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Specify Web Portal (Version 2.0)

The Specify Collections Consortium is funded by its member institutions. The Consortium web site is: http://wwww.specifysoftware.org

Specify Web Portal Copyright © 2020 Specify Collections Consortium. Specify comes with ABSOLUTELY NO WARRANTY. This is free software licensed under GNU General Public License 2 (GPL2).

Specify Collections Consortium
Biodiversity Institute
University of Kansas
1345 Jayhawk Blvd.
Lawrence, KS 66045 USA

Configuration Instructions

Instructions on customizing the Web Portal configuration are available on the Specify Communtiy Forum:

Web Portal Configuration Instructions

Developer Instructions

After completing these instructions you will be able to run Specify Web Portal 2.0.

These instructions are for deployment on a server running Ubuntu. An export file for a single collection is required for setting up the Specify Web Portal. This can be accomplished using the Schema Mappging tool tool within the Specify 6 application together with the stand alone Specify Data Export tool.

Install system dependencies

  • Python 2.7
  • Nginx webserver
  • JRE for running Solr
  • GNUMake
  • Unzip utility
  • cURL utility
  • python-lxml

Installation Instructions

These instructions illustrate the fewest steps needed to install the web portal.

  1. These instructions assume the Web Portal is being setup under a user account with the name specify. If a different account is used, the directory paths in these instructions will need to be updated accordingly.

    You will also need to update the webportal-solr.service file to use the correct user and group.

  2. Clone the Web Portal 2.0 repository using git:

    specify@wp:~$ git clone https://github.com/specify/webportal-installer.git

    This will create the directory webportal-installer.

  3. Configure nginx to proxy the Solr requests and serve the static files by copying the provided webportal-nginx.conf to /etc/nginx/sites-available/:

    root@wp:~# install -o root -g root -m644 /home/specify/webportal-installer/webportal-nginx.conf /etc/nginx/sites-available/

    N.B. this file will require changes if the webportal-installer is in a different location.

  4. Disable the default nginx site and enable the portal site:

    root@wp:~# rm /etc/nginx/sites-enabled/default
root@wp:~# ln -s /etc/nginx/sites-available/webportal-nginx.conf /etc/nginx/sites-enabled/
root@wp:~# systemctl restart nginx

  5. Use the Specify Data Export tool to create a Web Portal export zip file (see the Specify 6 Data Export documentation) for each collection to be hosted in the portal. If aggregated collections are desired, replace the single colleciton with the aggregated collections file after the initial Web Portal installation.

  6. Copy the zip files from the Specify Data Export into the webportal-installer/specify_exports directory. The copied files should be given names that are suitable for use in URLs; so no spaces, capital letters, slashes or other problematic characters. E.g. kufish.zip

  7. Build the Solr app:

    specify@wp:~/webportal-installer$ make clean-all && make build-all

  8. Copy the provided webportal-solr.service systemd unit file to /etc/systemd/system/webportal-solr.service and reload the systemd daemon.

    root@wp:~# install -o root -g root -m644 /home/specify/webportal-installer/webportal-solr.service /etc/systemd/system/
root@wp:~# systemctl daemon-reload

    N.B. this file will require changes if the webportal-installer is in a different location.

  9. Start and enable the service:

    root@wp:~# systemctl start webportal-solr.service
root@wp:~# systemctl enable webportal-solr.service

  10. Load the Specify data into Solr:

    specify@wp:~/webportal-installer$ make load-data

    When completing this step you will receive output consisting of blocks of JSON. This is normal unless one of the blocks includes an error message.

  11. The Web Portal is now running and can be tested by visiting the server's address with a web browser.

  12. Be aware that the Solr admin page is available by default on port 8983. This can be useful for troubleshooting but should be blocked in production using firewall rules such as the following:

    root@wp:~# ufw default deny incoming
root@wp:~# ufw default allow outgoing
root@wp:~# ufw allow ssh
root@wp:~# ufw allow http
root@wp:~# ufw --force enable

Customization

Certain customizations of the webportal are possible such as background images. To enable customizations, after the webportal is built with make build-all, copy the folders inside webportal-installer/build/setting_templates/ into webportal-installer/custom_settings/ and edit the files in each folder as desired. Afterwards, make build-html will incorporate the customizations into the portal without restarting any services.

The provided webportal-nginx.conf serves the directory /home/specify/custom-images/ at /custom-images/ allowing files place there to be used in customization.

Data-only Updates

The portal can be updated with new data from exported collections without restarting the Solr service if the export mappings are the same.

To update the Specify data in the webportal follow these steps.

  1. Use the Specify Data Export tool to create a Web Portal export zip file (see the Specify 6 Data Export documentation) for each collection to be updated. If aggregated collections are desired, replace the single colleciton with the aggregated collections file after the initial Web Portal installation.

  2. Copy the zip files from the Specify Data Export into the webportal-installer/specify_exports directory. The copied files in the specify_exports directory must have the same names as the original exports.

  3. Load the Specify data into Solr:

    specify@wp:~/webportal-installer$ make load-data

  4. Only export files newer than the last update will be loaded. The target make force-load-data will force all collections to be reloaded.

Full Updates

If new collections are to be added to the portal or mappings of existing collections change, the Solr service has to be stopped and the cores rebuilt.

  1. Stop the webportal-solr systemd service:

    root@wp:~# systemctl stop webportal-solr.service

  2. Use the Specify Data Export tool to create a Web Portal export zip file (see the Specify 6 Data Export documentation) for each collection to be hosted in the portal. If aggregated collections are desired, replace the single colleciton with the aggregated collections file after the initial Web Portal installation.

  3. Copy the zip files from the Specify Data Export into the webportal-installer/specify_exports directory. The copied files should be given names that are suitable for use in URLs; so no spaces, capital letters, slashes or other problematic characters. E.g. kufish.zip

  4. Build the Solr app:

    specify@wp:~/webportal-installer$ make build-all

  5. Start the webportal-solr service:

    root@wp:~# systemctl start webportal-solr.service

  6. Load the Specify data into Solr:

    specify@wp:~/webportal-installer$ make load-data

  7. The Web Portal is now running and can be tested by visiting the server's address with a web browser.