Merge pull request #419 from NASA-PDS/i415

Reorganizes Jenkins- and Docker-specific assets into subdirectories `jenkins` and `docker`, respectively

.github/dependabot.yml

@@ -5,7 +5,8 @@
 
 version: 2
 updates:
-  - package-ecosystem: "" # See documentation for possible values
-    directory: "/" # Location of package manifests
-    schedule:
-      interval: "weekly"
+    -
+        package-ecosystem: "pip"
+        directory: "/"
+        schedule:
+            interval: "weekly"

.github/workflows/codeql-analysis.yml

@@ -40,6 +40,11 @@ jobs:
     - name: Checkout repository
       uses: actions/checkout@v3
 
+    - name: Setup python 3.9
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
       uses: github/codeql-action/init@v2

README.md

@@ -115,14 +115,15 @@ To run the server on a Docker container, please execute the following from the p
 
 ```console
 $ # building the image
-$ docker image build --tag pds-doi-service .
+$ docker image build --tag pds-doi-service --file docker/Dockerfile .
 $ # starting up a container
 $ docker container run --publish 8080:8080 pds-doi-service
 ```
 
 However, note that when launching the container via `docker container run`, all configuration values are derived from the default INI file bundled with the repository. To override the configuration, it is recommended to launch the service via a Docker Composition:
 
 ```console
+$ cd docker
 $ # Make a copy of the docker composition environment template:
 $ cp doi_service.env.in doi_service.env
 $ # Edit the environment file, setting the credentials within:
@@ -131,7 +132,7 @@ $ # Start the composition; on some systems, `docker compose` is `docker-compose`
 $ docker compose up
 ```
 
-This will launch the DOI Service container using the top-level `docker-compose.yml` file, which specifies that environment variables be imported from `doi_service.env`. Modify `doi_service.env` (after copying it from `doi_service.env.in`) to define any configuration values to override when the service is launched.
+This will launch the DOI Service container using the `docker-compose.yaml` file in the `docker` subdirectory, which specifies that environment variables be imported from `doi_service.env`. Modify `doi_service.env` (after copying it from `doi_service.env.in`) to define any configuration values to override when the service is launched.
 
 ## Test
 
@@ -147,7 +148,13 @@ Testing details are detailed in this section.
 - linting
 - building the rich documentation.
 
-To launch the full set of tests, simply run:
+To launch the full set of tests, simply set the following environment variables:
+
+- `CI` should be set to `true`
+- `DATACITE_USER` should be set to the PDS username of the testing Datacite instance
+- `DATACITE_PASSWORD` should be set to that username's password
+
+Then run:
 
     tox
 

docker/doi_service.env.in

@@ -0,0 +1,69 @@
+# Copyright © 2021–2023, California Institute of Technology ("Caltech").
+# U.S. Government sponsorship acknowledged.
+#
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#
+# • Redistributions of source code must retain the above copyright notice,
+#   this list of conditions and the following disclaimer.
+# • Redistributions must reproduce the above copyright notice, this list of
+#   conditions and the following disclaimer in the documentation and/or other
+#   materials provided with the distribution.
+# • Neither the name of Caltech nor its operating division, the Jet Propulsion
+#   Laboratory, nor the names of its contributors may be used to endorse or
+#   promote products derived from this software without specific prior written
+#   permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+# This file is used with docker-compose.yaml to specify a number of environment
+# variable key/value pairs to add to the DOI Service's environment when
+# launching the container via docker compose up.
+
+# The DOI Service prioritizes environment variables over the included INI,
+# so this file may be used to inject credentials or any other supported
+# options into the DOI Service when in a containerized context.
+
+# The naming convention for expected environment variables follows from the
+# format of the INI, where the section name and option name are concatenated
+# with an underscore and converted to uppercase, for example:
+
+#   OSTI_USER=username -> overrides the "user" option of the [OSTI] INI section.
+
+# If the default values from the bundled INI are desired, do not specify
+# environment variables for them here or they will be overridden.
+
+# Also note that Docker performs "no special handling of quotation marks" for
+# values. This means that they become part of the value provided to the DOI Service.
+
+# [PDS4_DICTIONARY]
+PDS4_DICTIONARY_URL=https://pds.nasa.gov/pds4/pds/v1/PDS4_PDS_JSON_1D00.JSON
+
+# [LANDING_PAGES]
+LANDING_PAGES_URL=https://pds.nasa.gov/ds-view/pds/view{}.jsp?identifier={}&version={}
+
+# [OTHER]
+[email protected]
+OTHER_PDS_REGISTRATION_DOI_TOKEN=10.17189
+OTHER_LOGGING_LEVEL=DEBUG
+
+# [OSTI]
+#
+# This last 2 lines of this file *must* be OSTI_USER and OSTI_PASSWORD for
+# Jenkins to work!
+
+OSTI_URL=https://www.osti.gov/iad2test/api/records
+OSTI_USER=username
+OSTI_PASSWORD=secret

Jenkinsfile → jenkins/Jenkinsfile

@@ -1,5 +1,5 @@
 /*
- * Copyright © 2022, California Institute of Technology ("Caltech").
+ * Copyright © 2022–2023, California Institute of Technology ("Caltech").
  * U.S. Government sponsorship acknowledged.
  *
  * All rights reserved.
@@ -49,7 +49,7 @@ pipeline {
         shutdown_timeout = "30"
 
         // Basic composition command:
-        compose = "docker-compose --file ${env.WORKSPACE}/jenkins-compose.yaml"
+        compose = "docker-compose --file ${env.WORKSPACE}/jenkins/jenkins-compose.yaml --project-directory ${env.WORKSPACE}/jenkins"
 
         // Network morphology
         PDS_DOI_PUBLISHED_PORT = "3176"
@@ -70,10 +70,10 @@ pipeline {
                 withCredentials([
                     usernamePassword(credentialsId: 'datacite-dev', passwordVariable: 'p', usernameVariable: 'u')
                 ]) {
-                    sh "rm --force doi_service.env"
-                    sh "head --lines=-2 doi_service.env.in > doi_service.env"
-                    sh 'echo "OSTI_USER=$u" >> doi_service.env'
-                    sh 'echo "OSTI_PASSWORD=$p" >> doi_service.env'
+                    sh "rm --force jenkins/doi_service.env"
+                    sh "head --lines=-2 docker/doi_service.env.in > jenkins/doi_service.env"
+                    sh 'echo "OSTI_USER=$u" >> jenkins/doi_service.env'
+                    sh 'echo "OSTI_PASSWORD=$p" >> jenkins/doi_service.env'
                 }
                 sh "$compose pull --quiet"
             }

src/pds_doi_service/api/util.py

@@ -74,7 +74,7 @@ def _deserialize(data, klass):
         return deserialize_date(data)
     elif klass == datetime.datetime:
         return deserialize_datetime(data)
-    elif type(klass) == typing.GenericMeta:
+    elif type(klass) is typing.GenericMeta:
         if klass.__extra__ == list:
             return _deserialize_list(data, klass.__args__[0])
         if klass.__extra__ == dict:

tox.ini

@@ -10,7 +10,7 @@ passenv = CI DATACITE_USER DATACITE_PASSWORD
 [testenv:docs]
 deps = .[dev]
 whitelist_externals = python
-commands = python setup.py build_sphinx
+commands = sphinx-build docs/source docs/build
 
 [testenv:lint]
 deps = pre-commit