This post chronicles the steps I took to push my local dg.localdomain project, an ISLE v1.3.0 build, to staging on node DGDockerX as https://isle-stage.grinnell.edu using my dg-isle and dg-islandora repositories.

Directories

I’ll begin by opening a terminal on the staging host, DGDockerX as user islandora. Then I very carefully (note the use of the --recursive flags!) clone the aforementioned projects to DGDockerX like so:

Host / DGDockerX Commands
cd /opt git clone –recursive https://github.com/Digital-Grinnell/dg-isle.git git clone –recursive https://github.com/Digital-Grinnell/dg-islandora.git cd dg-isle git checkout staging

One Useful Git Config Change

One thing I learned during this process is that all of the dg-isle config files that I’ve modified and/or mapped into the containers show up as “modified” when I do a git status on the host. The only apparent “modification” is that these are all owned on the host by mcfatem:mcfatem, but prior to spin-up these were owned by islandora:islandora. The files/directories are:

  • config/apache/settings_php/settings.staging.php,
  • config/fedora/gsearch/foxmlToSolr.xslt,
  • config/fedora/gsearch/islandora_transforms/, and
  • config/solr/schema.xml

This is apparently a known condition that does no harm, but it can be easily ignored by specifying:

Host / DGDockerX Commands
cd /opt/dg-isle git config core.fileMode false

Thank you, Noah Smith for sharing that bit of wisdom!

Starting the Stack

Having cloned the projects to the host as indicated above, we visit our host terminal and…

Host / DGDockerX Commands
cd /opt/dg-isle docker-compose up -d docker logs -f isle-apache-dg

The startup will take a couple of minutes, and it does not “signal” when it’s done, so that’s the reason for the last command above. The -f option will keep the output spooling to your terminal so that you don’t have to keep repeating the command over and over again. You will know the startup is complete when you see the following at the bottom of the log output:

...
Done setting proper permissions on files and directories
XDEBUG OFF
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 192.168.0.7. Set the 'ServerName' directive globally to suppress this message
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 192.168.0.7. Set the 'ServerName' directive globally to suppress this message
[Mon Dec 16 18:28:44.428224 2019] [mpm_prefork:notice] [pid 67455] AH00163: Apache/2.4.41 (Ubuntu) configured -- resuming normal operations
[Mon Dec 16 18:28:44.428317 2019] [core:notice] [pid 67455] AH00094: Command line: '/usr/sbin/apache2 -D FOREGROUND'

Press ctrl-c to interrupt the docker logs... command and get your terminal back.

Some Settings Are Missing

I found some settings were missing the first time I started the stack like this. A little research and debugging led me to believe that not all of the required configuration commands had been executed properly. In particular, I found that my large image (TIFF image) viewer wasn’t displaying anything at all, presumably because the database I imported from production was setup to use Adore-Djatoka, not IIIF Cantaloupe. The remedy was to take a snapshot of the server, then run the required migration_site_vsets.sh script inside the Apache container. Unfortunately that didn’t work for me at first and I got lots of messages indicating that Command variable-set needs a higher bootstrap level to run.... That error basically means that the drush commands inside the script need to be run from the appropriate directory so that drush can find the site and its database. So, to run it properly inside the Apache container…

Apache Container Commands
cd /var/www/html/sites/default /utility-scripts/isle_drupal_build_tools/migration_site_vsets.sh

Note the cd command and path before the script is run, and there’s no “dot” in front of /utility-scripts.... This time everything worked except for a phpmailerException at the end of the run, but that’s of no consequence, and to be expected since this is a staging server and has no mail facilities of its own.

A quick visit to the staging site shows that large images (for example see https://isle-stage.grinnell.edu/islandora/object/grinnell:25511) are working properly. It sure would be nice to have an automated test to verify that for me, automatically… but we’ll address that issue a little later in this post. 😄

Backup the Site Database

For now, let’s just make a backup of the site database for safe-keeping. We can do this by visiting the site’s home page and using the Quick Backup block at the bottom of the right-hand sidebar and selecting Backup Destination: Manual Backups Directory. This operation makes a backup of the site database and stores it in a pre-determined place… in our case the docker-compose.staging.yml configuration file tells us that it’s stored somewhere in /mnt/data/DG-FEDORA/site-public. More specifically, this backup is /mnt/data/DG-FEDORA/site-public/backup_migrate/manual/DigitalGrinnell-2019-12-17T15-03-10.mysql.gz on the host, DGDockerX.

Missing CModels and No PDF Viewer

While visiting the site moments ago I noticed two more issues:

So, remember back in the Installing the Missing Islandora and Custom Modules section of post 058, we commented out the installation of islandora_binary_object and islandora_pdfjs_reader like so:

cd /var/www/html/sites/all/modules/islandora
git submodule add https://github.com/DigitalGrinnell/dg7.git
git submodule add https://github.com/DigitalGrinnell/idu.git
# git submodule add git://github.com/discoverygarden/islandora_binary_object.git
git submodule add https://github.com/discoverygarden/islandora_collection_search
git submodule add https://github.com/DigitalGrinnell/islandora_mods_display.git
git submodule add https://github.com/Islandora-Labs/islandora_solution_pack_oralhistories.git
# git submodule add git://github.com/nhart/islandora_pdfjs_reader.git
git submodule add https://github.com/Islandora-Labs/islandora_solr_collection_view.git
chown -R islandora:www-data *
cd /var/www/html/sites/default
drush cc all

Well, it’s evidently time to put them back! So, I’m taking a new snapshot of the server then I’ll try to solve this mystery. A little research tells me that the islandora_binary_object command above is pointing to the wrong project for Islandora v7 (it points to an Islandora v8 module). Also, the islandora_pdfjs_reader module has apparently been replaced by islandora_pdfjs, and it just requires some additional configuration. So, the entire command stream on the host should be:

Host / DGDockerX Commands
sudo su cd /opt/dg-islandora git submodule add https://github.com/Islandora-Labs/islandora_binary_object sites/all/modules/islandora/islandora_binary_object chown -R islandora:www-data *

A look at the Installation and Configuration guidance provided in the islandora_pdfjs module’s README.md file suggests that I need to do a little more work in the Apache container so I did as it said, then selected the new PDF viewer at

Then taking a look at our example PDF object, https://isle-stage.grinnell.edu/islandora/object/grinnell:25500, shows that it works!

Binary Objects

The https://github.com/discoverygarden/islandora_binary_object repository that Digital.Grinnell formerly used is now home to an Islandora version 8 module. :sad: That won’t do. Fortuntely, there is a version 7 copy of the old binary content model residing at https://github.com/Islandora-Labs/islandora_binary_object.

There’s no mention of islandora_binary_object in the host’s /opt/dg-islandora/.gitmodules file, so lets add this submodule with the following commands executed from the host:

Host / DGDockerX Commands
sudo su cd /opt/dg-islandora git submodule add https://github.com/Islandora-Labs/islandora_binary_object sites/all/modules/islandora/islandora_binary_object chown -R mcfatem:33 sites/all/modules/islandora/.

Next step then is to enable the new module, and I did this by visiting the site’s module administration page. But when I toggled the Islandora Binary Object Storage on and submitted the form I got this:

DatabaseSchemaObjectExistsException: Table islandora_binary_object_thumbnail_associations already exists. in DatabaseSchema->createTable() (line 663 of /var/www/html/includes/database/schema.inc).
DatabaseSchemaObjectExistsException: Table islandora_binary_object_thumbnail_mappings already exists. in DatabaseSchema->createTable() (line 663 of /var/www/html/includes/database/schema.inc).

Apparently the offending tables, presumably database leftovers from the production site, need to be removed before the new module can be installed. So, in the Apache container I’ll run this:

Apache Container Commands
cd /var/www/html/sites/default drush sql-query “drop table islandora_binary_object_thumbnail_associations” drush sql-query “drop table islandora_binary_object_thumbnail_mappings” drush dis islandora_binary_object -y drush en islandora_binary_object -y drush cc all

That seems to have done the trick. I’ll test it in the morning to confirm, right after another database backup.

Backup the Site Database, Again

Once again, we will visit the site’s home page and use the Quick Backup block at the bottom of the right-hand sidebar and selecting Backup Destination: Manual Backups Directory. This time our backup is /mnt/data/DG-FEDORA/site-public/backup_migrate/manual/DigitalGrinnell-2019-12-18T21-14-02.mysql.gz on the host, DGDockerX.

Not quite a wrap. Be back soon…