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Instructions for the Linux system is included in this section.

Contents

• Downloading and Installing Metacat
  • Installing on Linux
    • Downloading Metacat
    • Installing and Configuring Required Software
    • Installing Metacat
    • Optional Installation Options (LSID Server)

In addition to meeting the recommended system requirements, the server on whichyou wish to install Metacat must have the following software installed andrunning correctly:

• Apache Ant (if building from source)
• 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.
• Java 8 (Note: Java 7 is deprecated)

System requirements for running Metacat:

• a server running PostgreSQL database
• at least 512MB RAM
• 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).

This section contains instructions for downloading and installing Metacat onLinux systems. As Mac OS X is based on BSD Unix, these Linux instructions canbe adapted to also work on Mac OS X (although the exact commands fordownloading and installing packages will differ due to the different packagemanagement approaches on the Mac).

For the impatient or those who have already installed Metacat and know whatthey are doing, here are the steps needed to install Metacat. Detailedinstructions for each step are in the next section.

1. Download and install prerequisites (Java 8, Apache Tomcat 7, PostgreSQL, Apache HTTPD Server)
2. Create a database in PostgreSQL named ‘metacat’ and authorize access to it in pb_hba.conf for the user ‘metacat’
3. Log in to PostgreSQL and create the ‘metacat’ user
4. Download Metacat from the Metacat Download Page and extract the archive
5. sudomkdir/var/metacat;sudochown-R<tomcat_user>/var/metacat
6. sudocp<metacat_package_dir>/metacat.war<tomcat_app_dir>
7. sudocp<metacat_package_dir>/metacat-index.war<tomcat_app_dir>
8. sudocp<metacat_package_dir>/metacatui.war<tomcat_app_dir>
9. sudo/etc/init.d/tomcat7restart
10. Configure Metacat through the Web interface

Before installing Metacat, please ensure that all required software isinstalled and running correctly. To obtain a Metacat WAR file, which is neededfor installation, download one of the following:

• the Metacat installer, which has a pre-built WAR file,
• 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 downloadingthe installer (described in the next section) is the simplest way to getstarted.

Downloading the Metacat Installer is the simplest way to get started with theapplication. To download the installer:

1. Browse to the Metacat Download Page. In the Metacat section, select the link to the “GZIP file” (the link should look like: metacat-bin-X.X.X.tar.gz, where X.X.X is the latest version of Metacat e.g., 2.14.1)
2. Save the file locally.
3. Extract the Metacat package files by typing:

You should see a WAR file and several sample supporting files (Table 2.1). Theextraction location will be referred to as the <metacat_package_dir> for theremainder of this documentation.

To get the Metacat source distribution:

1. Browse to the Metacat Download Page. In the Metacat section, select the link to the Metacat Source code (it will look something like this: metacat-src-X.X.X.tar.gz, where X.X.X is the latest version of Metacat, e.g., 2.14.1).
2. Save the file locally.
3. Extract the Metacat package files by typing (replace X.X.X with the current version number):

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

Note that you do not need to create the WAR file directly because the Antbuild-file has an “install” target that will build and deploy the WAR for you.

To clone the repository from GitHub, go to the directory where you would like thecode to live and type:

The entire Metacat repository will be cloned to your local machine and the current branch is the master branch which is constantly maintained in a state ready for release. Detailed information about the code contribution please see:

Note that you do not need to create the WAR file directly because the Antbuild-file has an “install” target that will build and deploy the WAR for you.

Before you can install and run Metacat, you must ensure that a recent Java SDK,PostgreSQL, Ant (ifinstalling from source), and Tomcat are installed and running correctly. Wealso highly recommend that you install Apache Web server, as it provides a morerobust Web-serving environment and is required by some Metacat functionality.

• Apache HTTPD Server (Highly Recommended)
• PostgreSQL Database
• Apache Ant (if building from Source)

To run Metacat, you should use Java 8. Make sure that the JAVA_HOMEenvironment variable is properly set and that both java and javacare on your PATH.

To install Java if you are running Ubuntu/Debian, you can install using apt-get:

If you are not using Ubuntu/Debian, you can get Java from the Oracle website and install using the RPM installer.

We recommend that you install Tomcat 6 or 7 or 8 into the directory of your choice. The newer versions are preferred.Included with the Metacat download is a Tomcat-friendly start-up script thatshould be installed as well.

Note: we will refer to the Tomcat installation directory as <tomcat_home> forthe remainder of the documentation.

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

Otherwise, get Tomcat from the Apache Tomcat page.

After installing Tomcat, you can switch back to the Sun JDK by typing:

and selecting the correct Java installation.

If using Tomcat with Apache/mod_jk, enable the AJP connector on port 8009 by uncommenting that section in:

For DataONE deployments edit:

to include:

Note: If you’re running Tomcat using systemd, systemd sandboxes Tomcat limitingthe directories it can write to and prevents Metacat from operating correctly.Ensure the following lines exist in the service file for Tomcat (paths may vary depending on your configuration):

Although you have the option of running Metacat with only the Tomcat server, wehighly recommend that you run it behind the Apache Web server for severalreasons; running Tomcat with the Apache server provides a more robust Webserving environment. The Apache Web server is required if you wish toinstall and run the Metacat Registry or to use the Metacat Replication feature.

This section contains instructions for installing and configuring the ApacheWeb server for Metacat on an Ubuntu/Debian system. Instructions for configuringApache 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:

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If you are installing the Apache server on an Ubuntu/Debian system, and youinstalled Apache using apt-get as described above, the Metacat code will havehelper 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:

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

4. Apache needs to know about the Metacat site. The helper file named “metacat-site.conf” has rules that tell Apache which traffic to route to Metacat. Set up Metacat site by dropping the metacat-site file into the sites-available directory and running a2ensite to enable the site:

5. Disable the default Apache site configuration:

6. Restart Apache to bring in changes by typing:

Currently Metacat only supports PostgreSQL. You can choose the release versions of PostgreSQL 8, 9, 10 or 11. The newer versions are preferred. To install and configure PostgreSQL:

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

On other systems, install the rpms for postgres.

2. Start the database by running:

3. Change to postgres user:

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

Add the following line to the configuration file:

Save the file and then create the Metacat instance:

5. Log in to postgreSQL by typing:

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

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

7. Exit PostgreSQL by typing

8. Restart the PostgreSQL database to bring in changes:

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

10. Test the installation and Metacat account by typing:

11. Log out of postgreSQL:

The Metacat servlet automatically creates the required database schema. Formore information about configuring the database, please see DatabaseConfiguration.

From version 2.13.0, Metacat uses the external Solr HTTP server as thesearch engine. Unfortunately the Solr Debian packages that come with the Ubuntu operatingsystem are obsoleted and you have to install the binary packages by yourself. This sectionprovides guidance on how to setup Solr to run in production on *nix platforms, such as Ubuntu.

Metacat support Solr 8.4.1 and newer versions. You might download the binary releases from:

1. Go to the directory which contains the Solr release file and extract the installation script file by typing (assume the download file being solr-8.4.1.tgz):

2. Install Solr as the root user:

3. Ensure the Solr defaults file is group writable:

4. Check if the Solr service is running:

5. Make sure the firewall is running and the default port 8983 isn’t exposed externally (assume you are using ufw):

6. Increase Memory

By default, Solr sets the maximum Java heap size to 512M (-Xmx512m). Values between 10 and 20 gigabytes are not uncommon for production servers. When you need to change the memory settings for your Solr server, use the SOLR_JAVA_MEM variable in the environment specific include file (e.g. /etc/default/solr.in.sh) such as:

7. Tomcat and Solr User Management

The interaction of the Tomcat and Solr services can cause the file permission issues.Add the tomcat8 user to the solr group and the solr user to tomcat8 group to fix the problem:

8. Restart Solr server to make the new group setting effective (Important)

9. Check that the tomcat8 user and solr user are members of the appropriate groups with:

Note: If you’re running Tomcat using systemd, systemd sandboxes Tomcat limitingthe directories it can write to and prevents Metacat from operating correctly.Ensure the following lines exist in the service file for Tomcat (paths may vary depending on your configuration):

If you are building Metacat from a source distribution or from source codechecked out from SVN, Ant is required. (Users installing Metacat from thebinary distribution do not require it.) Ant is a Java-based build applicationsimilar to Make on UNIX systems. It takes build instructions from a file named“build.xml”, which is found in the root installation directory. Metacat sourcecode comes with a default “build.xml” file that may require some modificationupon installation.

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

Otherwise, get Ant from the Apache Ant homepage.

Ant should be installed on your system and the “ant” executable shell scriptshould be available in the user’s path. The latest Metacat release was testedwith Ant 1.8.2.

Instructions for a new install, an upgrade, and a source install are includedbelow.

Before installing Metacat, please ensure that all required applications areinstalled, configured to run with Metacat, and running correctly. If you areupgrading an existing Metacat servlet, please skip to Upgrade. For informationabout 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:

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):

3. Install the Metacat, Metacat-index and MetacatUI WAR in the Tomcat web-application directory. For instructions on downloading the Metacat WAR, please see Downloading Metacat. Typically, Tomcat will look for its application files (WAR files) in the <tomcat_home>/webapps directory (e.g., /usr/share/tomcat7/webapps). Your instance of Tomcat may be configured to look in a different directory. We will refer to the Tomcat application directory as <tomcat_app_dir>. NOTE: The name of the WAR file (e.g., metacat.war) provides the application context, which appears in the URL of the Metacat (e.g., http://yourserver.com/metacat/). To change the context, simply change the name of the WAR file to the desired name before copying it. To install the Metacat WAR:

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 installedcorrectly, 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 aboutconfiguring Metacat, please see the Configuration Section.

The Authentication Configuration screen appears the first time you open anew installation of Metacat.

To upgrade an existing binary Metacat installation follow the steps in thissection. The steps for upgrading Metacat from source are the same as theinstructions 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:

Warning: Do not backup the files to the <web_app_dir> directory. Tomcat willtry 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 tolook 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.

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 installedMetacat application, using a URL of the form:

You should substitute your context name for “yourcontext” in the URL above(your context will be “metacat” unless you change the name of the metacat.war file tosomething else). If everything is working correctly, you should be presentedwith Metacat’s Authorization Configuration screen. Note that if you do not haveTomcat integrated with Apache you will probably have to typehttp://yourserver.yourdomain.com:8080/yourcontext/

Whether you are building Metacat from the source distribution or source codechecked out from SVN, you will need Apache Ant to do the build (see Installingand 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 youdownloaded Metacat. Note: Throughout the instructions, we will refer to thisdirectory 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. Forinstance: 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

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2. In the <metacat_src_dir>, run:

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You will see the individual modules get built. You should see a “BUILDSUCCESSFUL” message at the end.

You should see a new file named metacat.war in your application deploymentdirectory.

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

Your context will be “metacat” unless you changed the name of the metacat.war file tosomething else. The servlet may require a few seconds to start up, but once itis running, you will be presented with the Authorization Configuration screen.

Note

The support for LSID identifiers is deprecated, and is being replaced withsupport for DOI identifiers in a future release. We are maintaining supportfor LSIDs on one particular site, but this support will be removed in afuture version of Metacat.

Metacat’s optional LSID server allows Metacat to use a standardized syntax foridentifying data sets, in addition to Metacat’s internal, custom scheme foridentifiers. LSID’s were designed to identify complex biological entities withshort identifiers (much like DOIs in publishing) that are both computer andhuman readable. LSID identifiers are URIs and are therefore usable in manyInternet applications, but they also cleanly separate the identity of a dataset (i.e., its permenant identifier) from its current location (e.g., the listof URLs from which it might be retrieved). LSIDs accomplish this by using alevel of indirection; the identifier represents simply a name without location,but an associated resolver service can be used to locate the current locationof the data and medata for the data set. This is accomplished by establishinga well-known location for the resolution service for each authority using aninfrequently used feature of the domain name system called SRV records. At itsmost basic, resolution of an identifier is performed when a client looks up theSRV record for an LSID by querying DNS, which returns the current host and portof the authority web service, which is in turn used to locate the data andmetadata.

Using LSIDs to identify data records is being debated among members of theTaxonomic Databases Working Group (TDWG). There are several alternatetechnologies that are under consideration (e.g., DOI, plain http URIs), and soat this time the support for LSIDs in Metacat has been created on anexperimental basis only. If the LSID approach is ratified by the broadercommunity, we will expand support for LSIDs in Metacat, but until then it is anoptional and experimental feature.

The format of an LSID is:

When you enable the Metacat LSID support, you can use LSID clients (such asLSID Launchpad) and LSID notation to query Metacat for data and metadata. LSIDnotation can be used directly in Metacat HTTP queries as well. For example, adata 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:

Notice that in the HTTP query strings, the periods in the data package ID havebeen replaced with colons. The authority (ecoinformatics.org) must be properlyconfigured by the Metacat administrator. Note: In order to configure theauthority, you must have access to the DNS server for the Metacat domain.Further instructions are provided below.

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’ssites-available directory and running a2ensite to enable the site:

3. Restart Tomcat. Log in as the user that runs your Tomcat server (often“tomcat”) and type:

4. Restart Apache to bring in changes by typing:

5. See notes beneath LSID server source installation for instructions formodifying the SRV record(s)

1. In the build.properties file found in the directory into which youextracted the Metacat source code, set the authority and config.lsidauthorityproperties. For example:

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

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

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 recommendedconfiguration), set up and enable the authority service site configurations bytyping:

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

6. Restart Apache to bring in changes by typing:

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 beadded to the master zone file for the metacat’s DNS server:

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

For example, the value of <metacat.edu> for the below example URL would beexample.com:

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

We keep and update a list of common problems and their solutions on the KNBwebsite. See http://knb.ecoinformatics.org/software/metacat/troubleshooting.htmlfor more information.

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Most Popular Metadata Editor Software for 2016 is Bulk Metadata Editor

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Bulk metadata editor software provides searching and replacing multiple metadata fields with ease and fast. It also allows bulk updating of metadata fields. It enables tagging for items as well as exhibits. It also provides themes with CSS changes and configuration that are easy to adapt. It is easy-to-use software. You can also see XML Sitemap Generator

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Metadata editor software is widely used to verify metadata information on various files and change them easily. They allow editing metadata for a large number of files in one stretch and they are very simple to use. They can handle a variety of file formats including video files and very useful software for various industries.