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Merge branch 'BioComputeDev' into hadley-dev
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Merge after rebase on galaxy/dev

Changes to be committed:
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	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/manage_repository.mako
	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako
	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/rate_repository.mako
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	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changelog.mako
	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_changeset.mako
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	modified:   lib/tool_shed/webapp/templates/webapps/tool_shed/repository/view_tool_metadata.mako
	modified:   packages/tool_util/HISTORY.rst
	modified:   packages/tool_util/galaxy/project_galaxy_tool_util.py
	modified:   run_tests.sh
	modified:   scripts/bootstrap_history.py
	modified:   scripts/cleanup_datasets/pgcleanup.py
	modified:   scripts/common_startup.sh
	modified:   scripts/common_startup_functions.sh
	modified:   scripts/tool_shed/build_ts_whoosh_index.py
	new file:   static/erricon.ico
	modified:   templates/show_params.mako
	modified:   test/docker/base/Dockerfile
	modified:   test/docker/base/ansible_vars.yml
	modified:   test/docker/base/run_test_wrapper.sh
	modified:   test/functional/tools/collection_creates_dynamic_nested.xml
	modified:   test/functional/tools/column_param.xml
	modified:   test/integration/conftest.py
	new file:   test/integration/objectstore/test_swift_objectstore.py
	modified:   test/integration/test_config_defaults.py
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	modified:   test/integration/test_datatype_upload.py
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	modified:   test/integration/test_fail_job_tool_unavailable.py
	modified:   test/integration/test_interactivetools_api.py
	modified:   test/integration/test_kubernetes_runner.py
	new file:   test/integration/test_pulsar_embedded_mq.py
	modified:   test/integration/test_repository_operations.py
	modified:   test/integration/uses_shed.py
	new file:   test/unit/config/test_config_values.py
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	modified:   test/unit/config/test_path_resolves_to.py
	modified:   test/unit/config/test_reload_config.py
	modified:   test/unit/config/test_schema.py
	modified:   test/unit/jobs/test_expression_run.py
	new file:   test/unit/objectstore/irods_object_store_conf.xml
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	new file:   test/unit/objectstore/irods_object_store_conf_no_extra_dir.xml
	new file:   test/unit/objectstore/test_irods.py
	new file:   test/unit/shed_unit/test_shed_index.py
	modified:   test/unit/test_model_store.py
	modified:   test/unit/tools/test_history_imp_exp.py
	modified:   test/unit/tools/test_toolbox.py
	modified:   test/unit/unittest_utils/galaxy_mock.py
	new file:   tools/data_source/sra.xml
	modified:   tools/extract/extract_genomic_dna.py
	new file:   tools/interactive/interactivetool_climate_notebook.xml
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	new file:   tools/interactive/interactivetool_vcf_iobio.xml
	modified:   tox.ini
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@HadleyKing
HadleyKing committed Apr 22, 2020
2 parents 51cb0dc + 5670064 commit 4376c73
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1 change: 1 addition & 0 deletions .ci/jenkins/api-py3
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api
3 changes: 0 additions & 3 deletions .ci/jenkins/api-py3/run_tests.sh
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1 change: 1 addition & 0 deletions .ci/jenkins/framework-py3
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framework
3 changes: 0 additions & 3 deletions .ci/jenkins/framework-py3/run_tests.sh
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1 change: 1 addition & 0 deletions .ci/jenkins/integration-py3
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integration
3 changes: 0 additions & 3 deletions .ci/jenkins/integration-py3/run_tests.sh
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1 change: 1 addition & 0 deletions .ci/jenkins/main-tools-py3
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main-tools
3 changes: 0 additions & 3 deletions .ci/jenkins/main-tools-py3/run_tests.sh
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5 changes: 2 additions & 3 deletions .ci/jenkins/selenium-compose/run_galaxy.bash
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Expand Up @@ -20,8 +20,7 @@ virtualenv "$GALAXY_VIRTUAL_ENV"
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"

cd /galaxy
HOME=/galaxy
sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }

echo "Waiting for postgres to become available"
while ! nc -z postgres 5432;
Expand All @@ -34,7 +33,7 @@ echo "Creating postgres database for Galaxy"
createdb -w -U postgres -h postgres galaxy

echo "Starting and waiting for Galaxy daemon(s)"
sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait

echo "Galaxy daemon ready, monitoring Galaxy logs"
tail -f "$GALAXY_ROOT/main.log"
1 change: 1 addition & 0 deletions .ci/jenkins/selenium-py3
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selenium
26 changes: 0 additions & 26 deletions .ci/jenkins/selenium-py3/run_tests.sh
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33 changes: 3 additions & 30 deletions .circleci/config.yml
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Expand Up @@ -81,22 +81,6 @@ jobs:
key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
paths:
- ~/repo
py27_lint:
docker:
- image: circleci/python:2.7
<<: *set_workdir
steps:
- *restore_repo_cache
- *install_tox
- run: tox -e py27-lint
py27_unit:
docker:
- image: circleci/python:2.7
<<: *set_workdir
steps:
- *restore_repo_cache
- *install_tox
- run: tox -e py27-unit
py35_docstring:
docker:
- image: circleci/python:3.5
Expand All @@ -105,14 +89,6 @@ jobs:
- *restore_repo_cache
- *install_tox
- run: tox -e py35-lint_docstring_include_list
py27_first_startup:
docker:
- image: circleci/python:2.7
<<: *set_workdir
steps:
- *restore_repo_cache
- *install_tox
- run: tox -e py27-first_startup
py35_lint:
docker:
- image: circleci/python:3.5
Expand All @@ -135,6 +111,9 @@ jobs:
<<: *set_workdir
steps:
- *restore_repo_cache
# Use this job to test the latest migrations
- run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
- run: mv db_gx_rev_0141.sqlite database/universe.sqlite
- *install_tox
- run: tox -e py35-first_startup
validate_test_tools:
Expand Down Expand Up @@ -190,12 +169,6 @@ workflows:
get_code_and_test:
jobs:
- get_code
- py27_lint:
<<: *requires_get_code
- py27_unit:
<<: *requires_get_code
- py27_first_startup:
<<: *requires_get_code
- py35_docstring:
<<: *requires_get_code
- py35_lint:
Expand Down
17 changes: 11 additions & 6 deletions .github/workflows/converter_tests.yaml
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Expand Up @@ -9,9 +9,14 @@ jobs:
matrix:
python-version: [3.7]
steps:
- uses: actions/checkout@v1
- uses: actions/checkout@v2
with:
fetch-depth: 1
path: 'galaxy root'
- name: Clone galaxyproject/galaxy-test-data
uses: actions/checkout@v2
with:
repository: galaxyproject/galaxy-test-data
path: galaxy-test-data
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
Expand All @@ -20,10 +25,10 @@ jobs:
id: pip-cache
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
- name: fetch test data
run: git clone https://github.com/galaxyproject/galaxy-test-data && cp -R galaxy-test-data/* test-data
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Move test data
run: rsync -av --remove-source-files --exclude .git galaxy-test-data/ 'galaxy root/test-data/'
- name: Install planemo
run: pip install planemo
- name: Run tests
run: 'planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root . lib/galaxy/datatypes/converters/*xml'
run: planemo test --galaxy_python_version ${{ matrix.python-version }} --galaxy_root 'galaxy root' 'galaxy root'/lib/galaxy/datatypes/converters/*xml
21 changes: 16 additions & 5 deletions .github/workflows/integration.yaml
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Expand Up @@ -2,8 +2,8 @@ name: Integration
on: [push, pull_request]
env:
GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
GALAXY_TEST_AMQP_URL: 'amqp://localhost:5672//'
jobs:

test:
name: Test
runs-on: ubuntu-18.04
Expand All @@ -20,21 +20,31 @@ jobs:
POSTGRES_DB: postgres
ports:
- 5432:5432
rabbitmq:
image: rabbitmq
ports:
- 5672:5672
steps:
- name: Prune unused docker image, volumes and containers
run: docker system prune -a -f
- name: Clean dotnet folder for space
if: matrix.subset == 'kubernetes'
run: rm -Rf /usr/share/dotnet
- name: Setup Minikube
if: matrix.subset == 'kubernetes'
id: minikube
uses: CodingNagger/minikube-setup-action@v1.0.2
uses: CodingNagger/minikube-setup-action@v1.0.3
with:
minikube-version: "1.9.0-0_amd64"
- name: Launch Minikube
if: matrix.subset == 'kubernetes'
run: eval ${{ steps.minikube.outputs.launcher }}
- name: Check pods
if: matrix.subset == 'kubernetes'
run: |
kubectl get pods
- uses: actions/checkout@v1
- uses: actions/checkout@v2
with:
fetch-depth: 1
path: 'galaxy root'
- uses: actions/setup-python@v1
with:
Expand All @@ -44,6 +54,7 @@ jobs:
id: pip-cache
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('requirements.txt') }}
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Run tests
run: './run_tests.sh -integration test/integration -- -k "${{ matrix.subset }}"'
working-directory: 'galaxy root'
17 changes: 9 additions & 8 deletions .github/workflows/mulled.yaml
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Expand Up @@ -9,19 +9,20 @@ jobs:
matrix:
python-version: [3.7]
steps:
- name: Cache tox dir
uses: actions/cache@v1
id: cache-tox-mulled
with:
path: .tox/mulled
key: tox-mulled-${{ matrix.python-version }}
- uses: actions/checkout@v1
- uses: actions/checkout@v2
with:
fetch-depth: 1
path: 'galaxy root'
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Cache pip dir
uses: actions/cache@v1
id: pip-cache
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Install tox
run: pip install tox
- name: run tests
run: tox -e mulled
working-directory: 'galaxy root'
28 changes: 28 additions & 0 deletions .github/workflows/osx_startup.yaml
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@@ -0,0 +1,28 @@
name: OSX
on: [push, pull_request]
jobs:

test:
name: Startup test
runs-on: macos-latest
steps:
- uses: actions/checkout@v2
with:
path: 'galaxy root'
- name: Cache pip dir
uses: actions/cache@v1
id: pip-cache
with:
path: ~/Library/Caches/pip
# scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6
key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Install tox
run: pip install tox
- name: Install and activate miniconda # use this job to test using Python from a conda environment
uses: goanpeca/setup-miniconda@v1
with:
activate-environment: ''
- name: run tests
run: tox -e first_startup
shell: bash -l {0} # need this to have CONDA_EXE set
working-directory: 'galaxy root'
37 changes: 37 additions & 0 deletions .github/workflows/toolshed.yaml
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@@ -0,0 +1,37 @@
name: Toolshed
on: [push, pull_request]
env:
GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
TOOL_SHED_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
jobs:
test:
name: Test
runs-on: ubuntu-18.04
strategy:
matrix:
python-version: [3.7]
services:
postgres:
image: postgres:11
env:
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
POSTGRES_DB: postgres
ports:
- 5432:5432
steps:
- uses: actions/checkout@v2
with:
path: 'galaxy root'
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Cache pip dir
uses: actions/cache@v1
id: pip-cache
with:
path: ~/.cache/pip
key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
- name: Run tests
run: './run_tests.sh -toolshed'
working-directory: 'galaxy root'
30 changes: 0 additions & 30 deletions .travis.yml
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1 change: 1 addition & 0 deletions CONTRIBUTORS.md
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Expand Up @@ -86,6 +86,7 @@ The following individuals have contributed code to Galaxy:
* Joachim Jacob <joachim.jacob@gmail.com>
* Xiaoqian Jiang <jxq198409@hotmail.com>
* Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
* Kaivan Kamali <kxk302@gmail.com>
* Radhesh Kamath <radhesh@bx.psu.edu>
* Iyad Kandalaft <ik@iyadk.com>
* Jan Kanis <jan.code@jankanis.nl>
Expand Down
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