在Debian 7系统里测试安装Ambra

感谢 tctia* 的支持。

有用户要求测试安装Ambra，现将过程记录，虽然未成功，但希望给其他人带来帮助。

环境：
软件：Debian 7.10 64位，JDK 7，tomcat 6，mysql server 5.5。
ECS配置：1核心，2GB内存。

个人总结：

Ambra官方网站里的文档相对较旧，很久没更新了
Ambra官方网站里提供的联系方法（邮件列表）无人审核，无法发邮件提问，获取帮助
Java生手（如我），不建议尝试，在前面两个原因前提下，完成测试有难度

过程：

1.更新软件源：
apt-get update

2.安装默认JDK版本（1.7.0_111）
apt-get install default-jdk

3.安装tomcat6
apt-get install tomcat6

4.安装mysql，假设设置mysql的密码为root
apt-get instal mysql-server

5.停止 tomcat6 服务，移走原有/var/lib/tomcat/webapps目录内容
service tomcat6 stop

6.用官方上手教程里方法，编译的webapp版本是2.9.5，官方PLOS支是2.11，这里下载官方编译好的2.11.war来测试，放到 /var/lib/tomcat/webapps/ROOT.war

wget http://ambraproject.org/maven2/release/org/ambraproject/ambra-webapp/2.11.0/ambra-webapp-2.11.0.war

7.从官方上手教程里下载相应的组件，如 tomcat-jdbc.jar, tomcat-juli.jar, log4j-1.2.14.jar 到 /usr/share/tomcat6/lib 目录（前两者是mysql连接要用到的，后边的是用于记录日志的），同时在该目录里创建log4j.properties的配置文件，让tomcat记录详细的输出信息

log4j.rootLogger=ERROR,consoleAppender
log4j.appender.consoleAppender=org.apache.log4j.ConsoleAppender
log4j.appender.consoleAppender.Target=System.out
log4j.appender.consoleAppender.layout=org.apache.log4j.PatternLayout
log4j.appender.consoleAppender.layout.ConversionPattern=%-5p %c{1} - %m%n
log4j.logger.org.ambraproject=DEBUG
log4j.logger.org.ambraproject.ambra.configuration=FATAL

8.编辑tomcat配置文件，/etc/tomcat6/context.xml ，在标签间加入以下内容，其中 jdbc:mysql://localhost/ambra 中的 ambra 是程序要用到的数据库名称，上一行的password是数据库用户的密码，路径 /mytest/dongshan/ambra 是程序要用到的文件路径，这里随意创建了 /mytest/dongshan 的路径，请作相应的更改

<WatchedResource>WEB-INF/web.xml</WatchedResource>
  <Resource name="jdbc/AmbraDS"
    auth="Container"
    type="javax.sql.DataSource"
    factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
    validationQuery="SELECT 1"
    testOnBorrow="true"
    driverClassName="com.mysql.jdbc.Driver"
    username="root"
    password="aqtest38"
    url="jdbc:mysql://localhost/ambra" />
<Resource name="ambra/FileStore"
    type="org.ambraproject.filestore.FileStoreService"
    factory="org.ambraproject.filestore.impl.LocalFileStoreFactory"
    baseDir="/mytest/dongshan"
    domain="ambra" />

9.创建好空数据库 ambra，导入从官方“上手教程”里的 ambra_schema.sql 数据库文件

10.创建ambra的配置文件，/etc/ambra/ambra.xml ，内容如下。这里主要是设置文件（ehcache.xml）和目录（ingest、ingestdestination、AmbraJournal和templates）的路径，还有默认杂志名称（AmbraJournal），请根据实际情况修改：

<config>
  <ambra>
    <network>
      <hosts>
        <default>localhost</default>
        <ambra>${ambra.network.hosts.default}</ambra>
      </hosts>
    </network>
    <services>
      <ehcache>
        <configFileLocation>/mytest/dongshan/ehcache.xml</configFileLocation>
      </ehcache>
      <search>
        <server>
          <url>http://localhost:8080/solr</url>
        </server>
      </search>
      <documentManagement>
        <ingestSourceDir>/mytest/dongshan/ingest</ingestSourceDir>
        <ingestDestinationDir>/mytest/dongshan/ingestdestination</ingestDestinationDir>
      </documentManagement>
    </services>
    <virtualJournals>
      <templateDir>/mytest/dongshan/templates</templateDir>
      <default>AmbraJournal</default>
      <journals>AmbraJournal</journals>
    </virtualJournals>
  </ambra>
</config>

11.创建杂志目录（/mytest/dongshan/templates/journals/AmbraJournal/webapp）及配置文件，如 /mytest/dongshan/templates/journals/AmbraJournal/configuration/journal.xml，内容如下：

<?xml version="1.0" encoding="UTF-8" ?>
<!--
  This file is the Ambra template for the Default AmbraJournal journal
-->
<config>
  <ambra>
    <!-- virtual journal config -->
    <virtualJournals>
      <AmbraJournal>
        <journal>AmbraJournal</journal>
        <eIssn>1111-2222</eIssn>
        <description>Ambra</description>
        <rules>
          <host>.*ambra.*</host>
        </rules>
        <url>http://ambrajournal.example.org</url>
        <!-- Does the journal have a taxonomy browser? -->
        <taxonomyBrowser>false</taxonomyBrowser>
        <ambra>
          <services>
            <feed>
              <title>Ambra Journal</title>
              <id>info:doi/10.1371/feed.ambr</id>
            </feed>
          </services>
        </ambra>
        <!-- Configuration keys for displaying recent articles tab widget on home page -->
        <recentArticles>
          <numDaysInPast>14</numDaysInPast>
          <numArticlesToShow>5</numArticlesToShow>
          <typeUriArticlesToShow>
            <articleTypeUri>http://rdf.plos.org/RDF/articleType/Research%20Article</articleTypeUri>
          </typeUriArticlesToShow>
        </recentArticles>
        <isIncludeInCrossJournalSearch>false</isIncludeInCrossJournalSearch>
      </AmbraJournal>
    </virtualJournals>
    <freemarker>
      <!--
        # This section defines the various journals and the css and javascript files which should be
        # included on each page as well as the page title.  The values within the <default> tag are used
        # if any of the values are missing in the <page> definitions.  Note, that the title, css, and
        # javascript level values are entirely replaced, they are not additive.  Override config files
        # may define values for each of those three variables and they will supsercede values present
        # in subsequent config values.  The lookup for values is as follows:
        # 1. Page defined in journal
        # 2. Default value defined in journal
        # 3. Page defined in default journal
        # 4. Default value in default journal
        # To define an empty value for a certain page so that it doesn't use defaults, just put the
        # element tag with no value, e.g. <javascript></javascript>
      -->
      <!--AmbraJournal-->
      <journal>
        <name>AmbraJournal</name>
        <metaKeywords>Ambra\, Default\, Journal</metaKeywords>
        <metaDescription>Ambra Journal: Defaults</metaDescription>
        <articleTitlePrefix>Ambra Journal :</articleTitlePrefix>
        <displayName>Ambra Journal</displayName>
        <default>
          <title>Ambra Journal : An Open-Access, Semantic, Journal Publishing System</title>
          <css>
            <file>/css/global.css</file>
            <file>/css/lte_ie7.css</file>
          </css>
          <javascript>
            <file>/javascript/js.js</file>
          </javascript>
        </default>
        <page>
          <name>/index.ftl</name>
          <css>
            <file>/css/global.css</file>
            <file>/css/lte_ie7.css</file>
          </css>
          <javascript>
            <file>/javascript/jquery-1.8.1.js</file>
            <file>/javascript/global.js</file>
          </javascript>
        </page>
      </journal>
    </freemarker>
  </ambra>
</config>

12.如果tomcat6提示缺少co请在相应的镜像站点下载 commons-logging-1.2-bin.tar.gz，将解压出来commons-logging-1.2.jar的文件，放到tomcat的lib目录/usr/share/tomcat6/lib
wget http://apache.mirror.iweb.ca//commons/logging/binaries/commons-logging-1.2-bin.tar.gz

13.启动tomcat6，在浏览器访问，看测试结果：
service tomcat6 start

14.如浏览器显示404页面找不到，请查看tomcat日志：
tail -300 /var/log/tomcat6/catalina.out

15.测试中，如果用官方PLOS树中的ambra-webapp-2.11.0.war，很可能会出现500错误，提示找不到 includes/article_variables.ftl 文件，我是直接将 /var/lib/tomcat6/webapps/ROOT/includes/global_variables.ftl 复制为 /var/lib/tomcat6/webapps/ROOT/includes/article_variables.ftl

freemarker.template.TemplateException: Error reading included file includes/article_variables.ftl