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 @@ - + + +