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‎Makefile

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# This file is part of workflow-service
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# https://github.com/common-workflow-language/workflow-service/, and is
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# Contact: [email protected]
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# make format to fix most python formatting errors
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# make pylint to check Python code for enhanced compliance including naming
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# and documentation
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# make coverage-report to check coverage of the python scripts by the tests
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MODULE1=wes_client
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MODULE2=wes_service
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PACKAGE=wes-service
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EXTRAS=
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# `SHELL=bash` doesn't work for some, so don't use BASH-isms like
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# `[[` conditional expressions.
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PYSOURCES=$(shell find $(MODULE1) -name "*.py") $(shell find $(MODULE2) -name "*.py")\
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$(wildcard test/*.py) $(wildcard *.py)
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DEVPKGS=build diff_cover pylint pep257 pydocstyle 'tox<4' tox-pyenv \
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wheel autoflake pyupgrade bandit auto-walrus \
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-rlint-requirements.txt -rtest-requirements.txt -rmypy-requirements.txt
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DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pydocstyle sloccount \
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python-flake8 python-mock shellcheck
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VERSION=v$(shell grep version pyproject.toml | awk -F\" '{print $2}')
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mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
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UNAME_S=$(shell uname -s)
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## all : default task (install wes-service in dev mode)
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all: dev
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## help : print this help message and exit
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help: Makefile
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@sed -n 's/^##//p' $<
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## cleanup : shortcut for "make sort_imports format flake8 diff_pydocstyle_report"
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cleanup: sort_imports format flake8 diff_pydocstyle_report
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## install-dep : install most of the development dependencies via pip
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install-dep: install-dependencies
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install-dependencies:
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pip install -U pip setuptools wheel
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pip install --upgrade $(DEVPKGS)
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## install-deb-dep : install many of the dev dependencies via apt-get
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install-deb-dep:
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sudo apt-get install $(DEBDEVPKGS)
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## install : install the wes-service package and the scripts
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install: FORCE
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pip install .$(EXTRAS)
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## dev : install the wes-service package in dev mode
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dev: install-dep
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pip install -U pip setuptools wheel
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pip install -e .$(EXTRAS)
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## dist : create a module package for distribution
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dist: dist/${MODULE}-$(VERSION).tar.gz
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dist/${MODULE}-$(VERSION).tar.gz: $(SOURCES)
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python -m build
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## clean : clean up all temporary / machine-generated files
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clean: FORCE
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rm -f ${MODULE}/*.pyc tests/*.pyc
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rm -Rf .coverage
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rm -f diff-cover.html
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# Linting and code style related targets
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## sort_import : sorting imports using isort: https://github.com/timothycrosley/isort
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sort_imports: $(PYSOURCES)
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isort $^
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remove_unused_imports: $(PYSOURCES)
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autoflake --in-place --remove-all-unused-imports $^
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pep257: pydocstyle
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## pydocstyle : check Python docstring style
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pydocstyle: $(PYSOURCES)
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pydocstyle --add-ignore=D100,D101,D102,D103 $^ || true
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pydocstyle_report.txt: $(PYSOURCES)
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pydocstyle $^ > $@ 2>&1 || true
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## diff_pydocstyle_report : check Python docstring style for changed files only
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diff_pydocstyle_report: pydocstyle_report.txt
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diff-quality --compare-branch=main --violations=pydocstyle --fail-under=100 $^
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## codespell : check for common misspellings
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codespell:
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codespell -w $(shell git ls-files | grep -v mypy-stubs)
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## format : check/fix all code indentation and formatting (runs black)
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format: $(PYSOURCES) FORCE
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black $(PYSOURCES)
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format-check: $(PYSOURCES)
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black --diff --check $^
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## pylint : run static code analysis on Python code
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pylint: $(PYSOURCES)
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ -j0|| true
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pylint_report.txt: $(PYSOURCES)
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pylint --msg-template="{path}:{line}: [{msg_id}({symbol}), {obj}] {msg}" \
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$^ -j0> $@ || true
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diff_pylint_report: pylint_report.txt
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diff-quality --compare-branch=main --violations=pylint pylint_report.txt
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.coverage: testcov
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coverage: .coverage
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coverage report
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coverage.xml: .coverage
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coverage xml
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coverage.html: htmlcov/index.html
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htmlcov/index.html: .coverage
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coverage html
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@echo Test coverage of the Python code is now in htmlcov/index.html
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coverage-report: .coverage
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coverage report
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diff-cover: coverage.xml
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diff-cover --compare-branch=main $^
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diff-cover.html: coverage.xml
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diff-cover --compare-branch=main $^ --html-report $@
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## test : run the wes-service test suite
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test: $(PYSOURCES)
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python -m pytest -rsx ${PYTEST_EXTRA}
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## testcov : run the wes-service test suite and collect coverage
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testcov: $(PYSOURCES)
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pytest --cov ${PYTEST_EXTRA}
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sloccount.sc: $(PYSOURCES) Makefile
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sloccount --duplicates --wide --details $^ > $@
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## sloccount : count lines of code
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sloccount: $(PYSOURCES) Makefile
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sloccount $^
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list-author-emails:
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@echo 'name, E-Mail Address'
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@git log --format='%aN,%aE' | sort -u | grep -v 'root'
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mypy3: mypy
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mypy: ${PYSOURCES}
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MYPYPATH=$$MYPYPATH:mypy-stubs mypy $^
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shellcheck: FORCE
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shellcheck release-test.sh
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pyupgrade: $(PYSOURCES)
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pyupgrade --exit-zero-even-if-changed --py38-plus $^
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auto-walrus $^
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release-test: FORCE
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git diff-index --quiet HEAD -- || ( echo You have uncommitted changes, please commit them and try again; false )
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./release-test.sh
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release: release-test
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. testenv2/bin/activate && \
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pip install build && \
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python -m build testenv2/src/${PACKAGE} && \
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pip install twine && \
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twine upload testenv2/src/${PACKAGE}/dist/* && \
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git tag ${VERSION} && git push --tags
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flake8: $(PYSOURCES)
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flake8 $^
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FORCE:
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# Use this to print the value of a Makefile variable
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# Example `make print-VERSION`
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# From https://www.cmcrossroads.com/article/printing-value-makefile-variable
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print-% : ; @echo $* = $($*)

‎cwl_flask.py

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from flask import Flask, Response, request, redirect
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import subprocess
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import tempfile
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import copy
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import json
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import yaml
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import signal
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import subprocess
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import tempfile
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import threading
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import time
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import copy
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import yaml
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from flask import Flask, Response, redirect, request
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app = Flask(__name__)
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‎cwltool_stream.py

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#!/usr/bin/env python
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import json
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import logging
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import sys
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import cwltool.main
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import tempfile
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import logging
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import cwltool.main
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import StringIO
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import json
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_logger = logging.getLogger("cwltool")
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_logger.setLevel(logging.ERROR)

‎test/test_client_util.py

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import unittest
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import os
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import logging
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import os
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import subprocess
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import sys
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import unittest
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pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), "..")) # noqa
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sys.path.insert(0, pkg_root) # noqa

‎test/test_integration.py

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import unittest
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import time
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import logging
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import os
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import subprocess
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import signal
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import shutil
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import logging
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import signal
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import subprocess
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import sys
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import requests
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import time
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import unittest
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import pytest
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import requests
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pkg_root = os.path.abspath(os.path.join(os.path.dirname(__file__), "..")) # noqa
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sys.path.insert(0, pkg_root) # noqa

‎wes_client/util.py

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import os
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import glob
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import json
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import logging
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import os
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from subprocess import DEVNULL, CalledProcessError, check_call
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from urllib.request import pathname2url, urlopen
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import requests
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import schema_salad.ref_resolver
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from subprocess import check_call, DEVNULL, CalledProcessError
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import yaml
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import glob
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import requests
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import logging
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from wes_service.util import visit
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from urllib.request import urlopen, pathname2url
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def two_seven_compatible(filePath):
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"""Determines if a python file is 2.7 compatible by seeing if it compiles in a subprocess"""

‎wes_client/wes_client_main.py

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#!/usr/bin/env python
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import pkg_resources # part of setuptools
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import json
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import time
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import sys
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import os
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import argparse
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import json
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import logging
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import os
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import sys
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import time
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import pkg_resources # part of setuptools
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import requests
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from requests.exceptions import InvalidSchema, MissingSchema
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from wes_client.util import modify_jsonyaml_paths, WESClient
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from wes_client.util import WESClient, modify_jsonyaml_paths
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def main(argv=sys.argv[1:]):

‎wes_service/arvados_wes.py

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import arvados
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import arvados.util
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import arvados.collection
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import arvados.errors
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import os
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import connexion
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import functools
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import json
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import logging
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import os
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import shutil
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import subprocess
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import tempfile
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import functools
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import threading
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import logging
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import shutil
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from wes_service.util import visit, WESBackend
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import arvados
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import arvados.collection
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import arvados.errors
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import arvados.util
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import connexion
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from wes_service.util import WESBackend, visit
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class MissingAuthorization(Exception):

‎wes_service/cwl_runner.py

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[runner, "--version"], stderr=subprocess.PIPE
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).communicate()
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r = {
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"workflow_type_versions": {"CWL": {"workflow_type_version": ["v1.0", "v1.1", "v1.2"]}},
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"workflow_type_versions": {
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"CWL": {"workflow_type_version": ["v1.0", "v1.1", "v1.2"]}
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},
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"supported_wes_versions": ["0.3.0", "1.0.0"],
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"supported_filesystem_protocols": ["file", "http", "https"],
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"workflow_engine_versions": {"cwl-runner": str(stderr)},

‎wes_service/toil_wes.py

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import json
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import logging
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import os
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import shutil
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import subprocess
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import time
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import logging
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import uuid
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import shutil
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from multiprocessing import Process
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from wes_service.util import WESBackend
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logging.basicConfig(level=logging.INFO)

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