README.txt

#
# Copyright (c) 2006, 2014, Oracle and/or its affiliates. All rights reserved.
#


OpenGrok - a wicked fast source browser
---------------------------------------

1.  Introduction
2.  Requirements
3.  Usage
4.  OpenGrok install
5.  OpenGrok setup
6.  Optional Command Line Interface Usage
7.  Change web application properties or name
8.  OpenGrok systray
9.  Information for developers
10.  Tuning OpenGrok for large code bases
11.  Authors
12. Contact us


1. Introduction
---------------

OpenGrok is a fast and usable source code search and cross reference
engine, written in Java. It helps you search, cross-reference and navigate
your source tree. It can understand various program file formats and
version control histories like SCCS, RCS, CVS, Subversion, Mercurial etc.

Offical page of the project is on:

  http://opengrok.github.com/OpenGrok/

2. Requirements
---------------

    * Latest Java (At least 1.7, 1.8 is supported)
      http://www.oracle.com/technetwork/java/
    * A servlet container like Tomcat (7.x or later)
      supporting Servlet 2.4 and JSP 2.0
      http://tomcat.apache.org/
    * Exuberant Ctags
      http://ctags.sourceforge.net/
    * Source Code Management installation
      depending on type of repositories indexed
    * If you want to build OpenGrok:
      - Ant (1.9.3 and later)
        http://ant.apache.org/
      - JFlex
        http://www.jflex.de/
      - Netbeans (optional, at least 8.0, will need Ant 1.9.3)
        http://netbeans.org/

3. Usage
--------

OpenGrok usually runs in servlet container (e.g. Tomcat).

SRC_ROOT environment variable refers to the directory containing your source
tree. OpenGrok analyzes the source tree and builds a search index along with
cross-referenced hypertext versions of the source files. These generated
data files will be stored in directory referred to with environment variable
called DATA_ROOT.

3.1 Projects
------------

OpenGrok has a concept of Projects - one project is one directory underneath
SRC_ROOT directory which usually contains a checkout of a project sources.
(this can be branch, version, ...) 

Projects effectively replace the need to have more web applications, each with
opengrok .war file. Instead it leaves you with one indexer and one web
application serving multiple source code repositories - projects.
Then you have a simple update script and simple index refresher script in
place, which simplifies management of more repositories.

A nice concept is to have a naming convention for directories underneath
SRC_ROOT, thereby creating a good overview of projects (e.g.
name-version-branch).

For example, the SRC_ROOT directory can contain the following directories:

  openssl-head
  openssl-0.9.8-stable
  openssl-1.0.0-stable

Each of these directories was created with 'cvs checkout' command (with
appropriate arguments to get given branch) and will be treated by OpenGrok
as a project.


4. OpenGrok install
-----------------

4.1 Installing on Solaris from *.p5p file
-----------------

4.1.0 Install
-----------------

The file <package_name>.p5p you can easily use as a new publisher for the pkg command.

  # pkg install --no-refresh -g /path/to/file/<package_name>.p5p opengrok


4.1.1 Update
-----------------

You can also update OpenGrok software with the *.p5p file by running a command

  # pkg update --no-refresh -g /path/to/file/<package_name>.p5p 'pkg://<publisher>/*'


5. OpenGrok setup
-----------------

To setup OpenGrok it is needed to prepare the source code, let OpenGrok index
it and start the web application.

5.1 Setting up the sources
--------------------------

Source base should be available locally for OpenGrok to work efficiently.
No changes are required to your source tree. If the code is under source
control management (SCM) OpenGrok requires the checked out source tree under
SRC_ROOT.

By itself OpenGrok does not perform the setup of the source code repositories
or sychronization of the source code with its origin. This needs to be done by
the user or by using automatic scripts.

It is possible for SCM systems which are not distributed (Subversion, CVS)
to use a remote repository but this is not recommended due to the performance
penalty. Special option when running the OpenGrok indexer is needed to enable
remote repository support ("-r on").

In order for history indexing to work for any SCM system it is necessary
to have environment for given SCM systems installed and in a path accessible
by OpenGrok.

Note that OpenGrok ignores symbolic links.

If you want to skip indexing the history of a particular directory
(and all of it's subdirectories), you can touch '.opengrok_skip_history' file
at the root of that directory.


5.2 Using Opengrok wrapper script to create indexes
---------------------------------------------------

For *nix systems there is a shell script called OpenGrok which simplifies most
of the tasks. It has been tested on Solaris and Linux distributions.

5.2.1 - Deploy the web application
----------------------------------

First please change to opengrok directory where the OpenGrok shell script is
stored (can vary on your system).

Note that now you might need to change to user which owns the target 
directories for data, e.g. on Solaris you'd do:

  # pfexec su - webservd
  $ cd /usr/opengrok/bin

and run 

  $ ./OpenGrok deploy

This command will do some sanity checks and will deploy the source.war in
its directory to one of detected web application containers.
Please follow the error message it provides.

If it fails to discover your container, please refer to optional steps on
changing web application properties below, which explains how to do this.

Note that OpenGrok script expects the directory /var/opengrok to be
available to user running opengrok with all permissions. In root user case
it will create all the directories needed, otherwise you have to manually
create the directory and grant all permissions to the user used.

5.2.2 - Populate DATA_ROOT Directory
------------------------------------

During this process the indexer will generate OpenGrok XML configuration file
configuration.xml and sends the updated configuration to your web app.

The indexing can take a lot of time. After this is done, indexer automatically
attempts to upload newly generated configuration to the web application.
Most probably you will not be able to use Opengrok before this is done for the
first time.

Please change to opengrok directory (can vary on your system)

  $ cd /usr/opengrok/bin

and run, if your SRC_ROOT is prepared under /var/opengrok/src

  $ ./OpenGrok index

otherwise (if SRC_ROOT is in different directory) run:

  $ ./OpenGrok index <absolute_path_to_your_SRC_ROOT>

The above command attempts to upload the latest index status reflected into
configuration.xml to a running source web application.
Once above command finishes without errors
(e.g. SEVERE: Failed to send configuration to localhost:2424),
you should be able to enjoy your opengrok and search your sources using
latest indexes and setup.

It is assumed that any SCM commands are reachable in one of the components
of the PATH environment variable (e.g. 'git' command for Git repositories).
Likewise, this should be maintained in the environment of the user which runs
the web server instance.

Congratulations, you should now be able to point your browser to
http://<YOUR_WEBAPP_SERVER>:<WEBAPPSRV_PORT>/source to work with your fresh
OpenGrok installation! :-)

At this time we'd like to point out some customization to OpenGrok script
for advanced users.
A common case would be, that you want the data in some other directory than
/var/opengrok. This can be easily achieved by using environment variable
OPENGROK_INSTANCE_BASE.

E.g. if opengrok data directory is /tank/opengrok and source root is
in /tank/source then to get more verbosity run the indexer as:

  $ OPENGROK_VERBOSE=true OPENGROK_INSTANCE_BASE=/tank/opengrok \
       ./OpenGrok index /tank/source 

Since above will also change default location of config file, beforehands(or
restart your web container after creating this symlink) I suggest doing
below for our case of having opengrok instance in /tank/opengrok :

  $ ln -s /tank/opengrok/etc/configuration.xml \
      /var/opengrok/etc/configuration.xml 

More customizations can be found inside the script, you just need to
have a look at it, eventually create a configuration out of it and use
OPENGROK_CONFIGURATION environment variable to point to it. Obviously such
setups can be used for nightly cron job updates of index or other automated
purposes.

5.3 Using SMF service (Solaris) to maintain OpenGrok indexes
------------------------------------------------------------

If you installed OpenGrok from the OSOLopengrok package, it will work out of
the box. Should you need to configure it (e.g. because of non-default SRC_ROOT
or DATA_ROOT paths) it is done via the 'opengrok' property group of the
service like this:

  # svccfg -s opengrok setprop \
       opengrok/srcdir="/absolute/path/to/your/sourcetree"
  # svccfg -s opengrok setprop opengrok/maxmemory="2048"

Then make the service start the indexing, at this point it would be nice if 
the web application is already running.

Now enable the service:

  # svcadm enable -rs opengrok

Note that this will enable tomcat6 service as dependency.

When the service starts indexing for first time, it's already enabled and
depending on tomcat6, so at this point the web application should be 
already running.

Note that indexing is not done when the opengrok service is disabled.

To rebuild the index later (e.g. after source code changed) just run:

  # svcadm refresh opengrok

The service makes it possible to supply part of the configuration via the
'opengrok/readonly_config' service property which is set to
/etc/opengrok/readonly_configuration.xml by default.

Note: before removing the package please disable the service.
If you don't do it, it will not be removed automatically.
In such case please remove it manually.

5.4 Using command line interface to create indexes
--------------------------------------------------

There are 2 (or 3) steps needed for this task.

5.4.1 - Populate DATA_ROOT Directory
------------------------------------

Option 1. OpenGrok: There is a sample shell script OpenGrok that is suitable
for using in a cron job to run regularly. Modify the variables in the script
to point appropriate directories, or as the code suggests factor your local
configuration into a separate file and simplify future upgrades.

Option 2. opengrok.jar: You can also directly use the Java application. If
the sources are all located in a directory SRC_ROOT and the data and
hypertext files generated by OpenGrok are to be stored in DATA_ROOT, run

     $ java -jar opengrok.jar -s $SRC_ROOT -d $DATA_ROOT

See opengrok.jar manual below for more details.

5.4.2 - Configure and Deploy source.war Webapp
----------------------------------------------

To configure the webapp source.war, look into the parameters defined in
web.xml of source.war file and change them (see note1) appropriately.

    * HEADER: is the fragment of HTML that will be used to display title or
              logo of your project
    * SRC_ROOT: absolute path name of the root directory of your source tree
    * DATA_ROOT: absolute path of the directory where OpenGrok data
                 files are stored
       - Header file 'header_include' can be created under DATA_ROOT.
	 The contents of this file file will be appended to the header of each
	 web page after the OpenGrok logo element.
       - Footer file 'footer_include' can be created under DATA_ROOT.
	 The contents of this file file will be appended to the footer of each
	 web page after the information about last index update.

5.4.3 - Path Descriptions (optional)
------------------------------------

OpenGrok can use path descriptions in various places (e.g. while showing
directory listings or search results). Example descriptions are in paths.tsv
file (delivered as /usr/opengrok/doc/paths.tsv by OpenGrok package on Solaris).
The paths.tsv file is read by OpenGrok indexing script from the configuration
directory (the same where configuration.xml is located) which will create file
dtags.eftar in the index subdirectory under DATA_ROOT directory which will
then be used by the webapp to display the descriptions.

The file contains descriptions for directories one per line. Path to the
directory and its description are separated by tab. The path to the directory
is absolute path under the SRC_ROOT directory.

For example, if the SRC_ROOT directory contains the following directories:

foo
bar
bar/blah
random
random/code

then the paths.tsv file contents can look like this:

/foo	source code for foo
/bar	source code for bar
/bar/blah	source code for blah

Note that only some paths can have a description.

5.4.4 - Changing webapp parameters (optional)
---------------------------------------------

web.xml is the deployment descriptor for the web application. It is in a Jar
file named source.war, you can change it as follows:

    * Option 1: Unzip the file to TOMCAT/webapps/source/ directory and
     change the source/WEB-INF/web.xml and other static html files like
     index.html to customize to your project. 
    
    * Option 2: Extract the web.xml file from source.war file

     $ unzip source.war WEB-INF/web.xml

     edit web.xml and re-package the jar file. 

     $ zip -u source.war WEB-INF/web.xml

     Then copy the war files to <i>TOMCAT</i>/webapps directory.

    * Option 3: Edit the Context container element for the webapp

     Copy source.war to TOMCAT/webapps

     When invoking OpenGrok to build the index, use -w <webapp> to set the 
     context. If you change this(or set using OPENGROK_WEBAPP_CONTEXT) later, 
     FULL clean reindex is needed.

     After the index is built, there's a couple different ways to set the
     Context for the servlet container:
     - Add the Context inside a Host element in TOMCAT/conf/server.xml

     <Context path="/<webapp>" docBase="source.war">
        <Parameter name="DATA_ROOT" value="/path/to/data/root" override="false" />
        <Parameter name="SRC_ROOT" value="/path/to/src/root" override="false" />
        <Parameter name="HEADER" value='...' override="false" />
     </Context>

     - Create a Context file for the webapp

     This file will be named `<webapp>.xml'.

     For Tomcat, the file will be located at:
     `TOMCAT/conf/<engine_name>/<hostname>', where <engine_name>
     is the Engine that is processing requests and <hostname> is a Host
     associated with that Engine.  By default, this path is
     'TOMCAT/conf/Catalina/localhost' or 'TOMCAT/conf/Standalone/localhost'.

     This file will contain something like the Context described above.

5.4.5 Custom ctags configuration
--------------------------------

To make ctags recognize additional symbols/definitions/etc. it is possible to
specify configuration file with extra configuration options for ctags.

This can be done by setting OPENGROK_CTAGS_OPTIONS_FILE environment variable
when running the OpenGrok shell script (or directly with the -o option for
opengrok.jar). Default location for the configuration file in the OpenGrok
shell script is etc/ctags.config under the OpenGrok base directory (by default
the full path to the file will be /var/opengrok/etc/ctags.config).

Sample configuration file for Solaris code base is delivered in the doc/
directory.

5.5 Using Java DB for history cache
-----------------------------------

By default OpenGrok stores history indexes in gzipped xml files. An alternative
is to use Java DB instead. This has the advantage of less disk space and
incremental indexing. Also, for some Source Code Management systems the
History view will show a list of files modified with given change.
On the other hand it consumes more system memory because the database has to
run in background.

Versions of Java DB from 10.5.3 to 10.8.3.0 are known to work.
Java DB 10.10.x.y versions are known to NOT work.
To install it perform the following steps:

Solaris 11:

   # pkg install library/java/javadb

Debian/Ubuntu:

  # apt-get install sun-java6-javadb

Other:

  Fetch the db-derby bundle from db.apache.org, and unpack to your preferred path.

1) Start the server:

  There are two modes, having Java DB embedded, or running a Java DB server.
  Java DB server is the default option, we will not describe how to set up the
  embedded one.

  Solaris 11:

    Use one of the following methods to start the database:
  
    a) via SMF (preferred):
  
       # svcadm enable javadb
  
    b) from command line:
  
       $ mkdir -p $DATA_ROOT/derby
       $ java -Dderby.system.home=$DATA_ROOT/derby \
           -jar /opt/SUNWjavadb/lib/derbynet.jar start
  
  Debian:

    $ mkdir -p $DATA_ROOT/derby
    $ java -Dderby.system.home=$DATA_ROOT/derby \
          -jar /usr/lib/jvm/java-6-sun/db/lib/derbynet.jar start


2) Copy derbyclient.jar to the lib directory 

  The derbyclient.jar is provided with Java DB installation.
  The lib directory is the one where opengrok.jar is located.
  E.g. for Tomcat it is located in the WEB-INF directory which was created
  as a result of deploying the source.war file.

Copy it over from:

  Solaris 11: /opt/SUNWjavadb/lib/derbyclient.jar
  Debian: /usr/lib/jvm/java-6-sun/db/lib/derbyclient.jar

  For example on Solaris 11 with bundled Java DB and Tomcat and OpenGrok
  installed from the OSOLopengrok package the command will be:

    # cp /opt/SUNWjavadb/lib/derbyclient.jar \
          /var/tomcat6/webapps/source/WEB-INF/lib/
    # cp /opt/SUNWjavadb/lib/derbyclient.jar \
          /usr/opengrok/lib

3) Use these options with indexer when indexing/generating the configuration:
   -D -H

   This is achieved by setting the OPENGROK_DERBY environment variable when
   using the OpenGrok shell script.

The Java DB server has to be running during indexing and for the web
application.

Note: To use a bigger database buffer, which may improve performance of both
indexing and fetching of history, create a file named derby.properties in
the JavaDB data directory and add this line to it:

  - If using specific data directory:

    # echo "derby.storage.pageCacheSize=25000" >> \
          $DATA_ROOT/derby/derby.properties

  - Using default directory on Solaris with JavaDB being run from SMF:

    # echo "derby.storage.pageCacheSize=25000" >> \
          /var/lib/javadb/data/derby.properties


6. Optional Command Line Interface Usage
----------------------------------------

You need to pass location of project file + the query to Search class, e.g.
for fulltext search for project with above generated configuration.xml you'd
do:

  $ java -cp ./opengrok.jar org.opensolaris.opengrok.search.Search -R \
        /var/opengrok/etc/configuration.xml -f fulltext_search_string

 For quick help run:

  $ java -cp ./opengrok.jar org.opensolaris.opengrok.search.Search

7. Change web application properties or name
--------------------------------------------

You might need to modify the web application if you don't store the
configuration file in the default location
(/var/opengrok/etc/configuration.xml).

To configure the webapp source.war, look into the parameters defined in
WEB-INF/web.xml of source.war (use jar or zip/unzip or your preferred zip
tool to get into it - e.g. extract the web.xml file from source.war ($ unzip
source.war WEB-INF/web.xml) file, edit web.xml and re-package the jar file
(zip -u source.war WEB-INF/web.xml) ) file and change those web.xml
parameters appropriately. These sample parameters need modifying(there are
more options, refer to manual or read param comments).

    * CONFIGURATION - the absolute path to XML file containing project
    * configuration (e.g. /var/opengrok/etc/configuration.xml )
    * ConfigAddress - port for remote updates to configuration, optional,
    * but advised(since there is no authentication) to be set to
    * localhost:<some_port> (e.g. localhost:2424), if you choose some_port
    * below 1024 you have to have root privileges

If you need to change name of the web application from source to something
else you need to use special option -w <new_name> for indexer to create
proper xrefs, besides changing the .war file name. Be sure that when this
changed you reindex cleanly from scratch. Examples below show just
deploying source.war, but you can use it to deploy your new_name.war too.

Deploy the modified .war file in glassfish/Sun Java App Server:

  * Option 1: Use browser and log into glassfish web administration interface

    Common Tasks / Applications / Web Applications , button Deploy and point
    it to your source.war webarchive

  * Option 2: Copy the source.war file to
    GLASSFISH/domains/YOURDOMAIN/autodeploy directory, glassfish will try
    to deploy it "auto magically".
    
  * Option 3: Use cli from GLASSFISH directory:

    # ./bin/asadmin deploy /path/to/source.war

Deploy the modified .war file in tomcat:

  * just copy the source.war file to TOMCAT_INSTALL/webapps directory.

8. OpenGrok systray
-------------------

The indexer can be setup with agent and systray GUI control application.
This is optional step for those who wish to monitor and configure OpenGrok
from their desktop using systray application.

An example opengrok-agent.properties file is provided, which can be used when
starting special OpenGrok Agent, where you can connect with a systray GUI
application.

To start the indexer with configuration run:

  $ java -cp ./opengrok.jar org.opensolaris.opengrok.management.OGAgent \
        --config opengrok-agent.properties

Then from the remote machine one can run:

  $ java -cp ./opengrok.jar \
        org.opensolaris.opengrok.management.client.OpenGrokTrayApp

assuming configuration permits remote connections (i.e. not listening on
localhost, but rather on a physical network interface).

This agent is work in progress, so it might not fully work.

9. Information for developers
-----------------------------

9.0 Building
------------

Just run 'ant' from command line in the top-level directory or use build
process driven by graphical developer environment such as Netbeans.

Note: in case you are behind http proxy, use ANT_OPTS to download jflex, lucene
E.g. $ ANT_OPTS="-Dhttp.proxyHost=?.? -Dhttp.proxyPort=80" ant


9.0.1 Package build
-------------------

Run 'ant package' to create package (specific for the operating system this is
being executed on) under the dist/ directory.

9.1 Unit testing
----------------

Note: For full coverage report your system has to provide proper junit test 
environment, that would mean:

  - you have to use Ant 1.7 and above
  - at least junit-4.10.jar has to be in ant's classpath (e.g. in ./lib)
    - Example install in the top of the opengrok repository:

      $ cd lib
      $ wget http://.../junit-4.10.jar
      $ jar -xf junit-4.10.jar

  - install derby.jar to ant's classpath so that Java DB tests can be run
  - your PATH must contain directory with exuberant ctags binary
    - Note: make sure that the directory which contains exuberant ctags binary
      is prepended before the directory with plain ctags program.
  - your PATH variable must contain directories which contain binaries of
    appropriate SCM software which means commands hg, sccs, cvs, git, bzr, svn
    (svnadmin too). They must be available for the full report.

The tests are then run as follows:

  $ ant -lib ./lib test

To check if the test completed without error look for AssertionFailedError
occurences in the TESTS-TestSuites.xml file produced by the test run.

9.2 Using Findbugs
------------------

If you want to run Findbugs (http://findbugs.sourceforge.net/) on OpenGrok,
you have to download Findbugs to your machine, and install it where you have 
checked out your OpenGrok source code, under the lib/findbugs directory,
like this:

  $ cd ~/.ant/lib
  $ wget http://..../findbugs-x.y.z.tar.gz
  $ gtar -xf findbugs-x.y.z.tar.gz
  $ mv findbugs-x.y.z findbugs

You can now run ant with the findbugs target:

  $ ant findbugs
  ...
  findbugs:
   [findbugs] Executing findbugs from ant task
   [findbugs] Running FindBugs...
   [findbugs] Warnings generated: nnn
   [findbugs] Output saved to findbugs/findbugs.html

Now, open findbugs/findbugs.html in a web-browser, and start fixing bugs !

If you want to install findbugs some other place than ~/.ant/lib, you can
untar the .tar.gz file to a directory, and use the findbugs.home property to
tell ant where to find findbugs, like this (if you have installed fundbugs
under the lib directory):

  $ ant findbugs -Dfindbugs.home=lib/findbug

There is also a findbugs-xml ant target that can be used to generate XML files
that can later be parsed, e.g. by Jenkins.

9.3 Using Emma
--------------

If you want to check test coverage on OpenGrok, download Emma from
http://emma.sourceforge.net/. Place emma.jar and emma-ant.jar in the
opengrok/trunk/lib directory, or ~/.ant/lib.

Now you can instrument your classes, and create a jar file:

  $ ant emma-instrument

If you are using NetBeans, select File - "opengrok" Properties 
- libraries - Compile tab. Press the "Add JAR/Folder" and select
lib/emma.jar and lib/emma_ant.jar

If you are not using netbeans, you have to edit the file 
nbproject/project.properties, and add "lib/emma.jar" and 
"lib/emma_ant.jar" to the javac.classpath inside it.

Now you can put the classes into jars and generate distributable:

  $ ant dist

The classes inside opengrok.jar should now be instrumented.
If you use opengrok.jar for your own set of tests, you need 
emma.jar in the classpath.If you want to specify where to store 
the run time analysis, use these properties:

   emma.coverage.out.file=path/coverage.ec
   emma.coverage.out.merge=true

The coverage.ec file should be placed in the opengrok/trunk/coverage
directory for easy analyze.

If you want to test the coverage of the unit tests, you can
run the tests:

   $ ant test   
   
Alternatively press Alt+F6 in NetBeans to achieve the same.

Now you should get some output saying that Emma is placing runtime 
coverage data into coverage.ec.

To generate reports, run ant again:

  $ ant emma-report

Look at coverage/coverage.txt, coverage/coverage.xml and 
coverage/coverage.html to see how complete your tests are.

9.4 Using Checkstyle
--------------------

To check that your code follows the standard coding conventions,
you can use checkstyle from http://checkstyle.sourceforge.net/

First you must download checkstyle from http://checkstyle.sourceforge.net/ ,
You need Version 5.3 (or newer). Extract the package you have
downloaded, and create a symbolic link to it from ~/.ant/lib/checkstyle,
e.g. like this:

   $ cd ~/.ant/lib
   $ unzip ~/Desktop/checkstyle-5.3.zip
   $ ln -s checkstyle-5.3 checkstyle

You also have to create symbolic links to the jar files:

   $ cd checkstyle
   $ ln -s checkstyle-5.3.jar checkstyle.jar
   $ ln -s checkstyle-all-5.3.jar checkstyle-all.jar

To run checkstyle on the source code, just run ant checkstyle:

   $ ant checkstyle

Output from the command will be stored in the checkstyle directory.

If you want to install checkstyle some other place than ~/.ant/lib, you can
untar the .tar.gz file to a directory, and use the checkstyle.home property
to tell ant where to find checkstyle, like this (if you have installed 
checkstyle under the lib directory):

  $ ant checkstyle -Dcheckstyle.home=lib/checkstyle

9.5 Using PMD and CPD
---------------------

To check the quality of the OpenGrok code you can also use PMD
from http://pmd.sourceforge.net/.

How to install:

  $ cd ~/.ant/lib
  $ unzip ~/Desktop/pmd-bin-5.0.0.zip
  $ ln -s pmd-5.0.0/ pmd

You also have to make links to the jar files:

  $ cd ~/.ant/lib/pmd/lib
  $ ln -s pmd-5.0.0.jar pmd.jar
  $ ln -s jaxen-1.1.1.jar jaxen.jar
  $ ln -s asm-3.2.jar asm.jar

To run PMD on the rource code, just run ant pmd:

  $ ant pmd

Outout from the command will be stored in the pmd subdirectory:

  $ ls pmd
  pmd_report.html  pmd_report.xml

If you want to install PMD some other place than ~/.ant/lib, you can
unzip the .zip file to a directory, and use the pmd.home property
to tell ant where to find PMD, like this (if you have installed 
PMD under the lib directory):

  $ ant pmd -Dpmd.home=lib/pmd-5.0.0

To run CPD, just use the same as above, but use targets:

  $ ant cpd cpd-xml

Which will result in:

  $ ls pmd
  cpd_report.xml cpd_report.txt

9.6 Using JDepend
-----------------

To see dependencies in the source code, you can use JDepend from
http://clarkware.com/software/JDepend.html.

How to install:

  $ cd ~/.ant/lib
  $ unzip ~/Desktop/jdepend-2.9.zip
  $ ln -s jdepend-2.9/ jdepend
  $ cd jdepend/lib
  $ ln -s jdepend-2.9.jar jdepend.jar

How to analyze:

  $ ant jdepend

Output is stored in the jdepend directory:

  $ ls jdepend/
  report.txt  report.xml

9.7 Using SonarQube
-------------------

Use a sonar runner with included sonar-project.properties properties, 
e.g. using bash:

  $ cd <checkout_dir> # it has to contain sonar-project.properties!
  $ export SONAR_RUNNER_OPTS="-Xmx768m -XX:MaxPermSize=256m"
  $ export SERVERIP=10.163.26.78
  $ ~//Projects/sonar-runner-2.3/bin/sonar-runner \
    -Dsonar.host.url=http://${SERVERIP}:9000 
    -Dsonar.jdbc.url=jdbc:h2:tcp://${SERVERIP}:9092/sonar

9.8 Using Travis CI
-------------------

Please see .travis.yml, if your branch has this file,
you should be able to connect your Github to Travis CI.
OpenGroks Travis is here: https://travis-ci.org/OpenGrok/OpenGrok


10. Tuning OpenGrok for large code bases
---------------------------------------

While indexing big source repos you might consider using ZFS filesystem to give 
you advantage of datasets which can be flipped over or cloned when needed.
If the machine is strong enough it will also give you an option to 
incrementally index in parallel to having the current sources and index in sync.
(So tomcat sees certain zfs datasets, then you just stop it, flip datasets to 
the ones that were updated by SCM/index and start tomcat again - outage is 
minimal, sources+indexes are ALWAYS in sync, users see the truth)

OpenGrok script by default uses 2G of heap and 16MB per thread for flush size of 
lucene docs indexing(when to flush to disk).
It also uses default 32bit JRE.
This MIGHT NOT be enough. You might need to consider this:
Lucene 4.x sets indexer defaults:
 DEFAULT_RAM_PER_THREAD_HARD_LIMIT_MB = 1945;
 DEFAULT_MAX_THREAD_STATES = 8;
 DEFAULT_RAM_BUFFER_SIZE_MB = 16.0; 
 - which might grow as big as 16GB (though DEFAULT_RAM_BUFFER_SIZE_MB shouldn't
 really allow it, but keep it around 1-2GB)

 - the lucenes RAM_BUFFER_SIZE_MB can be tuned now using the parameter -m, so 
running a 8GB 64 bit server JDK indexer with tuned docs flushing(on Solaris 11):

 # export JAVA=/usr/java/bin/`isainfo -k`/java
 (or use /usr/java/bin/amd64/java )
 # export JAVA_OPTS="-Xmx8192m -server"
 # OPENGROK_FLUSH_RAM_BUFFER_SIZE="-m 256" ./OpenGrok index /source

Tomcat by default also supports only small deployments. For bigger ones you
MIGHT need to increase its heap which might necessitate the switch to 64-bit 
Java. It will most probably be the same for other containers as well.
For tomcat you can easily get this done by creating conf/setenv.sh:

 # cat conf/setenv.sh
 # 64-bit Java
 JAVA_OPTS="$JAVA_OPTS -d64 -server"

 # OpenGrok memory boost to cover all-project searches
 # (7 MB * 247 projects + 300 MB for cache should be enough)
 # 64-bit Java allows for more so let's use 8GB to be on the safe side.
 # We might need to allow more for concurrent all-project searches.
 JAVA_OPTS="$JAVA_OPTS -Xmx8g"

 export JAVA_OPTS


For tomcat you might also hit a limit for http header size (we use it to send 
the project list when requesting search results):
 - increase(add) in conf/server.xml maxHttpHeaderSize
  connectionTimeout="20000"
 maxHttpHeaderSize="65536"
  redirectPort="8443" />

Refer to docs of other containers for more info on how to achieve the same.


11. Authors
-----------

The project has been originally conceived in Sun Microsystems by Chandan B.N.

Chandan B.N, (originally Sun Microsystems) http://blogs.oracle.com/chandan/
Trond Norbye, norbye.org
Knut Pape, eBriefkasten.de
Martin Englund, (originally Sun Microsystems)
Knut Anders Hatlen, Oracle. http://blogs.oracle.com/kah/
Lubos Kosco, Oracle. http://blogs.oracle.com/taz/
Vladimir Kotal, Oracle. http://blogs.oracle.com/vlad/

12. Contact us
--------------

Feel free to participate in discussion on discuss@opengrok.java.net.

You can subscribe via web interface on:

  http://java.net/projects/opengrok/lists