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patch - Concatenate Microbial fastq files #3958

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merged 13 commits into from
Nov 25, 2024
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remove unused import
diitaz93 committed Nov 21, 2024
commit 9246508bac07eb662fc1506740b2bfaa8bb5db33
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from unittest.mock import MagicMock

import pytest
from pydantic.v1 import BaseModel
from pydantic import BaseModel

from cg.constants import DataDelivery, Workflow
from cg.services.deliver_files.deliver_files_service.deliver_files_service import (
@@ -25,7 +25,6 @@
from cg.services.deliver_files.tag_fetcher.sample_and_case_service import (
SampleAndCaseDeliveryTagsFetcher,
)
from cg.store.store import Store


class DeliveryScenario(BaseModel):
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Unchanged files with check annotations Beta

ENV CG_SQL_DATABASE_URI="sqlite:///:memory:"
ENV CG_SECRET_KEY="key"

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Sensitive data should not be used in the ARG or ENV commands

SecretsUsedInArgOrEnv: Do not use ARG or ENV instructions for sensitive data (ENV "CG_SECRET_KEY") More info: https://docs.docker.com/go/dockerfile/rule/secrets-used-in-arg-or-env/
ENV LIMS_HOST="mocklims.scilifelab.se"
ENV LIMS_USERNAME="limsadmin"
ENV LIMS_PASSWORD="limsadminpassword"

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GitHub Actions / docker-image-push

Sensitive data should not be used in the ARG or ENV commands

SecretsUsedInArgOrEnv: Do not use ARG or ENV instructions for sensitive data (ENV "LIMS_PASSWORD") More info: https://docs.docker.com/go/dockerfile/rule/secrets-used-in-arg-or-env/
ENV MAIL_CONTAINER_URI="http://127.0.0.1:port/container"
ENV OSTICKET_EMAIL="support@system.email"
ENV OSTICKET_API_KEY=None

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GitHub Actions / docker-image-push

Sensitive data should not be used in the ARG or ENV commands

SecretsUsedInArgOrEnv: Do not use ARG or ENV instructions for sensitive data (ENV "OSTICKET_API_KEY") More info: https://docs.docker.com/go/dockerfile/rule/secrets-used-in-arg-or-env/
ENV OSTICKET_DOMAIN=None
ENV OSTICKET_TIMEOUT="1"
ENV GOOGLE_OAUTH_CLIENT_ID="1"
ENV GOOGLE_OAUTH_CLIENT_SECRET="1"

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GitHub Actions / docker-image-push

Sensitive data should not be used in the ARG or ENV commands

SecretsUsedInArgOrEnv: Do not use ARG or ENV instructions for sensitive data (ENV "GOOGLE_OAUTH_CLIENT_SECRET") More info: https://docs.docker.com/go/dockerfile/rule/secrets-used-in-arg-or-env/
ENV TRAILBLAZER_HOST="host"
ENV TRAILBLAZER_SERVICE_ACCOUNT="service_account"
ENV TRAILBLAZER_SERVICE_ACCOUNT_AUTH_FILE="auth_file"

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GitHub Actions / docker-image-push

Sensitive data should not be used in the ARG or ENV commands

SecretsUsedInArgOrEnv: Do not use ARG or ENV instructions for sensitive data (ENV "TRAILBLAZER_SERVICE_ACCOUNT_AUTH_FILE") More info: https://docs.docker.com/go/dockerfile/rule/secrets-used-in-arg-or-env/
WORKDIR /home/src/app
COPY cg ./cg
CMD gunicorn \

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JSON arguments recommended for ENTRYPOINT/CMD to prevent unintended behavior related to OS signals

JSONArgsRecommended: JSON arguments recommended for CMD to prevent unintended behavior related to OS signals More info: https://docs.docker.com/go/dockerfile/rule/json-args-recommended/
--workers=$GUNICORN_WORKERS \
--bind=$GUNICORN_BIND \
--threads=$GUNICORN_THREADS \