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Merge branch 'master' into VED-357-terraform-folder-changes-only
2 parents 24feded + 41be795 commit 24caab8

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‎.github/workflows/sonarcloud.yml‎

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@@ -40,7 +40,7 @@ jobs:
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id: filenameprocessor
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continue-on-error: true
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run: |
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poetry env use 3.10
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poetry env use 3.11
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poetry install
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poetry run coverage run -m unittest discover || echo "filenameprocessor tests failed" >> ../failed_tests.txt
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poetry run coverage xml -o ../filenameprocessor-coverage.xml
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id: recordprocessor
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continue-on-error: true
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run: |
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poetry env use 3.10
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poetry env use 3.11
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poetry install
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poetry run coverage run -m unittest discover || echo "recordprocessor tests failed" >> ../failed_tests.txt
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poetry run coverage xml -o ../recordprocessor-coverage.xml

‎README.md‎

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@@ -108,11 +108,17 @@ Once connected, you should see the path as something similar to: `/mnt/d/Source/
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5. Configure pyenv.
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```
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pyenv install --list | grep "3.10"
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pyenv install 3.10.16 #current latest
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pyenv install --list | grep "3.11"
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pyenv install 3.11.13 #current latest
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```
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6. Install poetry
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6. Install direnv if not already present, and hook it to the shell.
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```
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sudo apt-get update && sudo apt-get install direnv
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echo 'eval "$(direnv hook bash)"' >> ~/.bashrc
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```
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7. Install poetry
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```
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pip install poetry
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```
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Steps:
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1. Set the python version in the folder with the code used by lambda for example `./backend` (see [lambdas](#lambdas)) folder.
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```
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pyenv local 3.10.16 # Set version in backend (this creates a .python-version file)
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pyenv local 3.11.13 # Set version in backend (this creates a .python-version file)
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```
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Note: consult the lambda's `pyproject.toml` file to get the required Python version for this lambda. At the time of writing, this is `~3.10` for the batch lambdas and `~3.11` for all the others.
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2. Configure poetry
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```
@@ -203,4 +210,13 @@ The root (`immunisation-fhir-api`) should point to `/mnt/d/Source/immunisation-f
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## Verified commits
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Please note that this project requires that all commits are verified using a GPG key.
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To set up a GPG key please follow the instructions specified here:
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https://docs.github.com/en/authentication/managing-commit-signature-verification
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https://docs.github.com/en/authentication/managing-commit-signature-verification
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## AWS configuration: Getting credentials for AWS federated user account
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In the 'Access keys' popup menu under AWS Access Portal:
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**NOTE** that AWS's 'Recommended' method of getting credentials **(AWS IAM Identity Center credentials)** will break mocking in unit tests; specifically any tests calling `dynamodb_client.create_table()` will fail with `botocore.errorfactory.ResourceInUseException: Table already exists`.
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Instead, use **Option 2 (Add a profile to your AWS credentials file)**.

‎config/common/disease_mapping.json‎

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[
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{
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"vacc_type": "COVID19",
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"diseases": [
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{
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"code": "840539006",
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"term": "Disease caused by severe acute respiratory syndrome coronavirus 2"
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}
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]
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},
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{
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"vacc_type": "FLU",
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"diseases": [
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{
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"code": "6142004",
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"term": "Influenza caused by seasonal influenza virus (disorder)"
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}
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]
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},
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{
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"vacc_type": "HPV",
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"diseases": [
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{
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"code": "240532009",
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"term": "Human papillomavirus infection"
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}
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]
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},
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{
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"vacc_type": "MMR",
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"diseases": [
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{
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"code": "14189004",
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"term": "Measles (disorder)"
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},
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{
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"code": "36989005",
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"term": "Mumps (disorder)"
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},
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{
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"code": "36653000",
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"term": "Rubella (disorder)"
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}
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]
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},
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{
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"vacc_type": "MMRV",
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"diseases": [
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{
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"code": "14189004",
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"term": "Measles (disorder)"
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},
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{
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"code": "36989005",
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"term": "Mumps (disorder)"
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},
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{
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"code": "36653000",
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"term": "Rubella (disorder)"
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},
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{
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"code": "38907003",
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"term": "Varicella (disorder)"
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}
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]
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},
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{
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"vacc_type": "RSV",
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"diseases": [
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{
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"code": "55735004",
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"term": "Respiratory syncytial virus infection (disorder)"
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}
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]
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},
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{
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"vacc_type": "PERTUSSIS",
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"diseases": [
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{
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"code": "27836007",
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"term": "Pertussis (disorder)"
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}
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]
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},
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{
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"vacc_type": "SHINGLES",
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"diseases": [
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{
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"code": "4740000",
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"term": "Herpes zoster"
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}
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]
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},
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{
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"vacc_type": "PCV13",
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"diseases": [
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{
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"code": "16814004",
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"term": "Pneumococcal infectious disease"
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}
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]
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},
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{
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"vacc_type": "3in1",
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"diseases": [
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{
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"code": "398102009",
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"term": "Acute poliomyelitis"
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},
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{
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"code": "397430003",
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"term": "Diphtheria caused by Corynebacterium diphtheriae"
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},
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{
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"code": "76902006",
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"term": "Tetanus (disorder)"
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}
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]
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},
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{
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"vacc_type": "MENACWY",
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"diseases": [
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{
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"code": "23511006",
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"term": "Meningococcal infectious disease"
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}
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]
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}
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]

‎config/dev/permissions_config.json‎

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[
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{
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"supplier": "DPSFULL",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "DPSREDUCED",
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"permissions": [
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"COVID19.CRUD",
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"FLU.CRUD",
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"MMR.CRUD",
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"RSV.CRUD"
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]
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},
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{
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"supplier": "MAVIS",
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"permissions": [
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"HPV.CRUDS",
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"3IN1.CRUDS",
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"MENACWY.CRUDS",
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"MMR.CRUDS",
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"FLU.CRUDS"
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]
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},
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{
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"supplier": "EMIS",
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"permissions": [
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"RSV.U"
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]
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},
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{
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"supplier": "PINNACLE",
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"permissions": []
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},
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{
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"supplier": "SONAR",
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"permissions": [
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"FLU.CD"
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]
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},
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{
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"supplier": "TPP",
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"permissions": []
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},
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{
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"supplier": "AGEM-NIVS",
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"permissions": []
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},
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{
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"supplier": "NIMS",
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"permissions": []
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},
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{
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"supplier": "EVA",
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"permissions": [
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"COVID19.CUD"
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]
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},
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{
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"supplier": "RAVS",
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"permissions": [
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "AGEM-RAVS-Integration",
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"permissions": [
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "MEDICAL_DIRECTOR",
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"permissions": []
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},
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{
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"supplier": "COVID19_VACCINE_RESOLUTION_SERVICEDESK",
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"permissions": []
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},
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{
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"supplier": "Test_App",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS",
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"HPV.CRUDS",
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"MENACWY.CRUDS",
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"PERTUSSIS.CRUDS",
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"3IN1.CRUDS"
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]
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},
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{
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"supplier": "Postman_Auth",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS",
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"HPV.CRUDS",
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"MENACWY.CRUDS",
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"PERTUSSIS.CRUDS",
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"3IN1.CRUDS"
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]
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}
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]

‎config/preprod/permissions_config.json‎

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[
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{
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"supplier": "DPSFULL",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "DPSREDUCED",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "MAVIS",
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"permissions": [
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"HPV.CRUDS",
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"3IN1.CRUDS",
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"MENACWY.CRUDS",
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"MMR.CRUDS",
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"FLU.CRUDS"
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]
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},
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{
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"supplier": "RAVS",
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"permissions": [
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "Test_App",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS",
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"HPV.CRUDS",
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"MENACWY.CRUDS",
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"PERTUSSIS.CRUDS",
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"3IN1.CRUDS"
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]
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},
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{
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"supplier": "Postman_Auth",
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"permissions": [
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"COVID19.CRUDS",
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"FLU.CRUDS",
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"MMR.CRUDS",
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"RSV.CRUDS",
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"HPV.CRUDS",
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"MENACWY.CRUDS",
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"PERTUSSIS.CRUDS",
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"3IN1.CRUDS"
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]
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}
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]

‎config/prod/permissions_config.json‎

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[
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{
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"supplier": "DPSFULL",
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"permissions": [
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "DPSREDUCED",
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"permissions": [
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"RSV.CRUDS"
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]
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},
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{
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"supplier": "RAVS",
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"permissions": [
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"RSV.RS"
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]
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}
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]

‎filenameprocessor/Dockerfile‎

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FROM public.ecr.aws/lambda/python:3.10 AS base
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FROM public.ecr.aws/lambda/python:3.11 AS base
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# Create non-root user
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RUN mkdir -p /home/appuser && \

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