{"action":"created","issue":{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/116","repository_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml","labels_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/116/labels{/name}","comments_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/116/comments","events_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/116/events","html_url":"https://github.com/matthiaskoenig/cy3sbml/issues/116","id":166591462,"number":116,"title":"Support Combine archive files (.omex) and ResearchObjects (.ro)","user":{"login":"matthiaskoenig","id":900538,"avatar_url":"https://avatars.githubusercontent.com/u/900538?v=3","gravatar_id":"","url":"https://api.github.com/users/matthiaskoenig","html_url":"https://github.com/matthiaskoenig","followers_url":"https://api.github.com/users/matthiaskoenig/followers","following_url":"https://api.github.com/users/matthiaskoenig/following{/other_user}","gists_url":"https://api.github.com/users/matthiaskoenig/gists{/gist_id}","starred_url":"https://api.github.com/users/matthiaskoenig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthiaskoenig/subscriptions","organizations_url":"https://api.github.com/users/matthiaskoenig/orgs","repos_url":"https://api.github.com/users/matthiaskoenig/repos","events_url":"https://api.github.com/users/matthiaskoenig/events{/privacy}","received_events_url":"https://api.github.com/users/matthiaskoenig/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/milestones/12","html_url":"https://github.com/matthiaskoenig/cy3sbml/milestones/0.3.0","labels_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/milestones/12/labels","id":1902093,"number":12,"title":"0.3.0","description":"SBML package release\r\nThe missing package support will be implemented.","creator":{"login":"matthiaskoenig","id":900538,"avatar_url":"https://avatars.githubusercontent.com/u/900538?v=3","gravatar_id":"","url":"https://api.github.com/users/matthiaskoenig","html_url":"https://github.com/matthiaskoenig","followers_url":"https://api.github.com/users/matthiaskoenig/followers","following_url":"https://api.github.com/users/matthiaskoenig/following{/other_user}","gists_url":"https://api.github.com/users/matthiaskoenig/gists{/gist_id}","starred_url":"https://api.github.com/users/matthiaskoenig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthiaskoenig/subscriptions","organizations_url":"https://api.github.com/users/matthiaskoenig/orgs","repos_url":"https://api.github.com/users/matthiaskoenig/repos","events_url":"https://api.github.com/users/matthiaskoenig/events{/privacy}","received_events_url":"https://api.github.com/users/matthiaskoenig/received_events","type":"User","site_admin":false},"open_issues":9,"closed_issues":14,"state":"open","created_at":"2016-07-25T10:30:38Z","updated_at":"2016-08-19T14:07:49Z","due_on":"2016-08-14T00:00:00Z","closed_at":null},"comments":8,"created_at":"2016-07-20T14:12:41Z","updated_at":"2016-08-19T17:09:26Z","closed_at":null,"body":"Allow to read all SBML files from a given OMEX file.\r\nNecessary to register an additional file filter for `*.omex` and read the SBML files from the manifest file.\r\n"},"comment":{"url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/comments/241076432","html_url":"https://github.com/matthiaskoenig/cy3sbml/issues/116#issuecomment-241076432","issue_url":"https://api.github.com/repos/matthiaskoenig/cy3sbml/issues/116","id":241076432,"user":{"login":"matthiaskoenig","id":900538,"avatar_url":"https://avatars.githubusercontent.com/u/900538?v=3","gravatar_id":"","url":"https://api.github.com/users/matthiaskoenig","html_url":"https://github.com/matthiaskoenig","followers_url":"https://api.github.com/users/matthiaskoenig/followers","following_url":"https://api.github.com/users/matthiaskoenig/following{/other_user}","gists_url":"https://api.github.com/users/matthiaskoenig/gists{/gist_id}","starred_url":"https://api.github.com/users/matthiaskoenig/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthiaskoenig/subscriptions","organizations_url":"https://api.github.com/users/matthiaskoenig/orgs","repos_url":"https://api.github.com/users/matthiaskoenig/repos","events_url":"https://api.github.com/users/matthiaskoenig/events{/privacy}","received_events_url":"https://api.github.com/users/matthiaskoenig/received_events","type":"User","site_admin":false},"created_at":"2016-08-19T17:09:26Z","updated_at":"2016-08-19T17:09:26Z","body":"Some update:\r\nFinally got the Maven dependencies running. The trick is to split up the jena-osgi bundle and than import the components while including and updating the compontents.\r\n\r\nInstead of\r\n```\r\n<dependency>\r\n            <groupId>org.apache.taverna.language</groupId>\r\n            <artifactId>taverna-robundle</artifactId>\r\n            <version>0.15.1-incubating</version>\r\n</dependency>\r\n```\r\n\r\n```\r\n<dependency>\r\n            <groupId>org.apache.taverna.language</groupId>\r\n            <artifactId>taverna-robundle</artifactId>\r\n            <version>0.15.1-incubating</version>\r\n            <exclusions>\r\n                <exclusion>\r\n                    <groupId>org.slf4j</groupId>\r\n                    <artifactId>slf4j-log4j12</artifactId>\r\n                </exclusion>\r\n                <exclusion>\r\n                    <groupId>org.slf4j</groupId>\r\n                    <artifactId>jcl-over-slf4j</artifactId>\r\n                </exclusion>\r\n                <!-- problems with newer OSGI and necessary to split in components\r\n                     for exclusion of xerces -->\r\n                <exclusion>\r\n                    <groupId>org.apache.jena</groupId>\r\n                    <artifactId>jena-osgi</artifactId>\r\n                </exclusion>\r\n            </exclusions>\r\n        </dependency>\r\n\r\n        <!-- include split components -->\r\n        <dependency>\r\n            <groupId>org.apache.jena</groupId>\r\n            <artifactId>jena-core</artifactId>\r\n            <version>3.1.0</version>\r\n            <exclusions>\r\n                <exclusion>\r\n                <groupId>xerces</groupId>\r\n                <artifactId>xercesImpl</artifactId>\r\n                </exclusion>\r\n            </exclusions>\r\n        </dependency>\r\n        <dependency>\r\n            <groupId>xerces</groupId>\r\n            <artifactId>xercesImpl</artifactId>\r\n            <version>2.11.0</version>\r\n            <scope>provided</scope>\r\n        </dependency>\r\n\r\n        <dependency>\r\n            <groupId>org.apache.jena</groupId>\r\n            <artifactId>jena-arq</artifactId>\r\n            <version>3.1.0</version>\r\n        </dependency>\r\n        <dependency>\r\n            <groupId>org.apache.jena</groupId>\r\n            <artifactId>jena-iri</artifactId>\r\n            <version>3.1.0</version>\r\n        </dependency>\r\n        <dependency>\r\n            <groupId>org.apache.jena</groupId>\r\n            <artifactId>jena-tdb</artifactId>\r\n            <version>3.1.0</version>\r\n        </dependency>\r\n        <!--\r\n        Update dependencies to fix:\r\n        https://issues.apache.org/jira/browse/JENA-1178\r\n        -->\r\n        <dependency>\r\n            <groupId>org.apache.httpcomponents</groupId>\r\n            <artifactId>httpclient</artifactId>\r\n            <version>4.5.2</version>\r\n        </dependency>\r\n        <dependency>\r\n            <groupId>org.apache.httpcomponents</groupId>\r\n            <artifactId>httpclient-cache</artifactId>\r\n            <version>4.5.2</version>\r\n        </dependency>\r\n        <dependency>\r\n            <groupId>com.github.jsonld-java</groupId>\r\n            <artifactId>jsonld-java</artifactId>\r\n            <version>0.8.3</version>\r\n        </dependency>\r\n```"}}
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