jhu-idc / idc-isle-dc

Islandora Digital Collections (IDC) development environment
MIT License
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IDC development platform

Leverages ISLE to provide a local development environment for the IDC stack, with particular focus on development/testing of the Drupal site.

Contents

Quick Start

To start the IDC development environment, run

make up

This will build a docker-compose file, run composer install to locally install all dependencies for our site (which will take a few minutes when done the first time, but will be much quicker subsequent times), and start the stack. The stack will start from a known snapshot state, which currently is an entirely empty (but initialized) Drupal.

To reset to a known Drupal state, run

make reset

This will remove all content from volumes that you may have added, remove all php files downloaded by composer, launch using the snapshot as its initial state, then import any config from config/sync.
composer install will run automatically as part of the startup process.

A slightly quicker way to reset to a known state is:

docker-compose down -v
make up

This removes all content from volumes, restores from the last snapshot, pulls in config from config/sync, but does not remove composer-managed PHP files. composer install will still run upon startup, but it needs to do much less.

To dump the site's configuration so that it can be committed to git, do

make config-export

Make targets

There are several Make targets in the Makefile, and its idc-specific companion idc.Makefile (which are included by default, so no need to do anything special other than make to invoke them). A few useful targets are as follows:

A few specialized targets are:

Running tests

To run all tests, with the environment (configuration, modules, content) reset between each test, run make test. This is the make target used to run tests during CI. To run an individual test, run make test test=<name of test>, where <name of test> is the name of a test script in the tests directory, e.g. make test test=01-end-to-end.sh.

When a single test is specified with the test= argument, the environment is not reset for the execution of the test. That is, the existing configuration, content, and modules present in the current codebase are used. This is the recommended (and really only supported way) of running your tests while iterating.

Some additional notes about the test execution environment:

S3 file storage

Drupal is configured to store media on the private:// filesystem, backed by S3. The s3fs module provides this s3-backed implementation of the private:// filesystem. For the idc-isle-dc development environment, minio ([https://minio-idc.traefik.me][https://minio-idc.traefik.me]) provides the S3 API. Cloud/production instances will use Amazon S3.

Configuration

Configuration is via environment variables

Env Var Default Value Description
DRUPAL_DEFAULT_MIGRATIONS_VALIDATE true Determines whether migrations will perform validation
DRUPAL_DEFAULT_S3_ACCESS_KEY - S3 access key
DRUPAL_DEFAULT_S3_SECRET_KEY - S3 secret key
DRUPAL_DEFAULT_S3_BUCKET idc S3 bucket name
DRUPAL_DEFAULT_S3_USE_CUSTOMHOST false Connect to an S3-compatible storage service other than Amazon.
DRUPAL_DEFAULT_S3_HOSTNAME - S3 hostname; use only if DRUPAL_DEFAULT_USE_CUSTOMHOST is true
DRUPAL_DEFAULT_S3_USE_CNAME false Serve files from a custom domain by using an appropriately named bucket, e.g. "mybucket.mydomain.com".
DRUPAL_DEFAULT_S3_USE_PATH_STYLE_ENDPOINT false Send requests to a path-style endpoint, instead of a virtual-hosted-style endpoint. For example, http://s3.amazonaws.com/bucket, insead of http://bucket.s3.amazonaws.com.

Debugging

TL;DR

Supported Env Vars

Env Var Default Value Description
XDEBUG_CONFIG n/a Allows for multiple XDebug config params to be set in a string. Used for CLI debugging.
XDEBUG_SESSION n/a Enables XDebug when present. Used for CLI debugging.
XDEBUG_MODE develop,debug,trace Supported XDebug modes. Used for browser-based debugging
XDEBUG_LOG /var/www/drupal/xdebug.log XDebug logfile. Used for browser-based debugging
XDEBUG_LOGLEVEL 7 XDebug log level. Used for browser-based debuggging.
XDEBUG_DISCOVERCLIENTHOST false If XDebug should attempt to discover the debugging client host. Used for browser-based debugging.
XDEBUG_CLIENTHOST host.docker.internal The address of the debugging client host. Used for browser-based debugging.

About

Allows a developer to launch Drupal with step-wise debugging enabled. The three supported use cases are:

Each use case requires setting a different combination of XDebug settings. By default, the Drupal development image is configured to support the primary use-case, step-enabled debugging of PHP from a browser. Enabling all the use cases at once would be counter-productive from a performance standpoint.

Debugging Drupal interactively from a browser requires the installation of an XDebug helper plugin, so if you don't have one installed, you'll need to do so.

To run the debugging container:

When your debugging session is over, it is important to remember to run make dev-down

In your IDE, configure a PHP/XDebug development session. Your IDE must listen for debugging requests on port 9003. Set a breakpoint. In your browser, activate the XDebug helper by selecting "Debug", then make a request to Drupal which will activate your breakpoint. Your browser should prompt you to map the file from the remote server to your local filesystem, and then you can perform step-by-step debugging.

There are a few ways to determine whether you've successfully started the development environment correctly:

.gitignore is set up to ignore any file that is prefixed with xdebug. If you need to create files to support your debug session, or store output from your debug session, name them xdebug<something> to avoid committing debug artifacts.

If first two conditions are met, you should be able to start a debug session. If you can't, then check for the presence of xdebug.log in the codebase directory for clues, double check your IDE settings, and check the output of php -v in the drupal-dev container. The IDE must accept connections on port 9003, and XDebug must know the IP address of your machine. By default, XDebug connects to host.docker.internal, which is a special DNS name for the host computer.

To switch back from the debugging container:

Snapshots

Snapshots are Docker images that contain Drupal state (content files, database, SOLR indexes, Fedora files, etc). When Docker starts, all Docker volumes will be populated with files from the snapshot image. The net result is that an environment will start quickly, from a known state, with pre-populated content.

After Docker starts from a snapshot, data subsequent in Docker's volumes is ephemeral. It will persist across stop and down, but can be wiped out by

docker-compose down -v

When docker subsequently starts, it will start from the known snapshot state. You are free to take a snapshot whenever you want a checkpoint you can reliably reset Drupal to.

Images

The image used for the snapshot is specified via environment variables in .env. For example:

# Docker image and tag for snapshot image
SNAPSHOT_IMAGE=birkland/snapshot
SNAPSHOT_TAG=upstream-20201007-739693ae-12-ga409e4d8.1602146397

When the docker-compose.yml make target is run, that image and tag will be specified in the docker-compose file. The images contain data that are copied to Docker volumes upon initial startup of the stack (i.e. snapshots are deployed only once, until all volumes are wiped out via docker-compose down -v). Because they are just regular docker images, they can be pushed and puled from container registry as usual.

Taking and publishing snapshots

To take a snapshot, run

make snapshot

This will do the following:

If you want to commit that snapshot so that others can use it, you need to commit .env (which contains the tag of the snapshot image), and publish the snapshot image to a Docker registry via

make snapshot-push

Make sure you do both steps! You need to push the image (so others can pull it), and push .env (so others can check out and run it).

SAML Configuration

Drupal incorporates its own SAML Service Provider using SimpleSAMLphp; an Apache-based SP proxy (c.f. PASS SAML configuration) is not used, and would be incompatible with Drupal. The SimpleSAMLphp SP will be used in development and production environments (including all cloud-based instances).

The developer environment includes a mock Shibboleth Identity Provider (IdP) and LDAP user store to serve as a backend for user attributes. These services would also be used when running integration tests, e.g. as a part of a PR or locally-executed tests. The production environment would not deploy these mock services.

SimpleSAMLphp has an administrative web interface which supports:

Clicking on the Federation tab, and then click on the link labeled Show metadata under the heading “SAML 2.0 SP Metadata” will generate the SAML metadata to provide to the IdP. Testing authentication and attributes presented by the IdP is best performed using this admin interface.

Runtime parameterization of the IdP and SP is accomplished using a mixture of environment variables and secrets. Two containers use these secrets: the idp and drupal containers. Secrets are defined in docker-compose.yml from the consitutient service definitions in docker-compose.saml.yml and docker-compose.local.yml.

For a deeper understanding of SAML certificate roles, this primer may help.

Requested Attributes

Allocation1 SAML 12 SAML 23
eduPersonAffiliation urn:mace:dir:attribute-def:eduPersonAffiliation 1.3.6.1.4.1.5923.1.1.1.1
eduPersonUniqueId urn:oid:1.3.6.1.4.1.5923.1.1.1.13 1.3.6.1.4.1.5923.1.1.1.13
eduPersonPrincipalName urn:mace:dir:attribute-def:eduPersonPrincipalName 1.3.6.1.4.1.5923.1.1.1.6
eduPersonScopedAffiliation urn:mace:dir:attribute-def:eduPersonScopedAffiliation 1.3.6.1.4.1.5923.1.1.1.9
eduPersonAffiliation urn:mace:dir:attribute-def:eduPersonAffiliation 1.3.6.1.4.1.5923.1.1.1.1
employeeNumber urn:mace:dir:attribute-def:employeeNumber 2.16.840.1.113730.3.1.3
displayName urn:mace:dir:attribute-def:displayName 2.16.840.1.113730.3.1.241
givenName urn:mace:dir:attribute-def:givenName 2.5.4.42
departmentNumber urn:mace:dir:attribute-def:departmentNumber 2.16.840.1.113730.3.1.2
mail urn:mace:dir:attribute-def:mail urn:oid:0.9.2342.19200300.100.1.3

1 urn:oasis:names:tc:SAML:2.0:attrname-format:basic

2 urn:mace:shibboleth:1.0:attributeNamespace:uri

3 urn:oasis:names:tc:SAML:2.0:attrname-format:uri

The authsources.php file contains the requested attributes. These are hardcoded, and are not parameterized.

See the SimpleSAMLphp User Sync page for how these attributes may be mapped to Drupal user attributes or role selection.

Note: 'mail' and 'eduPersonPrincipleName' are required attributes

Env vars

These are truly environment variables (in the sense that they are not secrets). Cloud-based installations will need to update these to expected values.

Variable Name Default Value Location Description
SP_BASEURL https://islandora-idc.traefik.me .env file Base URL for SP services. Cloud-based installations will need to update these to expected values.
SP_ENTITYID https://islandora-idc.traefik.me/sp/shibboleth .env file SP entity ID (a URI). Cloud-based installations will need to update these to expected values.
IDP_BASEURL https://islandora-idp.traefik.me:4443 .env file Base URL for IdP services. Cloud-based installations will need to update these to expected values.
IDP_ENTITYID https://islandora-idp.traefik.me/idp/shibboleth .env file IdP entity ID (a URI). Cloud-based installations will need to update these to expected values.
DRUPAL_DEFAULT_SITE_URL https://islandora-idc.traefik.me docker-compose.env.yml Use to derive the SimpleSAMLphp baseurlpath
DRUPAL_SP_TECHCONTACTNAME Moo Cow docker-compose.env.yml Some information about the technical persons running this installation. The email address will be used as the recipient address for error reports, and also as the technical contact in generated metadata.
DRUPAL_SP_TECHCONTACTEMAIL moo@cow.org docker-compose.env.yml Some information about the technical persons running this installation. The email address will be used as the recipient address for error reports, and also as the technical contact in generated metadata.
DRUPAL_SP_PROTECTINDEXPAGE false docker-compose.env.yml Set this options to true if you want to require administrator password to access the web interface or the metadata pages, respectively.
DRUPAL_SP_PROTECTMETADATAPAGE false docker-compose.env.yml Set this options to true if you want to require administrator password to access the web interface or the metadata pages, respectively.
DRUPAL_SP_CHECKFORUPDATES true docker-compose.env.yml Set this option to false if you don't want SimpleSAMLphp to check for new stable releases when visiting the configuration tab in the web interface.
DRUPAL_SP_ASSERTIONALLOWEDCLOCKSKEW 180 docker-compose.env.yml Set the allowed clock skew between encrypting/decrypting assertions
DRUPAL_SP_SESSION_DURATIONSECONDS 28800 docker-compose.env.yml This value is the duration of the session in seconds. Make sure that the time duration of cookies both at the SP and the IdP exceeds this duration.
DRUPAL_SP_SESSION_DATASTORETIMEOUTSECONDS 14400 docker-compose.env.yml Sets the duration, in seconds, data should be stored in the datastore. As the data store is used for login and logout requests, this option will control the maximum time these operations can take.
DRUPAL_SP_SESSION_STATETIMEOUTSECONDS 3600 docker-compose.env.yml Sets the duration, in seconds, auth state should be stored.
DRUPAL_SP_SESSION_COOKIENAME SimpleSAMLSessionID docker-compose.env.yml Option to override the default settings for the session cookie name
DRUPAL_SP_SESSION_COOKIELIFETIMESECONDS 0 docker-compose.env.yml Expiration time for the session cookie, in seconds. Defaults to 0, which means that the cookie expires when the browser is closed.
DRUPAL_SP_SESSION_COOKIEPATH / docker-compose.env.yml Limit the path of the cookies. Can be used to limit the path of the cookies to a specific subdirectory.
DRUPAL_SP_SESSION_COOKIESECURE false docker-compose.env.yml Set the secure flag in the cookie. Set this to TRUE if the user only accesses your service through https. If the user can access the service through both http and https, this must be set to FALSE.
DRUPAL_SP_LOGGING_LEVEL INFO simplesaml_config.patch, <vendor dir>/simplesamlphp/simplesamlphp/config/config.php Set the log level used by the SimpleSAMLphp SP. Valid values are 'ERR', 'WARNING', 'NOTICE', 'INFO', 'DEBUG'
DRUPAL_SP_LOGGING_HANDLER errorlog simplesaml_config.patch, <vendor dir>/simplesamlphp/simplesamlphp/config/config.php Sets the log handler used by the SimpleSAMLphp SP. Valid values are 'syslog', 'file', 'errorlog', 'stderr'

SAML Secrets

It should be said immediately that not every key/value pair in the saml-secrets.yml file is strictly a secret. For example, public keys (in the form of X509 certs) would not be considered a secret. However, to facilitate uniform processing of private/public key pairs and other values, using a single secrets file together with the confd file backend makes sense. saml-secrets.yml uses a structure well-known to the containers that process its contents. Renaming, removing, or adding keys may impact the processing of its content by the idp or drupal containers.

In the Docker environment, there are unfortunate layers of indirection when it comes to the use of secrets.

First and foremost, secrets are defined in docker-compose.yml, which is formed by constituent service files including docker-compose.local.yml (which defines the drupal service) and docker-compose.saml.yml (which defines the idp service). The first indirection decouples the location of the secret from the name of the secret: the secrets are exposed to the containers by their name, independent of their location in the repository.

Generally, a named secret defines a single value. The exception is the secret named saml_secrets; it contains multiple secrets. This is the second indirection, whereby a single named secret can securely expose multiple secret values. (This is in order to leverage the file backend of confd) Values in saml-secrets.yml may themselves be environment variables, which must be processed before they are used. This is the third indirection.

Finally, some values from saml_secrets may be written out to files. This depends on the capabilities of the consumer: some read configuration values inline, others read them from files.

Composer Secret Name Composer Location Confd Key Container(s) Used By Referenced As References Notes
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/signing-key idp Shibboleth IdP file idp.properties Ends with: 'opm/rxS83hCrTsIX3Il3T8Fpb97kdF+unCiWEaxrPEurjW8lB506'
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/signing-cert idp,drupal Shibboleth IdP, SimpleSAMLphp file, inline idp.properties, idp-metadata.xml, shib13-idp-remote.php Ends with: 's00xrv14zLifcc8oj5DYzOhYRifRXgHX'
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/encryption-key idp Shibboleth IdP file idp.properties Ends with: 'qX7ZsBuOT72RwVEa8fpT6IZ6IpOOEPmUid/f2VM2aAcXgaF//vMjxA=='
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/encryption-cert idp,drupal Shibboleth IdP, SimpleSAMLphp file, inline idp.properties, idp-metadata.xml, shib13-idp-remote.php Ends with: 'p+tGUbGS2l873J5PrsbpeKEVR/IIoKo='
idp_sealer /secrets/idp/sealer.jks - idp Shibboleth IdP file idp.properties -
idp_backchannel /secrets/idp/idp-backchannel.p12 - idp Jetty file backchannel.ini Runs on port 8443, may not be used
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/backchannel-signing-cert idp,drupal Shibboleth IdP, SimpleSAMLphp inline idp-metadata.xml, shib13-idp-remote.php PEM version of the PKCS 12 encoded idp_backchannel; ends with: 't6Lf23Kb8yD6ZR7dihMZAGHnYQ/hlhM='
idp_browser /secrets/idp/idp-browser.p12 - idp Jetty file ssl.ini Runs on port 4443; this is the cert presented to HTTPS clients for IdP requests
saml_secrets /secrets/saml-secrets.yml /saml-secrets/idp/browser-cert - - - - PEM version of the PKCS 12 encoded idp_browser, seems unused; ends with '7vawjZs0YP5qGifhos34g2GKW81m6sjoxpstLMK7pNQRy/pR/kv/jiXEn8xHRE6s'
saml_secrets /secrets/saml-secrets.yml /saml-secrets/sp/admin-pw drupal SimpleSAMLphp inline config.php Contains the administrative password for the SimpleSAMLphp interface
saml_secrets /secrets/saml-secrets.yml /saml-secrets/sp/signing-cert idp,drupal Shibboleth IdP, SimpleSAMLphp inline sp-metadata.xml, authsources.php Ends with: 'lQQUhxyEXTBJx3luLlpIjoloFKIute9K7pE5qAENjg=='
saml_secrets /secrets/saml-secrets.yml /saml-secrets/sp/hashing-salt drupal SimpleSAMLphp inline config.php Used by SimpleSAMLphp to create secure hashes
saml_secrets /secrets/saml-secrets.yml /saml-secrets/sp/signing-key drupal SimpleSAMLphp file authsources.php Ends with: 'HPxmTTEX5graPtXeDM3hz5A='

SAML env and secrets processing

Two containers use SAML env vars and secrets: the idp container (the mock Shibboleth Identity Provider) and the drupal container (SimpleSAMLphp Service Provider). Secrets are defined in their accompanying docker-compose files, docker-compose.local.yml and docker-compose.saml.yml.

There are a number of files which contribute to the SAML environment, distributed across the idc-isle-dc and idc-isle-buildkit repositories, and multiple methods used for processing. The complexity is high for a couple of reasons:

An example may help: you wish to know how/where the IdP signing key is used. Using the table above, a starting point would be to search the idc-isle-buildkit repo for occurrences of idp/signing-key key. The only hits will be confd configuration, where you see that it is written out to /tmp/idp_signing. Perform a second search for /tmp/idp_signing, and you'll see it used in the idp.properties confd template (which in turn writes idp.properties to /opt/shibboleth-idp/conf/idp.properties).

A second, more complex example: you wish to know how/where the IdP signing cert is used. Using the table, start by searching the idc-isle-buildkit repo for occurrences of idp/signing-cert key. You'll see it referenced by a couple of confd templates which in turn will lead you to idp.properties (references the value in the file /tmp/idp_signing.crt) and idp-metadata.xml (the value is used inline). You will also want to perform a similar search of the idc-isle-dc repository. To cast a wide net, search for the string signing-cert (you'll get some hits from both the SP and IdP). You'll note that the file shib13-idp-remote.php uses PHP to parse the value from the saml_secrets YAML structure (essentially inline use). As things evolve, I do not expect the table below to be kept up-to-date, so it is worth understanding how to discover where and how various secrets are used.

Tips:

IdP env and secrets processing

The IdP entrypoint uses confd to interpolate a number of configuration files that dictate SAML request processing. Because saml_secrets can use environment variables as secret values, the configuration files are subsequently processed through envsubst.

Note that the IdP configuration files may refer to any named secrets that are exposed by Docker, not just the secrets present in saml_secrets.

Finally, processing logic occurs in the idp entrypoint which resides in the idc-isle-buildkit repository. Secrets are defined in the idc-isle-dc repository. The names of secrets are shared between the two repositories; if the name of a secret changes, it must be changed in both.

SP env and secrets processing

The Service Provider (SimpleSAMLphp) runs in the drupal container, installed as a vendored composer dependency. A number of PHP configuration files have been modified to reference secrets and environment variables where it makes sense. For example, in config.php 'assertion.allowed_clock_skew' => 180 has been changed to 'assertion.allowed_clock_skew' => intval(getenv('DRUPAL_SP_ASSERTIONALLOWEDCLOCKSKEW')). Instead of inlining certificates, shib-13-idp-remote.php parses saml_secrets. These modifications reside in a patch file managed in the idc-isle-dc repository.

The PHP interpreter executes under PHP-FPM, therefore environment variables must be explicitly passed from NGINX. Confd is used to process SP-related environment variables (using the env backend) and expose them to PHP-FPM via the include file drupal_sp_fastcgi_params. Confd is executed on container start, and is managed in the idc-isle-buildkit repository.

======= Note: In order for the push to be successful, you need to be "logged in" to the container registry via

docker login ghcr.io

See the guide to the github container registry for more information.