diff --git a/.secrets.baseline b/.secrets.baseline index 5bccf9b..48e51c4 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -3,7 +3,7 @@ "files": null, "lines": null }, - "generated_at": "2021-07-16T13:28:46Z", + "generated_at": "2024-11-19T22:00:45Z", "plugins_used": [ { "name": "AWSKeyDetector" @@ -68,15 +68,21 @@ ], "poetry.lock": [ { - "hashed_secret": "04bc1e75a811cb16d5b276b9f02d083c6c62d936", + "hashed_secret": "3fe4cfda6b6d913d6ba809208c22b9cc682de7c6", "is_verified": false, - "line_number": 147, + "line_number": 191, "type": "Hex High Entropy String" }, { - "hashed_secret": "683bf5e8b3f78752cab86cc2524104180d43d7d7", + "hashed_secret": "02e1ed68101272a29b85bb1623070c60e6a017cb", "is_verified": false, - "line_number": 603, + "line_number": 224, + "type": "Hex High Entropy String" + }, + { + "hashed_secret": "5bca853943adcb8e1f858addeb33fcde3ecea5a5", + "is_verified": false, + "line_number": 773, "type": "Hex High Entropy String" } ] diff --git a/Dockerfile b/Dockerfile index b0ae3ee..880c7dd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,22 +1,43 @@ -FROM quay.io/cdis/python-nginx:pybase3-1.5.0 +ARG AZLINUX_BASE_VERSION=master -RUN pip install --upgrade pip -RUN apk add --update \ - postgresql-libs postgresql-dev libffi-dev libressl-dev \ - linux-headers musl-dev gcc g++ \ - curl bash git vim logrotate -RUN apk --no-cache add --update \ - aspell aspell-en ca-certificates \ - && mkdir -p /usr/share/dict/ \ - && aspell -d en dump master > /usr/share/dict/words +# Base stage with python-build-base +FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base -COPY . /src/ -WORKDIR /src +ENV appname=dictionaryutils -RUN pip install poetry \ - && poetry config virtualenvs.create false \ - && poetry install -vv --no-interaction +COPY --chown=gen3:gen3 . /${appname} -COPY . /dictionaryutils +WORKDIR /${appname} -CMD cd /dictionary; rm -rf build dictionaryutils dist gdcdictionary.egg-info; python setup.py install --force && cp -r /dictionaryutils . && cd /dictionary/dictionaryutils; pip uninstall -y gen3dictionary; pytest tests -s -v; export SUCCESS=$?; cd ..; rm -rf build dictionaryutils dist gdcdictionary.egg-info; exit $SUCCESS +# Builder stage +FROM base AS builder + +RUN dnf install -y python3-devel postgresql-devel gcc + +USER gen3 + +COPY poetry.lock pyproject.toml /${appname}/ + +RUN poetry install -vv --no-interaction --without dev + +COPY --chown=gen3:gen3 . /${appname} + +# Run poetry again so this app itself gets installed too +# include dev because we need data-simulator to run the unit tests. +RUN poetry install -vv --no-interaction + +ENV PATH="$(poetry env info --path)/bin:$PATH" + +# Final stage +FROM base + +COPY --from=builder /${appname} /${appname} + +# Switch to non-root user 'gen3' for the serving process +USER gen3 + +WORKDIR /${appname} + +RUN chmod +x "/${appname}/dockerrun.bash" + +CMD ["/bin/bash", "-c", "/${appname}/dockerrun.bash"] diff --git a/README.md b/README.md index 79060ba..16b3f14 100644 --- a/README.md +++ b/README.md @@ -21,8 +21,7 @@ Then from the directory containing the `gdcdictionary` directory run `testdict`. If you wish to generate fake simulated data you can also do that with dictionaryutils and the data-simulator. ``` -simdata() { docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master /bin/sh -c "cd /dictionary && python setup.py install --force; python /src/datasimulator/bin/data-simulator simulate --path /simdata/ $*; export SUCCESS=$?; rm -rf build dictionaryutils dist gdcdictionary.egg-info; chmod -R a+rwX /simdata; exit $SUCCESS"; } -simdataurl() { docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master /bin/sh -c "python /src/datasimulator/bin/data-simulator simulate --path /simdata/ $*; chmod -R a+rwX /simdata"; } +simdata() { docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master; /bin/bash -c "cd /dictionary/dictionaryutils; bash dockerrun.bash; cd /dictionary/dictionaryutils; poetry run python bin/simulate_data.py --path /dictionary/simdata $*; export SUCCESS=$?; cd /dictionary; rm -rf build dictionaryutils dist gdcdictionary.egg-info; chmod -R a+rwX /simdata; exit $SUCCESS "; } ``` @@ -39,11 +38,28 @@ The `--max_samples` argument will define a default number of nodes to simulate, ``` Then run the following: ``` -docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master /bin/sh -c "cd /dictionary && python setup.py install --force; python /src/datasimulator/bin/data-simulator simulate --path /simdata/ --program workshop --project project1 --max_samples 10 --node_num_instances_file instances.json; export SUCCESS=$?; rm -rf build dictionaryutils dist gdcdictionary.egg-info; chmod -R a+rwX /simdata; exit $SUCCESS"; +docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master /bin/bash -c "cd /dictionaryutils; bash dockerrun.bash; cd /dictionary/dictionaryutils; poetry run python bin/simulate_data.py --path /simdata/ --program workshop --project project1 --max_samples 10 --node_num_instances_file /dictionary/instances.json; export SUCCESS=$?; rm -rf build dictionaryutils dist gdcdictionary.egg-info; chmod -R a+rwX /simdata; exit $SUCCESS"; ``` Then you'll get 100 each of `case` and `demographic` nodes and 10 each of everything else. Note that the above example also defines `program` and `project` names. -You can also run the simulator for an arbitrary json url by using `simdataurl --url https://datacommons.example.com/schema.json`. +You can also run the simulator for an arbitrary json url with the `--url` parameter. The alias can be simplified to skip the set up of the parent directory virtual env (ie, skip the `docker_run.bash`): +``` +simdataurl() { docker run --rm -v $(pwd):/dictionary -v $(pwd)/simdata:/simdata quay.io/cdis/dictionaryutils:master /bin/bash -c "python /dictionaryutils/bin/simulate_data.py simulate --path /simdata/ $*; chmod -R a+rwX /simdata"; } + +``` + +Then run `simdataurl --url https://datacommons.example.com/schema.json`. + +## Using a local build of the Docker image + +It is possible to use a local build of the `dictionaryutils` Docker image instead of the master branch stored in `quay`. + +From a local copy of the `dictionaryutils` repo, build and tag a Docker image, for example +``` +docker build -t dictionaryutils-mytag . +``` +Then use this image in any of the aliases and commands mentioned +above by replacing `quay.io/cdis/dictionaryutils:master` with `dictionaryutils-mytag`. ## Use dictionaryutils to load a dictionary diff --git a/bin/simulate_data.py b/bin/simulate_data.py new file mode 100644 index 0000000..1c86716 --- /dev/null +++ b/bin/simulate_data.py @@ -0,0 +1,67 @@ +import argparse + +from datasimulator import main as simulator + + +def parse_arguments(): + parser = argparse.ArgumentParser() + + parser.add_argument( + "--path", required=True, help="path to save files to", nargs="?" + ) + parser.add_argument( + "--program", required=False, help="program to generate data", nargs="?" + ) + parser.add_argument( + "--project", required=False, help="project to generate data", nargs="?" + ) + parser.add_argument( + "--max_samples", + required=False, + help="max number of samples for each node", + default=1, + nargs="?", + ) + parser.add_argument( + "--node_num_instances_file", + required=False, + help="max number of samples for each node stored in a file", + nargs="?", + ) + parser.add_argument( + "--random", help="randomly generate data numbers for nodes", action="store_true" + ) + parser.add_argument( + "--required_only", help="generate only required fields", action="store_true" + ) + parser.add_argument( + "--skip", help="skip raising an exception if gets an error", action="store_true" + ) + parser.add_argument("--url", required=False, help="s3 dictionary link.", nargs="?") + + return parser.parse_args() + + +def main(): + + args = parse_arguments() + + graph = simulator.initialize_graph( + dictionary_url=args.url if hasattr(args, "url") else None, + program=args.program if hasattr(args, "program") else None, + project=args.project if hasattr(args, "project") else None, + consent_codes=args.consent_codes if hasattr(args, "consent_codes") else None, + ) + + simulator.run_simulation( + graph, + args.path, + args.max_samples, + args.node_num_instances_file, + args.random, + args.required_only, + args.skip, + ) + + +main() diff --git a/dockerrun.bash b/dockerrun.bash new file mode 100644 index 0000000..3085cf0 --- /dev/null +++ b/dockerrun.bash @@ -0,0 +1,49 @@ +#!/bin/bash + +# This script sets up the poetry environment for running tests +# against a local build of a dictionary repo. +# This will remove the default gdcdictionary (eg, version 2.0.0) +# and install the local dictionary (eg, version 0.0.0). +# +# Similar to +# https://github.com/uc-cdis/.github/blob/master/.github/workflows/dictionary_push.yaml + +cd /dictionary +if [ -f pyproject.toml ]; then + export USE_POETRY=1 +else + export USE_POETRY=0 +fi + +echo "Removing old dictionaryutils" +rm -rf build dictionaryutils dist gdcdictionary.egg-info + +echo "Installing dictionary" +if [ $USE_POETRY -eq 1 ]; then + echo "Via poetry" + poetry install -v --all-extras --no-interaction || true +fi + +cp -r /dictionaryutils . +cd /dictionary/dictionaryutils + +echo "Removing old gdcdictionary" +if [ $USE_POETRY -eq 1 ]; then + poetry run pip uninstall -y gen3dictionary + poetry run pip uninstall -y gdcdictionary +else + poetry remove gdcdictionary + poetry run pip uninstall -y gen3dictionary +fi + +echo "Reinstall dictionary" +poetry run pip install .. + +echo "The following schemas from dictionary will be tested:" +ls `poetry run python -c "from gdcdictionary import SCHEMA_DIR; print(SCHEMA_DIR)"` + +echo "Ready to run tests" +poetry run pytest -v tests +export SUCCESS=$? + +exit $SUCCESS diff --git a/poetry.lock b/poetry.lock index fc3abeb..9e7624d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -57,101 +57,116 @@ files = [ [[package]] name = "charset-normalizer" -version = "3.3.2" +version = "3.4.0" description = "The Real First Universal Charset Detector. 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