mmi orr migration to xdomes vm

MMI ORR migration to xdomes VM

Many thanks to Felimon Gayanilo and Phil Hale (TAMUCC), and John Graybeal (Stanford) for your assistance.

Status

• 2020-04-01 - Migration completed
• 2020-04-12 - Satisfactory testing of all services

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As part of this task:

• MMI ORR is now running version 3.8.9 (from 3.7.0).
• MMI ORR is now running in a dockerized way (like other ORR instances out there).

Cutover steps

Carlos:

• Shutdown tomcat on current mmisw
• Final Mongo DB and ontology files transfer
• Repopulate triple store (Carlos)
• Basic functionality tests against https://xdomes.tamucc.edu/mmisw.org/ont/
• Adjust ORR config to revert the temporary URL settings so they are now mmisw.org-based
• Disable all cronjobs on current mmisw:
  • ORR launch
  • documentation webhook
  • cf2rdf watchdog

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Felimon / TAMUCC IT:

• Set virtual host on xdomes for mmisw.org and enable any relevant certificates.

  What's basically needed is something like the following:

  <VirtualHost mmisw.org:443>
      DocumentRoot "/var/www/html/mmisw.org"
      ProxyPass        /ont    http://localhost:39090/ont
      ProxyPassReverse /ont    http://localhost:39090/ont
      ProxyPass        /sparql http://localhost:30035/repositories/mmiorr
      ProxyPassReverse /sparql http://localhost:30035/repositories/mmiorr
  
      # TAMUCC IT: certificate-related settings.
      # ...
  </VirtualHost>
  

• Remove the temporary "MMI ORR" settings in /etc/httpd/conf.d/ssl-vhosts.conf

    ProxyPass        /mmisw.org/ont    http://localhost:39090/ont
    ProxyPassReverse /mmisw.org/ont    http://localhost:39090/ont
    ProxyPass        /mmisw.org/sparql http://localhost:30035/repositories/mmiorr
    ProxyPassReverse /mmisw.org/sparql http://localhost:30035/repositories/mmiorr    
    Alias "/mmisw.org"  "/var/www/html/mmisw.org"
  

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John:

• Apply IP cutover with domain name provider

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Carlos:

• Enable mmisw-related cronjobs on xdomes:

  • documentation webhook
  • cf2rdf watchdog

• Documentation and webhook for doc update https://mmisw.org/orrdoc/

  • supporting software in place

• API DOC: https://mmisw.org/ontapi/

• CF vocabulary "watchdog"

  • cronjob enabled

• CF browser https://mmisw.org/cfsn/

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All:

• Tests against mmisw.org as IP cutover propagates (new IP for mmisw.org is 64.71.82.34)

  • https://mmisw.org/ont
  • https://mmisw.org/ont/sparql
  • https://mmisw.org/orrdoc/
  • https://mmisw.org/ontapi/
  • https://mmisw.org/cfsn/
  • https://mmisw.org/experimental/vbrowser/

• Declare victory

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Additional notes

Software installed

During the migration process:

• installed java, required to run the CF watchdog program

  $ sudo yum install java-1.8.0-openjdk-devel
  
  $ java -version
  openjdk version "1.8.0_242"
  

• installed mkdocs, required to generate MMI ORR documentation

  $ sudo yum install mkdocs
  
  $ mkdocs --version
  mkdocs, version 0.14.0
  

Migration scripts

• export-mongo-collections.sh to export mongo data on previous mmisw machine:

  for c in organizations users ontologies; do
    echo "exporting $c ..."
    mongoexport --collection=$c --db=orr-ont --out=$c.json
  done
  

• import-mongo-collections.sh to import mongo data on xdomes machine:

  for c in organizations users ontologies; do
    echo "importing $c ..."
    mongoimport --collection=$c --db=orr-ont --mode=upsert --file=$c.json
  done
  

  Note that this script, along with the exported *.json files are first docker cp-ed to the mmisw-mongo container, where the script is then run.

mmisw.org directory

• Located at /var/www/html/mmisw.org, this is the DocumentRoot for the mmisw.org VirtualHost.

• Fixed permission issue with contents under experimental with: chcon -R unconfined_u:object_r:httpd_sys_content_t:s0 experimental. See https://cwiki.apache.org/confluence/display/HTTPD/13PermissionDenied.