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EcatDeployment  
short summary of how applications and databases are deployed on the ECAT servers at GBIF
Updated Jul 22, 2010 by wixner@googlemail.com

bla5 Production Server

production server hosting tomcat webapps, apache for ecat-dev (see below), dwca-adapters, ecat-data directory

Apache setup

apache on bla5 is configured to wire up all services for this domain.

See /etc/httpd/conf.d/virt_ecat-dev.conf for the latest version of the apache config file:

<VirtualHost *:80>
 ServerName ecat-dev.gbif.org
 CustomLog logs/ecat-dev_access_log combined

Alias /crossdomain.xml  /var/www/html/crossdomain.xml

Alias /tmp /mnt/extra/ecat-data/tmp
<Directory /mnt/extra/ecat-data/tmp>
  Options +Indexes
  Order allow,deny
  Allow from all
</Directory>

Alias /pbd /mnt/extra/ecat-data/pbd
<Directory /mnt/extra/ecat-data/pbd>
  Order allow,deny
  Allow from all
</Directory>

Alias /repository /mnt/extra/ecat-data/sources
<Directory /mnt/extra/ecat-data/sources>
  Options +Indexes
  Order allow,deny
  Allow from all
</Directory>
<Directory /mnt/extra/ecat-data/sources/protected>
  Order Deny,Allow
  Deny from all
  Allow from gbif.org
  Allow from 192.38.28
  Options +Indexes
</Directory>

Alias /glossary /var/www/html/glossary
<Directory /var/www/html/glossary>
  Order allow,deny
  Allow from all
</Directory>

Alias /console /var/www/html/console
<Directory /var/www/html/console>
  Order allow,deny
  Allow from all
</Directory>

Alias /taxontagger /var/www/html/taxontagger
<Directory /var/www/html/taxontagger>
  Order allow,deny
  Allow from all
</Directory>

ProxyPass /tf http://db2.gbif.org/webservices/find
ProxyPass /ws ajp://localhost:8009/ecat-ws/
ProxyPass /ws-sdr http://db2.gbif.org/ws-sdr/
ProxyPass /ws-sdr2 ajp://localhost:8009/ecat-ws-sdr/
ProxyPass /dwca-validator ajp://localhost:8009/dwca-validator
ProxyPass /manager  ajp://localhost:8009/manager

# mount the portal as the root application via mod_proxy
# need to exclude above urls from the root, otherwise its all served from the portal webapp
ProxyPass /icons !
ProxyPass /tmp !
ProxyPass /pbd !
ProxyPass /glossary !
ProxyPass /console !
ProxyPass /taxontagger !
ProxyPass /repository !
ProxyPass /crossdomain.xml !
ProxyPass /  ajp://localhost:8009/ecat-portal/

</VirtualHost>

ecat-dev.gbif.org

static ecat-dir

ecat-dir, used for indexing, tmp files, user uploads and dwca repository hosted at /mnt/extra/ecat-data Parts of this data-dir are exposed via apache on bla5:

/tmp

/mnt/extra/ecat-data/tmp temporary files

/pbd

/mnt/extra/ecat-data/pbd intended for hosting species occurrence map tiles. Currently only single passer domesticus species for demo maps

/repository

/mnt/extra/ecat-data/repository exposing dwca source files from the repo

clb portal

the latest ECAT portal

clb webservices

the latest ECAT services

sdr webservices

old version of ECAT services running on the static SDR database. Used only by SDR website and deprecated for further use!

see db2 for details

sdr2 webservices

the latest ECAT services running on the static SDR database. Used by mountain biodiv

dwca-adapter

/root/dwc-adapters

bla5.gbif.org

only accessible via VPN. Contains tomcat manager

using the CLB commandline tool

 cd /mnt/extra/ecat-data/bin
./clb.sh clb-test --help

# drop & recreate the public schema of database "clb-test" on boma to init a new db:
./clb.sh clb-test --init

# add catalog of life compound checklist
./clb.sh clb-test --addCompound /mnt/extra/ecat-data/sources/col

# add a single resource via URL and instantly import it to CLB
./clb.sh clb-test -a http://ecat-dev.gbif.org/repository/taxonomic/itis_archive.zip -i now

# run lexical grouping and nub building in one go
./clb.sh clb-test --lex --nub

# import all occurrence soruces and run lexical grouping & nub building in one go
./clb.sh clb-test --addAll /mnt/extra/ecat-data/sources/occurrences -i now --lex --nub

# search for checklist via its title, resource key or id:
./clb.sh clb-test --search Cat

db2 Development Server

development server currently in transformation. Still hosting a few applications exposed via bla: taxon finder, ruby webservices, old sdr clb webservice. Should only host true development apps which are not exposed to public at all. Used for staging before production deployment.

db2.gbif.org

only accessible via VPN

sdr webservices

the latest ECAT services running on the static SDR database. Used by mountain biodiv

Taxon Finder

  • ruby webservice running on db2
    • /var/www/ruby/webservices
    • see db2 apache config for configuration

Database Servers

boma

PostgreSQL databases:

  • clb / clb2: current checklist bank database and a second one for rollovers/indexing
  • clb-test: for clb testing, development apps
  • clb-sdr: old, static database for the old ecat services feeding the SDR site. Nub=current portal nub with old IDs so all taxonIDs can be used to link to portal and EOL map tiles
  • clb-sdr2: content the same as clb-sdr, but using the latest checklist bank db structure so it can be used with the latest services. Being used by Mountain Biodiv site

mogo

  • col2010ac
  • itis


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