ala-install
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AtlasOfLivingAustralia
ala-demo: Rough ala-bie
Still running the command below.
ansible-playbook -i inventories/ala-demo ala-demo-cassandra3-solr6.yml --become --ask-become-pass
This is what does dot work
- Exception while issuing a simple search
Error 500: Internal Server Error
URI
/ala-bie/search
Class
java.lang.NoClassDefFoundError
Message
Handler dispatch failed; nested exception is java.lang.NoClassDefFoundError: org/apache/commons/httpclient/util/URIUtil
Caused by
org/apache/commons/httpclient/util/URIUtil
Trace
Line | Method
->> 44 | getQueryString in au.org.ala.bie.webapp2.SearchRequestParamsDTO
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
| 14 | searchBie in au.org.ala.bie.BieService
| 82 | doCall . . . . . in au.org.ala.bie.SpeciesController$_closure2
| 223 | invoke in org.grails.core.DefaultGrailsControllerClass$MethodHandleInvoker
| 188 | invoke . . . . . in org.grails.core.DefaultGrailsControllerClass
| 90 | handle in org.grails.web.mapping.mvc.UrlMappingsInfoHandlerAdapter
| 967 | doDispatch . . . in org.springframework.web.servlet.DispatcherServlet
| 901 | doService in ''
| 970 | processRequest . in org.springframework.web.servlet.FrameworkServlet
| 861 | doGet in ''
| 846 | service . . . . in ''
| 55 | doFilterInternal in org.springframework.boot.web.filter.ApplicationContextHeaderFilter
| 77 | doFilterInternal in org.grails.web.servlet.mvc.GrailsWebRequestFilter
| 203 | doFilter in au.org.ala.cas.client.UriFilter
| 97 | doFilter . . . . in org.jasig.cas.client.session.SingleSignOutFilter
| 67 | doFilterInternal in org.grails.web.filters.HiddenHttpMethodFilter
| 117 | doFilter . . . . in org.springframework.boot.web.support.ErrorPageFilter
| 61 | access$000 in ''
| 92 | doFilterInternal in org.springframework.boot.web.support.ErrorPageFilter$1
| 110 | doFilter in org.springframework.boot.web.support.ErrorPageFilter
| 1149 | runWorker . . . in java.util.concurrent.ThreadPoolExecutor
| 624 | run in java.util.concurrent.ThreadPoolExecutor$Worker
^ 748 | run . . . . . . in java.lang.Thread
- ala-bie seems not to be using CSS styles at all.
ive reproduced this too. Im attempting to fix the ala-bie build which is currently broken due to missing SNAPSHOT dependencies
This has happened again with bie-plugin version 1.4.4. Can't see what has caused it this time, as no missing SNAPSHOT deps are present. Seems like some libs are simply not being included in the jar file...
org/apache/commons/httpclient/util/URIUtil is a class from commons-httpclient-3, which isn't on the classpath looking at what is deployed on nectar-bie-test. Could be useful to upgrade the code to use httpclient-4 which is on the classpath.
We're pulling it in via compile "commons-httpclient:commons-httpclient:3.1". When running "in line" I can click though to this library from the code that is calling it (which fails above).
The diff of the dependent jars in WEB-INF/libs between ala-bie-1.4.3 and ala-bie-1.4.5 is fairly large (reduced from 223 jars to 139 jars):
$ diff -u ala-bie-1.4.*
--- ala-bie-1.4.3-deps.txt 2018-10-23 12:36:43.000000000 +1100
+++ ala-bie-1.4.5-deps.txt 2018-10-23 12:36:56.000000000 +1100
@@ -1,60 +1,27 @@
-HikariCP-2.4.7.jar
-activation-1.1.jar
ala-admin-plugin-2.0.jar
ala-auth-3.1.0.jar
ala-bootstrap3-3.0.6.jar
ala-cas-client-2.4.jar
-ala-charts-plugin-2.0.jar
-ala-name-matching-2.4.7.jar
-amqp-client-3.1.4.jar
-aopalliance-1.0.jar
args4j-2.0.26.jar
-asm-3.3.1.jar
aspectjrt-1.8.10.jar
aspectjweaver-1.8.10.jar
asset-pipeline-core-2.14.1.jar
asset-pipeline-grails-2.14.1.jar
-bie-plugin-1.4.2.2.jar
+bie-plugin-1.4.5.jar
cache-3.0.3.jar
cas-client-core-3.4.1.jar
-cglib-2.2.2.jar
-checklistbank-common-2.61.jar
classmate-1.3.3.jar
closure-compiler-externs-v20160713.jar
closure-compiler-unshaded-v20160713.jar
-commons-beanutils-1.9.3.jar
-commons-cli-1.2.jar
commons-codec-1.10.jar
commons-collections-3.2.2.jar
-commons-compress-1.10.jar
-commons-digester3-3.2.jar
-commons-httpclient-3.1.jar
-commons-io-2.5.jar
commons-lang-2.6.jar
-commons-lang3-3.5.jar
commons-logging-1.2.jar
-commons-math3-3.6.1.jar
commons-validator-1.5.1.jar
concurrentlinkedhashmap-lru-1.4.2.jar
converter-moshi-2.4.0.jar
dom4j-1.6.1.jar
-download-query-tools-1.18.jar
-dwc-api-1.17.jar
-dwca-io-1.32.jar
-ehcache-core-2.0.0.jar
external-config-1.1.1.jar
-ezmorph-1.0.6.jar
-freemarker-2.3.26-incubating.jar
-gbif-api-0.55.jar
-gbif-common-0.37.jar
-gbif-common-mybatis-0.28.jar
-gbif-common-service-0.16.jar
-gbif-common-ws-0.40.jar
-gbif-doi-1.5.jar
-gbif-httputils-0.10.jar
-gbif-parsers-0.30.jar
-gbif-postal-service-0.24.jar
-gmetric4j-1.0.7.jar
gpars-1.2.1.jar
grails-async-3.2.11.jar
grails-bootstrap-3.2.11.jar
@@ -108,68 +75,28 @@
gs-collections-api-5.1.0.jar
gson-2.7.jar
guava-19.0.jar
-guice-4.0.jar
-guice-multibindings-4.0.jar
-guice-servlet-4.0.jar
h2-1.4.194.jar
hibernate-jpa-2.1-api-1.0.0.Final.jar
hibernate-validator-5.4.2.Final.jar
-http-builder-0.7.1.jar
httpclient-4.5.3.jar
httpcore-4.4.6.jar
-images-client-plugin-1.0.jar
jackson-annotations-2.8.8.jar
jackson-core-2.8.8.jar
-jackson-core-asl-1.9.13.jar
jackson-databind-2.8.8.jar
-jackson-datatype-guava-1.9.2.jar
-jackson-jaxrs-1.9.13.jar
-jackson-mapper-asl-1.9.13.jar
-jackson-xc-1.9.2.jar
javassist-3.20.0-GA.jar
-javax.inject-1.jar
-jaxb-api-2.2.2.jar
-jaxb-impl-2.2.3-1.jar
jboss-logging-3.3.1.Final.jar
jcl-over-slf4j-1.7.25.jar
-jcommander-1.60.jar
-jersey-apache-client4-1.19.3.jar
-jersey-client-1.19.3.jar
-jersey-core-1.19.3.jar
-jersey-guice-1.19.3.jar
-jersey-json-1.19.3.jar
-jersey-server-1.19.3.jar
-jersey-servlet-1.19.3.jar
-jettison-1.1.jar
-json-lib-2.3-jdk15.jar
-jsoup-1.8.3.jar
jsr166y-1.7.0.jar
-jsr250-api-1.0.jar
-jsr305-3.0.1.jar
-jsr311-api-1.1.1.jar
+jsr305-1.3.9.jar
jta-1.1.jar
-jts-1.13.jar
jul-to-slf4j-1.7.25.jar
-log4j-1.2.17.jar
log4j-over-slf4j-1.7.25.jar
logback-classic-1.1.11.jar
logback-core-1.1.11.jar
-mail-1.4.7.jar
-metrics-core-3.1.4.jar
-metrics-ganglia-3.1.4.jar
moshi-1.5.0.jar
moshi-adapters-1.5.0.jar
-mybatis-3.4.1.jar
-mybatis-ehcache-1.0.0.jar
-mybatis-guice-3.7.1.jar
-name-parser-2.24.jar
-nekohtml-1.9.22.jar
okhttp-3.10.0.jar
okio-1.14.0.jar
-oncrpc-1.0.7.jar
-opencsv-2.4.jar
-owasp-java-html-sanitizer-20160924.1.jar
-postgresql-9.4.1212.jre7.jar
protobuf-java-2.5.0.jar
reactive-streams-1.0.0.jar
reactor-bus-2.0.8.RELEASE.jar
@@ -177,17 +104,11 @@
reactor-spring-context-2.0.7.RELEASE.jar
reactor-spring-core-2.0.7.RELEASE.jar
reactor-stream-2.0.8.RELEASE.jar
-registry-doi-2.71.jar
-registry-identity-2.71.jar
-registry-metadata-2.71.jar
-registry-surety-2.71.jar
-registry-ws-client-2.71.jar
retrofit-2.4.0.jar
rhino-1.7R4.jar
serializer-2.7.2.jar
sitemesh-2.4.jar
slf4j-api-1.7.25.jar
-slf4j-log4j12-1.7.25.jar
snakeyaml-1.17.jar
spring-aop-4.3.9.RELEASE.jar
spring-aspects-4.3.9.RELEASE.jar
@@ -207,9 +128,6 @@
spring-tx-4.3.9.RELEASE.jar
spring-web-4.3.9.RELEASE.jar
spring-webmvc-4.3.9.RELEASE.jar
-stax-api-1.0-2.jar
-threetenbp-1.3.2.jar
-tika-core-1.15.jar
tomcat-embed-core-8.5.13.jar
tomcat-embed-el-8.5.13.jar
tomcat-embed-logging-log4j-8.5.2.jar
@@ -218,6 +136,4 @@
tomcat-juli-8.5.13.jar
userdetails-service-client-1.4.0.jar
validation-api-1.1.0.Final.jar
-xercesImpl-2.11.0.jar
xml-apis-1.4.01.jar
-xml-resolver-1.2.jar
I've found the problem. The bie-plugin had a publishing task in build.gradle (link) that resulted in the travis triggering 2 publishing events, one of type publishMavenJarPublicationToNexusRepository and another of publishMavenPublicationToNexusRepository. The problem with release versions was the second event would fail, as it was trying to (re-)generate the jar file (and pom file, etc) on nexus and would fail due to the restriction of not allowing files to be overridden for release versions.
The fix was to remove the publishing section (which had a mavenJar(MavenPublication) entry - note the jar reference) from build.gradle and allow just publishMavenPublicationToNexusRepository to run. We originally had this code in the file to remove any dependencies with NO version info, but it appears this was a work-around for a Grails issue that has since been resolved and so its not needed any more.