Merge branch 'dev' into biotools

.ci/check_test_class_names.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+TEST=$(mktemp)
+TEST_EXTRA_CLASSES=$(mktemp)
+
+pytest --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST"
+pytest -o python_classes='Test* *Test *TestCase' --collect-only --ignore=test/functional lib/galaxy_test/ test/ > "$TEST_EXTRA_CLASSES"
+
+n_tests=$(grep 'tests collected' "$TEST" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+n_tests_extra_classes=$(grep 'tests collected' "$TEST_EXTRA_CLASSES" | sed -e 's/[^0-9]*\([0-9]*\) tests collected.*/\1/')
+
+if [ "$n_tests_extra_classes" -gt "$n_tests" ]; then
+    echo "New test class with name not starting with Test introduced, change it to have tests collected by pytest"
+    diff "$TEST" "$TEST_EXTRA_CLASSES"
+    exit 1
+fi

.ci/eslint_wrapper.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+set -e
+
+# Setting NODE_PATH and config appropriately, using dependencies from
+# client/node_modules, run eslint against args passed to this script.
+# Primary use case here is for a pre-commit check.
+NODE_PATH=src/ node client/node_modules/eslint/bin/eslint.js -c client/.eslintrc.js "$@"

.ci/first_startup.sh

@@ -1,16 +1,45 @@
 #!/bin/sh
+case "$1" in
+    galaxy|"")
+        SCRIPT=./run.sh
+        PORT=8080
+        LOGFILE=galaxy.log
+        GRAVITY_LOGFILE=database/gravity/log/gunicorn.log
+        SUPERVISORD_LOGFILE=database/gravity/supervisor/supervisord.log
+        ;;
+    reports)
+        SCRIPT=./run_reports.sh
+        PORT=9001
+        LOGFILE=reports_webapp.log
+        ;;
+    *)
+        echo "ERROR: Unrecognized app"
+        exit 1
+        ;;
+esac
 TRIES=120
-URL=http://localhost:8080
+URL=http://localhost:$PORT
 EXIT_CODE=1
 i=0
 echo "Testing for correct startup:"
-bash run.sh --daemon && \
+$SCRIPT --daemon && \
     while [ "$i" -le $TRIES ]; do
-        curl "$URL" && EXIT_CODE=0 && break
+        curl --max-time 1 "$URL" && EXIT_CODE=0 && break
         sleep 1
         i=$((i + 1))
     done
-kill -9 "$(cat galaxy.pid)"
+$SCRIPT --skip-wheels --stop-daemon
 echo "exit code:$EXIT_CODE, showing startup log:"
-cat galaxy.log
+if [ -f "$LOGFILE" ]; then
+    cat "$LOGFILE"
+elif [ ! -f "$LOGFILE" -a -f "$GRAVITY_LOGFILE" ]; then
+    echo "Warning: $LOGFILE does not exist, showing gravity startup log instead"
+    cat "$GRAVITY_LOGFILE"
+elif [ ! -f "$LOGFILE" -a ! -f "$GRAVITY_LOGFILE" -a -f "$SUPERVISORD_LOGFILE" ]; then
+    echo "Warning: $LOGFILE and $GRAVITY_LOGFILE do not exist, showing supervisord startup log instead"
+    cat "$SUPERVISORD_LOGFILE"
+else
+    echo "ERROR: No log files found!"
+    ls -lR database/gravity
+fi
 exit $EXIT_CODE

.ci/flake8_ignorelist.txt

@@ -0,0 +1,18 @@
+.git
+.tox
+.venv*
+packages/*/.venv
+packages/*/build
+packages/*/dist
+packages/venv
+node_modules
+database
+doc/build
+eggs
+lib/galaxy/web/proxy/js/node_modules
+lib/tool_shed/test/test_data/repos
+static/maps
+static/scripts
+test/functional/tools/cwl_tools/v1.?/
+build
+dist

.ci/flake8_wrapper.sh

@@ -2,7 +2,7 @@
 
 set -e
 
-flake8 --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
+flake8 --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore=D --max-line-length=150 lib/galaxy/jobs/runners/util/
+flake8 --ignore=E203,D --max-line-length=150 lib/galaxy/jobs/runners/util/

.ci/flake8_wrapper_docstrings.sh

@@ -17,5 +17,5 @@ if [ "$1" = "--include" ];
 then
     flake8 $args $(paste -sd' ' .ci/flake8_docstrings_include_list.txt)
 else
-    flake8 $args --exclude $(paste -sd, .ci/flake8_blacklist.txt) .
+    flake8 $args --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
 fi

.ci/ignore-spelling.txt

@@ -0,0 +1,3 @@
+hda
+implementors
+purgable