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OpenTreeOfLife / oti

indexing service for the OpenTreeOfLife nexson repository
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Uninformative error message 'ArrayIndexOutOfBoundsException' #25

Closed jar398 closed 10 years ago

jar398 commented 10 years ago

There aren't even any numbers in the request.

curl -X POST http://api.opentreeoflife.org/oti/v1/singlePropertySearchForStudies -d '{"property": "ot:studyId", "value" : "pg_1707"}' { "message" : "1", "exception" : "ArrayIndexOutOfBoundsException", "fullname" : "java.lang.ArrayIndexOutOfBoundsException", "stacktrace" : [ "org.neo4j.server.rest.repr.formats.UrlFormFormat.readMap(UrlFormFormat.java:99)", "org.neo4j.server.rest.repr.RepresentationFormat.readParameterList(RepresentationFormat.java:97)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]

chinchliff commented 10 years ago

It's because you're missing the -H "content-type:application/json" argument to curl. A very annoying error, I agree. Not one I think we have much ability to affect from within the neo4j plugin extensions though.

On Thu, Aug 28, 2014 at 3:20 PM, Jonathan A Rees notifications@github.com wrote:

There aren't even any numbers in the request.

curl -X POST http://api.opentreeoflife.org/oti/v1/singlePropertySearchForStudies -d '{"property": "ot:studyId", "value" : "pg_1707"}' { "message" : "1", "exception" : "ArrayIndexOutOfBoundsException", "fullname" : "java.lang.ArrayIndexOutOfBoundsException", "stacktrace" : [ "org.neo4j.server.rest.repr.formats.UrlFormFormat.readMap(UrlFormFormat.java:99)", "org.neo4j.server.rest.repr.RepresentationFormat.readParameterList(RepresentationFormat.java:97)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/oti/issues/25.

chinchliff commented 10 years ago

You'll also need to use devapi, as the production server seems to still be using an oti version with bug that Jim tracked down a few weeks ago. This should work:

curl -X POST http://devapi.opentreeoflife.org/oti/v1/singlePropertySearchForStudies -H "content-type:application/json" -d '{"property": "ot:studyId", "value" : "pg_1707"}'

On Thu, Aug 28, 2014 at 3:45 PM, Cody Hinchliff cody.hinchliff@gmail.com wrote:

It's because you're missing the -H "content-type:application/json" argument to curl. A very annoying error, I agree. Not one I think we have much ability to affect from within the neo4j plugin extensions though.

On Thu, Aug 28, 2014 at 3:20 PM, Jonathan A Rees <notifications@github.com

wrote:

There aren't even any numbers in the request.

curl -X POST http://api.opentreeoflife.org/oti/v1/singlePropertySearchForStudies -d '{"property": "ot:studyId", "value" : "pg_1707"}' { "message" : "1", "exception" : "ArrayIndexOutOfBoundsException", "fullname" : "java.lang.ArrayIndexOutOfBoundsException", "stacktrace" : [ "org.neo4j.server.rest.repr.formats.UrlFormFormat.readMap(UrlFormFormat.java:99)", "org.neo4j.server.rest.repr.RepresentationFormat.readParameterList(RepresentationFormat.java:97)", "org.neo4j.server.rest.web.ExtensionService.invokeGraphDatabaseExtension(ExtensionService.java:122)", "java.lang.reflect.Method.invoke(Method.java:606)", "org.neo4j.server.rest.security.SecurityFilter.doFilter(SecurityFilter.java:112)" ]

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/oti/issues/25.

jar398 commented 10 years ago

Thanks!

jimallman commented 10 years ago

Yes, that's a hideous error from (iirc) neo4j. In this case, your call is missing the Content-Type header:

curl -X POST http://devapi.opentreeoflife.org/oti/v1/singlePropertySearchForStudies \
  -d '{"property": "ot:studyId", "value" : "pg_1707"}' \
  -H "Content-Type: application/json"

EDIT: I had reported another (underlying) error, but that was due to my test calling api.opentreeoflife.org. devapi should give a good result.

chinchliff commented 10 years ago

@jimallman, it's the same bug you tracked down before. The fix just hasn't been pushed to production yet.

On Thu, Aug 28, 2014 at 3:51 PM, Jim Allman notifications@github.com wrote:

Yes, that's a hideous error from (iirc) neo4j. In this case, your call is missing the Content-Type header:

curl -X POST http://api.opentreeoflife.org/oti/v1/singlePropertySearchForStudies \ -d '{"property": "ot:studyId", "value" : "pg_1707"}' \ -H "Content-Type: application/json"

This call now returns a more sensible error message, though I'm not sure why. (We had a similar problem with the indexing of ot:studyId properties, but this is now working in our tests for duplicate studies.)

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/oti/issues/25#issuecomment-53786266.