Merge pull request #8147 from nsoranzo/misc_fixes

Testing framework fixes

.ci/validate_test_tools.sh

@@ -1,11 +1,11 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
 xsd_path="lib/galaxy/tools/xsd/galaxy.xsd"
 # Lint the XSD
 xmllint --noout "$xsd_path"
 
 test_tools_path='test/functional/tools'
-tool_files_list=$(ls "$test_tools_path"/*xml | grep -v '_conf.xml$')
+tool_files_list=$(ls "$test_tools_path"/*.xml | grep -v '_conf.xml$')
 sh scripts/validate_tools.sh $tool_files_list

.circleci/config.yml

@@ -25,7 +25,7 @@ variables:
 jobs:
   get_code:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       # Replace standard code checkout with shallow clone to speed things up.
@@ -83,7 +83,7 @@ jobs:
             - ~/repo
   py27_lint:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -91,7 +91,7 @@ jobs:
       - run: tox -e py27-lint
   py27_unit:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -99,7 +99,7 @@ jobs:
       - run: tox -e py27-unit
   py27_docstring:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -107,7 +107,7 @@ jobs:
       - run: tox -e py27-lint_docstring_include_list
   py27_first_startup:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -139,14 +139,14 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - *install_tox
       - run: sudo apt-get update
       # For uwsgi
       - run: sudo apt-get install -y libpython3.5-dev
+      - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
@@ -160,10 +160,11 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: bash packages/test.sh
+      - *install_tox
+      - run: tox -e test_galaxy_packages
   check_py3_compatibility:
     docker:
-      - image: circleci/python:2.7.15
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache

create_db.sh

@@ -1,9 +1,9 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
 setup_python
 
-python ./scripts/create_db.py $@
+python ./scripts/create_db.py "$@"

extract_dataset_parts.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
@@ -9,5 +9,5 @@ setup_python
 for file in $1/split_info*.json
 do
     # echo processing $file
-    python ./scripts/extract_dataset_part.py $file
+    python ./scripts/extract_dataset_part.py "$file"
 done

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -15,6 +15,7 @@ mock = "*"
 NoseHTML = "*"
 pygithub3 = {version = "*", markers = "python_version < '3'"}
 pytest = "*"
+pytest-cov = "*"
 pytest-html = "*"
 pytest-pythonpath = "*"
 pytest-postgresql = "*"

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -10,13 +10,14 @@ chardet==3.0.4
 commonmark==0.9.0
 configparser==3.7.4 ; python_version < '3.2'
 contextlib2==0.5.5 ; python_version < '3.5'
+coverage==4.5.3
 docutils==0.14
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.17.1
 gunicorn==19.9.0
 idna==2.8
 imagesize==1.1.0
-importlib-metadata==0.17
+importlib-metadata==0.18
 jinja2==2.10.1
 lxml==4.3.4
 markdown==2.6.11
@@ -31,16 +32,17 @@ pathlib2==2.3.2 ; python_version < '3'
 pathtools==0.1.2
 pluggy==0.12.0
 port-for==0.4
-psutil==5.6.2
+psutil==5.6.3
 py==1.8.0
 pygithub3==0.5.1 ; python_version < '3'
 pygments==2.4.2
 pyparsing==2.4.0
+pytest-cov==2.7.1
 pytest-html==1.20.0
 pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
-pytest==4.6.2
+pytest==4.6.3
 pytz==2019.1
 pyyaml==5.1.1
 recommonmark==0.5.0

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -29,7 +29,7 @@ bleach==3.1.0
 boltons==19.1.0
 boto3==1.9.114
 boto==2.49.0
-botocore==1.12.165
+botocore==1.12.167
 bx-python==0.8.2
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
@@ -118,7 +118,7 @@ pathlib2==2.3.2 ; python_version < '3'
 pbr==5.2.1
 prettytable==0.7.2
 prov==1.5.1
-psutil==5.6.2
+psutil==5.6.3
 pulsar-galaxy-lib==0.12.1
 pyasn1-modules==0.2.5
 pyasn1==0.4.5

lib/galaxy/tools/test.py

@@ -21,7 +21,7 @@ log = logging.getLogger(__name__)
 @nottest
 def parse_tests(tool, tests_source):
     """
-    Build ToolTestBuilder objects for each "<test>" elements and
+    Build ToolTestDescription objects for each "<test>" elements and
     return default interactor (if any).
     """
     raw_tests_dict = tests_source.parse_tests_to_dict()

packages/test.sh

@@ -5,8 +5,9 @@ set -e
 # Change to packages directory.
 cd "$(dirname "$0")"
 
+# Use a throw-away virtualenv
 TEST_PYTHON=${TEST_PYTHON:-"python"}
-TEST_ENV_DIR=${TEST_ENV_DIR:-`mktemp -d -t gxpkgtestenvXXXXXX`}
+TEST_ENV_DIR=${TEST_ENV_DIR:-$(mktemp -d -t gxpkgtestenvXXXXXX)}
 
 virtualenv -p "$TEST_PYTHON" "$TEST_ENV_DIR"
 . "${TEST_ENV_DIR}/bin/activate"
@@ -31,13 +32,11 @@ for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do
 
     cd "$package_dir"
     pip install -e .
-    if [ "$package_dir" = "util" ];
-    then
+    if [ "$package_dir" = "util" ]; then
         pip install -e '.[template,jstree]'
     fi
 
-    if [[ "$run_tests" == "1" ]];
-    then
+    if [[ "$run_tests" == "1" ]]; then
         pytest --doctest-modules galaxy tests
     fi
     cd ..

run_tests.sh

@@ -1,7 +1,6 @@
 #!/bin/sh
 
-pwd_dir=$(pwd)
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 rm -f run_functional_tests.log
 
@@ -318,8 +317,8 @@ then
         -e "GALAXY_TEST_DATABASE_TYPE=$db_type" \
         -e "LC_ALL=C" \
         --rm \
-        -v `pwd`:/galaxy \
-        -v `pwd`/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh $DOCKER_IMAGE "$@"
+        -v "$(pwd)":/galaxy \
+        -v "$(pwd)"/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh "$DOCKER_IMAGE" "$@"
     exit $?
 fi
 
@@ -374,7 +373,6 @@ do
               api_script="./test/api"
               shift 1
           fi
-          coverage_file="api_coverage.xml"
           ;;
       -selenium|--selenium)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -412,15 +410,15 @@ do
           shift
           ;;
       --external_url)
-          GALAXY_TEST_EXTERNAL=$2
+          export GALAXY_TEST_EXTERNAL=$2
           shift 2
           ;;
       --external_master_key)
-          GALAXY_CONFIG_MASTER_KEY=$2
+          export GALAXY_CONFIG_MASTER_API_KEY=$2
           shift 2
           ;;
       --external_user_key)
-          GALAXY_TEST_USER_API_KEY=$2
+          export GALAXY_TEST_USER_API_KEY=$2
           shift 2
           ;;
       -f|-framework|--framework)
@@ -428,7 +426,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="framework_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -437,7 +434,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_framework_tests.html"
-          coverage_file="main_tools_coverage.xml"
           framework_test=1;
           shift 1
           ;;
@@ -445,7 +441,6 @@ do
           marker="-m data_manager"
           test_script="pytest"
           report_file="run_data_managers_tests.html"
-          coverage_file="data_managers_coverage.xml"
           data_managers_test=1;
           shift 1
           ;;
@@ -454,7 +449,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_migrated_tests.html"
-          coverage_file="migrated_coverage.xml"
           migrated_test=1;
           shift
           ;;
@@ -463,7 +457,6 @@ do
           marker="-m tool"
           test_script="pytest"
           report_file="run_installed_tests.html"
-          coverage_file="installed_coverage.xml"
           installed_test=1;
           shift
           ;;
@@ -503,7 +496,6 @@ do
           # Must have coverage installed (try `which coverage`) - only valid with --unit
           # for now. Would be great to get this to work with functional tests though.
           coverage_arg="--with-coverage"
-          NOSE_WITH_COVERAGE=true
           shift
           ;;
       --debug)
@@ -523,7 +515,6 @@ do
               unit_extra="$unit_extra lib test/unit"
               shift 1
           fi
-          coverage_file="unit_coverage.xml"
           ;;
       -i|-integration|--integration)
           GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
@@ -535,7 +526,6 @@ do
           else
               integration_extra="./test/integration"
               shift 1
-          coverage_file="integration_coverage.xml"
           fi
           ;;
       --no_cleanup)
@@ -616,7 +606,7 @@ elif [ -n "$toolshed_script" ]; then
 elif [ -n "$api_script" ]; then
     extra_args="$api_script"
 elif [ -n "$section_id" ]; then
-    extra_args=`python tool_list.py $section_id`
+    extra_args=$(python tool_list.py "$section_id")
 elif [ -n "$unit_extra" ]; then
     extra_args="$unit_extra"
 elif [ -n "$integration_extra" ]; then
@@ -645,8 +635,8 @@ else
 fi
 export GALAXY_TEST_TOOL_CONF
 if [ "$test_script" = 'pytest' ]; then
-    if [ "$coverage_arg" = "--with_coverage" ]; then
-        coverage_arg="--cov-report term --cov-report xml:cov-unit.xml --cov=lib"
+    if [ "$coverage_arg" = '--with-coverage' ]; then
+        coverage_arg="--cov-report term --cov=lib"
     fi
     "$test_script" -v --html "$report_file" $coverage_arg  $xunit_args $extra_args "$@"
 else

scripts/cleanup_datasets/delete_datasets.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r "$@" >> ./scripts/cleanup_datasets/delete_datasets.log

scripts/cleanup_datasets/delete_userless_histories.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 "$@" >> ./scripts/cleanup_datasets/delete_userless_histories.log

scripts/cleanup_datasets/populate_uuid.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 export PYTHONPATH=./lib/
-python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini $@
+python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini "$@"

scripts/cleanup_datasets/purge_datasets.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r "$@" >> ./scripts/cleanup_datasets/purge_datasets.log

scripts/cleanup_datasets/purge_folders.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r "$@" >> ./scripts/cleanup_datasets/purge_folders.log

scripts/cleanup_datasets/purge_histories.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r "$@" >> ./scripts/cleanup_datasets/purge_histories.log

scripts/cleanup_datasets/purge_libraries.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r "$@" >> ./scripts/cleanup_datasets/purge_libraries.log

scripts/cleanup_datasets/update_metadata.sh

@@ -6,4 +6,4 @@
 . ./scripts/get_python.sh
 . ./setup_paths.sh
 
-$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini $@
+"$GALAXY_PYTHON" ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini "$@"

scripts/maintenance.sh

@@ -6,7 +6,7 @@
 set -e
 
 display_help(){
-  scriptname=`basename $0`
+  scriptname=$(basename "$0")
   printf "./$scriptname [--help] [--no-dry-run] [--days 10] 
 Will run the galaxy cleanup scripts in the recommend order. By default a 'dry-run' is started. Specify --no-dry-run to do the actual cleanup.
 
@@ -52,7 +52,7 @@ do
   esac
 done
 
-cd "$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"/../
+cd "$(dirname "$0")"/..
 
 . scripts/common_startup_functions.sh
 

scripts/migrate_tools/0002_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml "$@"

scripts/migrate_tools/0003_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml "$@"

scripts/migrate_tools/0004_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml "$@"

scripts/migrate_tools/0005_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml "$@"

scripts/migrate_tools/0006_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml "$@"

scripts/migrate_tools/0007_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml "$@"

scripts/migrate_tools/0008_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml "$@"

scripts/migrate_tools/0009_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml "$@"

scripts/migrate_tools/0010_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml "$@"

scripts/migrate_tools/0011_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml "$@"

scripts/migrate_tools/0012_tools.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml "$@"

scripts/tool_shed/migrate_tools_to_repositories.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 python ./scripts/tool_shed/migrate_tools_to_repositories.py ./community_wsgi.ini >> ./scripts/tool_shed/migrate_tools_to_repositories.log

scripts/validate_tools.sh

@@ -1,33 +1,31 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
 GALAXY_SKIP_CLIENT_BUILD=1 ./scripts/common_startup.sh
 GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
-if [ -d "$GALAXY_VIRTUAL_ENV" ];
-then
+if [ -d "$GALAXY_VIRTUAL_ENV" ]; then
     printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 xsd_path="lib/galaxy/tool_util/xsd/galaxy.xsd"
 
-err_tmp=`mktemp`
+err_tmp=$(mktemp)
 count=0
 exit=0
 for p in "$@"; do
     count=$((count+1))
     path="$p"
-    echo $path
+    echo "$path"
     PYTHONPATH=lib:$PYTHONPATH
     export PYTHONPATH
-    result=`python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"`
-    if [ $? -eq 0 ]
-    then
+    python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"
+    if [ $? -eq 0 ]; then
         echo "ok $count";
     else
         echo "not ok $count $path";
-        cat "$err_tmp" | sed 's/^/    /'
+        sed 's/^/    /' "$err_tmp"
         exit=1
     fi
 done

tox.ini

@@ -1,7 +1,7 @@
 [tox]
 # envlist is the list of environments that are tested when `tox` is run without any option
 # hyphens in an environment name are used to delimit factors
-envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, validate_test_tools
+envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
 skipsdist = True
 
 [testenv]
@@ -35,6 +35,9 @@ commands = bash .ci/flake8_wrapper_docstrings.sh --exclude
 [testenv:py27-lint_docstring_include_list]
 commands = bash .ci/flake8_wrapper_docstrings.sh --include
 
+[testenv:test_galaxy_packages]
+commands = bash packages/test.sh
+
 [testenv:validate_test_tools]
 commands = bash .ci/validate_test_tools.sh