Java examples: AnnotateText throws FileNotFoundException

[jvendetti]

Executing the main method in AnnotateText.java throws the following exception:

java.io.FileNotFoundException: http://data.bioontology.org/ontologies/OHMI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)
	at AnnotateText.get(AnnotateText.java:97)
	at AnnotateText.printAnnotations(AnnotateText.java:50)
	at AnnotateText.main(AnnotateText.java:27)
Class details
com.fasterxml.jackson.databind.JsonMappingException: No content to map due to end-of-input
 at [Source: java.io.StringReader@6cd8737; line: 1, column: 1]
	at com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingException.java:164)
	at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:2836)
	at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:2778)
	at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:1659)
	at AnnotateText.jsonToNode(AnnotateText.java:75)
	at AnnotateText.printAnnotations(AnnotateText.java:50)
	at AnnotateText.main(AnnotateText.java:27)
Exception in thread "main" java.lang.NullPointerException
	at AnnotateText.printAnnotations(AnnotateText.java:52)
	at AnnotateText.main(AnnotateText.java:27)

[jvendetti]

The exception is thrown when the code encounters a particular class in the set of annotated classes returned for which the "self" link is invalid. Screen shot of the offending class:

Issuing the REST call for the "self" link results in the following 404 response:

"Resource 'http://purl.obolibrary.org/obo/DOID_1909' not found in ontology OHMI submission 5"

According to @mdorf, we need to regenerate BioPortal's annotator cache. There is currently no mechanism in the code that deletes class data from the annotator cache when a class that existed in previous submissions is removed in the latest submission of any given ontology.

[jvendetti]

This issue was reported again today (identical exception) by @juanlossio.

The annotator cache should be regenerated because Annotator result sets contain annotatedClass objects for which the "self" link is invalid. To observe this behavior, issue the example call to the Annotator that's provided in our REST API documentation. The first result is this annotatedClass:

Issuing a REST call for the "self" link results in a 404:

"Resource 'http://purl.obolibrary.org/obo/NCIT_C3224' not found in ontology CHEAR submission 15"