Merge pull request #45 from TheJacksonLaboratory/task/update-kustomiz…

…ation-definitions

Task/update kustomization definitions

.compass/compass.yml

@@ -0,0 +1,103 @@
+name: geneweaver-api
+id: 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/ac8655e4-ce94-4576-adb6-15a785b0161b'
+description: null
+configVersion: 1
+typeId: SERVICE
+ownerId: 'ari:cloud:teams::team/0d1a489d-e157-4c61-8d94-7e5c651eb9cc'
+fields:
+  tier: 2
+  lifecycle: Active
+links:
+  - name: null
+    type: REPOSITORY
+    url: 'https://github.com/TheJacksonLaboratory/geneweaver-api'
+  - name: null
+    type: PROJECT
+    url: 'https://jacksonlaboratory.atlassian.net/browse/G3'
+  - name: ''
+    type: DOCUMENT
+    url: 'https://thejacksonlaboratory.github.io/geneweaver-docs/'
+  - name: Swagger Page
+    type: OTHER_LINK
+    url: 'https://geneweaver.jax.org/api/docs'
+  - name: GeneWeaver Slack
+    type: CHAT_CHANNEL
+    url: 'https://thejacksonlaboratory.slack.com/archives/GGKCSAWCF'
+  - name: GeneWeaver JCPG Slack
+    type: CHAT_CHANNEL
+    url: 'https://thejacksonlaboratory.slack.com/archives/C05G32L2SLX'
+relationships:
+  DEPENDS_ON:
+    - 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/f1375e59-b539-46b4-a44c-2cf1bce3637a'
+    - 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/a95bd6b6-cf4f-4635-bb62-693ef9df2f69'
+    - 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/37625f97-0774-42ba-9e0e-9a6b4c87a707'
+    - 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/43044a89-087b-4469-86a8-34f9ded06b4c'
+    - 'ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:component/90bb0329-f6c5-429a-abbc-8d174535ad21/71eb9358-bf9c-4bb2-b30f-2918b099ed57'
+labels: null
+customFields:
+  - name: 'FIN: Funding End Date'
+    type: text
+    value: null
+  - name: 'FIN: Funding Sources'
+    type: text
+    value: null
+  - name: 'FIN: Hosting Cost'
+    type: number
+    value: null
+  - name: 'FIN: Incurred Development Cost'
+    type: number
+    value: null
+  - name: 'FIN: Maintenance Cost'
+    type: number
+    value: null
+  - name: 'INFO: Business Owner'
+    type: text
+    value: 'Erich Baker, Elissa Chesler'
+  - name: 'INFO: Creation Date'
+    type: text
+    value: null
+  - name: 'INFO: Data Type(s)'
+    type: text
+    value: null
+  - name: 'INFO: FAIR Compliance'
+    type: text
+    value: null
+  - name: 'INFO: Usage Statistics'
+    type: text
+    value: null
+  - name: 'INFO: User Statistics'
+    type: text
+    value: null
+  - name: 'TECH: Authentication Type'
+    type: text
+    value: null
+  - name: 'TECH: Authorization'
+    type: text
+    value: null
+  - name: 'TECH: Automated Deployments'
+    type: boolean
+    value: true
+  - name: 'TECH: Containerized'
+    type: boolean
+    value: false
+  - name: 'TECH: Deployment Location'
+    type: text
+    value: jax-cluster
+  - name: 'TECH: Deployment OS'
+    type: text
+    value: null
+  - name: 'TECH: Open Source Code'
+    type: boolean
+    value: true
+  - name: 'TECH: Other'
+    type: text
+    value: null
+  - name: 'TECH: Point of Contact'
+    type: text
+    value: null
+  - name: 'TECH: Public Domain Name'
+    type: boolean
+    value: false
+  - name: 'TECH: Stack'
+    type: text
+    value: 'python, fastapi'

.github/workflows/_check-coverage-action.yml

@@ -65,6 +65,32 @@ jobs:
         with:
           name: coverage-report-html
           path: htmlcov
+      - name: Upload coverage to Compass
+        run: |
+          METRIC_VALUE=$(cat coverage_report.txt | grep 'Total coverage:' | awk '{print $NF}' | sed 's/%//')
+          curl --request POST \
+          --url https://jacksonlaboratory.atlassian.net/gateway/api/compass/v1/metrics \
+          --user "${{ vars.ATLASSIAN_COMPASS_EMAIL }}:${{ secrets.ATLASSIAN_COMPASS_KEY }}" \
+          --header "Accept: application/json" \
+          --header "Content-Type: application/json" \
+          --data "{
+            \"metricSourceId\": \"ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:metric-source/90bb0329-f6c5-429a-abbc-8d174535ad21/f2a60ca2-5065-4c10-ae99-cb844715b5e3\",
+            \"value\": $METRIC_VALUE,
+            \"timestamp\": \"$(date -u +'%Y-%m-%dT%H:%M:%SZ')\"
+          }"
+      - name: Upload complexity to Compass
+        run: |
+          METRIC_VALUE=$(poetry run radon cc src --total-average | grep 'Average complexity:' | awk '{print $NF}' | sed 's/[\(\)]//g')
+          curl --request POST \
+          --url https://jacksonlaboratory.atlassian.net/gateway/api/compass/v1/metrics \
+          --user "${{ vars.ATLASSIAN_COMPASS_EMAIL }}:${{ secrets.ATLASSIAN_COMPASS_KEY }}" \
+          --header "Accept: application/json" \
+          --header "Content-Type: application/json" \
+          --data "{
+            \"metricSourceId\": \"ari:cloud:compass:44257862-6c68-4d47-8211-da38d2bb001b:metric-source/90bb0329-f6c5-429a-abbc-8d174535ad21/480dd6d8-7e86-492f-b929-3cea59711691\",
+            \"value\": $METRIC_VALUE,
+            \"timestamp\": \"$(date -u +'%Y-%m-%dT%H:%M:%SZ')\"
+          }"
   comment-coverage-report:
     needs: [ check_coverage ]
     runs-on: ubuntu-latest

CONTRIBUTING.md

@@ -0,0 +1,15 @@
+The full contribution guide can be found at [Geneweaver Documentation](https://thejacksonlaboratory.github.io/geneweaver-docs/reference/contributing-guide/).
+
+This package is developed and maintained by the Computational Sciences department at 
+the Jackson Laboratory.
+
+For more information, please visit 
+[our website](https://www.jax.org/research-and-faculty/resources/scientific-research-services/computational-sciences).
+
+For questions, comments, bug reports and security vulnerability reporting, please reach
+out to us as [email protected].
+
+Other Geneweaver packages are community developed and can be found at on GitHub:
+- [Geneweaver Testing](https://github.com/bergsalex/geneweaver-testing)
+- [Geneweaver Tools](https://github.com/bergsalex/geneweaver-tools)
+- [Geneweaver AON](https://github.com/bergsalex/geneweaver-aon)

README.md

@@ -1,5 +1,9 @@
 # Geneweaver 3 API
 
+[![GitHub deployments](https://img.shields.io/github/deployments/thejacksonlaboratory/geneweaver-api/jax-cluster-prod-10--prod?style=for-the-badge&label=Deployment%20Status)](https://geneweaver.jax.org/aon/api/docs)
+[![Website](https://img.shields.io/website?url=https%3A%2F%2Fgeneweaver.jax.org%2Fapi%2Fdocs&up_message=available&down_message=down&style=for-the-badge&logo=swagger&label=Swagger%20Page&link=https%3A%2F%2Fgeneweaver.jax.org%2Fapi%2Fdocs)](https://geneweaver.jax.org/api/docs)
+[![Website](https://img.shields.io/website?url=https%3A%2F%2Fthejacksonlaboratory.github.io%2Fgeneweaver-docs%2F&up_message=AVAILABLE&style=for-the-badge&logo=materialformkdocs&label=Documentation)](https://thejacksonlaboratory.github.io/geneweaver-docs/)
+
 Description: The API for the Geneweaver v3 application ecosystem.
 
 ## Setup

deploy/k8s/base/global-labels.yaml

@@ -0,0 +1,14 @@
+apiVersion: builtin
+kind: LabelTransformer
+metadata:
+  name: global-labels
+labels:
+  jax.org/owner-team: geneweaver
+  jax.org/owner-team-id: 0d1a489d-e157-4c61-8d94-7e5c651eb9cc
+  jax.org/billing-group: geneweaver
+  jax.org/system-group: geneweaver
+  jax.org/component-id: ac8655e4-ce94-4576-adb6-15a785b0161b
+  jax.org/component-tier: 2
+fieldSpecs:
+- path: metadata/labels
+  create: true

deploy/k8s/base/kustomization.yaml

@@ -1,9 +1,8 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
+transformers:
+  - global-labels.yaml
 resources:
   - configmap.yaml
   - deployment.yaml
   - service.yaml
-  # TODO: Uncomment the following line to enable ingress
-  # - ingress.yaml

deploy/k8s/overlays/jax-cluster-dev-10--dev/kustomization.yaml

@@ -1,15 +1,6 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
 namespace: dev
-
-bases:
-- ../../base
-
-# NOTE: When applying production ingress, replace this with a patch
 resources:
+  - ../../base
   - ingress.yaml
-
-#patchesStrategicMerge:
-#  - configmap.yaml
-#  - ingress.yaml

deploy/k8s/overlays/jax-cluster-dev-10--sqa/kustomization.yaml

@@ -1,15 +1,6 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
 namespace: sqa
-
-bases:
-- ../../base
-
-# NOTE: When applying production ingress, replace this with a patch
 resources:
+  - ../../base
   - ingress.yaml
-
-#patchesStrategicMerge:
-#  - configmap.yaml
-#  - ingress.yaml

deploy/k8s/overlays/jax-cluster-prod-10--prod/kustomization.yaml

@@ -1,13 +1,8 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
 namespace: prod
-
-bases:
-- ../../base
-
+resources:
+  - ../../base
+  - ingress.yaml
 patchesStrategicMerge:
   - configmap.yaml
-
-resources:
-  - ingress.yaml

deploy/k8s/overlays/jax-cluster-prod-10--stage/kustomization.yaml

@@ -1,13 +1,8 @@
 apiVersion: kustomize.config.k8s.io/v1beta1
 kind: Kustomization
-
 namespace: stage
-
-bases:
-- ../../base
-
+resources:
+  - ../../base
+  - ingress.yaml
 patchesStrategicMerge:
   - configmap.yaml
-
-resources:
-  - ingress.yaml