{"action":"opened","issue":{"url":"https://api.github.com/repos/petermr/norma/issues/11","labels_url":"https://api.github.com/repos/petermr/norma/issues/11/labels{/name}","comments_url":"https://api.github.com/repos/petermr/norma/issues/11/comments","events_url":"https://api.github.com/repos/petermr/norma/issues/11/events","html_url":"https://github.com/petermr/norma/issues/11","id":93736199,"number":11,"title":"Problems with newest version of norma (from Jenkins)","user":{"login":"rossmounce","id":824120,"avatar_url":"https://avatars.githubusercontent.com/u/824120?v=3","gravatar_id":"","url":"https://api.github.com/users/rossmounce","html_url":"https://github.com/rossmounce","followers_url":"https://api.github.com/users/rossmounce/followers","following_url":"https://api.github.com/users/rossmounce/following{/other_user}","gists_url":"https://api.github.com/users/rossmounce/gists{/gist_id}","starred_url":"https://api.github.com/users/rossmounce/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rossmounce/subscriptions","organizations_url":"https://api.github.com/users/rossmounce/orgs","repos_url":"https://api.github.com/users/rossmounce/repos","events_url":"https://api.github.com/users/rossmounce/events{/privacy}","received_events_url":"https://api.github.com/users/rossmounce/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-07-08T08:48:18Z","updated_at":"2015-07-08T08:48:18Z","closed_at":null,"body":"Version of norma (installed from https://jenkins.ch.cam.ac.uk/view/AMI2/job/norma/ , yesterday at 6pm)\r\nUsing this in the Neuro workshop VM.\r\nRan getpapers to get 25 peerj papers in valid ctree structure:\r\n\r\n```\r\ngetpapers --query 'JOURNAL:\"PeerJ\" AND FIRST_PDATE:[2015-04-01 TO 2015-04-20]' -x -p --outdir peerj\r\n```\r\n\r\nRunning NORMA\r\nold style commands (worked in previous version on norma, but now perhaps depreciated?):\r\n```\r\nworkshop@crunchbang:~/workshop/test/peerj$ norma -q PMC4389270 -i fulltext.xml -o scholarly.html -x nlm2html\r\n0    [main] WARN  org.xmlcml.norma.NormaArgProcessor  - option --xsl is deprecated); use --transform instead\r\nError \r\n  I/O error reported by XML parser processing null:\r\n  /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\njava.lang.RuntimeException: invoke transform fails\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:698)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:582)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:564)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:742)\r\n\tat org.xmlcml.norma.Norma.run(Norma.java:23)\r\n\tat org.xmlcml.norma.Norma.main(Norma.java:18)\r\nCaused by: java.lang.reflect.InvocationTargetException\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\r\n\tat java.lang.reflect.Method.invoke(Method.java:606)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:696)\r\n\t... 5 more\r\nCaused by: java.lang.RuntimeException: cannot transform: \r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:191)\r\n\tat org.xmlcml.norma.NormaTransformer.applyXSLDocumentListToCurrentCMDir(NormaTransformer.java:176)\r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:94)\r\n\tat org.xmlcml.norma.NormaArgProcessor.runTransform(NormaArgProcessor.java:214)\r\n\tat org.xmlcml.norma.NormaArgProcessor.transform(NormaArgProcessor.java:208)\r\n\t... 10 more\r\nCaused by: net.sf.saxon.trans.XPathException: I/O error reported by XML parser processing null: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\n\tat net.sf.saxon.event.Sender.sendSAXSource(Sender.java:467)\r\n\tat net.sf.saxon.event.Sender.send(Sender.java:171)\r\n\tat net.sf.saxon.Controller.transform(Controller.java:1690)\r\n\tat net.sf.saxon.s9api.XsltTransformer.transform(XsltTransformer.java:547)\r\n\tat net.sf.saxon.jaxp.TransformerImpl.transform(TransformerImpl.java:180)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:167)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:117)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:104)\r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:189)\r\n\t... 14 more\r\nCaused by: java.io.FileNotFoundException: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\n\tat java.io.FileInputStream.open(Native Method)\r\n\tat java.io.FileInputStream.<init>(FileInputStream.java:146)\r\n\tat java.io.FileInputStream.<init>(FileInputStream.java:101)\r\n\tat sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)\r\n\tat sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)\r\n\tat org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)\r\n\tat org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.XMLParser.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)\r\n\tat org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)\r\n\tat net.sf.saxon.event.Sender.sendSAXSource(Sender.java:440)\r\n\t... 22 more\r\nException in thread \"main\" java.lang.RuntimeException: cannot process argument: --xsl (FileNotFoundException: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory))\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:586)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:564)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:742)\r\n\tat org.xmlcml.norma.Norma.run(Norma.java:23)\r\n\tat org.xmlcml.norma.Norma.main(Norma.java:18)\r\n```\r\n\r\nnew commands (still not giving desired output, or I'm getting it wrong):\r\n```\r\nworkshop@crunchbang:~/workshop/test/peerj$ norma -q PMC4389270 -i fulltext.xml -o scholarly.html --transform nlm2html\r\nError \r\n  I/O error reported by XML parser processing null:\r\n  /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\njava.lang.RuntimeException: invoke runTransform fails\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:698)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:582)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:564)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:742)\r\n\tat org.xmlcml.norma.Norma.run(Norma.java:23)\r\n\tat org.xmlcml.norma.Norma.main(Norma.java:18)\r\nCaused by: java.lang.reflect.InvocationTargetException\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r\n\tat sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)\r\n\tat sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)\r\n\tat java.lang.reflect.Method.invoke(Method.java:606)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.instantiateAndRunMethod(DefaultArgProcessor.java:696)\r\n\t... 5 more\r\nCaused by: java.lang.RuntimeException: cannot transform: \r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:191)\r\n\tat org.xmlcml.norma.NormaTransformer.applyXSLDocumentListToCurrentCMDir(NormaTransformer.java:176)\r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:94)\r\n\tat org.xmlcml.norma.NormaArgProcessor.runTransform(NormaArgProcessor.java:214)\r\n\t... 10 more\r\nCaused by: net.sf.saxon.trans.XPathException: I/O error reported by XML parser processing null: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\n\tat net.sf.saxon.event.Sender.sendSAXSource(Sender.java:467)\r\n\tat net.sf.saxon.event.Sender.send(Sender.java:171)\r\n\tat net.sf.saxon.Controller.transform(Controller.java:1690)\r\n\tat net.sf.saxon.s9api.XsltTransformer.transform(XsltTransformer.java:547)\r\n\tat net.sf.saxon.jaxp.TransformerImpl.transform(TransformerImpl.java:180)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:167)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:117)\r\n\tat org.xmlcml.norma.util.TransformerWrapper.transformToXML(TransformerWrapper.java:104)\r\n\tat org.xmlcml.norma.NormaTransformer.transform(NormaTransformer.java:189)\r\n\t... 13 more\r\nCaused by: java.io.FileNotFoundException: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory)\r\n\tat java.io.FileInputStream.open(Native Method)\r\n\tat java.io.FileInputStream.<init>(FileInputStream.java:146)\r\n\tat java.io.FileInputStream.<init>(FileInputStream.java:101)\r\n\tat sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)\r\n\tat sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)\r\n\tat org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLEntityManager.startEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLEntityManager.startDTDEntity(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDTDScannerImpl.setInputSource(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDocumentScannerImpl$DTDDispatcher.dispatch(Unknown Source)\r\n\tat org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)\r\n\tat org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.XMLParser.parse(Unknown Source)\r\n\tat org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)\r\n\tat org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)\r\n\tat net.sf.saxon.event.Sender.sendSAXSource(Sender.java:440)\r\n\t... 21 more\r\nException in thread \"main\" java.lang.RuntimeException: cannot process argument: --transform (FileNotFoundException: /home/workshop/workshop/test/peerj/JATS-archivearticle1.dtd (No such file or directory))\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runMethodsOfType(DefaultArgProcessor.java:586)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runRunMethodsOnChosenArgOptions(DefaultArgProcessor.java:564)\r\n\tat org.xmlcml.cmine.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:742)\r\n\tat org.xmlcml.norma.Norma.run(Norma.java:23)\r\n\tat org.xmlcml.norma.Norma.main(Norma.java:18)\r\n```\r\n"}}