diff --git a/common-bundles/commons-collections-3.2.1.jar b/common-bundles/commons-collections-3.2.1.jar
new file mode 100644
index 000000000..c35fa1fee
Binary files /dev/null and b/common-bundles/commons-collections-3.2.1.jar differ
diff --git a/common-bundles/javax.activation_1.1.0.v201105071233.jar b/common-bundles/javax.activation_1.1.0.v201105071233.jar
new file mode 100644
index 000000000..cb3591344
Binary files /dev/null and b/common-bundles/javax.activation_1.1.0.v201105071233.jar differ
diff --git a/org.bridgedb.webservice.cronos/META-INF/MANIFEST.MF b/org.bridgedb.webservice.cronos/META-INF/MANIFEST.MF
index 3de8a4a9e..fe7a4cd70 100644
--- a/org.bridgedb.webservice.cronos/META-INF/MANIFEST.MF
+++ b/org.bridgedb.webservice.cronos/META-INF/MANIFEST.MF
@@ -3,132 +3,6 @@ Bundle-ManifestVersion: 2
Bundle-Name: Cronos
Bundle-SymbolicName: org.bridgedb.webservice.cronos
Bundle-Version: 1.1.0
-Bundle-ClassPath: cronos.jar,
- lib/axis-1_4/lib/axis-ant.jar,
- lib/axis-1_4/lib/axis.jar,
- lib/axis-1_4/lib/commons-discovery-0.2.jar,
- lib/axis-1_4/lib/commons-logging-1.0.4.jar,
- lib/axis-1_4/lib/jaxrpc.jar,
- lib/axis-1_4/lib/log4j-1.2.8.jar,
- lib/axis-1_4/lib/saaj.jar,
- lib/axis-1_4/lib/wsdl4j-1.5.1.jar
-Export-Package: com.ibm.wsdl,
- com.ibm.wsdl.extensions,
- com.ibm.wsdl.extensions.http,
- com.ibm.wsdl.extensions.mime,
- com.ibm.wsdl.extensions.schema,
- com.ibm.wsdl.extensions.soap,
- com.ibm.wsdl.factory,
- com.ibm.wsdl.util,
- com.ibm.wsdl.util.xml,
- com.ibm.wsdl.xml,
- javax.wsdl,
- javax.wsdl.extensions,
- javax.wsdl.extensions.http,
- javax.wsdl.extensions.mime,
- javax.wsdl.extensions.schema,
- javax.wsdl.extensions.soap,
- javax.wsdl.factory,
- javax.wsdl.xml,
- javax.xml.messaging,
- javax.xml.namespace,
- javax.xml.rpc,
- javax.xml.rpc.encoding,
- javax.xml.rpc.handler,
- javax.xml.rpc.handler.soap,
- javax.xml.rpc.holders,
- javax.xml.rpc.server,
- javax.xml.rpc.soap,
- javax.xml.soap,
- org.apache.axis,
- org.apache.axis.attachments,
- org.apache.axis.client,
- org.apache.axis.client.async,
- org.apache.axis.collections,
- org.apache.axis.components.compiler,
- org.apache.axis.components.encoding,
- org.apache.axis.components.image,
- org.apache.axis.components.jms,
- org.apache.axis.components.logger,
- org.apache.axis.components.net,
- org.apache.axis.components.script,
- org.apache.axis.components.threadpool,
- org.apache.axis.components.uuid,
- org.apache.axis.configuration,
- org.apache.axis.constants,
- org.apache.axis.deployment.wsdd,
- org.apache.axis.deployment.wsdd.providers,
- org.apache.axis.description,
- org.apache.axis.encoding,
- org.apache.axis.encoding.ser,
- org.apache.axis.encoding.ser.castor,
- org.apache.axis.handlers,
- org.apache.axis.handlers.http,
- org.apache.axis.handlers.soap,
- org.apache.axis.holders,
- org.apache.axis.i18n,
- org.apache.axis.management,
- org.apache.axis.management.jmx,
- org.apache.axis.message,
- org.apache.axis.monitor,
- org.apache.axis.providers,
- org.apache.axis.providers.java,
- org.apache.axis.schema,
- org.apache.axis.security,
- org.apache.axis.security.servlet,
- org.apache.axis.security.simple,
- org.apache.axis.server,
- org.apache.axis.session,
- org.apache.axis.soap,
- org.apache.axis.strategies,
- org.apache.axis.tools.ant.axis,
- org.apache.axis.tools.ant.foreach,
- org.apache.axis.tools.ant.wsdl,
- org.apache.axis.transport.http,
- org.apache.axis.transport.java,
- org.apache.axis.transport.jms,
- org.apache.axis.transport.local,
- org.apache.axis.transport.mail,
- org.apache.axis.types,
- org.apache.axis.utils,
- org.apache.axis.utils.bytecode,
- org.apache.axis.utils.cache,
- org.apache.axis.wsdl,
- org.apache.axis.wsdl.fromJava,
- org.apache.axis.wsdl.gen,
- org.apache.axis.wsdl.symbolTable,
- org.apache.axis.wsdl.toJava,
- org.apache.commons.discovery,
- org.apache.commons.discovery.ant,
- org.apache.commons.discovery.jdk,
- org.apache.commons.discovery.log,
- org.apache.commons.discovery.resource,
- org.apache.commons.discovery.resource.classes,
- org.apache.commons.discovery.resource.names,
- org.apache.commons.discovery.tools,
- org.apache.commons.logging,
- org.apache.commons.logging.impl,
- org.apache.log4j,
- org.apache.log4j.chainsaw,
- org.apache.log4j.config,
- org.apache.log4j.helpers,
- org.apache.log4j.jdbc,
- org.apache.log4j.jmx,
- org.apache.log4j.lf5,
- org.apache.log4j.lf5.config,
- org.apache.log4j.lf5.util,
- org.apache.log4j.lf5.viewer,
- org.apache.log4j.lf5.viewer.categoryexplorer,
- org.apache.log4j.lf5.viewer.configure,
- org.apache.log4j.lf5.viewer.images,
- org.apache.log4j.net,
- org.apache.log4j.nt,
- org.apache.log4j.or,
- org.apache.log4j.or.jms,
- org.apache.log4j.or.sax,
- org.apache.log4j.spi,
- org.apache.log4j.varia,
- org.apache.log4j.xml,
- org.bridgedb.webservice.cronos
+Export-Package: org.bridgedb.webservice.cronos
Require-Bundle: org.bridgedb;bundle-version="1.1.0",
org.bridgedb.bio;bundle-version="1.1.0"
diff --git a/org.bridgedb.webservice.picr/.classpath b/org.bridgedb.webservice.picr/.classpath
index 2ca59f1f3..8320d31a9 100644
--- a/org.bridgedb.webservice.picr/.classpath
+++ b/org.bridgedb.webservice.picr/.classpath
@@ -4,8 +4,6 @@
-
-
diff --git a/org.bridgedb.webservice.picr/META-INF/MANIFEST.MF b/org.bridgedb.webservice.picr/META-INF/MANIFEST.MF
index bbe738387..fa56c3daa 100644
--- a/org.bridgedb.webservice.picr/META-INF/MANIFEST.MF
+++ b/org.bridgedb.webservice.picr/META-INF/MANIFEST.MF
@@ -3,293 +3,7 @@ Bundle-ManifestVersion: 2
Bundle-Name: Picr
Bundle-SymbolicName: org.bridgedb.webservice.picr
Bundle-Version: 1.1.0
-Bundle-ClassPath: picr.jar,
- lib/activation-1.1.jar,
- lib/commons-collections-3.2.jar,
- lib/jaxb-api-2.1.jar,
- lib/jaxb-impl-2.1.2.jar,
- lib/jaxb-xjc-2.1.2.jar,
- lib/jaxws-api-2.1.jar,
- lib/jaxws-rt-2.1.jar,
- lib/jaxws-tools-2.1.jar,
- lib/jsr173_api-1.0.jar,
- lib/jsr181-api-1.0-MR1.jar,
- lib/jsr250-api-1.0.jar,
- lib/resolver.jar,
- lib/saaj-api-1.3.jar,
- lib/sjsxp-SNAPSHOT.jar,
- lib/stax-api-1.0.jar,
- lib/stax-ex-1.0.jar,
- lib/streambuffer-0.4.jar,
- lib/xfire-jsr181-api-1.0-M1.jar,
- lib/saaj-impl-1.3.2.jar
-Export-Package: com.sun.activation.registries,
- com.sun.activation.viewers,
- com.sun.codemodel,
- com.sun.codemodel.fmt,
- com.sun.codemodel.util,
- com.sun.codemodel.writer,
- com.sun.dtdparser,
- com.sun.istack,
- com.sun.istack.tools,
- com.sun.istack.ws,
- com.sun.org.apache.xml.internal.resolver,
- com.sun.org.apache.xml.internal.resolver.helpers,
- com.sun.org.apache.xml.internal.resolver.readers,
- com.sun.org.apache.xml.internal.resolver.tools,
- com.sun.tools.jxc,
- com.sun.tools.jxc.apt,
- com.sun.tools.jxc.gen.config,
- com.sun.tools.jxc.model.nav,
- com.sun.tools.resourcegen,
- com.sun.tools.ws,
- com.sun.tools.ws.ant,
- com.sun.tools.ws.api,
- com.sun.tools.ws.api.wsdl,
- com.sun.tools.ws.processor,
- com.sun.tools.ws.processor.generator,
- com.sun.tools.ws.processor.model,
- com.sun.tools.ws.processor.model.exporter,
- com.sun.tools.ws.processor.model.java,
- com.sun.tools.ws.processor.model.jaxb,
- com.sun.tools.ws.processor.modeler,
- com.sun.tools.ws.processor.modeler.annotation,
- com.sun.tools.ws.processor.modeler.wsdl,
- com.sun.tools.ws.processor.util,
- com.sun.tools.ws.resources,
- com.sun.tools.ws.spi,
- com.sun.tools.ws.util,
- com.sun.tools.ws.util.xml,
- com.sun.tools.ws.wscompile,
- com.sun.tools.ws.wsdl.document,
- com.sun.tools.ws.wsdl.document.http,
- com.sun.tools.ws.wsdl.document.jaxws,
- com.sun.tools.ws.wsdl.document.mime,
- com.sun.tools.ws.wsdl.document.schema,
- com.sun.tools.ws.wsdl.document.soap,
- com.sun.tools.ws.wsdl.framework,
- com.sun.tools.ws.wsdl.parser,
- com.sun.tools.xjc,
- com.sun.tools.xjc.addon.at_generated,
- com.sun.tools.xjc.addon.code_injector,
- com.sun.tools.xjc.addon.episode,
- com.sun.tools.xjc.addon.locator,
- com.sun.tools.xjc.addon.sync,
- com.sun.tools.xjc.api,
- com.sun.tools.xjc.api.impl.j2s,
- com.sun.tools.xjc.api.impl.s2j,
- com.sun.tools.xjc.api.util,
- com.sun.tools.xjc.generator.annotation.ri,
- com.sun.tools.xjc.generator.annotation.spec,
- com.sun.tools.xjc.generator.bean,
- com.sun.tools.xjc.generator.bean.field,
- com.sun.tools.xjc.generator.util,
- com.sun.tools.xjc.model,
- com.sun.tools.xjc.model.nav,
- com.sun.tools.xjc.outline,
- com.sun.tools.xjc.reader,
- com.sun.tools.xjc.reader.dtd,
- com.sun.tools.xjc.reader.dtd.bindinfo,
- com.sun.tools.xjc.reader.gbind,
- com.sun.tools.xjc.reader.internalizer,
- com.sun.tools.xjc.reader.relaxng,
- com.sun.tools.xjc.reader.xmlschema,
- com.sun.tools.xjc.reader.xmlschema.bindinfo,
- com.sun.tools.xjc.reader.xmlschema.ct,
- com.sun.tools.xjc.reader.xmlschema.parser,
- com.sun.tools.xjc.runtime,
- com.sun.tools.xjc.util,
- com.sun.tools.xjc.writer,
- com.sun.xml.bind,
- com.sun.xml.bind.annotation,
- com.sun.xml.bind.api,
- com.sun.xml.bind.api.impl,
- com.sun.xml.bind.marshaller,
- com.sun.xml.bind.unmarshaller,
- com.sun.xml.bind.util,
- com.sun.xml.bind.v2,
- com.sun.xml.bind.v2.bytecode,
- com.sun.xml.bind.v2.model.annotation,
- com.sun.xml.bind.v2.model.core,
- com.sun.xml.bind.v2.model.impl,
- com.sun.xml.bind.v2.model.nav,
- com.sun.xml.bind.v2.model.runtime,
- com.sun.xml.bind.v2.runtime,
- com.sun.xml.bind.v2.runtime.output,
- com.sun.xml.bind.v2.runtime.property,
- com.sun.xml.bind.v2.runtime.reflect,
- com.sun.xml.bind.v2.runtime.reflect.opt,
- com.sun.xml.bind.v2.runtime.unmarshaller,
- com.sun.xml.bind.v2.schemagen,
- com.sun.xml.bind.v2.schemagen.episode,
- com.sun.xml.bind.v2.schemagen.xmlschema,
- com.sun.xml.bind.v2.util,
- com.sun.xml.dtdparser,
- com.sun.xml.dtdparser.resources,
- com.sun.xml.messaging.saaj,
- com.sun.xml.messaging.saaj.client.p2p,
- com.sun.xml.messaging.saaj.packaging.mime,
- com.sun.xml.messaging.saaj.packaging.mime.internet,
- com.sun.xml.messaging.saaj.packaging.mime.util,
- com.sun.xml.messaging.saaj.soap,
- com.sun.xml.messaging.saaj.soap.dynamic,
- com.sun.xml.messaging.saaj.soap.impl,
- com.sun.xml.messaging.saaj.soap.name,
- com.sun.xml.messaging.saaj.soap.ver1_1,
- com.sun.xml.messaging.saaj.soap.ver1_2,
- com.sun.xml.messaging.saaj.util,
- com.sun.xml.messaging.saaj.util.transform,
- com.sun.xml.stream,
- com.sun.xml.stream.buffer,
- com.sun.xml.stream.buffer.sax,
- com.sun.xml.stream.buffer.stax,
- com.sun.xml.stream.dtd,
- com.sun.xml.stream.dtd.nonvalidating,
- com.sun.xml.stream.events,
- com.sun.xml.stream.util,
- com.sun.xml.stream.writers,
- com.sun.xml.stream.xerces.impl.io,
- com.sun.xml.stream.xerces.impl.msg,
- com.sun.xml.stream.xerces.util,
- com.sun.xml.stream.xerces.xni,
- com.sun.xml.stream.xerces.xni.parser,
- com.sun.xml.txw2,
- com.sun.xml.txw2.annotation,
- com.sun.xml.txw2.output,
- com.sun.xml.ws,
- com.sun.xml.ws.addressing,
- com.sun.xml.ws.addressing.model,
- com.sun.xml.ws.addressing.v200408,
- com.sun.xml.ws.api,
- com.sun.xml.ws.api.addressing,
- com.sun.xml.ws.api.client,
- com.sun.xml.ws.api.fastinfoset,
- com.sun.xml.ws.api.message,
- com.sun.xml.ws.api.message.stream,
- com.sun.xml.ws.api.model,
- com.sun.xml.ws.api.model.soap,
- com.sun.xml.ws.api.model.wsdl,
- com.sun.xml.ws.api.pipe,
- com.sun.xml.ws.api.pipe.helper,
- com.sun.xml.ws.api.server,
- com.sun.xml.ws.api.streaming,
- com.sun.xml.ws.api.wsdl.parser,
- com.sun.xml.ws.api.wsdl.writer,
- com.sun.xml.ws.binding,
- com.sun.xml.ws.client,
- com.sun.xml.ws.client.dispatch,
- com.sun.xml.ws.client.sei,
- com.sun.xml.ws.developer,
- com.sun.xml.ws.developer.servlet,
- com.sun.xml.ws.encoding,
- com.sun.xml.ws.encoding.fastinfoset,
- com.sun.xml.ws.encoding.soap,
- com.sun.xml.ws.encoding.soap.streaming,
- com.sun.xml.ws.encoding.xml,
- com.sun.xml.ws.fault,
- com.sun.xml.ws.handler,
- com.sun.xml.ws.message,
- com.sun.xml.ws.message.jaxb,
- com.sun.xml.ws.message.saaj,
- com.sun.xml.ws.message.source,
- com.sun.xml.ws.message.stream,
- com.sun.xml.ws.model,
- com.sun.xml.ws.model.soap,
- com.sun.xml.ws.model.wsdl,
- com.sun.xml.ws.protocol.soap,
- com.sun.xml.ws.protocol.xml,
- com.sun.xml.ws.resources,
- com.sun.xml.ws.server,
- com.sun.xml.ws.server.provider,
- com.sun.xml.ws.server.sei,
- com.sun.xml.ws.server.servlet,
- com.sun.xml.ws.spi,
- com.sun.xml.ws.streaming,
- com.sun.xml.ws.transport,
- com.sun.xml.ws.transport.http,
- com.sun.xml.ws.transport.http.client,
- com.sun.xml.ws.transport.http.server,
- com.sun.xml.ws.transport.http.servlet,
- com.sun.xml.ws.util,
- com.sun.xml.ws.util.exception,
- com.sun.xml.ws.util.localization,
- com.sun.xml.ws.util.pipe,
- com.sun.xml.ws.util.resources,
- com.sun.xml.ws.util.xml,
- com.sun.xml.ws.wsdl.parser,
- com.sun.xml.ws.wsdl.writer,
- com.sun.xml.ws.wsdl.writer.document,
- com.sun.xml.ws.wsdl.writer.document.http,
- com.sun.xml.ws.wsdl.writer.document.soap,
- com.sun.xml.ws.wsdl.writer.document.soap12,
- com.sun.xml.ws.wsdl.writer.document.xsd,
- com.sun.xml.xsom,
- com.sun.xml.xsom.impl,
- com.sun.xml.xsom.impl.parser,
- com.sun.xml.xsom.impl.parser.state,
- com.sun.xml.xsom.impl.scd,
- com.sun.xml.xsom.impl.util,
- com.sun.xml.xsom.parser,
- com.sun.xml.xsom.util,
- com.sun.xml.xsom.visitor,
- data,
- javax.activation,
- javax.annotation,
- javax.annotation.security,
- javax.jws,
- javax.jws.soap,
- javax.xml,
- javax.xml.bind,
- javax.xml.bind.annotation,
- javax.xml.bind.annotation.adapters,
- javax.xml.bind.attachment,
- javax.xml.bind.helpers,
- javax.xml.bind.util,
- javax.xml.namespace,
- javax.xml.soap,
- javax.xml.stream,
- javax.xml.stream.events,
- javax.xml.stream.util,
- javax.xml.ws,
- javax.xml.ws.handler,
- javax.xml.ws.handler.soap,
- javax.xml.ws.http,
- javax.xml.ws.soap,
- javax.xml.ws.spi,
- javax.xml.ws.wsaddressing,
- org.apache.commons.collections,
- org.apache.commons.collections.bag,
- org.apache.commons.collections.bidimap,
- org.apache.commons.collections.buffer,
- org.apache.commons.collections.collection,
- org.apache.commons.collections.comparators,
- org.apache.commons.collections.functors,
- org.apache.commons.collections.iterators,
- org.apache.commons.collections.keyvalue,
- org.apache.commons.collections.list,
- org.apache.commons.collections.map,
- org.apache.commons.collections.set,
- org.bridgedb.webservice.picr,
- org.jvnet.staxex,
- org.kohsuke.rngom.ast.builder,
- org.kohsuke.rngom.ast.om,
- org.kohsuke.rngom.ast.util,
- org.kohsuke.rngom.binary,
- org.kohsuke.rngom.binary.visitor,
- org.kohsuke.rngom.digested,
- org.kohsuke.rngom.dt,
- org.kohsuke.rngom.dt.builtin,
- org.kohsuke.rngom.nc,
- org.kohsuke.rngom.parse,
- org.kohsuke.rngom.parse.compact,
- org.kohsuke.rngom.parse.host,
- org.kohsuke.rngom.parse.xml,
- org.kohsuke.rngom.util,
- org.kohsuke.rngom.xml.sax,
- org.kohsuke.rngom.xml.util,
- org.relaxng.datatype,
- org.relaxng.datatype.helpers,
- uk.ac.ebi.demo.picr.business,
- uk.ac.ebi.demo.picr.soap,
- uk.ac.ebi.demo.picr.swing
-Require-Bundle: org.bridgedb;bundle-version="1.1.0"
+Export-Package: org.bridgedb.webservice.picr
+Require-Bundle: org.bridgedb;bundle-version="1.1.0",
+ org.apache.commons.collections;bundle-version="3.2.1",
+ javax.activation;bundle-version="1.1.0"
diff --git a/org.bridgedb.webservice.picr/build.xml b/org.bridgedb.webservice.picr/build.xml
index 09e7f47e6..16c37e4f5 100644
--- a/org.bridgedb.webservice.picr/build.xml
+++ b/org.bridgedb.webservice.picr/build.xml
@@ -8,6 +8,10 @@
+
+
+
+
@@ -20,7 +24,9 @@
-
+
+
+
diff --git a/org.bridgedb.webservice.picr/lib/activation-1.1.jar b/org.bridgedb.webservice.picr/lib/activation-1.1.jar
deleted file mode 100644
index 53f82a1c4..000000000
Binary files a/org.bridgedb.webservice.picr/lib/activation-1.1.jar and /dev/null differ
diff --git a/org.bridgedb.webservice.picr/lib/commons-collections-3.2.jar b/org.bridgedb.webservice.picr/lib/commons-collections-3.2.jar
deleted file mode 100644
index 75580be25..000000000
Binary files a/org.bridgedb.webservice.picr/lib/commons-collections-3.2.jar and /dev/null differ
diff --git a/org.bridgedb.webservice.synergizer/META-INF/MANIFEST.MF b/org.bridgedb.webservice.synergizer/META-INF/MANIFEST.MF
index 9eb17a399..71ab562d6 100644
--- a/org.bridgedb.webservice.synergizer/META-INF/MANIFEST.MF
+++ b/org.bridgedb.webservice.synergizer/META-INF/MANIFEST.MF
@@ -3,9 +3,5 @@ Bundle-ManifestVersion: 2
Bundle-Name: Synergizer
Bundle-SymbolicName: org.bridgedb.webservice.synergizer
Bundle-Version: 1.1.0
-Bundle-ClassPath: synergizer.jar,
- lib/synergizer.jar
-Export-Package: org.bridgedb.webservice.synergizer,
- org.json,
- synergizer
+Export-Package: org.bridgedb.webservice.synergizer
Require-Bundle: org.bridgedb;bundle-version="1.1.0"
diff --git a/org.bridgedb.webservice.synergizer/build.xml b/org.bridgedb.webservice.synergizer/build.xml
index 5d4398804..0b7154b52 100644
--- a/org.bridgedb.webservice.synergizer/build.xml
+++ b/org.bridgedb.webservice.synergizer/build.xml
@@ -21,7 +21,9 @@
-
+
+
+