tarrow/ami-plugin

ami-plugin's Issues

resNotFiles fails in practice.

vagrant@vagrant-ubuntu-trusty-64:~$ ~/ami-plugin/target/appassembler/bin/ami2-gene -q zika -i scholarly.html --g.gene --g.type human
java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:993)
at org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:889)
at org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:870)
at org.xmlcml.ami2.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:163)
at org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:1054)
at org.xmlcml.ami2.plugins.gene.GenePlugin.main(GenePlugin.java:36)
Caused by: java.lang.RuntimeException: Cannot read HGNC file: src/main/resources/org/xmlcml/ami2/plugins/gene/hgnc/hgnc_complete_set.json
at org.xmlcml.ami2.dictionary.gene.HGNCDictionary.readHGNCJson(HGNCDictionary.java:84)
at org.xmlcml.ami2.dictionary.gene.HGNCDictionary.readHGNCXML(HGNCDictionary.java:59)
at org.xmlcml.ami2.dictionary.gene.HGNCDictionary.init(HGNCDictionary.java:54)
at org.xmlcml.ami2.dictionary.gene.HGNCDictionary.(HGNCDictionary.java:50)
at org.xmlcml.ami2.plugins.gene.GeneArgProcessor.getOrCreateCurrentDictionary(GeneArgProcessor.java:113)
at org.xmlcml.ami2.plugins.AMISearcher.getOrCreateCurrentDictionary(AMISearcher.java:289)
at org.xmlcml.ami2.plugins.AMISearcher.search(AMISearcher.java:284)
at org.xmlcml.ami2.plugins.AMIArgProcessor.searchSectionElements(AMIArgProcessor.java:286)
at org.xmlcml.ami2.plugins.gene.GeneArgProcessor.runExtractGene(GeneArgProcessor.java:64)
... 10 more
Caused by: java.lang.RuntimeException: cannot parse/read stream:
at org.xmlcml.xml.XMLUtil.parseQuietlyToDocument(XMLUtil.java:1075)
at org.xmlcml.cmine.lookup.DefaultStringDictionary.createFromInputStream(DefaultStringDictionary.java:51)
at org.xmlcml.ami2.dictionary.gene.HGNCDictionary.readHGNCJson(HGNCDictionary.java:69)
... 18 more
Caused by: java.lang.NullPointerException: Null InputStream
at nu.xom.Builder.build(Unknown Source)
at org.xmlcml.xml.XMLUtil.parseQuietlyToDocument(XMLUtil.java:1073)
... 20 more
0 [main] DEBUG org.xmlcml.cmine.args.DefaultArgProcessor - or --g.gene; (0,0); null; STRING: null / null; null; null

Need to check why or how we should make this? Shouldn't the xml be there already?