Docker vn

.python-version

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+3.9.1

CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Kuzma"
+  given-names: "Kori"
+- family-names: "Stevenson"
+  given-names: "James"
+- family-names: "Liu"
+  given-names: "Jiachen"
+- family-names: "Coffman"
+  given-names: "Adam"
+- family-names: "Henkenjohann"
+  given-names: "Richard"
+- family-names: "Babb"
+  given-names: "Lawrence"
+- family-names: "Liu"
+  given-names: "Xuelu"
+- family-names: "Wagner"
+  given-names: "Alex H."
+  orcid: "https://orcid.org/0000-0002-2502-8961"
+doi: 10.5281/zenodo.5894937
+title: "VICC Variation Normalization Service"
+version: 0.2.16dev
+date-released: 2022-01-23
+url: "https://github.com/cancervariants/variation-normalization"

Dockerfile

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+# A simple container for variant-service.
+# Runs service on port 80.
+# Healthchecks service up every 5m.  
+
+FROM python:3.9
+RUN apt update ; apt install -y rsync
+RUN pip install pipenv uvicorn[standard]
+ENV SEQREPO_ROOT_DIR=/usr/local/share/seqrepo/2021-01-29
+#ENV GENE_NORM_DB_URL=http://localhost:8001
+ENV GENE_NORM_DB_URL=http://dynamodb:8001
+ENV AWS_ACCESS_KEY_ID = 'DUMMYIDEXAMPLE'
+ENV AWS_SECRET_ACCESS_KEY = 'DUMMYEXAMPLEKEY'
+ENV AWS_DEFAULT_REGION = 'us-west-2'
+COPY . /app
+WORKDIR /app
+RUN if [ ! -f "Pipfile.lock" ] ; then pipenv lock ; else echo Pipfile.lock exists ; fi
+RUN pipenv sync
+EXPOSE 80
+HEALTHCHECK --interval=5m --timeout=3s \
+    CMD curl -f http://localhost/variation || exit 1
+
+CMD pipenv run uvicorn variation.main:app --log-level debug --port 80 --host 0.0.0.0
+#CMD pipenv run uvicorn variation.main:app --reload

EBSampleApp-Python.iml

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+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="GoLibraries">
+    <option name="urls">
+      <set>
+        <option value="file://$MODULE_DIR$" />
+      </set>
+    </option>
+  </component>
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/build" />
+    </content>
+    <orderEntry type="jdk" jdkName="Python 3.6 (NEWRELEASE)" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>

LICENSE

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+MIT License
+
+Copyright (c) 2018-2023 VICC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Pipfile

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+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+pytest = "*"
+pytest-asyncio = "*"
+pytest-cov = "*"
+pre-commit = "*"
+variation-normalizer = {editable = true, path = "."}
+jupyter = "*"
+ipykernel = "*"
+psycopg2-binary = "*"
+ruff = "*"
+black = "*"
+
+[packages]
+"biocommons.seqrepo" = "*"
+fastapi = "*"
+uvicorn = "*"
+pydantic = "==2.*"
+"ga4gh.vrs" = {version = "~=2.0.0a2", extras = ["extras"]}
+gene-normalizer = "~=0.3.0.dev1"
+boto3 = "*"
+cool-seq-tool = "~=0.4.0.dev1"
+bioutils = "*"