Metacat

Downloading and Installing Metacat

==================================

-------------------

you wish to install Metacat must have the following software installed and

running correctly:

* `Apache Ant`_ (if building from source)

* `Apache Tomcat`_

* `Apache HTTPD Server`_ (recommended)

  * In order to use the Metacat Registry (and for a more robust Web-serving environment in general), the Apache Web server should be installed with Tomcat and the two should be integrated. See the installing Apache for more information.

.. _PostgreSQL: http://www.postgresql.org/

.. _Oracle: http://www.oracle.com/

.. _Apache Ant: http://ant.apache.org/

.. _Apache Tomcat: http://tomcat.apache.org/

.. _Apache HTTPD Server: http://httpd.apache.org/

System requirements for running Metacat:

* a server running an SQL92-compliant database (PostgreSQL_ recommended)

* 200 MB disk space (Note: The amount of disk space required depends on the size of your RDBMS tablespace and the the size and number of documents stored. Metacat itself requires only about 140 MB of free space after installation).

-------------------

Linux systems. As Mac OS X is based on BSD Unix, these Linux instructions can

be adapted to also work on Mac OS X (although the exact commands for

downloading and installing packages will differ due to the different package

management approaches on the Mac).

Quick Start Overview

~~~~~~~~~~~~~~~~~~~~

they are doing, here are the steps needed to install Metacat. Detailed

instructions for each step are in the next section.

3. Log in to PostgreSQL and create the 'metacat' user

4. Download Metacat from the `Metacat Download Page`_ and extract the archive

5. ``sudo mkdir /var/metacat; sudo chown -R <tomcat_user> /var/metacat``

.. _Metacat Download Page: http://knb.ecoinformatics.org/software/metacat/

~~~~~~~~~~~~~~~~~~~

installed and running correctly. To obtain a Metacat WAR file, which is needed

for installation, download one of the following:

* the Metacat source distribution, which must be built in order to create a WAR file,

* the Metacat source code from SVN. You must build the source code in order to create a WAR file.

Instructions for all three options are discussed below. Note that downloading

the installer (described in the next section) is the simplest way to get

started.

..............................

application. To download the installer:

3.  Extract the Metacat package files by typing:

::

  tar -xvzf metacat-bin-X.X.X.tar.gz

remainder of this documentation.

					Optional unless Metacat UI is being used.

metacat-ui.war     The Metacat UI - can be deployed as a webapp or directly in webserver

					Metacat UI requires metacat-index be deployed and configured.

............................

3. Extract the Metacat package files by typing (replace X.X.X with the current version number):

::

  tar -xvzf metacat-src-X.X.X.tar.gz

4. Rename the metacat-X.X.X directory to metacat.

Note that you do not need to create the WAR file directly because the Ant

build-file has an "install" target that will build and deploy the WAR for you.

.......................................................

    If you have not already installed Subversion and you are running Ubuntu/Debian,

    you can get the SVN client by typing:

    ::

        sudo apt-get install subversion

    Otherwise, you can get the SVN client from The Subversion homepage

    (http://subversion.tigris.org/).

If you wish to work with the most recent Metacat code, or you'd like to extend

the Metacat code yourself, you may wish to check out the Metacat source code

from SVN. You will need a Subversion (SVN) client installed and configured on

your system (see the end of this section for information about obtaining an SVN

client).

To check out the code from SVN, go to the directory where you would like the

code to live and type::

  svn co https://code.ecoinformatics.org/code/metacat/tags/METACAT_<rev> metacat

To check out the head, type::

  svn co https://code.ecoinformatics.org/code/metacat/trunk metacat

You should see a list of files as they check out.

Note that you do not need to create the WAR file directly because the Ant

build-file has an "install" target that will build and deploy the WAR for you.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

also highly recommend that you install Apache Web server, as it provides a more

robust Web-serving environment and is required by some Metacat functionality.

* `Apache HTTPD Server`_ (Highly Recommended)

* PostgreSQL_ Database (or Oracle_)

* `Apache Ant`_ (if building from Source)

are on your PATH.

.. _Ubuntu: http://www.ubuntu.com/

Apache Tomcat

.............

should be installed as well.

Note: we will refer to the Tomcat installation directory as ``<tomcat_home>`` for

the remainder of the documentation.

If you are running Ubuntu_/Debian, get Tomcat by typing::

Otherwise, get Tomcat from the `Apache Tomcat`_ page.

  sudo update-alternatives --config java

  <tomcat_home>/conf/server.xml

For DataONE deployments edit::

to include::

	org.apache.tomcat.util.buf.UDecoder.ALLOW_ENCODED_SLASH=true

	org.apache.catalina.connector.CoyoteAdapter.ALLOW_BACKSLASH=true

........................................

Although you have the option of running Metacat with only the Tomcat server, we

highly recommend that you run it behind the Apache Web server for several

reasons; running Tomcat with the Apache server provides a more robust Web

install and run the Metacat Registry or to use the Metacat Replication feature.

.. sidebar:: Configuring Apache on an OS other than Ubuntu/Debian

  If you are running on an O/S other than Ubuntu/Debian (e.g., Fedora Core or

  RedHat Linux) or if you installed the Apache source or binary, you must

  manually edit the Apache configuration file, where <apache_install_dir> is the

  directory in which Apache is installed:

  ::

    <apache_install_dir>/conf/httpd.conf

  1. Configure the log location and level for Mod JK. If your configuration file does not already have the following section, add it and set the log location to any place you'd like:

    ::

      <IfModule mod_jk.c>

        JkLogFile "/var/log/tomcat/mod_jk.log"

        JkLogLevel info

      </IfModule>

  2. Configure apache to route traffic to the Metacat application. ServerName should be set to the DNS name of the Metacat server. ScriptAlias and the following Directory section should both point to the cgi-bin directory inside your Metacat installation:

    ::

      <VirtualHost XXX.XXX.XXX.XXX:80>

        DocumentRoot /var/www

        ServerName dev.nceas.ucsb.edu

        ErrorLog /var/log/httpd/error_log

        CustomLog /var/log/httpd/access_log common

        <Directory /var/www/cgi-bin/>

          Options ExecCGI

          Order allow,deny

          Allow from all

        </Directory>

        <Directory "/var/www/webapps/metacat/cgi-bin/">

          Options ExecCGI

          Order allow,deny

          Allow from all

        </Directory>

        JkMount /metacat ajp13

        JkMount /metacat/* ajp13

        JkUnMount /metacat/cgi-bin/* ajp13

        JkMount /*.jsp ajp13

  3. Copy the "workers.properties" file provided by Metacat into your Apache configuration directory (<apache_install_dir>/conf/).  Depending on whether you are installing from binary distribution or source, the workers.properties file will be in one of two locations:

    * the directory in which you extracted the Metacat distribution (for binary distribution)

    * <metacat_code_dir>/src/scripts/workers.properties (for both the source distribution and source code checked out from SVN)

  4. Edit the workers.properties file and make sure the following properties are set correctly:

    ::

      workers.tomcat_home -  set to the Tomcat install directory.

      workers.java_home - set to the Java install directory.

  5. Restart Apache to bring in changes by typing:

    ::

      sudo /etc/init.d/apache2 restart

This section contains instructions for installing and configuring the Apache

Web server for Metacat on an Ubuntu_/Debian system. Instructions for configuring

Apache running on other Linux systems are included in the sidebar.

1. Install the Apache and Mod JK packages (Mod JK is the module Apache uses to talk to Tomcat applications) by typing:

::

  sudo apt-get install apache2 libapache2-mod-jk

If you are installing the Apache server on an Ubuntu/Debian system, and you

installed Apache using apt-get as described above, the Metacat code will have

helper files that can be dropped into directories to configure Apache.

Depending on whether you are installing from binary distribution or source,

these helper files will be in one of two locations:

* the directory in which you extracted the distribution (for binary distribution)

* ``<metacat_code_dir>/src/scripts`` (for both the source distribution and source code checked out from SVN).  We will refer to the directory with the helper scripts as ``<metacat_helper_dir>`` and the directory where Apache is installed (e.g., ``/etc/apache2/``) as ``<apache_install_dir>``.

2. Set up Mod JK apache configuration by typing:

::

  sudo cp <metacat_helper_dir>/debian/workers.properties <apache_install_dir>

3. Disable and re-enable the Apache Mod JK module to pick up the new changes:

::

  sudo a2dismod jk

  sudo a2enmod jk

::

  sudo a2ensite metacat-site.conf

5. Disable the default Apache site configuration:

6. Restart Apache to bring in changes by typing:

  sudo /etc/init.d/apache2 restart

Metacat has been most widely tested with PostgreSQL_ and we recommend using it.

Instructions for installing and configuring Oracle are also included in the

next section.  To install and configure PostgreSQL_:

1. If you are running Ubuntu_/Debian, get PostgreSQL by typing:

  ::

    sudo apt-get install postgresql

  On other systems, install the rpms for postgres.

2. Start the database by running:

  ::

3. Change to postgres user:

  ::

    sudo su - postgres

4. Set up an empty Metacat database instance by editing the postgreSQL configuration file:

  ::

  Add the following line to the configuration file:

  ::

    host metacat metacat 127.0.0.1 255.255.255.255 password

  Save the file and then create the Metacat instance:

  ::

    createdb metacat

5. Log in to postgreSQL by typing:

  ::

    psql metacat

6. At the psql prompt, create the Metacat user by typing:

  ::

    CREATE USER metacat WITH UNENCRYPTED PASSWORD 'your_password';

  where 'your_password' is whatever password you would like for the Metacat user.

7. Exit PostgreSQL by typing

  ::

    \q

8. Restart the PostgreSQL database to bring in changes:

  ::

9. Log out of the postgres user account by typing:

  ::

    logout

10. Test the installation and Metacat account by typing:

  ::

    psql -U metacat -W -h localhost metacat

11. Log out of postgreSQL:

  ::

    \q

The Metacat servlet automatically creates the required database schema. For

more information about configuring the database, please see Database

Configuration.

Enable it by logging in as an Oracle user and typing::

recommended). You must also create and enable a username specific to Metacat.

The Metacat user must have most normal permissions including: CREATE SESSION,

CREATE TABLE, CREATE INDEX, CREATE TRIGGER, EXECUTE PROCEDURE, EXECUTE TYPE,

etc. If an action is unexplainably rejected by Metacat, the user permissions

are (most likely) not correctly set.

The Metacat servlet automatically creates the required database schema. For

more information, please see Database Configuration.

Apache Ant (if building from Source)

....................................

If you are building Metacat from a source distribution or from source code

checked out from SVN, Ant is required. (Users installing Metacat from the

binary distribution do not require it.) Ant is a Java-based build application

similar to Make on UNIX systems. It takes build instructions from a file named

"build.xml", which is found in the root installation directory. Metacat source

code comes with a default "build.xml" file that may require some modification

upon installation.

If you are running Ubuntu/Debian, get Ant by typing::

  sudo apt-get install ant

Otherwise, get Ant from the `Apache Ant`_ homepage.

Ant should be installed on your system and the "ant" executable shell script

should be available in the user's path. The latest Metacat release was tested

~~~~~~~~~~~~~~~~~~

below.

...........

Before installing Metacat, please ensure that all required applications are

installed, configured to run with Metacat, and running correctly. If you are

upgrading an existing Metacat servlet, please skip to Upgrade. For information

about installing from source, skip to Source Install and Upgrade.

To install a new Metacat servlet:

1. Create the Metacat directory. Metacat uses a base directory to store data, metadata, temporary files, and configuration backups. This directory should be outside of the Tomcat application directory so that it will not get wiped out during an upgrade. Typically, the directory is '/var/metacat', as shown in the instructions. If you choose a different location, remember it. You will be asked to configure Metacat to point to the base directory at startup.  Create the Metacat directory by typing:

  ::

    sudo mkdir /var/metacat

2. Change the ownership of the directory to the user that will start Tomcat by typing (note: If you are starting Tomcat as the root user, you do not need to run the chown command):

  ::

    sudo chown -R <tomcat_user> /var/metacat

  ::

4. Restart Tomcat. Log in as the user that runs your Tomcat server (often "tomcat") and type:

  ::

Congratulations! You have now installed Metacat. If everything is installed

correctly, you should see the Authentication Configuration screen (Figure 2.1)

when you type http://yourserver.com/yourcontext/ (e.g.,

http://knb.ecoinformatics.org/knb) into a browser. For more information about

configuring Metacat, please see the Configuration Section.

   The Authentication Configuration screen appears the first time you open a

   new installation of Metacat.

Upgrade Metacat

...............

To upgrade an existing binary Metacat installation follow the steps in this

section. The steps for upgrading Metacat from source are the same as the

instructions for installing from source:

1. Download and extract the new version of Metacat. For more information about downloading and extracting Metacat, please see Downloading Metacat.

2. Stop running Metacat. To stop Metacat, log in as the user that runs your Tomcat server (often "tomcat") and type:

  ::

3. Back up the existing Metacat installation. Although not required, we highly recommend that you back up your existing Metacat to a backup directory (<backup_dir>) before installing a new one. You can do so by typing:

  ::

    cp <web_app_dir>/metacat.war <backup_dir>/metacat.war.<yyyymmdd>

  Warning: Do not backup the files to the ``<web_app_dir>`` directory.  Tomcat will

  try to run the backup copy as a service.

4. Copy the new Metacat WAR file in to the Tomcat applications directory:

  ::

  Note: Typically, Tomcat will look for its application files (WAR files) in the

  ``<tomcat_home>/webapps`` directory. Your instance of Tomcat may be configured to

  look in a different directory.

5. If you have been (or would like to start) running an LSID server, copy the new authority.war file to the Tomcat applications directory. For more information about the LSID server, please see Optional Installation Options.

  ::

    sudo cp <metacat_package_dir>/authority.war <tomcat_app_dir>

6. Restart Tomcat (and Apache if you have Tomcat integrated with it). Log in as the user that runs your Tomcat server (often "tomcat"), and type:

  ::

7. Run your new Metacat servlet. Go to a Web browser and visit your installed

Metacat application, using a URL of the form:

  ::

    http://yourserver.yourdomain.com/yourcontext/

You should substitute your context name for "yourcontext" in the URL above

with Metacat's Authorization Configuration screen. Note that if you do not have

Tomcat integrated with Apache you will probably have to type

http://yourserver.yourdomain.com:8080/yourcontext/

Source Install and Upgrade

..........................

Whether you are building Metacat from the source distribution or source code

checked out from SVN, you will need Apache Ant to do the build (see Installing

and Configuring Required Software for more information about Ant).

To install Metacat from source:

1. Edit the build.properties file found in the directory in which you

   downloaded Metacat. Note: Throughout the instructions, we will refer to this

   directory as ``<metacat_src_dir>``.

  * Set the build.tomcat.dir property to your Tomcat installation directory.

    Metacat will use some of the native Tomcat libraries during the build. For

    instance: build.tomcat.dir=/usr/local/tomcat

  * Set the app.deploy.dir property to your application deployment directory.

    For instance: app.deploy.dir=/usr/local/tomcat/webapps

2. In the ``<metacat_src_dir>``, run:

  ::

    sudo ant clean install

  You will see the individual modules get built. You should see a "BUILD

  SUCCESSFUL" message at the end.

To run your new Metacat servlet, open a Web browser and type::

  http://yourserver.yourdomain.com/yourcontext/

is running, you will be presented with the Authorization Configuration screen.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

  The support for LSID identifiers is deprecated, and is being replaced with

  support for DOI_ identifiers in a future release. We are maintaining support

  for LSIDs on one particular site, but this support will be removed in a

  future version of Metacat.

.. _DOI: http://www.doi.org/

Metacat's optional LSID server allows Metacat to use a standardized syntax for

identifying data sets, in addition to Metacat's internal, custom scheme for

identifiers. LSID's were designed to identify complex biological entities with

short identifiers (much like DOIs in publishing) that are both computer and

human readable. LSID identifiers are URIs and are therefore usable in many

Internet applications, but they also cleanly separate the identity of a data

set (i.e., its permenant identifier) from its current location (e.g., the list

of URLs from which it might be retrieved).  LSIDs accomplish this by using a

level of indirection; the identifier represents simply a name without location,

but an associated resolver service can be used to locate the current location

of the data and medata for the data set.  This is accomplished by establishing

a well-known location for the resolution service for each authority using an

infrequently used feature of the domain name system called SRV records.  At its

most basic, resolution of an identifier is performed when a client looks up the

SRV record for an LSID by querying DNS, which returns the current host and port

of the authority web service, which is in turn used to locate the data and

metadata.

Using LSIDs to identify data records is being debated among members of the

Taxonomic Databases Working Group (TDWG).  There are several alternate

technologies that are under consideration (e.g., DOI_, plain http URIs), and so

at this time the support for LSIDs in Metacat has been created on an

experimental basis only.  If the LSID approach is ratified by the broader

community, we will expand support for LSIDs in Metacat, but until then it is an

optional and experimental feature.

The format of an LSID is::

  urn:lsid:<Authority>:<Namespace>:<ObjectID>[:<Version>]

  e.g., urn:lsid:ecoinformatics.org:tao:12039:1

When you enable the Metacat LSID support, you can use LSID clients (such as

LSID Launchpad) and LSID notation to query Metacat for data and metadata. LSID

notation can be used directly in Metacat HTTP queries as well. For example, a

data package with an ID tao.12039.1 that is stored in a Metacat available at:

http://example.com:9999 can be accessed by the following HTTP Metacat queries::

  http://example.com:9999/authority/data?lsid=urn:lsid:ecoinformatics.org:tao:12039:1

  (To return the data)

  http://example.com:9999/authority/metadata?lsid=urn:lsid:ecoinformatics.org:tao:12039:1

  (To return the metadata)

Notice that in the HTTP query strings, the periods in the data package ID have

been replaced with colons. The authority (ecoinformatics.org) must be properly

configured by the Metacat administrator. Note: In order to configure the

authority, you must have access to the DNS server for the Metacat domain.

Further instructions are provided below.

Install and configure the LSID Server shipped with Metacat

..........................................................

To install the LSID server using the binary installation:

1. Copy the authority.war file to Tomcat:

  ::

2. Set up the LSID server by dropping the authority file into Apache's

   sites-available directory and running a2ensite to enable the site:

   ::

     sudo cp <metacat_helper_dir>/authority /etc/apache2/sites-available

     sudo a2ensite authority

3. Restart Tomcat. Log in as the user that runs your Tomcat server (often

   "tomcat") and type:

   ::

     /etc/init.d/tomcat5.5 restart

4. Restart Apache to bring in changes by typing:

  ::

    sudo /etc/init.d/apache2 restart

5. See notes beneath LSID server source installation for instructions for

   modifying the SRV record(s)

To install the LSID server from a source

........................................

1. In the build.properties file found in the directory into which you

   extracted the Metacat source code, set the authority and config.lsidauthority

   properties. For example:

  ::

   authority.context=authority

   config.lsidauthority=ecoinformatics.org

2. In the <metacat-src-dirctory> create the authority.war by running:

  ::

    sudo ant war-lsid

3. Copy the LSID WAR file into the Tomcat application directory.

  ::

    sudo cp <metacat_package_dir>/dist/authority.war <tomcat_app_dir>

4. Restart Tomcat. Log in as the user that runs your Tomcat server (often

   "tomcat") and type:

  ::

5. If you are running Tomcat behind the Apache server (the recommended

   configuration), set up and enable the authority service site configurations by

   typing:

  ::

    sudo cp <metacat_helper_dir>/authority <apache_install_dir>/sites-available

    sudo a2ensite authority

  Where <metacat_helper_dir> can be found in <metacat_code_dir>/src/scripts

6.  Restart Apache to bring in changes by typing:

  ::

    sudo /etc/init.d/apache2 restart

  Once the authority.war is installed, you must also modify the SRV record(s)

  on the DNS server for the domain hosting the Metacat. The record should be

  added to the master zone file for the metacat's DNS server:

    ::

      _lsid._tcp      IN      SRV     1       0       8080    <metacat.edu>.

  Where <metacat.edu> is the name of the machine that will serve as the

  physical location of the AuthorityService.

  For example, the value of <metacat.edu> for the below example URL would be

  example.com:

    ::

      http://example.com:9999/authority/data?lsid=urn:lsid:ecoinformatics.org:tao:12039:1

  For more information, please see http://www.ibm.com/developerworks/opensource/library/os-lsid/

~~~~~~~~~~~~~~~

website. See http://knb.ecoinformatics.org/software/metacat/troubleshooting.html

for more information.

Installing on Windows

---------------------

section for downloading Metacat, installing the required software, and

installing Metacat. Note that Registry and Data Upload functionality has not

been tested on Windows.

Download Metacat

~~~~~~~~~~~~~~~~

To obtain a Metacat WAR file, which is used when installing the Metacat

servlet:

1. Browse to the KNB Software Download Page. In the Metacat section, select

   the link that looks like: metacat-bin-X.X.X.zip, where X.X.X is the latest

2. Choose to download and Save the file locally.

3. Extract the Metacat package files using your Windows zip utility. You

   should see a WAR file and several supporting files (we will only use the WAR

   file when installing Metacat).

Note: The location where these files were extracted will be referred to as the

``<metacat_package_dir>`` for the remainder of this documentation.

Note: Before installing Metacat, please ensure that all required software is

installed and running correctly.

Install Required Software

~~~~~~~~~~~~~~~~~~~~~~~~~

Before you can install and run Metacat, you must ensure that a recent Java SDK,

PostgreSQL and Tomcat are installed, configured, and running correctly.

* PostgreSQL_ Database

are on your PATH.

To download and install Java:

   the instructions to download JDK 7.

2. Run the downloaded installer to install Java.

3. Set the JAVA_HOME environment variable: In "My Computer" properties, go to

   "advanced settings > environment variables". Add:

  ::

Apache Tomcat

.............

3. Extract Tomcat files to C:\Program Files\tomcat using the windows zip

   utility.

PostgreSQL Database

...................

Metacat can be run with several SQL92-compliant database systems, but it has

been most widely tested with PostgreSQL_. Instructions for installing and

configuring PostgreSQL for use with Metacat are included in this section.

To download and install PostgreSQL:

1. Browse to http://www.postgresql.org/download/windows and download the

   one-click installer

2. Run the installer

3. Edit C:\Program Files\PostgreSQL\8.3\data and add:

  ::

    host metacat metacat 127.0.0.1 255.255.255.255 password

4. Create a super user. At the command line, enter:

  ::

    C:\Program Files\PostgreSQL\8.3\bin

    createdb -U postgres metacat (enter super user password)

5. Log in to PostgreSQL:

  ::

    psql -U postgres metacat (enter super user password)

6. Create a Metacat user:

  ::

    CREATE USER metacat WITH UNENCRYPTED PASSWORD 'your_password'

7. Exit PostgreSQL:

  ::

    \q

8. Restart PostgreSQL from the start menu by selecting:

  ::

    run start/All Programs/PostgreSQL 8.3/Stop Server

    run start/All Programs/PostgreSQL 8.3/Start Server

9. Test the installation by logging in as the metacat user:

  ::

10. Exit PostgreSQL:

  ::

    \q

The Metacat servlet automatically creates the required database schema. For

more information, please see Database Configuration.

Installing Metacat

~~~~~~~~~~~~~~~~~~

Instructions for a new install and for an upgrade are included below.

New Install

...........

Before installing Metacat, please ensure that all required applications are

installed, configured to run with Metacat, and running correctly. If you are

upgrading an existing Metacat servlet, please skip to Upgrade.

To install a new Metacat servlet:

1. Create the Metacat base directory at:

  ::

    C:/Program Files/metacat

2. Copy the Metacat WAR file to Tomcat (for information about obtaining a

   Metacat WAR file, see Download Metacat):

  ::

3.  Restart Tomcat:

  ::

    C:\Program Files\tomcat\shutdown.bat

    C:\Program Files\tomcat\startup.bat

Congratulations! You are now ready to configure Metacat. Please see the

Configuration Section for more information.

Upgrade

.......

To upgrade an existing Metacat installation:

1. Download and extract the new version of Metacat. For more information about

   downloading and extracting Metacat, please see Download Metacat.

2. Back up the existing Metacat installation. Although not required, we highly

   recommend that you back up your existing Metacat to a backup directory

   (<backup_dir>) before installing a new version. You can do so by copying:

  ::

    <web_app_dir>/metacat.war to <backup_dir>/metacat.war.<yyyymmdd>

3.  Copy the new Metacat WAR file in to Tomcat applications directory:

  ::

4.  Restart Tomcat:

  ::

    C:\Program Files\tomcat\shutdown.bat

    C:\Program Files\tomcat\startup.bat

Congratulations! You are now ready to configure Metacat. Please see Configuring

Metacat for more information.