u2g mmisw

Log

Base location

/opt/MMI-ORR/:

$ sudo mkdir /opt/MMI-ORR
$ sudo chown `whoami` /opt/MMI-ORR
$ df -h
Filesystem            Size  Used Avail Use% Mounted on
/dev/mapper/vg_internal-lv_root
                      240G  2.3G  226G   1% /
tmpfs                 2.9G     0  2.9G   0% /dev/shm
/dev/sda1             485M   63M  397M  14% /boot

$ mkdir /opt/MMI-ORR/code

Software installed

Required

GCC

$ sudo yum groupinstall 'Development Tools'
$ gcc --version
gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Java (installation on centos)

$ cd /opt/MMI-ORR/Downloads
$ # get the file from oracle (jdk-7u21-linux-x64.rpm)
$ sudo rpm -Uvh jdk-7u21-linux-x64.rpm
$ sudo alternatives --config java
There are 5 programs which provide 'java'.

  Selection    Command
-----------------------------------------------
*+ 1           /usr/lib/jvm/jre-1.7.0-openjdk.x86_64/bin/java
   2           /usr/lib/jvm/jre-1.6.0-openjdk.x86_64/bin/java
   3           /usr/lib/jvm/jre-1.5.0-gcj/bin/java
   4           /usr/java/latest/jre/bin/java
   5           /usr/java/jdk1.7.0_21/jre/bin/java

Enter to keep the current selection[+], or type selection number: 5
[__@mmisw MMI-ORR]$ java -version
java version "1.7.0_21"
Java(TM) SE Runtime Environment (build 1.7.0_21-b11)
Java HotSpot(TM) 64-Bit Server VM (build 23.21-b01, mixed mode)

Apache HTTP server (devel)

$ sudo yum install httpd-devel.x86_64

Apache Tomcat

$ wget "http://apache.mirrors.tds.net/tomcat/tomcat-7/v7.0.40/bin/apache-tomcat-7.0.40.tar.gz"
$ cd /opt/
$ sudo tar zxf ~-/apache-tomcat-7.0.40.tar.gz
$ sudo ln -s /opt/apache-tomcat-7.0.40 ./tomcat
$ sudo chown -R tomcat:tomcat /opt/tomcat/

Subversion

$ sudo yum install subversion
$ svn --version
svn, version 1.6.11 (r934486)
   compiled Apr 11 2013, 16:13:51

Apache Ant

$ wget "http://mirror.cogentco.com/pub/apache//ant/binaries/apache-ant-1.9.0-bin.tar.gz"
$ cd /opt/
$ sudo tar zxf ~-/apache-ant-1.9.0-bin.tar.gz
$ vi ~/.bash_profile  # to set ANT_HOME

Google Web Toolkit (GWT)

The ORR Portal GWT application, currently requiring a 1.5.x version:

cd /opt/MMI-ORR/Downloads/
wget http://google-web-toolkit.googlecode.com/files/gwt-linux-1.5.2.tar.bz2
bunzip2 gwt-linux-1.5.2.tar.bz2
cd /opt/
sudo tar xf /opt/MMI-ORR/Downloads/gwt-linux-1.5.2.tar

GWT gets installed in /opt/gwt-linux-1.5.2

Not required (but useful)

w3m -- sudo yum install w3m

Apache and Tomcat configs

Building mod_jk

$ wget "http://mirror.reverse.net/pub/apache/tomcat/tomcat-connectors/jk/tomcat-connectors-1.2.37-src.tar.gz"

$ cd /opt/MMI-ORR/code
$ tar zxf /opt/MMI-ORR/Downloads/tomcat-connectors-1.2.37-src.tar.gz
$ cd tomcat-connectors-1.2.37-src/
$ # according to BUILD.txt:
$ cd native/
$ ./configure --with-apxs=/usr/sbin/apxs
$ make
$ sudo make install

$ ls -l /usr/lib64/httpd/modules/mod_jk.so
-rwxr-xr-x. 1 root root 1113552 May 20 17:11 /usr/lib64/httpd/modules/mod_jk.so

Edit `/etc/httpd/conf/httpd.conf`

LoadModule jk_module modules/mod_jk.so
<IfModule mod_jk.c>
        JKWorkersFile /etc/httpd/conf/workers.properties
        JKLogFile /var/log/httpd/mod_jk.log
        JKLogLevel info
        JkShmFile /var/log/httpd/mod_jk.shm
        JKMount /*.jsp mmi
        JKMount /servlet/* mmi
        JKMount /examples/* mmi
</IfModule>

(and others to enable the mmi worker and configure a number of mappings)

Create `Create /etc/httpd/conf/workers.properties`

# MMISW
# Define some properties
workers.apache_log=/var/log/httpd/mod_jk.log
workers.tomcat_home=/opt/tomcat
workers.java_home=/usr/java/jdk1.7.0_21
worker.list=mmi
# Set properties for mmi (ajp13)
worker.mmi.type=ajp13
worker.mmi.host=localhost
worker.mmi.port=8009

Update `/etc/httpd/conf.d/ssl.conf`

...
# MMISW
RewriteEngine On
RewriteCond %{HTTPS} on
RewriteRule ^/(.*) http://%{HTTP_HOST}%{REQUEST_URI}

</VirtualHost>

Tomcat init

Created /etc/init.d/tomcat (copied/adapted from previous host's /etc/init.d/apache) and then:

$ sudo /sbin/chkconfig --add tomcat
$ sudo /sbin/chkconfig --level 345 tomcat on
$ sudo /sbin/chkconfig --list tomcat
tomcat          0:off   1:off   2:off   3:on    4:on    5:on    6:off

Note: There was already a 'tomcat' user but it was not playing well with a launch command, so I simply removed it (/usr/sbin/userdel) and added it again (/usr/sbin/useradd).

At this point: Apache HTTP and Tomcat are set up and running.

AllegroGraph server

Downloaded agraph-4.11-1.x86_64.rpm from http://www.franz.com/agraph/downloads/:

$ cd /opt/MMI-ORR/Downloads/
$ wget "http://www.franz.com/ftp/pri/acl/ag/ag4.11/linuxamd64.64/SE/agraph-4.11-1.x86_64.rpm"
$ ls -l agraph*
-rw-rw-r--. 1 uuuuu uuuuu 183921030 May 17 09:44 agraph-4.11-1.x86_64.rpm

According to http://www.franz.com/agraph/support/documentation/current/server-installation.html

$ rpm -i agraph-4.11-1.x86_64.rpm 
$ sudo /usr/bin/configure-agraph
Welcome to the AllegroGraph configuration program.  This script will
help you establish a baseline AllegroGraph configuration. 

You will be prompted for a few settings.  In most cases, you can hit return
to accept the default value.

Location of configuration file to create:
[/etc/agraph/agraph.cfg]: 
/etc/agraph does not exist.
Would you like me to create it?:
[y]: 
Directory to store data and settings:
[/var/lib/agraph]: /opt/MMI-ORR/workspace/agraph
/opt/MMI-ORR/workspace/agraph does not exist.
Would you like me to create it?:
[y]: y
Directory to store log files:
[/var/log/agraph]: 
Location of file to write server process id:
[/var/run/agraph/agraph.pid]: 
User to run as:
[agraph]: 

User 'agraph' doesn't exist on this system. 
Create agraph user:
[y]: 

Now you must set up an initial user account for AllegroGraph.  This
account will have "super user" privileges in AllegroGraph.

SuperUser account name:
[super]: 
SuperUser account password:
SuperUser account password (again):
Instance timeout seconds:
[604800]: 

/etc/agraph/agraph.cfg has been created.  

If desired, you may modify the configuration.  When you are satisfied,
you may start the agraph service.

You can start AllegroGraph by running: 
/sbin/service agraph start

You can stop AllegroGraph by running: 
/sbin/service agraph stop

First start:

$ sudo /sbin/service agraph start
AllegroGraph Server Edition 4.11, built on May 17, 2013 07:26:49 GMT-0700
Copyright (c) 2005-2013 Franz Inc.  All Rights Reserved.
AllegroGraph contains patented technology.
No patches loaded.
current-time: Monday, May 20, 2013 06:30:14 PM 
default-external-format: #<external-format :utf8 [(crlf-base-ef :utf8)]>

Daemonizing...
Server started normally: Running with free license of 5,000,000 triples; no-expiration.
Starting AllegroGraph:                                     [  OK  ]

AGWebView interface at http://mmisw.tamucc.edu:10035

The mmiorr repository was already created because of previous runs of the Ont service (ie. web interface no needed to create the repo).

$ sudo ls -lrth /opt/MMI-ORR/workspace/agraph/rootcatalog/mmiorr/
total 522M
-rw-r-----. 1 agraph agraph  524 May 20 22:57 parameters.dat
-rw-r-----. 1 agraph agraph    4 May 20 22:57 version
-rw-r-----. 1 agraph agraph   36 May 20 22:57 uuid
-rw-r-----. 1 agraph agraph 4.0G May 20 22:57 deleted
-rw-r-----. 1 agraph agraph 4.0M May 20 22:57 sstab-large-strings
-rw-r-----. 1 agraph agraph 256M May 20 22:57 freelog-307619580
-rw-r-----. 1 agraph agraph 1.5M May 20 22:57 sstab-chunk
-rw-r-----. 1 agraph agraph 4.0M May 20 22:57 sstab-strings
-rw-------. 1 agraph agraph 1.8K May 20 22:57 metadata.2
-rw-r-----. 1 agraph agraph 256M May 27 23:04 tlog-82e85810-d347-acf4-42fe-001dd8b71c56-0
-rw-------. 1 agraph agraph   13 May 27 23:04 ckpt
-rw-r-----. 1 agraph agraph   65 May 27 23:04 tlmgr
-rw-r-----. 1 agraph agraph   23 Jul  4 12:32 instance-info
-rw-r-----. 1 agraph agraph  330 Jul  4 12:32 storage
-rw-------. 1 agraph agraph 1.8K Jul  4 12:32 metadata.0
-rw-r-----. 1 agraph agraph    3 Jul  4 12:32 fti-state

To allow anonymous users to do queries against the mmiorr repository:

Log in as the 'super' user at http://mmisw.tamucc.edu:10035/repositories/mmiorr#users
click [add user], create 'anonymous', no password, and click OK.
Edit the created 'anonymous' user
grant 'read' on catalog '/' repository 'mmiorr'
click [ok]

AllegroGraph init

$ sudo /sbin/chkconfig --add agraph
$ sudo /sbin/chkconfig --level 345 agraph on
$ sudo /sbin/chkconfig --list agraph
agraph         	0:off	1:off	2:off	3:on	4:on	5:on	6:off

MySQL

(there was a mysql installation, but apparently incomplete)

$ sudo yum install mysql-server mysql php-mysql
$ mysql --version
mysql  Ver 14.14 Distrib 5.1.69, for redhat-linux-gnu (x86_64) using readline 5.1
$ sudo /sbin/chkconfig --levels 235 mysqld on
$ sudo /sbin/chkconfig --list  mysqld
mysqld         	0:off	1:off	2:on	3:on	4:off	5:on	6:off
$ sudo /sbin/service mysqld  start
Initializing MySQL database:  Installing MySQL system tables...
OK
...
                                                           [  OK  ]
Starting mysqld:                                           [  OK  ]

$ /usr/bin/mysql_secure_installation
...
Set root password? [Y/n] 
New password: 
Re-enter new password: 
Password updated successfully!
...
Remove anonymous users? [Y/n] 
 ... Success!
...
Disallow root login remotely? [Y/n] 
 ... Success!
...
Remove test database and access to it? [Y/n] n
 ... skipping.
Reload privilege tables now? [Y/n] 
 ... Success!
...
All done!  If you've completed all of the above steps, your MySQL
installation should now be secure.

BioPortal

Code checkout

$ cd /opt/MMI-ORR
$ mkdir -p code/bioportal
$ cd code/bioportal
$ svn checkout --username anonymous https://bmir-gforge.stanford.edu/svn/bioportal_core/tags/1005
# enter a blank password

Creation of dbs and users

$ mysql -u root -p
Enter password: 
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 12
Server version: 5.1.69 Source distribution

Copyright (c) 2000, 2013, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> create database bioportal;
Query OK, 1 row affected (0.00 sec)

mysql> create database bioportal_protege;
Query OK, 1 row affected (0.00 sec)

mysql> create database bioportal_lexgrid;
Query OK, 1 row affected (0.00 sec)

mysql> create user bioportal_user;
Query OK, 0 rows affected (0.00 sec)

mysql> create user bp_lexgrid_user;
Query OK, 0 rows affected (0.00 sec)

mysql> create user bp_protege_user;
Query OK, 0 rows affected (0.00 sec)

mysql> grant all on *.* to 'bioportal_user'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> grant all on *.* to 'bp_lexgrid_user'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> grant all on *.* to 'bp_protege_user'@'localhost';
Query OK, 0 rows affected (0.00 sec)

mysql> Bye

BioPortal build

$ cd /opt/MMI-ORR/code/bioportal/1005/

Before building BioPortal, edit and adjust WebRoot/WEB-INF/resources/xslt/ontology_light.xsl to add the line <xsl:copy-of select="urn" /> between the corresponding lines for "id" and "displayLabel":

<xsl:copy-of select="id" />
<xsl:copy-of select="urn" />
<xsl:copy-of select="displayLabel"/>

Then, continuing with the BioPortal instructions:

$ cp build.properties.sample build.properties
$ vi build.properties

The properties updated in build.properties are:

bioportal.resource.path=/opt/MMI-ORR/workspace/bioportal/resources
appserver.home=/opt/tomcat
appserver.lib=${appserver.home}/lib     # note: original has .../common/lib
bioportal.jdbc.username=uu
bioportal.jdbc.password=xxxx
protege.jdbc.username=uu
protege.jdbc.password=xxxx
lexgrid.db.user=uu
lexgrid.db.password=xxxx

Then:

$ mkdir -p /opt/MMI-ORR/workspace/bioportal/resources
$ sudo chown -R `whoami` /opt/MMI-ORR/workspace/bioportal  # to temporarily facilitate the build
$ ant clean
$ ant createwar
$ sudo ant deploywar
$ ls -l /opt/tomcat/webapps/bioportal.war
-rw-r--r--. 1 root root 49577775 May 20 22:35 /opt/tomcat/webapps/bioportal.war

Bioportal deployment test

OK.

Import database dumps and ontology files from previous hosting

Create database dumps

$ mkdir /opt/MMI-ORR/migration_to_tamu_cc
$ cd /opt/MMI-ORR/migration_to_tamu_cc/
$ PW=xxxx for db in bioportal bioportal_lexgrid bioportal_protege; do
    echo "$db" \
    mysqldump --user=root --password=$PW --protocol=tcp --add-drop-table $db > $db.sql \
  done
$ tar zcf dbdumps-2013-09-06-11.30am.tgz *.sql

Zip ontology files

$ cd /opt/MMI-ORR/workspace/bioportal/resources/
$ tar zcf /opt/MMI-ORR/migration_to_tamu_cc/bioportal_resources_uploads-2013-09-06-11.30am.tgz uploads/

Transfer files to sftp space

$ cd /opt/MMI-ORR/migration_to_tamu_cc/
$ sftp [email protected]
sftp> put bioportal_resources_uploads-2013-09-06-11.30am.tgz
sftp> put dbdumps-2013-09-06-11.30am.tgz

Transfer files from sftp space to new hosting

$ mkdir /opt/MMI-ORR/data_from_ucsd
$ cd /opt/MMI-ORR/data_from_ucsd/
$ sftp [email protected]
sftp> get bioportal_resources_uploads-2013-09-06-11.30am.tgz
sftp> get dbdumps-2013-09-06-11.30am.tgz

$ tar zxf dbdumps-2013-09-06-11.30am.tgz
$ mysql -u root -p bioportal < bioportal.sql
$ mysql -u root -p bioportal_lexgrid < bioportal_lexgrid.sql
$ mysql -u root -p bioportal_protege < bioportal_protege.sql

$ w3m "http://localhost:8080/ont?listall"   # => Looks good

Import files

$ cd /opt/MMI-ORR/workspace/bioportal/resources/
$ tar zxf /opt/MMI-ORR/data_from_ucsd/bioportal_resources_uploads-2013-09-06-11.30am.tgz
$ sudo chown -R tomcat:tomcat /opt/MMI-ORR/workspace

Repopulate triple store.

Use the internal command provided by the Ont service (see below) to repopulate the triple store.

MMISW Ont service

Using latest code from trunk:

$ cd /opt/MMI-ORR/code/
$ svn checkout http://mmisw.googlecode.com/svn/trunk/org.mmisw.ont
...Checked out revision 1416.
$ cd org.mmisw.ont
$ cp sample.build.properties build.properties
$ vi build.properties

The adjusted properties are:

appserver.home=/opt/tomcat
appserver.host=http://mmisw.tamucc.edu     # NOTE: while we get to the cutover
 
aquaportal.rest.url=http://localhost/bioportal/rest
aquaportal.resource.directory = /opt/MMI-ORR/workspace/bioportal/resources
aquaportal.voc2rdf.dir = /opt/MMI-ORR/workspace/mmiregistry/preuploads/voc2rdf/
aquaportal.jdbc.url=jdbc:mysql://localhost:3306/bioportal
aquaportal.jdbc.username=uu
aquaportal.jdbc.password=xxxx
 
portal.service.url=http://mmisw.tamucc.edu/orr
ont.internal.dir = /opt/MMI-ORR/workspace/mmiregistry/internal
 
agraph.version = 4.11
agraph.host = http://localhost
agraph.port = 10035
agraph.ts.dir = /opt/MMI-ORR/workspace/mmiregistry/agraph/ts
agraph.ts.name = mmiorr
agraph.username = super
agraph.password = xxx

Some of the mentioned working directories need to exist :

$ sudo mkdir -p /opt/MMI-ORR/workspace/mmiregistry/agraph/ts
$ sudo mkdir -p /opt/MMI-ORR/workspace/bioportal/resources
$ sudo mkdir -p /opt/MMI-ORR/workspace/mmiregistry/preuploads/voc2rdf
$ sudo mkdir -p /opt/MMI-ORR/workspace/mmiregistry/internal

We're ready to build Ont, but the following is needed so the MySQL JDBC driver is found at runtime: I copied the driver library directly to Tomcat's lib/ directory and restarted tomcat. I used the library coming with BioPortal (mysql-connector-java-5.1.6-bin.jar):

$ sudo cp -pi /opt/MMI-ORR/code/bioportal/1005/WebRoot/WEB-INF/lib/mysql-connector-java-5.1.6-bin.jar /opt/tomcat/lib/

Now build and deploy ont.war:

$ ant war
$ sudo chown -R tomcat:tomcat /opt/MMI-ORR/workspace/mmiregistry
$ sudo cp  _generated/ont.war /opt/tomcat/webapps/
$ tail -f /opt/tomcat/logs/catalina.out
2013-05-20 22:58:59,484 INFO  [org.mmisw.ont.OntServlet] - MMI Ontology and Term URI Resolver. Version 2.0.39.beta (201305202256): initializing
2013-05-20 22:58:59,486 DEBUG [org.mmisw.ont.OntConfig] - aquaportal.rest.url = http://localhost:8080/bioportal/rest
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - aquaportal.uploads.directory = /opt/MMI-ORR/workspace/bioportal/resources/uploads
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - aquaportal.datasource = java:comp/env/jdbc/BioPortalDataSource
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - aquaportal.voc2rdf.dir = /opt/MMI-ORR/workspace/mmiregistry/preuploads/voc2rdf/
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - appserver.host = http://mmisw.tamucc.edu
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - ont.service.url = http://mmisw.tamucc.edu/ont
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - portal.service.url = http://mmisw.tamucc.edu/orr
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - virtuoso.host = null
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - virtuoso.username = null
2013-05-20 22:58:59,487 DEBUG [org.mmisw.ont.OntConfig] - virtuoso.password = *****
2013-05-20 22:58:59,488 DEBUG [org.mmisw.ont.OntConfig] - jena.tdb.dir = null
2013-05-20 22:58:59,488 DEBUG [org.mmisw.ont.OntConfig] - jena.tdb.assembler = null
2013-05-20 22:58:59,488 DEBUG [org.mmisw.ont.OntConfig] - agraph.version = 4.11
2013-05-20 22:58:59,488 DEBUG [org.mmisw.ont.OntConfig] - agraph.host = http://localhost
2013-05-20 22:58:59,488 DEBUG [org.mmisw.ont.OntConfig] - agraph.port = 10035
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - agraph.ts.dir = /opt/MMI-ORR/workspace/mmiregistry/agraph/ts
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - agraph.ts.name = mmiorr
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - agraph.username = super
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - agraph.password = *****
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - ont.internal.dir = /opt/MMI-ORR/workspace/mmiregistry/internal
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - ga.uanumber = null
2013-05-20 22:58:59,489 DEBUG [org.mmisw.ont.OntConfig] - ga.domainName = null
2013-05-20 22:58:59,490 DEBUG [org.mmisw.ont.OntConfig] - ga.dir = null
2013-05-20 22:58:59,490 INFO  [org.mmisw.ont.db.Db] - init called.
2013-05-20 22:58:59,505 DEBUG [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - Ag4TripleStore instance created.
2013-05-20 22:58:59,505 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - init called.
2013-05-20 22:58:59,507 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - Credentials set to: host='localhost'; port=10035; username='super'; password=***
2013-05-20 22:58:59,508 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - Connecting to triple store...
2013-05-20 22:59:00,072 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - CONNECTION OPEN
2013-05-20 22:59:00,110 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - AllegroGraph Server version = 4.11
2013-05-20 22:59:00,126 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] -  Index flavors = [i, gospi, gposi, gspoi, ospgi, posgi, spogi]
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] -  #triples = 0
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - CONNECTION CLOSED
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.triplestore.allegro4.Ag4TripleStore] - init complete.
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.admin.AdminDispatcher] - init called.
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.admin.AdminDispatcher] - internalDir: /opt/MMI-ORR/workspace/mmiregistry/internal
2013-05-20 22:59:00,140 INFO  [org.mmisw.ont.admin.AdminDispatcher] - graphsFile: /opt/MMI-ORR/workspace/mmiregistry/internal/graphs.rdf
2013-05-20 22:59:00,320 INFO  [org.mmisw.ont.admin.AdminDispatcher] - /opt/MMI-ORR/workspace/mmiregistry/internal/graphs.rdf: model created.
2013-05-20 22:59:00,320 INFO  [org.mmisw.ont.util.Analytics] - Analytics.init: property ga.uanumber not provided
2013-05-20 22:59:00,320 INFO  [org.mmisw.ont.OntServlet] - MMI Ontology and Term URI Resolver. Version 2.0.39.beta (201305202256): init complete.

Basic tests OK:

Other preparations

Enabled workaround described at http://marinemetadata.org/mmiorrdeplmtech/log/log20110523a to avoid mysql connection problem:

Crontab:

0-59/5 * * * *  /home/uuuuu/bin/orr_heartbeat.sh

orr_heartbeat.sh:

# bioportal/rest/users:
TIME=`date`
CODE=`curl -s -w '%{http_code}' 'http://localhost/bioportal/rest/users' -o  /tmp/orr_bioportal_users.xml`
if [ "200" != "$CODE" ]; then
        echo "$TIME: error requesting bioportal/rest/users, code=$CODE";
fi
 
# ont?listall:
TIME=`date`
CODE=`curl -s -w '%{http_code}' 'http://localhost/ont?listall' -o  /tmp/orr_ont_listall.csv`
if [ "200" != "$CODE" ]; then
        echo "$TIME: error requesting ont?listall, code=$CODE";
fi

ORR Portal

Using latest code from trunk:

$ cd /opt/MMI-ORR/code/
$ svn checkout http://mmisw.googlecode.com/svn/trunk/org.mmisw.orrportal
$ cd org.mmisw.orrportal
$ cp sample.build.properties build.properties
$ vi build.properties

Adjusted properties:

GWT_HOME = /opt/gwt-linux-1.5.2
appserver.home = /opt/tomcat
appserver.host = http://mmisw.tamucc.edu
ont.service.url = http://mmisw.tamucc.edu/ont
ontbrowser.service.url = -
orrportal.pre.uploads.dir = /opt/MMI-ORR/workspace/mmiregistry/preuploads/
orrportal.voc2rdf.dir = /opt/MMI-ORR/workspace/mmiregistry/preuploads/voc2rdf/
orrportal.preview.dir = /opt/MMI-ORR/workspace/mmiregistry/previews/
orrportal.resource.dir = /opt/MMI-ORR/workspace/mmiregistry/resources/
mail.usr = [email protected]
mail.pw = xxxx
ga.uanumber = UA-16970585-1

$ sudo mkdir -p /opt/MMI-ORR/workspace/mmiregistry/previews
$ sudo mkdir -p /opt/MMI-ORR/workspace/mmiregistry/resources
$ sudo chown -R tomcat /opt/MMI-ORR/workspace
$ ant war
$ sudo cp _generated/orr.war /opt/tomcat/webapps/

orr.log and catalina.out show that the installation went OK.

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u2g mmisw

Log

Base location

Software installed

Required

Not required (but useful)

Apache and Tomcat configs

Building mod_jk

Edit `/etc/httpd/conf/httpd.conf`

Create `Create /etc/httpd/conf/workers.properties`

Update `/etc/httpd/conf.d/ssl.conf`

Tomcat init

AllegroGraph server

AllegroGraph init

MySQL

BioPortal

Creation of dbs and users

BioPortal build

Bioportal deployment test

Import database dumps and ontology files from previous hosting

Create database dumps

Zip ontology files

Transfer files to sftp space

Transfer files from sftp space to new hosting

Import files

Repopulate triple store.

MMISW Ont service

Other preparations

ORR Portal

Clone this wiki locally

u2g mmisw

Log

Base location

Software installed

Required

Not required (but useful)

Apache and Tomcat configs

Building mod_jk

Edit /etc/httpd/conf/httpd.conf

Create Create /etc/httpd/conf/workers.properties

Update /etc/httpd/conf.d/ssl.conf

Tomcat init

AllegroGraph server

AllegroGraph init

MySQL

BioPortal

Creation of dbs and users

BioPortal build

Bioportal deployment test

Import database dumps and ontology files from previous hosting

Create database dumps

Zip ontology files

Transfer files to sftp space

Transfer files from sftp space to new hosting

Import files

Repopulate triple store.

MMISW Ont service

Other preparations

ORR Portal

Clone this wiki locally

Edit `/etc/httpd/conf/httpd.conf`

Create `Create /etc/httpd/conf/workers.properties`

Update `/etc/httpd/conf.d/ssl.conf`