Setup pytest python3 API testing

lib/galaxy/dependencies/pipfiles/develop/Pipfile

@@ -19,6 +19,9 @@ selenium = "*"
 testfixtures = "*"
 watchdog = "*"
 pygithub3 = {version = "*", markers = "python_version < '3'"}
+pytest = "*"
+pytest-html = "*"
+pytest-pythonpath = "*"
 Sphinx = "<1.7"  # Docs do not build with sphinx 1.7 for some reason, can't find issue.
 sphinx_rtd_theme = "*"
 lxml = "!=4.2.2"

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

@@ -21,6 +21,9 @@ pathtools==0.1.2
 pbr==4.1.0
 pygithub3==0.5.1; python_version < '3'
 pygments==2.2.0
+pytest==3.7.0
+pytest-html==1.19.0
+pytest-pythonpath==0.7.2
 pytz==2018.5
 pyyaml==3.12
 recommonmark==0.4.0

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+log_cli=true
+log_level=DEBUG
+python_paths=lib

run_tests.sh

@@ -11,6 +11,7 @@ cat <<EOF
 '${0##*/} -sid ccc'                 for testing one section with sid 'ccc' ('ccc' is the string after 'section::')
 '${0##*/} -list'                    for listing all the tool ids
 '${0##*/} -api (test_path)'         for running all the test scripts in the ./test/api directory
+'${0##*/} -api_py3 (test_path)'     for running all the test scripts in the ./test/api directory using python 3
 '${0##*/} -toolshed (test_path)'    for running all the test scripts in the ./test/shed_functional/functional directory
 '${0##*/} -installed'               for running tests of Tool Shed installed tools
 '${0##*/} -framework'               for running through example tool tests testing framework features in test/functional/tools"
@@ -275,6 +276,10 @@ then
     DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""}
     DOCKER_RUN_EXTRA_ARGS=${DOCKER_RUN_EXTRA_ARGS:-""}
     DOCKER_IMAGE=${DOCKER_IMAGE:-${DOCKER_DEFAULT_IMAGE}}
+    if [ "$1" = "--python3" ]; then
+        DOCKER_RUN_EXTRA_ARGS="-e GALAXY_VIRTUAL_ENV=/galaxy_venv3 $DOCKER_RUN_EXTRA_ARGS"
+        shift 1
+    fi
     if [ "$1" = "--db" ]; then
        db_type=$2
        shift 2
@@ -350,6 +355,18 @@ do
               shift 1
           fi
           ;;
+      -api_py3|--api_py3)
+          with_framework_test_tools_arg="-with_framework_test_tools"
+          test_script="pytest"
+          report_file="./run_api_tests_python_3.html"
+          if [ $# -gt 1 ]; then
+              api_script=$2
+              shift 2
+          else
+              api_script="./test/api"
+              shift 1
+          fi
+          ;;
       -selenium|--selenium)
           with_framework_test_tools_arg="-with_framework_test_tools"
           test_script="./scripts/functional_tests.py"
@@ -595,7 +612,11 @@ else
 fi
 
 if [ -n "$xunit_report_file" ]; then
-    xunit_args="--with-xunit --xunit-file $xunit_report_file"
+    if [ "$test_script" = 'pytest' ]; then
+        xunit_args="--junit-xml $xunit_report_file"
+    else
+        xunit_args="--with-xunit --xunit-file $xunit_report_file"
+    fi
 else
     xunit_args=""
 fi
@@ -608,7 +629,11 @@ if [ -n "$with_framework_test_tools_arg" ]; then
     GALAXY_TEST_TOOL_CONF="config/tool_conf.xml.sample,test/functional/tools/samples_tool_conf.xml"
     export GALAXY_TEST_TOOL_CONF
 fi
-python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
+if [ "$test_script" = 'pytest' ]; then
+    python -m "$test_script" -v --html "$report_file" $xunit_args $extra_args "$@"
+else
+    python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $xunit_args $structured_data_args $extra_args "$@"
+fi
 exit_status=$?
 echo "Testing complete. HTML report is in \"$report_file\"." 1>&2
 exit ${exit_status}

scripts/plugin_staging.py

@@ -18,7 +18,10 @@ def link_up_static(f):
     elif not os.path.exists(dest_parent):
         # Create parent dir structure to symlink directly to static.
         os.makedirs(dest_parent)
-    os.symlink(src, dest)
+    try:
+        os.symlink(src, dest)
+    except Exception:
+        pass
 
 
 if __name__ == "__main__":

test/docker/base/Dockerfile

@@ -10,7 +10,9 @@ ENV DEBIAN_FRONTEND=noninteractive \
     MYSQL_MAJOR=5.7 \
     POSTGRES_MAJOR=9.5 \
     GALAXY_ROOT=/galaxy \
-    GALAXY_VIRTUAL_ENV=/galaxy_venv
+    GALAXY_VIRTUAL_ENV=/galaxy_venv \
+    GALAXY_VIRTUAL_ENV_2=/galaxy_venv \
+    GALAXY_VIRTUAL_ENV_3=/galaxy_venv3
 
 # Pre-install a bunch of packages to speed up ansible steps.
 RUN apt-get update -y && apt-get install -y software-properties-common apt-transport-https curl && \
@@ -79,11 +81,15 @@ RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 RUN cd $GALAXY_ROOT && \
-    ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; } && \
-    dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt && \
-    [ -f $dev_requirements ] && $GALAXY_VIRTUAL_ENV/bin/pip install -r $dev_requirements
+    for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
+        export GALAXY_VIRTUAL_ENV=$VENV && \
+        ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; } && \
+        dev_requirements=./lib/galaxy/dependencies/dev-requirements.txt && \
+        [ -f $dev_requirements ] && $VENV/bin/pip install -r $dev_requirements; done
 
-RUN . $GALAXY_VIRTUAL_ENV/bin/activate && \
+RUN for VENV in $GALAXY_VIRTUAL_ENV_2 $GALAXY_VIRTUAL_ENV_3; do \
+    export GALAXY_VIRTUAL_ENV=$VENV && \
+    . $GALAXY_VIRTUAL_ENV/bin/activate && \
     pip install psycopg2 && \
     pip install mysql && \
     cd $GALAXY_ROOT && \
@@ -101,7 +107,7 @@ RUN . $GALAXY_VIRTUAL_ENV/bin/activate && \
     echo "Prepopulating toolshed sqlite database" && \
     TOOL_SHED_CONFIG_DATABASE_CONNECTION="sqlite:////opt/galaxy/toolshed.sqlite" bash create_db.sh tool_shed && \
     echo "Prepopulating toolshed mysql database" && \
-    TOOL_SHED_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock" bash create_db.sh tool_shed
+    TOOL_SHED_CONFIG_DATABASE_CONNECTION="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock" bash create_db.sh tool_shed; done
 
 # bcftools for Galaxy.
 RUN mkdir -p /tmp/install && \

test/docker/base/run_test_wrapper.sh

@@ -18,7 +18,7 @@ echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and
 useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
 echo "Setting galaxy user password - the operation may fail."
 echo "galaxy:galaxy" | chpasswd | true
-chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /galaxy_venv
+chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "${GALAXY_VIRTUAL_ENV:-/galaxy_venv}"
 
 : ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
 if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];