Page History

...

• --version - display what released version the tool came from
• --help - display a synopsis of command args and switches

For example:

bash ${REPO_HOME}/etc/upgrade.sh --version
upgrade.sh from release 1.1-MS4.00 SCM revision 5422

...

The repository is distributed as a single Zip file. It contains a file README which identifies the software release it was built from. It is the artifact produced by the Maven project:

org.eagle-i:eagle-i-repository-dist

...

We will call this directory REPO_HOME and it will appear in commands and scripts below as ${REPO_HOME}.
Create the repository home directory in your file system. It is useful to have a base eagle-i directory to place data and configuration used by other eagle-i applications. For example,

mkdir /opt/eaglei
mkdir /opt/eaglei/repo

If necessary (i.e if you created it using your own user-id), change ownership of the directory to the user-id under which Tomcat is running. If you followed the example above, change the ownership of the two directories using the -R option. For example, if the user-id under which Tomcat executes is tomcat, 

chown -R tomcat /opt/eaglei

Initialize it as a variable in your shell environment. In this example (Bourne/bash shell) the repository home directory is /opt/eaglei/repo :

REPO_HOME=/opt/eaglei/repo

...

Unpack the distribution Zip archive in a directory under /tmp:

cd /tmp
unzip repository-dist.zip

Move the contents of the unzipped directory to your repository home directory. In this example the distribution is version 1.1-MS1.00-SNAPSHOT

mv /tmp/repository-1.1-MS1.00-SNAPSHOT/* ${REPO_HOME}/.

List the contents of the home directory:

cd ${REPO_HOME}
ls

It should contain the subdirectories etc/ lib/ and webapps/

...

We will call this directory CATALINA_HOME and it will appear in commands and scripts below as

${CATALINA_HOME}

Initialize it as a variable in your shell environment. In this example (in Bourne/bash shell) the Tomcat'shome directory is /opt/tomcat:

CATALINA_HOME=/opt/tomcat

...

Ensure that your Tomcat server is run with the following options on its JVM. The simplest way to accomplish this is to have the environment variable JAVA_OPTS include those options, but each platform, distro, package etc. of Tomcat has its own mechanism for setting this variable. For example, on Fedora 14, it should be in the file /etc/tomcat6/tomcat6.conf. If you can't find your distribution's configuration file, you may create a file setenv.sh in tomcat's bin directory to add the environment variable:

...(ONLY DO THIS if you can't find your distribution's config file)
cd ${CATALINA_HOME}/bin
touch setenv.sh

Edit the configuration file (tomcat6.conf, setenv.sh or whatever your distribution uses) and add the following line:

JAVA_OPTS="-XX:PermSize=64M -XX:MaxPermSize=256M -Xmx1024m"

Add the following two system properties to file conf/catalina.properties under the CATALINA_HOME directory -- the same directory where you'll find server.xml. The value for both of these properties is the absolute path of the repository home directory. In this example, it is /opt/eaglei/repo:

# example
org.eaglei.repository.home = /opt/eaglei/repo
derby.system.home= /opt/eaglei/repo

...

Look in your Tomcat installation's main lib directory. If there are no files named derby.jar or derby-version.jar, you must install the Derby jars from the "scripts" distribution, e.g.

cp ${REPO_HOME}/lib/derby-* ${CATALINA_HOME}/lib/

...

Bourne/bash shell version:

....(ONLY DO THIS when ALREADY running Apache Derby!) 
export DERBY_HOME=my-derby-installation-toplevel 

C Shell/csh version:

....(ONLY DO THIS when ALREADY running Apache Derby!)
setenv DERBY_HOME my-derby-installation-toplevel 

...

1. Navigate to Tomcat's webapps directory. If there exist a directory named ROOT, move it aside. The eagle-i repository must be the ROOT application

   Code Blocknoformat
   cd ${CATALINA_HOME}/webapps mv ROOT ROOT.original

2. Copy the repository webapp to the Tomcat webapps directory:

   Code Blocknoformat
   cp ${REPO_HOME}/webapps/ROOT.war ${CATALINA_HOME}/webapps/.

3. Create your initial administrative user login. Think of a USERNAME and PASSWORD and substitute them for the upper case words in this command:

   Code Blocknoformat
   bash ${REPO_HOME}/etc/prepare-install.sh USERNAME PASSWORD ${REPO_HOME}

4. Start up Tomcat.
5. Run the finish-install script, which loads the data model ontology among other things. Note that you can also give it additional options to specify a personal name and email box for the initial admin user.

   Code Blocknoformat
   bash ${REPO_HOME}/etc/finish-install.sh USERNAME PASSWORD https://localhost:8443

   ...or, with username metadata included:

   Code Blocknoformat
   bash ${REPO_HOME}/etc/finish-install.sh \ -f firstname \ -l lastname \ -m admin@ei.edu \ USERNAME PASSWORD https://localhost:8443

6. Run the upgrade.sh script, which preforms additional configurations.

   Code Blocknoformat
   bash ${REPO_HOME}/etc/upgrade.sh USERNAME PASSWORD https://localhost:8443

7. Edit the file configuration.properties located in {${REPO_HOME} to reflect your installation. See the #Configuration section below for details on the property definitions and expected values.
8. Restart Tomcat to pick up these configuration changes. Confirm that the eagle-i repository is running by visiting the admin page (login with USERNAME and PASSWORD):

   Code Blocknoformat
   https://localhost:8443/repository/admin

...

The repository release is distributed as a single Zip file. It contains a file README whcih identifies the software release it was built from. It is the artifact produced by the Maven project:

org.eagle-i:eagle-i-repository-dist

...

1. Unpack the distribution Zip archive in a directory e.g. under /tmp:

   Code Blocknoformat
   cd /tmp unzip repository-dist.zip

2. Shut down your Tomcat java servlet container.
3. Delete the old repo webapp subdirectory and WAR file, since there should not be any local modifcations there. For example:

   Code Blocknoformat
   rm -rf ${CATALINA_HOME}/webapps/ROOT*

4. Save the current release files in case you have to roll back:

   Code Blocknoformat
   cd ${REPO_HOME} mv etc etc.old mv lib lib.old mv webapps webapps.old

5. Copy the distribution into place (in this example the distribution is version 1.7-MS1.01) -- note there are 2 steps:

   Code Blocknoformat
   cp -f -rp /tmp/repository-1.7-MS1.01/* ${REPO_HOME} cp ${REPO_HOME}/webapps/ROOT.war ${CATALINA_HOME}/webapps/.

6. Start up your tomcat java servlet container.
7. Run the upgrade script, substituting your admin's username and password:

   Code Blocknoformat
   bash ${REPO_HOME}/etc/upgrade.sh USERNAME PASSWORD https://localhost:8443

   Watch the output of upgrade.sh very carefully! Pay particular attention to the final status and any messages beginning "WARN", they will indicate problems you MUST resolve.
8. Confirm that it worked: visit the repo admin page, check for new version, and then follow the link to Show Data Model Ontology versions to confirm that "loaded" and "available" versions of the ontology are the same.When running the upgrade script, there may be messages about out-of-date NG_Internal and NG_Query graphs. Most likely, these are nothing to worry about -- check the release notes. These graphs are only initialized from static files when the repository was created, and afterward they accumulate statements, so reloading a new copy of the original data is not practical. Some releases may include instructions for making changes in these graphs when upgrading from previous versions.
9. Download the data migration toolkit that corresponds to your repository version (in this example, version 1.7-MS1.02) and run the data migration script, substituting your admin's username and password:

   Code Blocknoformat
   wget wget -O ${REPO_HOME}/etc/eagle-i-datatools-datamanagement.jar \ http://infra.search.eagle-i.net:8081/nexus/content/repositories/\ releases/org/eagle-i/eagle-i-datatools-datamanagement/1.7-MS1.02/\ eagle-i-datatools-datamanagement-1.7-MS1.02.jar bash ${REPO_HOME}/etc/data-migration.sh USERNAME PASSWORD https://localhost:8443

   Watch the output of data-migration.sh very carefully! Pay particular attention to the final status and any messages beginning "WARN", they will indicate problems you MUST resolve. In addition to the output on screen, the data-migration script will place a data migration report in the logs directory directly under /etc.

...

If you are using the Apache Tomcat version 6 container (which is recommended), you can add these system properties to file conf/catalina.properties - add lines like these: (note that the path /opt/eaglei/repo is just shown as an example)

org.eaglei.repository.home = /opt/eaglei/repo
derby.system.home= /opt/eaglei/repo

...

• eaglei.repository.namespace - The namespace URI prefix for Eagle-I resource instances created in the repository.
  • Every administrator should set this to a reasonable value for his/her site, because the default is NOT desireable.
  • The value must be a fully qualified, resolvable, HTTP URL.
  • For example, http://foo.bar.edu/i/
  • Use the http scheme, NOT https, since the container will redirect to https if necessary, but it is not possible to direct back if it becomes preferable to use http later.
  • The system-generated default is the hostname followed by /i/ -- but this is often wrong, since Java's determination of hostnames in a servlet container environment is not reliable.
• eaglei.repository.title - the decorative title for UI pages, should be set for cosmetic reasons.
  • Set this to the name of your site, e.g. "Miskatonic University School of Medicine".
• eaglei.repository.logo - URL of the logo image for your site, may be either relative URL (to refer to a image embedded in the webapp) or an absolute URL to use an image hosted elsewhere. It should be about 50 pixels high and a suitable with given the proportions.
• eaglei.repository.index.url - Set this to the URL to which you want the site's "root" (top-level index) page redirected. Although the repository is installed as the root webapp to have control over resolving Semantic Web URIs, it does not need the root page so this allows you to configure your site as you like.
• eaglei.repository.admin.backgroundColor - Lets you change the background color for admin web UI pages, to give admins an obvious cue when they are operating on e.g. the production vs. test repos. Value is CSS color expression, e.g. crayon name like "bisque" or hex #CCFFCC (Added in Release 1.2MS2 or 3)
• eaglei.repository.instance.xslt - path to XSL stylesheet used to transform the HTML output of the instance dissemination service. A value for this key is required to produce XHTML in the dissemination service; without it, the service returns the internal XML document describing the instance.
  • If it is a relative path then it must be located relative to the root of the web application, if absolute then it is in the filesystem at large.
  • The advantage of keeping your stylesheets external to the webapp is that you can change them easily, and don't have to modify the webapp from its default installation.
  • An example is provided at repository/styles/example.xsl which creates very simple HTML, as a demonstration of how to write an XSL stylesheet.
• eaglei.repository.instance.css - URI of the CSS stylesheet resource to be used to style instance dissemination pages. It must be an absolute path or absolute URL. The default is:

  Code Blocknoformat
  eaglei.repository.instance.css = /repository/styles/i.css

  eaglei.repository.instance.js - Comma-separated list of URLs of JavaScript files to load in the default Instance HTML dissemination page. Note that the order may be significant. URLs may be absolute or relative to the webapp. The default value is required to support the contact email popup:

  Code Block
  eaglei.repository.instance.js = [http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js], /repository/styles/i.js

• eaglei.repository.tbox.graphs - a comma-separated list of graph URIs making up the "TBox".
  You should never have to set this! It is configurable "just in case", and for testing/experimenting. For more information, see the section on inferencing in the API Manual.
  By default, the TBox consists of:
  • The repository's internal ontology, http://eagle-i.org/ont/repo/1.0/
  • The eagle-i data model ontology, http://purl.obolibrary.org/obo/ero.owl
• eaglei.repository.datamodel.source - the full name of a resource within the webapp which its itself a property file describing the RDF data model ontology. You should not need to set this, the default is adequate for the eagle-i applicaiton. Default is eaglei-datamodel.properties which is a built-in resource file.
  For a description of the contents of this properties file, see the separate document Guide to Data Model Configuration Properties
• eaglei.repository.sesame.dir - directory where Sesame RDF database files are created.
  • Defaults to sesame subdirectory of home dir.
• eaglei.repository.log.dir - Directory where log files are created.
  • Defaults to logs subdirectory of the home dir. 
  • You can also configure log4j explicitly by adding log4j properties to this file.
• eaglei.repository.sesame.indexes - index configuration for Sesame triple store. Must be a comma-separated list of index specifiers, see Sesame NativeStore configuration documentation for details. Use this to change the internal indexes Sesame maintains to process queries. It takes effect on next servlet container (tomcat) restart.

  Warning
  title WARNING
  If you have a configured value and wish to go back to the default, do NOT just delete this configuration property. If you do, Sesame will simply keep the existing indexes. You must change it to the original default value, which is documented int he default configuration file.

• eaglei.repository.slow.query - Value in seconds of time after which a SPARQL query should be considered "slow" and logged as such. Only affects the SPARQL Protocol endpoint service. Default is 0, which never logs. Use this to check for performance problems, since it logs the full text of the query and time of occurance in the regular log at INFO level.
• eaglei.repository.sparqlprotocol.max.time - Time limit, in seconds, of the maximum time allowed for a query invoked by the SPARQL Protocol endpoint. Note that this does not affect any internally-generated SPARQL queries.
  • Any user can override this setting to impose a shorter timeout by giving a value for the nonstandard time argument.
  • Only the Administrator can override with a longer timeout.
  • The built-in default is 600 seconds (10 min) if nothing is configured.
  • If a SPARQL Protocol request cannot be complted within the timeout, it returns an HTTP 413 status (result too large - it was the standard response code that comes closest to the concept).
• eaglei.repository.anonymous.user - This is a hack, only intended for testing the Anonymous role. Its value is a username, e.g. "nobody". If configured, when the designated user logs in, their session is downgraded to the Anonymous role; this allows explicit testing of Anonymous (vs. Authenticated) access even when the webapp configuration does not allow unauthenticated access. ONLY TESTERS SHOULD EVER NEED TO SET THIS.
• Configuring Contact Hiding:*The following properties control the contact hiding extension, which restricts the display of "contact location" properties of instances and instead offers an anonymous email option. Red properties are required *only if you enable contact hiding:
  • eaglei.repository.hideContacts - true|false, enables the contact hiding function. When it is false, none of the other properties are used.
  • eaglei.repository.postmaster - email address of repository administrator(s). User-generated messages about resources without a contact email address get sent here, as well as diagnostic messages. We recommend using an email list or alias so it can be changed or directed to multiple people.
  • eaglei.repository.mail.host - hostname of SMTP server for outgoing mail, defaults to localhost.
  • eaglei.repository.mail.port - TCP port number of SMTP server for outgoing mail, only necessary if using a non-default port for your chosen type of service.
  • eaglei.repository.mail.ssl - Use SSL for connection to SMTP server for outgoing mail, value is true or false.
  • eaglei.repository.mail.username - Username with which to authenticate to SMTP server for outgoing mail, default is unauthenticated.
  • eaglei.repository.mail.password - password with which to authenticate to SMTP server for outgoing mail, default is none.

...

Note that the properties file may also contain Log4J configuration properties. For example you can turn on debugging log output by adding this line:

log4j.logger.org.eaglei.repository=DEBUG, repository

...

The default log4j configuration sets up an appender named repository with buffered I/O for efficiency. Note that this means log messages will not appear in the log file immediately, but only after the logging volume fills a buffer. This is useless for interactive debugging through the logs. If you are doing interactive debugging and want to see more log detail, along with immediate results, you should add the properties:

log4j.logger.org.eaglei.repository=DEBUG, repository
log4j.appender.repository.BufferedIO=false
log4j.appender.repository.ImmediateFlush=true

Also note that the default configuration turns off additivity in the repo root Logger; this means its log events do not propagate up to e.g. the root logger. If you wish to turn it back on, add this to your configuration:

log4j.additivity.org.eaglei.repository=true

Here are all of the default log4j configuration properties:

log4j.logger.org.eaglei.repository=INFO, repository
log4j.additivity.org.eaglei.repository=false
log4j.appender.repository=org.apache.log4j.RollingFileAppender
log4j.appender.repository.File=${eaglei.repository.log.dir}/repository.log
log4j.appender.repository.ImmediateFlush=false
log4j.appender.repository.BufferedIO=true
log4j.appender.repository.Append=true
log4j.appender.repository.Encoding=UTF-8
log4j.appender.repository.layout=org.apache.log4j.PatternLayout
log4j.appender.repository.layout.ConversionPattern=%d{ISO8601} %p %c - %m%n

IMPORTANT NOTE: If you add logger configurations to tweak the level of a subset of the repo log hierarchy, you must add an additivity configuration to prevent log4j from applying the ancestor logger as well, which would result in double log entries. For example, this fragment shows a default log level of INFO but adds DEBUG logging of RepositoryServlet to get elapsed time messages:

log4j.logger.org.eaglei.repository=INFO, repository
log4j.additivity.org.eaglei.repository=false
log4j.logger.org.eaglei.repository.servlet.RepositoryServlet=DEBUG, repository
log4j.additivity.org.eaglei.repository.servlet.RepositoryServlet=false
log4j.appender.repository.BufferedIO=false
log4j.appender.repository.ImmediateFlush=true

...

1. Dissemination HTML pages, the head element contains a meta tag with the name eaglei.version, e.g.

   Code Blocknoformat
   <meta name="eaglei.version" content="1.1-MS5.00-SNAPSHOT" />

2. The repository admin home page /repository/admin lists application version info in a human-readable format.
3. The page /repository/version gives a complete breakdown of component versions, including repo source and the version of the OpenRDF Sesame database. It is XHTML, and it includes meta tags to be easy to scrape or transform.

...

As of release 1.1MS5 the repo can log the elapsed time (in milliseconds) for each service request. You must enable DEBUG level logging for the RepositoryServlet, as in this configuration example.

log4j.logger.org.eaglei.repository=INFO, repository
log4j.additivity.org.eaglei.repository=false
log4j.logger.org.eaglei.repository.servlet.RepositoryServlet=DEBUG, repository
log4j.additivity.org.eaglei.repository.servlet.RepositoryServlet=false
log4j.appender.repository.BufferedIO=false
log4j.appender.repository.ImmediateFlush=true

As of release 1.2MS3 the repo will also show the time spent on internal SPARQL queries, which can be useful when tuning Sesame indexes. Add these log4j configuration lines to see just the query log messages:

log4j.logger.org.eaglei.repository.util.SPARQL = DEBUG, repository
log4j.additivity.org.eaglei.repository.util.SPARQL = false

Then, you'll see log entries like this which you can correlate to requests from your application:

...service invocation examples:

2011-01-27 14:28:06,483 T=http-8443-1 DEBUG org.eaglei.repository.servlet.RepositoryServlet -  
============== Ending Request /repository/update (2,159 mSec elapsed)

2011-01-27 14:27:58,023 T=http-8443-1 DEBUG org.eaglei.repository.servlet.RepositoryServlet -  
============== Ending Request /repository/workflow/push (1,763 mSec elapsed)

... (internal query example:)

2011-04-15 14:13:28,383 T=http-8443-1 DEBUG org.eaglei.repository.util.SPARQL -  
SPARQL Query executed by by 
org.eaglei.repository.model.User:findAll at line 227 in elapsed time (mSec) 15

...

NO MESSAGE is printed upon success, which lets it run under cron.

Usage

Synopsis:

make-snapshot.sh username password repo-URL directory

...

Given a dump created in e.g. ${DUMPDIR}, to restore this dump on a newly-created, empty, repository, use these commands: (where ${REPOSITORY} is URL prefix of the repo)

curl -D - -s -S -u ADMIN:PASSWORD -F type=user -F format=application/x-trig \
-F content=@${DUMPDIR}/users.trig -F duplicate=replace \
-F transform=no ${REPOSITORY}/repository/import

curl -s -S -D - -u ADMIN:PASSWORD -F action=replace -F all= \
-F "content=@${DUMPDIR}/resources.trig;type=application/x-trig" \
${REPOSITORY}/repository/graph

...

in a differently-named directory each day, rotating through a week:

make-snapshot.sh ADMIN PASSWORD [https://localhost:8443] "daily_cron_`date +%u`"

move-everything.sh: Copying Everything Between Repositories or Files

...

The synopsis for copying from repository to repository:

Usage: move-everything.sh [--version|--version] [ -f | --force ]
[-exclude-users user,user,..|-exclude-users user,user,..] [-nousers]
from-username from-password from-repo-URL
to-username to-password to-repo-URL

The synopsis for copying from file to repository:

Usage: move-everything.sh [--version|--version] [ -f | --force ]
[-exclude-users user,user,..|-exclude-users user,user,..] [-nousers]
--from-snapshot directory --from-prefix from-prefix
to-username to-password to-repo-URL

...

Here is an example that copies from the production Harvard repo to a local one:

move-everything.sh bigbird PASSWORD [ https://harvard.eagle-i.net] \
bigbird PASSWORD [https://localhost:8443]

Here is an example that copies a snapshot the production Harvard repo to a local one:

make-snapshot bigbird PASSWORD [https://harvard.eagle-i.net] \
harvard.monday


move-everything.sh -f \
--from-snapshot harvard.monday \
--from-prefix [http://harvard.eagle-i.net/i/] \
bigbird PASSWORD [https://localhost:8443]

Hints

We strongly recommend you avoid using the Superuser (administrator) login on the source repository, to prevent accidentally obliterating it by getting the argument order wrong. Use an account that has read access to every graph (e.g. the Admin-Read-Only role). This restricts you to using the --nousers version of the command but in most cases that is adequate. See the #Procedures section for recommendations on how to maintain copies of repositories this way.

...

Run it with -h to get the synopsis:

Usage: move-resources [-verbose] [-replace]
[--type published|workspace]{ --file source-file --prefix uri-prefix | --source source-repo-url 
	--user login:password --graph src-graph-URI }
dest-repo-url dest-login:dest-password dest-graph-URI



(options may be abbreviated to first letter, e.g. -f)

...

Here is an example command, it copies from the Published graph on qa.harvard to an "Experimental" graph on the local repo (on https://localhost:8443)

move-resources -s [https://qa.harvard.eagle-i.net:8443] -u bert:ernie \
-g [http://eagle-i.org/ont/repo/1.0/NG_Published] [https://localhost:8443] \
root:password [http://eagle-i.org/ont/repo/1.0/NG_Experimental]



Moved 4694 data statements and 322 metadata statements.

...

1. Shut down tomcat. This is major surgery, and tomcats don't like to be vivisected no matter how much more satisfying you may find it.
2. Disable Java Security -- alternately, you could try to configure all the authorization grants to give the repository webapp access to the filesystem and property resources it needs, but I found it much easier to just disable java security. DO NOT RUN THE TOMCAT PROCESS AS ROOT if you do this, but you should not be running it as root in any case. That's just insane.
   1. Edit the file /etc/init.d/tomcat6 and change the following variable to look like this:

      Code Blocknoformat
      TOMCAT6_SECURITY=no

3. Install Derby jars: ONLY IF DERBY IS NOT ALREADY INSTALLED IN THE COMMON AREA OF YOUR TOMCAT. If another webapp is already using Derby, they should share that version.
   1. Find the Derby jars in the lib/ subdirectory under where you installed the create-user.sh script.
   2. Copy them to the Tomcat common library directory:

      Code Blocknoformat
      cp ${REPO-ZIP-DIR}/lib/derby* /usr/share/tomcat6/lib/

4. Install the webapp: First, get rid of any existing root webapp, then copy in the webapp (ROOT.war file from your installation kit) and be sure it is readable by the tomcat6 user:

   Code Blocknoformat
   rm /var/lib/tomcat6/webapps/ROOT*cp ROOT.war /var/lib/tomcat6/webapps/ROOT.war

5. Install cached webapp context: This is VERY IMPORTANT, and the Tomcat docs does not even mention it, but without it your server will be mysteriously broken. The file /etc/tomcat6/Catalina/localhost/ROOT.xml must be a copy of your app's context.xml. Redo this command after installing every new ROOT.war:

   Code Blocknoformat
   mkdir -p /etc/tomcat6/Catalina/localhost unzip -p /var/lib/tomcat6/webapps/ROOT.war META-INF/context.xml > /etc/tomcat6/Catalina/localhost/ROOT.xml

6. Add System Properties: Be sure you have added system properties to the file /etc/tomcat6/catalina.properties e.g.

   Code Blocknoformat
   org.eaglei.repository.home = /opt/eaglei/repoderby.system.home = /opt/eaglei/repo

   ...of course, the value of these properties will be your Repository Home Directory path.
7. Start up Tomcat:

   Code Blocknoformat
   sudo /etc/init.d/tomcat6 start

8. Troubleshooting: If there are problems, check the following places for logs (because packaged apps make everything so much easier):
   • /var/log/daemon.log - really dire tomcat problems and stdout/stderr go to syslog
   • /var/log/tomcat6/* - normal catalina logging
   • ${REPOSITORY_HOME}/logs/repository.log - default repo log file in release 1.1; under 1.0 the filename was default.log.

...

1. Discover your machine's primary IP address and set the ADDR shell variable: (Note that this assumes eth0 is your primary network interface --use ifconfig -a to see them all)

   Code Blocknoformat
   ADDR=`ifconfig eth0 | perl -ne 'print "$1\n" if m/\sinet addr\:(\d+\.\d+\.\d+\.\d+)\s/;'`

2. Run these iptables commands to redirect all port 80 requests to port 8080.

   Code Blocknoformat
   iptables -t nat -A OUTPUT -d localhost -p tcp --dport 80 -j REDIRECT --to-ports 8080 iptables -t nat -A OUTPUT -d $ADDR -p tcp --dport 80 -j REDIRECT --to-ports 8080 iptables -t nat -A PREROUTING -d $ADDR -p tcp --dport 80 -j REDIRECT --to-ports 8080

3. (If using SSL) Run these iptables commands to redirect all port 443 requests to port 8443.

   Code Blocknoformat
   iptables -t nat -A OUTPUT -d localhost -p tcp --dport 443 -j REDIRECT --to-ports 8443 iptables -t nat -A OUTPUT -d $ADDR -p tcp --dport 443 -j REDIRECT --to-ports 8443 iptables -t nat -A PREROUTING -d $ADDR -p tcp --dport 443 -j REDIRECT --to-ports 8443

4. Save the rules in the canonical place to be reloaded on boot:

   Code Blocknoformat
   iptables-save > /etc/iptables.rules

5. Create a script to be run by the network startup infrastructure that will reload the iptables whenever the network is configured on:

   Code Blocknoformat
   cat << EOF > /etc/network/if-pre-up.d/iptablesload #!/bin/sh iptables-restore < /etc/iptables.rules exit 0 EOF

6. Test by accessing your server both locally and remotely by the port-80 URL. Then reboot the machine and try it again to be sure the iptables commands are run correctly on boot.

...

1. Run this iptables command to redirect all port 80 requests to port 8080.

   Code Blocknoformat
   /sbin/iptables -t nat -I PREROUTING -p tcp --dport 80 -j REDIRECT --to-port 8080

2. Save the rules in the canonical place to be reloaded on boot:

   Code Blocknoformat
   /sbin/iptables-save

3. Update the startup settings so iptables will run upon reboot:

   Code Blocknoformat
   chkconfig --level 35 iptables on

4. Test by accessing your server both locally and remotely by the port-80 URL. Then reboot the machine and try it again to be sure the iptables commands are run correctly on boot.

...

Typical command to make a backup, in TriG format to a file, e.g. all-dump.trig (here highlighted in yellow) from a server running locally on port 80. In practice, you'll probably need to change all the highlighted parts, such as the username:password login credentials, and the hostname in the target URL if not running locally.

curl -G -X GET -s -S -u username:password -o all-dump.trig -d all \
--write-out 'status=%{http_code}, %{time_total}sec\n' \
-d format=application/x-trig [https://localhost:8443/repository/graph]

Be sure the output shows a successful status code (namely 200), as shown here, since curl will return a successful status even if the HTTP service did not succeed; curl only reports on the success of the network request-and-response transaction.

status=200, 13.283sec

Restore Repository from Backup

...

curl -s -S -u username:password -F action=replace -F all= \
--write-out 'status=%{http_code}, %{time_total}sec\n' \
-F 'content=@all-dump.trig;type=application/x-trig' [https://localhost:8443/repository/graph]

Be sure the output shows a successful status code (namely 201, since it created graphs), as shown here, since curl will return a successful status even if the HTTP service did not succeed; curl only reports on the success of the network request-and-response transaction.

status=201, 13.283sec

Procedure: Saving and Restoring User Accounts

...

Now run a command like this to export the accounts into the file all-users.trig

curl -s -S -u username:password -G -d type=user -d format=application/x-trig \
--write-out 'status=%{http_code}\n' \
-o all-users.trig [https://hostname:8443/repository/export]

Note that you have to change the hostname and possibly the login. If there are accounts you do not want in the export, add an exclude argument to filter them out, with a space-separated list, e.g.

.... -d 'exclude=frankenstein moreau lizardo' ....

...

You can start with a newly-created repository which needs to have user accounts added. It only has the initial administrator login, e.g. bigbird. Use the import service to add users from the file you created in step 0. The following command adds all of the accounts except bigbird (since it already exists), and aborts without changing anything if there are already duplicates of any of the users on the destination repo. It will print "status=200" on success.

curl -s -S -u username:password -F type=user -F format=application/x-trig \
-F transform=yes --write-out 'status=%{http_code}\n' \
-F exclude=bigbird \
-F content=@all-users.trig [https://hostname:8443/repository/import]

Note that the transform=yes argument means import will translate the instance URIs of the new users to newly-created URIs in the repository's default namespace. This is usually what you want. If you are positively restoring users already in the correct namespace and you want to preserve the old URIs, substitute transform=no.

...

The easiest way to test the existence and details of a user is with the /whoami service. It does not show roles, however, you'll have to go to the repository administrative UI for that (or take it on faith). For example, after restoring users including curator, this is how you'd check that curator exists:

curl -s -S -u curator:password -G -d format=text/plain [https://hostname:8443/repository/whoami]

It's probably only necessary to test one user like this, and to make sure the output includes a URI, as a check that the whole import succeeded.

...

To export property grants, plug those URIs into the following command (you need to replace italicized words):

curl -G -k -u ADMIN:PASSWORD -d type=grant -d "include=HIDE,CONTACT" \
-d format=application/x-trig [https://localhost:8443/repository/export]

This writes a record of grants to the standard output. Since the URIs are the same between other repositories running the same data model, you should be able to import them with the command (shows standard input in the example):

curl -k -u ADMIN:PASSWORD -F type=grant \
-F duplicate=abort -F transform=no -F content=@- \
-F format=application/x-trig [https://localhost:8443/repository/import]