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jmchiltonjmchilton
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Tests for workflow testing script.
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‎.travis.yml‎

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language: python
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sudo: false
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sudo: true
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python: 2.7
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env:
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- TOX_ENV=py27-lint
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- TOX_ENV=py34-lint
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- TOX_ENV=py27-lint-readme
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- TOX_ENV=py27-lint-docs
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- TOX_ENV=py34-quick
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- TOX_ENV=py27
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- TOX_ENV=py34
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- TOX_ENV=py34-gx-1801
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- TOX_ENV=py34-gx-dev
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- TOX_ENV=py34-gx-1709
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- TOX_ENV=py27-lint-docstrings
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global:
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- PLANEMO_SKIP_REDUNDANT_TESTS=1
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- PLANEMO_ENABLE_POSTGRES_TESTS=1
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- PLANEMO_SKIP_GALAXY_CWL_TESTS=1
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- PLANEMO_TEST_WORKFLOW_RUN_PROFILE=travisworkflowtests
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matrix:
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- TOX_ENV=py27-lint
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- TOX_ENV=py34-lint
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- TOX_ENV=py27-lint-readme
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- TOX_ENV=py27-lint-docs
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- TOX_ENV=py34-quick
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- TOX_ENV=py27
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- TOX_ENV=py34
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- TOX_ENV=py34-gx-1801
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- TOX_ENV=py34-gx-dev
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- TOX_ENV=py34-gx-1709
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- TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=docker_test
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- TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=serve_and_test
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- TOX_ENV=py27-lint-docstrings
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install:
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- pip install tox coveralls
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matrix:
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allow_failures:
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- env: TOX_ENV=py27-lint-docstrings
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- TOX_ENV=py27-gxwf-test-test PLANEMO_TEST_STYLE=docker_test
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script: PLANEMO_SKIP_REDUNDANT_TESTS=1 PLANEMO_ENABLE_POSTGRES_TESTS=1 PLANEMO_SKIP_GALAXY_CWL_TESTS=1 PLANEMO_TEST_WORKFLOW_RUN_PROFILE=travisworkflowtests tox -e $TOX_ENV
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script: tox -e $TOX_ENV
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after_success:
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- coveralls
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services:
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- postgresql
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- postgresql
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- docker

‎Makefile‎

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@@ -81,6 +81,9 @@ test: ## run tests with the default Python (faster than tox)
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quick-test: ## run quickest tests with the default Python
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$(IN_VENV) PLANEMO_SKIP_SLOW_TESTS=1 PLANEMO_SKIP_GALAXY_TESTS=1 nosetests $(NOSE_TESTS)
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gxwf-test-test: ## run test of workflow testing script
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bash $(BUILD_SCRIPTS_DIR)/test_workflow_tests.sh
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tox: ## run tests with tox in the specified ENV, defaults to py27
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$(IN_VENV) tox -e $(ENV) -- $(ARGS)
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‎scripts/run_workflow_tests.sh‎

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#!/bin/bash
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: ${PLANEMO_TARGET:="planemo==0.50.1"}
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: ${PLANEMO_OPTIONS:="--verbose"}
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: ${PLANEMO_PROFILE_NAME:="wxflowtest"}
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: ${PLANEMO_SERVE_PORT:="9019"}
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: ${PLANEMO_TEST_STYLE:="serve_and_test"} # profile_serve_and_test, serve_and_test, docker_serve_and_test, test, docker_test
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: ${PLANEMO_SERVE_DATABASE_TYPE:="postgres"} # used if not using Docker with PLANEMO_TEST_STYLE
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: ${PLANEMO_DOCKER_GALAXY_IMAGE:="quay.io/bgruening/galaxy:18.01"} # used if used Docker with PLANEMO_TEST_STYLE
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GALAXY_URL="http://localhost:$PLANEMO_SERVE_PORT"
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# Ensure Planemo is installed.
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if [ ! -d .venv ]; then
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virtualenv .venv
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. .venv/bin/activate
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pip install -U pip
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# Intentionally expand wildcards in PLANEMO_TARGET.
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shopt -s extglob
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pip install ${PLANEMO_TARGET}
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fi
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. .venv/bin/activate
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# Run test.
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# This example shows off a bunch of different ways one could test with Planemo,
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# but for actual workflow testing projects - probably best just to take one of the last
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# two very easy invocations to simplify things.
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if [ "$PLANEMO_TEST_STYLE" = "profile_serve_and_test" ]; then
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planemo $PLANEMO_OPTIONS profile_create \
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--database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
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"$PLANEMO_PROFILE_NAME"
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planemo $PLANEMO_OPTIONS serve \
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--daemon \
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--profile "$PLANEMO_PROFILE_NAME" \
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--port "$PLANEMO_SERVE_PORT" \
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"$1"
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planemo $PLANEMO_OPTIONS test \
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--galaxy_url "$GALAXY_URL" \
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--engine external_galaxy \
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"$1"
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elif [ "$PLANEMO_TEST_STYLE" = "serve_and_test" ]; then
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planemo $PLANEMO_OPTIONS serve \
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--daemon \
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--database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
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--port "$PLANEMO_SERVE_PORT" \
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"$1"
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planemo $PLANEMO_OPTIONS test \
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--galaxy_url "$GALAXY_URL" \
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--engine external_galaxy \
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"$1"
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elif [ "$PLANEMO_TEST_STYLE" = "docker_serve_and_test" ]; then
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docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}"
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planemo $PLANEMO_OPTIONS serve \
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--daemon \
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--engine docker_galaxy \
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--docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \
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--docker_extra_volume . \
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--port "$PLANEMO_SERVE_PORT" \
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"$1"
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planemo $PLANEMO_OPTIONS test \
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--galaxy_url "$GALAXY_URL" \
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--engine external_galaxy \
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"$1"
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elif [ "$PLANEMO_TEST_STYLE" = "test" ]; then
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planemo $PLANEMO_OPTIONS test \
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--database_type "$PLANEMO_SERVE_DATABASE_TYPE" \
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"$1"
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elif [ "$PLANEMO_TEST_STYLE" = "docker_test" ]; then
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docker pull "${PLANEMO_DOCKER_GALAXY_IMAGE}"
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planemo $PLANEMO_OPTIONS test \
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--engine docker_galaxy \
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--docker_galaxy_image "${PLANEMO_DOCKER_GALAXY_IMAGE}" \
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--docker_extra_volume . \
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"$1" > /dev/null
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else
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echo "Unknown test style ${PLANEMO_TEST_STYLE}"
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exit 1
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fi

‎scripts/test_workflow_tests.sh‎

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#!/bin/bash
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# Ensure working directory is planemo project.
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SCRIPTS_DIRECTORY="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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PROJECT_DIRECTORY="${SCRIPTS_DIRECTORY}/.."
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TEMP_DIRECTORY=`mktemp -d 2>/dev/null || mktemp -d -t 'planemowftest'`
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cp "$SCRIPTS_DIRECTORY/run_workflow_tests.sh" "$TEMP_DIRECTORY"
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cp "$PROJECT_DIRECTORY/tests/data/"wf4* "$TEMP_DIRECTORY"
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cp "$PROJECT_DIRECTORY/tests/data/1.bed" "$TEMP_DIRECTORY"
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cd $PROJECT_DIRECTORY
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# Build Planemo wheel.
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make dist
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# Test against wheel.
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export PLANEMO_TARGET="$PROJECT_DIRECTORY/dist/planemo*whl"
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cd $TEMP_DIRECTORY
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bash run_workflow_tests.sh "wf4-distro-tools.gxwf.yml"

‎tox.ini‎

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# TODO: implement doc linting
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[tox]
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envlist = py{27,34}-lint, py{27,34,35}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}, py{27,34,35}-gx-{master,dev,1801,1709,1705}
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envlist = py{27,34}-lint, py{27,34,35}-quick, py27-lint-imports, py27-lint-docstrings, py27-lint-readme, py27-lint-docs, py{27,34,35}, py{27,34,35}-gx-{master,dev,1801,1709,1705}, py27-gxwf-test-test
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source_dir = planemo
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test_dir = tests
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deps =
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-rrequirements.txt
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-rdev-requirements.txt
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[testenv:py27-gxwf-test-test]
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commands = make gxwf-test-test
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skip_install = True
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whitelist_externals = make

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