoader implementations: -# -org.castor.mapping.loaderFactories=\ - org.castor.mapping.JDOMappingLoaderFactory,\ - org.castor.mapping.XMLMappingLoaderFactory - -# Cache implementations: -# -org.castor.cache.Factories=\ - org.castor.cache.simple.NoCacheFactory,\ - org.castor.cache.simple.TimeLimitedFactory,\ - org.castor.cache.simple.CountLimitedFactory,\ - org.castor.cache.simple.UnlimitedFactory,\ - org.castor.cache.distributed.FKCacheFactory,\ - org.castor.cache.distributed.JcsCacheFactory,\ - org.castor.cache.distributed.JCacheFactory,\ - org.castor.cache.distributed.CoherenceCacheFactory,\ - org.castor.cache.distributed.OsCacheFactory,\ - org.castor.cache.hashbelt.FIFOHashbeltFactory,\ - org.castor.cache.hashbelt.LRUHashbeltFactory,\ - org.castor.cache.distributed.EHCacheFactory,\ - org.castor.cache.distributed.GigaspacesCacheFactory - -# TransactionManagerFactory implementations: -# -org.castor.transactionmanager.Factories=\ - org.castor.transactionmanager.WebSphereTransactionManagerFactory,\ - org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\ - org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\ - org.castor.transactionmanager.LocalTransactionManagerFactory,\ - org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\ - org.castor.transactionmanager.JOTMTransactionManagerFactory - -# Selects whether the TransactionManager should be initialized at registration, -# or lazily when requested for the first time. -# Defaults to false. -# -org.castor.transactionmanager.InitializeAtRegistration=false - -# Instructs Castor JDO to use the JDBC 3.0-specific features to obtain -# the generated value of an identity column. -# Defaults to false. -# -org.castor.jdo.use.jdbc30=false - -# Specifies whether to use ANSI-compliant SQL for MS SQL Server. -# Defaults to false. -# -org.exolab.castor.jdo.sqlserver.ansi-compliant=false - -# Specifyies whether the ClassDescriptorResolver should (automatically) search -# for and consult with package mapping files (.castor.xml) to retrieve class -# descriptor information; on by default. -# Defaults to true. -# -#org.exolab.castor.xml.loadPackageMappings=false +# THE CASTOR PROPERTIES FILE +# This file specifies values for Castor run-time which may be configured +# by the user. +# $Id$ + +# This section defines Backwards compatibility switches. +# +# Hashtable/Map default mapping. +# For backward compatibility with 0.9.5.2 and earlier. +# +#org.exolab.castor.xml.saveMapKeys=false + +# Defines the default XML parser to be used by Castor. +# The parser must implement org.xml.sax.Parser. +# +org.exolab.castor.parser=org.apache.xerces.parsers.SAXParser + +# Defines the (default) XML serializer factory to use by Castor, which must +# implement org.exolab.castor.xml.SerializerFactory; default is +# org.exolab.castor.xml.XercesXMLSerializerFactory +# +# When using Castor XML with JDK 5.0, you may switch to the XercesJDK5XMLSerializerFactory +# which will use the Xerces instance as shipped with the JDK itself; this avoids +# having to download another Xerces instance and installing it. +org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesXMLSerializerFactory +#org.exolab.castor.xml.serializer.factory=org.exolab.castor.xml.XercesJDK5XMLSerializerFactory + +# Defines the NodeType for use with Java primitive types (int, long, boolean, +# etc). This value is only used by the Introspector. Valid values are either +# "attribute" or "element". By default, all primitives are marshaled as +# attributes. Uncomment the following line to change the NodeType to element. +# +#org.exolab.castor.xml.introspector.primitive.nodetype=element + +# Defines the Naming "style" or conventions to use when creating XML names +# from Java class or field names. +# Valid values are as follows: +# ----------------------------------------------------------------- +# lower (default) | All names are lowercase with hyphens +# | separating words. +# | +# | Example: personInfo = person-info +# ----------------------------------------------------------------- +# mixed | All names are mixed case, with Uppercase +# | character as the first letter of a new word. +# | +# | Example: personInfo = personInfo +# | Example: FooBar = fooBar +# ----------------------------------------------------------------- +# {Any ClassName} | Any Class which implements +# | org.exolab.castor.xml.XMLNaming +# ----------------------------------------------------------------- +# +# By default, all names are treated as the "lower" option. To preserve the +# Java mixed-case conventions, uncomment the following line. +# +#org.exolab.castor.xml.naming=mixed + +############################### +# REGULAR EXPRESSION EVALUATORS +# +# Defines the Regular Expression Evaluator to be used by Castor. +# The evaluator must implement org.exolab.castor.util.RegExpEvaluator. +# +# Uncomment the following to basically suppress Regular expressions evaluation: +#org.exolab.castor.regexp=org.exolab.castor.xml.util.AlwaysTrueRegExpEvaluator +# +# An implementation which uses the Jakarta RegExp library: +#org.exolab.castor.regexp=org.exolab.castor.util.JakartaRegExpEvaluator +# +# An implementation which uses the Jakarta ORO library: +org.exolab.castor.regexp=org.exolab.castor.util.JakartaOroEvaluator + +# True if all documents should be indented on output by default. +# Defaults to false. +# +#org.exolab.castor.indent=true + +# True if xml documents should be validated by the SAX Parser +# Defaults to false. +# +org.exolab.castor.parser.validation=false + +# True for parser to support Namespaces. +# Defaults to false. +# +org.exolab.castor.parser.namespaces=false + +# True if all documents should be validated by the marshaling framework +# Defaults to true. +# +org.exolab.castor.marshalling.validation=true + +# Comma separated list of SAX 2 features that should be enabled for the +# default parser. +# +#org.exolab.castor.sax.features= + +# Comma separated list of SAX 2 features that should be disabled for the +# default parser. +# +#org.exolab.castor.sax.features-to-disable + +# True if debugging output should be generated. +# Defaults to false. +# +org.exolab.castor.debug=false + +# List of collection handlers for Java 1.1 and Java 1.2 run-times: +# +org.exolab.castor.mapping.collections=\ + org.exolab.castor.mapping.loader.J1CollectionHandlers,\ + org.exolab.castor.mapping.loader.J2CollectionHandlers + +# List of persistence factories for the supported database servers: +# +org.exolab.castor.jdo.engines=\ + org.exolab.castor.jdo.drivers.OracleFactory,\ + org.exolab.castor.jdo.drivers.PostgreSQLFactory,\ + org.exolab.castor.jdo.drivers.SybaseFactory,\ + org.exolab.castor.jdo.drivers.SQLServerFactory,\ + org.exolab.castor.jdo.drivers.DB2Factory,\ + org.exolab.castor.jdo.drivers.InformixFactory,\ + org.exolab.castor.jdo.drivers.HsqlFactory,\ + org.exolab.castor.jdo.drivers.InstantDBFactory,\ + org.exolab.castor.jdo.drivers.InterbaseFactory,\ + org.exolab.castor.jdo.drivers.MySQLFactory,\ + org.exolab.castor.jdo.drivers.SapDbFactory,\ + org.exolab.castor.jdo.drivers.GenericFactory,\ + org.exolab.castor.jdo.drivers.DerbyFactory,\ + org.castor.jdo.drivers.PointbaseFactory,\ + org.castor.jdo.drivers.ProgressFactory + +# List of key generator factories: +# +org.exolab.castor.jdo.keyGeneratorFactories=\ + org.exolab.castor.jdo.keygen.MaxKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.HighLowKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.IdentityKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.SequenceKeyGeneratorFactory,\ + org.exolab.castor.jdo.keygen.UUIDKeyGeneratorFactory + +# Collection handlers for the source code generator: +# +org.exolab.castor.builder.type.j2=\ + org.exolab.castor.builder.FieldInfoFactoryJ2 +org.exolab.castor.builder.type.j1=\ + org.exolab.castor.builder.FieldInfoFactory +org.exolab.castor.builder.type.odmg=\ + org.exolab.castor.builder.FieldInfoFactoryODMG30 + +# Configures the default time zone to apply to dates/times fetched from +# database fields (if not already part of the data). Specify same format as +# in java.util.TimeZone.getTimeZone, or the empty string to use the computer's +# local time zone. Please see http://de.wikipedia.org/wiki/Zeitzone for +# detailed information about time zones. +# +org.exolab.castor.jdo.defaultTimeZone= +#org.exolab.castor.jdo.defaultTimeZone=GMT-8:00 + +# List of TxSynchronizeable implementations: +# +#org.exolab.castor.persist.TxSynchronizable= + +# Sets the buffer size in bytes for fetching LOBs (this is dependent upon +# the JDBC driver implementation). The value below == 5k. +# +org.exolab.castor.jdo.lobBufferSize=5120 + +# True if database configuration should be initalization +# when loading it (default: true). +# +#org.exolab.castor.jdo.DatabaseInitializeAtLoad=true + +# True if proxy classes should be used for JDBC connections and +# prepared statements. +# Defaults to true. +# +org.exolab.castor.persist.useProxies=false + +# MappingLoader implementations: +# +org.castor.mapping.loaderFactories=\ + org.castor.mapping.JDOMappingLoaderFactory,\ + org.castor.mapping.XMLMappingLoaderFactory + +# Cache implementations: +# +org.castor.cache.Factories=\ + org.castor.cache.simple.NoCacheFactory,\ + org.castor.cache.simple.TimeLimitedFactory,\ + org.castor.cache.simple.CountLimitedFactory,\ + org.castor.cache.simple.UnlimitedFactory,\ + org.castor.cache.distributed.FKCacheFactory,\ + org.castor.cache.distributed.JcsCacheFactory,\ + org.castor.cache.distributed.JCacheFactory,\ + org.castor.cache.distributed.CoherenceCacheFactory,\ + org.castor.cache.distributed.OsCacheFactory,\ + org.castor.cache.hashbelt.FIFOHashbeltFactory,\ + org.castor.cache.hashbelt.LRUHashbeltFactory,\ + org.castor.cache.distributed.EHCacheFactory,\ + org.castor.cache.distributed.GigaspacesCacheFactory + +# TransactionManagerFactory implementations: +# +org.castor.transactionmanager.Factories=\ + org.castor.transactionmanager.WebSphereTransactionManagerFactory,\ + org.castor.transactionmanager.WebSphere5TransactionManagerFactory,\ + org.castor.transactionmanager.WebSphere51TransactionManagerFactory,\ + org.castor.transactionmanager.LocalTransactionManagerFactory,\ + org.castor.transactionmanager.JNDIENCTransactionManagerFactory,\ + org.castor.transactionmanager.JOTMTransactionManagerFactory + +# Selects whether the TransactionManager should be initialized at registration, +# or lazily when requested for the first time. +# Defaults to false. +# +org.castor.transactionmanager.InitializeAtRegistration=false + +# Instructs Castor JDO to use the JDBC 3.0-specific features to obtain +# the generated value of an identity column. +# Defaults to false. +# +org.castor.jdo.use.jdbc30=false + +# Specifies whether to use ANSI-compliant SQL for MS SQL Server. +# Defaults to false. +# +org.exolab.castor.jdo.sqlserver.ansi-compliant=false + +# Specifyies whether the ClassDescriptorResolver should (automatically) search +# for and consult with package mapping files (.castor.xml) to retrieve class +# descriptor information; on by default. +# Defaults to true. +# +#org.exolab.castor.xml.loadPackageMappings=false diff --git a/test/jalview/ws/seqfetcher/DasSequenceFetcher.java b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java new file mode 100644 index 0000000..7f82252 --- /dev/null +++ b/test/jalview/ws/seqfetcher/DasSequenceFetcher.java @@ -0,0 +1,19 @@ +package jalview.ws.seqfetcher; + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class DasSequenceFetcher +{ + + @Test + public void testDasRegistryContact() + { + jalview.bin.Cache.getDasSourceRegistry().refreshSources(); + assertTrue( + "Expected to find at least one DAS source at the registry. Check config.", + jalview.bin.Cache.getDasSourceRegistry().getSources().size() > 0); + } + +}