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JBEI / ice

Web based Registry platform for managing synthetic biological parts
https://public-registry.jbei.org
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JBEI registry does not produce .gb files for specific registry entry #3

Closed ceiben closed 10 years ago

ceiben commented 10 years ago

To reproduce bug: Go to https://registry.jbei.org/#page=entry;id=25125 (plasmid name is pSY61_His_LIPS_LAT-LACP if you need to search the registry for it instead). On the header that says "Sequence" there are three options ["Open in VectorEditor" | Download | Hide Pigeon Image]. Select Download The browser will go to a new page, but a download pop up will never appear.

Tried opening in vector editor to download there. In this case I can download a .gb file, but it has nothing in it. There is clearly sequence and annotations visible in the registry, so it seems like something goes wrong when it tries to convert it to .gb format.

Sidenote: the 'a' in 'Download' appears to be a roman character and not the typical 'a' (on my screen anyway)

hplahar commented 10 years ago

stack trace:

java.lang.IllegalArgumentException: Must have at least two members at org.biojavax.bio.seq.CompoundRichLocation.(CompoundRichLocation.java:103) at org.biojavax.bio.seq.CompoundRichLocation.(CompoundRichLocation.java:84) at org.jbei.ice.lib.composers.formatters.GenbankFormatter.format(GenbankFormatter.java:165) at org.jbei.ice.lib.entry.sequence.SequenceController.compose(SequenceController.java:225) at org.jbei.ice.server.servlet.SequenceDownloadServlet.getGenbank(SequenceDownloadServlet.java:165) at org.jbei.ice.server.servlet.SequenceDownloadServlet.doGet(SequenceDownloadServlet.java:82) at javax.servlet.http.HttpServlet.service(HttpServlet.java:617) at javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.jbei.ice.server.servlet.filter.IceFilter.doFilter(IceFilter.java:33) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:563) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:615) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859) at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602) at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489) at java.lang.Thread.run(Thread.java:745)