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Rename adt to obds #115

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merged 10 commits into from
Oct 31, 2023
Merged

Rename adt to obds #115

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a65114e
removed adt everywhere, replaced it with obds
Oct 26, 2023
4f6f7c1
Merge branch 'master' into rename-adt-job
Oct 26, 2023
bc98991
replaced some more adts
Oct 26, 2023
a3d4c47
remove code editor config
Oct 26, 2023
a1a98ac
chore: bumps obds-to-fhir images
MarcelErpi Oct 26, 2023
7be7d17
chore: bumps obds-to-fhir
MarcelErpi Oct 27, 2023
6806cf4
Update ci.yaml
jasminziegler Oct 31, 2023
3c6946c
chore: make megalinter black happy
Oct 31, 2023
e6cc005
Merge branch 'rename-adt-job' of https://github.com/bzkf/diz-in-a-box…
Oct 31, 2023
8a59ef7
chore: markdownlint
Oct 31, 2023
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20 changes: 10 additions & 10 deletions .github/workflows/ci.yaml
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Expand Up @@ -18,11 +18,11 @@ permissions: read-all
env:
DIZBOX_NAMESPACE_NAME: bzkf-dizbox
DECOMPOSE_XML_IMAGE_NAME: ghcr.io/${{ github.repository }}/decompose-xmls
ADTFHIR_TO_OPAL_IMAGE_NAME: ghcr.io/${{ github.repository }}/adtfhir-to-opal
OBDS_FHIR_TO_OPAL_IMAGE_NAME: ghcr.io/${{ github.repository }}/obds-fhir-to-opal

jobs:
build-decompose-xml-image:
name: build decompose_xmls container image
name: build decompose-xmls container image
runs-on: ubuntu-22.04
permissions:
packages: write
Expand Down Expand Up @@ -64,15 +64,15 @@ jobs:
labels: ${{ steps.container_meta.outputs.labels }}
load: ${{ github.event_name == 'pull_request' }}

build-adtfhir-to-opal-image:
name: build adtfhir_to_opal container image
build-obds-fhir-to-opal-image:
name: build obds-fhir-to-opal container image
runs-on: ubuntu-22.04
permissions:
packages: write
outputs:
image-tags: ${{ steps.container_meta.outputs.tags }}
image-digest: ${{ steps.build.outputs.digest }}
image-name: ${{ env.ADTFHIR_TO_OPAL_IMAGE_NAME }}
image-name: ${{ env.OBDS_FHIR_TO_OPAL_IMAGE_NAME }}
steps:
- name: Checkout code
uses: actions/checkout@8ade135a41bc03ea155e62e844d188df1ea18608 # v4
Expand All @@ -85,7 +85,7 @@ jobs:
uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5
with:
images: |
${{ env.ADTFHIR_TO_OPAL_IMAGE_NAME }}
${{ env.OBDS_FHIR_TO_OPAL_IMAGE_NAME }}

- name: Login to GitHub Container Registry
uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3
Expand All @@ -99,7 +99,7 @@ jobs:
id: build
uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5
with:
context: src/adtfhir_to_opal
context: src/obds_fhir_to_opal
cache-from: type=gha
cache-to: type=gha,mode=max
push: ${{ github.event_name != 'pull_request' }}
Expand All @@ -113,7 +113,7 @@ jobs:
if: ${{ github.event_name == 'pull_request' }}
needs:
- build-decompose-xml-image
- build-adtfhir-to-opal-image
- build-obds-fhir-to-opal-image
steps:
- name: install k3s
run: |
Expand Down Expand Up @@ -173,7 +173,7 @@ jobs:
run: |
helm test diz-in-a-box

kubectl wait deployment/diz-in-a-box-stream-processors-onkoadt-to-fhir --for=condition=Available --timeout=300s
kubectl wait deployment/diz-in-a-box-stream-processors-obds-to-fhir --for=condition=Available --timeout=300s
kubectl wait deployment/diz-in-a-box-stream-processors-fhir-to-server --for=condition=Available --timeout=300s

- name: Print cluster logs
Expand Down Expand Up @@ -207,5 +207,5 @@ jobs:
packages: write
needs:
- build-decompose-xml-image
- build-adtfhir-to-opal-image
- build-obds-fhir-to-opal-image
uses: ./.github/workflows/release.yaml
2 changes: 1 addition & 1 deletion .github/workflows/release-please.yaml
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Expand Up @@ -24,7 +24,7 @@ jobs:
charts/prerequisites/Chart.yaml
README.md
docker-compose/compose.decompose-xmls.yaml
docker-compose/compose.adtfhir-to-opal.yaml
docker-compose/compose.obds-fhir-to-opal.yaml
changelog-types: |
[
{ "type": "feat", "section": "Features" },
Expand Down
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -15,3 +15,5 @@ __pycache__/

bundles-delta/
*.csv

.vscode
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -99,7 +99,7 @@ helm upgrade --install --wait --timeout=10m --version=1.6.2 diz-in-a-box oci://g
# test the installation
helm test diz-in-a-box

kubectl wait deployment/diz-in-a-box-stream-processors-onkoadt-to-fhir --for=condition=Available --timeout=300s
kubectl wait deployment/diz-in-a-box-stream-processors-obds-to-fhir --for=condition=Available --timeout=300s
kubectl wait deployment/diz-in-a-box-stream-processors-fhir-to-server --for=condition=Available --timeout=300s
```

Expand Down
6 changes: 3 additions & 3 deletions Taskfile.yaml
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Expand Up @@ -4,21 +4,21 @@ env:
COMPOSE_PROJECT_NAME: bzkf-diz-in-a-box

tasks:
adt-to-fhir:
obds-to-fhir:
dir: docker-compose/
cmds:
- |
docker compose \
-f compose.full.yaml \
-f compose.decompose-xmls.yaml \
-f compose.onkoadt-to-fhir.yaml up --detach
-f compose.obds-to-fhir.yaml up --detach

fhir-to-opal:
dir: docker-compose/
cmds:
- |
docker compose \
-f compose.adtfhir-to-opal.yaml up
-f compose.obds-to-opal.yaml up

clean:
dir: docker-compose/
Expand Down
2 changes: 1 addition & 1 deletion build-air-gapped-installer.sh
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Expand Up @@ -82,7 +82,7 @@ mkdir -p "$AIR_GAPPED_COMPOSE_INSTALL_DIR"
# generate save-images.sh
docker compose --profile=kafka-connect \
-f docker-compose/compose.full.yaml \
-f docker-compose/compose.onkoadt-to-fhir.yaml \
-f docker-compose/compose.obds-to-fhir.yaml \
-f docker-compose/compose.decompose-xmls.yaml \
-f docker-compose/compose.fhir-server.yaml \
-f docker-compose/compose.pseudonymization.yaml \
Expand Down
8 changes: 4 additions & 4 deletions charts/diz-in-a-box/README.md
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Expand Up @@ -45,10 +45,10 @@ Kubernetes: `>= 1.21.0`
| fhir-gateway.fhir-pseudonymizer.vfps.enabled | bool | `true` | |
| fhir-gateway.fhir-pseudonymizer.vfps.postgresql.auth.postgresPassword | string | `"vfps-postgres"` | |
| fhir-gateway.kafka.enabled | bool | `true` | |
| fhir-gateway.kafka.inputTopics[0] | string | `"fhir.onkoadt.MedicationStatement"` | |
| fhir-gateway.kafka.inputTopics[1] | string | `"fhir.onkoadt.Condition"` | |
| fhir-gateway.kafka.inputTopics[2] | string | `"fhir.onkoadt.Observation"` | |
| fhir-gateway.kafka.inputTopics[3] | string | `"fhir.onkoadt.Procedure"` | |
| fhir-gateway.kafka.inputTopics[0] | string | `"fhir.obds.MedicationStatement"` | |
| fhir-gateway.kafka.inputTopics[1] | string | `"fhir.obds.Condition"` | |
| fhir-gateway.kafka.inputTopics[2] | string | `"fhir.obds.Observation"` | |
| fhir-gateway.kafka.inputTopics[3] | string | `"fhir.obds.Procedure"` | |
| fhir-gateway.kafka.outputTopic | string | `"fhir.post-gateway"` | |
| fhir-gateway.kafka.securityProtocol | string | `"SSL"` | |
| fhir-gateway.kafka.strimziClusterName | string | `"bzkf-dizbox-cluster"` | |
Expand Down
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