Comments at the bottom. (Spoiler alert: Good news!)
On 11/01/2018 22:38, "Christopher Schultz" <ch...@christopherschultz.net> wrote: >-----BEGIN PGP SIGNED MESSAGE----- >Hash: SHA256 > >Sean, > >On 1/11/18 11:58 AM, Sean Brett wrote: >> On 11/01/2018 15:48, "Christopher Schultz" >> <ch...@christopherschultz.net> wrote: >> >> >>> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 >>> >>> Sean, >>> >>> (Thanks for moving to the mailing list; it's a much better forum >>> for getting into a protracted discussion. See below for more, >>> inline.) >>> >>> On 1/10/18 9:08 AM, Sean Brett wrote: >>>> I've been tasked with migrating a site from one institution to >>>> another. As part of the process we are attempting to update >>>> the versions the site uses. >>>> >>>> Initially I was asked to use Java 8 with Tomcat 5.5 (on >>>> Linux), which led to issues - not to mention Tomcat 5 being >>>> 'out of support¹. I have since tried to deploy the webapps to >>>> Tomcat 9 with Java 8. Some of the webapps appear to run fine >>>> (and resolve the issues I was having with Tomcat5). However, >>>> the main app (and 2 similar/smaller web apps) throws a >>>> JasperException when I go to the index.jsp - the same web apps >>>> deployed to Tomcat 5.5 load without issue. >>> >>> Moving to a later Tomcat version is best. We'll help you figure >>> out these issues so you can use a current version and be >>> better-equipped to stay current into the future. >>> >>>> Most of the similar issues I have found have suggested this >>>> would be related to the jar files and possibly some sort of >>>> conflict. However, the lib structure for tomcat 9 is different >>>> to tomcat5 and I'm not sure which jars could be causing this. >>>> e.g. >>>> https://stackoverflow.com/questions/22552244/tomcat-7-fails-to-compi >le >>> >>>> >- - -jsp- >>>> >>>> >>> pages >>> >>> JAR files might conflict, but that depends upon what you have >>> done so far. Easy questions: >>> >>> 1. Have you added anything to Tomcat's lib/ directory (that would >>> be CATALINA_HOME/lib or CATALINA_BASE/lib -- or both) after >>> installing Tomcat 8/9? >> >> Yes, I’ve added some jars. Some I can’t remember why I’ve added >> them but doubt they’d be connected to the problem. Here’s a list >> of the CATALINA_HOME/lib directory: (the last 4 being the ones that >> have been added) >> >> [snip] >> >> -rw-r--r--. 1 tomcat tomcat 313898 Dec 20 13:57 dom4j-1.6.1.jar >> -rw-r--r--. 1 tomcat tomcat 802494 Dec 20 13:57 >> freemarker-2.3.8.jar -rw-r--r--. 1 tomcat tomcat 355030 Dec 20 >> 13:57 mail.jar -rw-r--r--. 1 tomcat tomcat 713037 Dec 20 14:15 >> postgresql-42.1.4.jar > >Yup, those look "foreign". > >If possible, I'd move all of those except for the postgresql driver >into your web application's WEB-INF/lib folder. We can move them back >if absolutely necessary. > >Is "mail.jar" the JavaMail API/implementation? You'd only need that in >Tomcat's lib/ directory if you were asking Tomcat to provide mail >session via JNDI -- such would appear somewhere in either your web >applications' META-INF/context.xml file or some file under >CATALINA_BASE/conf/* > >Check your version of JavaMail. There are older versions which contain >vulnerabilities that have been patched. The API is (AFAICT) 100% >backward-compatible, so you should be able to upgrade to >JavaMail.latest without any problems. YMMV. > >>> 2. What JAR files are bundled with your application in >>> WEB-INF/lib ? >> >> -rw-r-----. 1 root root 97703 Jan 11 15:05 servlet-api.jar > >Remove that one. Tomcat should refuse to load it, but you should >remove it anyway. > >> -rw-r-----. 1 root root 8356134 Jan 11 15:05 rt.jar > >Is that the Java JDK's runtime library? If so, remove that as well. >Tomcat should refuse to load classes over-top of the standard java.*, >javax.*, and a few other top-level packages but it's always possible >something might sneak in there and confuse everything. > >> -rw-r-----. 1 root root 474746 Jan 11 15:05 >> postgresql-8.3-603.jdbc4.jar> -rw-r-----. 1 root root 355030 Jan >> 11 15:05 mail.jar > >If you have either (or both) of these in Tomcat's CATALINA_BASE/lib or >CATALINA_HOME/lib directories, you'll want to remove them from here. > >> -rw-r-----. 1 root root 352668 Jan 11 15:05 log4j-1.2.8.jar > >Ok. > >> -rw-r-----. 1 root root 55008 Jan 11 15:05 local-ldap-0.0.1.jar >> -rw-r-----. 1 root root 38114 Jan 11 15:05 ldap-src-0.0.1.jar >> -rw-r-----. 1 root root 38668 Jan 11 15:05 ldap.jar -rw-r-----. 1 >> root root 55827 Jan 11 15:05 ldap-0.0.1.jar > >Hmm. Does your application use LDAP directly? > >> -rw-r-----. 1 root root 146718 Jan 11 15:05 jdom.jar -rw-r-----. 1 >> root root 173211 Jan 11 15:05 IonoMap.jar -rw-r-----. 1 root root >> 457002 Jan 11 15:05 ibmjndi.jar -rw-r-----. 1 root root 38015 Jan >> 11 15:05 commons-logging-1.0.4.jar -rw-r-----. 1 root root 87776 >> Jan 11 15:05 commons-io-1.3.2.jar -rw-r-----. 1 root root 22379 >> Jan 11 15:05 commons-fileupload.jar -rw-r-----. 1 root root 57779 >> Jan 11 15:05 commons-fileupload-1.2.1.jar -rw-r-----. 1 root root >> 559366 Jan 11 15:05 commons-collections-3.1.jar -rw-r-----. 1 root >> root 58735 Jan 11 15:05 common-piims-src.jar -rw-r-----. 1 root >> root 175113 Jan 11 15:05 common-piims.jar -rw-r-----. 1 root root >> 55147 Jan 11 15:05 activation.jar > >Everything else looks okay. With Java 8, I'm not sure activation.jar >is necessary anymore. But JavaMail and the activation framework should >together (if activation.jar is still required). > >>>> I've also tried changing the index.jsp into a simpler >>>> (HelloWorld) form - removing any code. And tried deleting the >>>> 'work' directory before restarting Tomcat >>>> (http://grokbase.com/t/tomcat/users/072v2kf60h/java-permission-denie >d- >>> >>>> >error >>>> >>>> >>> - -in-tomcat). In both cases the exception is still thrown. >>> >>> Can you post the full text of HelloWorld.jsp? >>> >>> I'm wondering if you have some odd syntax or are expecting to use >>> a "custom base JSP servlet class" or something like that which is >>> no longer compatible with Tomcat's current JSP servlet. If so, >>> we'll try to figure out why the custom code was necessary and >>> make arrangements to replace it. >>> >>> - -chris >> >> I also wondered if it could be some incompatible code so stripped >> it down to the bare minimum as follows: >> >> <html> <head> <title>Ionomics Hub (iHUB) - Home</title> </head> >> <body class="tundra"> <p>iHub index page</p> </body> </html> > >It doesn't get any simpler than that. And it still completely dies >when you request that file from Tomcat? Weird. > >> Another suggestion >> (https://coderanch.com/t/689419/Jasper-Exception-Tomcat-works-Tomcat) >> was it may be something to do with precompiled jsps. > >Are you precompiling JSPS? If you don't know what I'm talking about, >you're not precompiling JSPs. > >> Excuse my ignorance but the file highlighted in the >> JasperException is only created when the war file is deployed by >> tomcat. So I’m not sure what I can do to influence this file. >> Pretty convinced this is a config issue. > >Your Tomcat may be broken in some way, too. Other than adding those 4 >JAR files (and dropping your webapp into CATALINA_BASE/webapps), did >you do anything else to Tomcat since you installed it? Any >configuration file changes? > >- -chris Thanks Chris, it looks like following your advice has resolved the issue - I’ve not been through the whole application but the first few pages are loading correctly. I haven’t narrowed down the cause yet but suspect it was the servlet-api.jar in the WEB-INF/lib folder that was causing the issue. As it stands I removed the dom4j-1.6.1.jar and freemarker-2.3.8.jar from $CATALINA_HOME/lib, I then removed servlet-api.jar, rt.jar from the web application's WEB-INF/lib directory. I needed the mail.jar for other web apps further down the chain. Thanks for your advice, it’s much appreciated. 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