Merge branch 'dev' into remove_toolshed_grids

.ci/flake8_lint_include_list.txt

@@ -57,6 +57,7 @@ lib/galaxy/managers/taggable.py
 lib/galaxy/model/
 lib/galaxy/objectstore/pulsar.py
 lib/galaxy/objectstore/s3_multipart_upload.py
+lib/galaxy/objectstore/s3.py
 lib/galaxy/openid/__init__.py
 lib/galaxy/quota/
 lib/galaxy/sample_tracking/data_transfer.py
@@ -81,6 +82,7 @@ lib/galaxy/visualization/tracks/
 lib/galaxy/web/base/
 lib/galaxy/web/buildapp.py
 lib/galaxy/web/formatting.py
+lib/galaxy/web/form_builder.py
 lib/galaxy/web/framework/base.py
 lib/galaxy/web/framework/decorators.py
 lib/galaxy/web/framework/helpers/grids.py
@@ -126,6 +128,7 @@ lib/galaxy/webapps/__init__.py
 lib/galaxy/webapps/reports/config.py
 lib/galaxy/webapps/reports/controllers/__init__.py
 lib/galaxy/webapps/reports/controllers/query.py
+lib/galaxy/webapps/reports/controllers/tools.py
 lib/galaxy/webapps/reports/__init__.py
 lib/galaxy/webapps/tool_shed/api/__init__.py
 lib/galaxy/webapps/tool_shed/controllers/groups.py

.ci/jenkins/selenium/Dockerfile

@@ -2,11 +2,11 @@ FROM toolshed/requirements
 MAINTAINER John Chilton, jmchilton@gmail.com
 
 RUN apt-get -qq update && \
-    apt-get install --no-install-recommends -y postgresql-client python-pip && \
+    apt-get install --no-install-recommends -y postgresql-client python-pip libffi-dev python-cffi && \
     apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 ENV GALAXY_ROOT=/galaxy \
-    GALAXY_CONFIG_OVERRIDE_ADMIN_USERS=admin@galaxy.org \
+    GALAXY_CONFIG_OVERRIDE_ADMIN_USERS=admin@galaxy.org,test@bx.psu.edu \
     GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DATASET_PURGE=true \
     GALAXY_CONFIG_OVERRIDE_ALLOW_LIBRARY_PATH_PASTE=true \
     GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_WORKFLOW_MODULES=true \

.ci/jenkins/selenium/docker-compose.yml

@@ -11,6 +11,8 @@ services:
       - postgres
     ports:
       - "${GALAXY_PORT}:8080"
+    environment:
+      GALAXY_TEST_UID: "${MY_UID}"
   selenium:
     image: selenium/standalone-chrome:3.5.2
     ports:

.ci/jenkins/selenium/galaxy.ini

@@ -6,6 +6,12 @@ host = 0.0.0.0
 use_threadpool = True
 threadpool_kill_thread_limit = 10800
 
+[filter:proxy-prefix]
+use = egg:PasteDeploy#prefix
+prefix = /galaxypf
+
 [app:main]
 
 paste.app_factory = galaxy.web.buildapp:app_factory
+
+filter-with = proxy-prefix

.ci/jenkins/selenium/run_galaxy.bash

@@ -2,6 +2,27 @@
 
 set -e
 
+# Same hacks to setup a Galaxy user as used in test/docker/base/run_test_wrapper.sh
+# We want to make sure Galaxy runs as the same user as the external user so the files have the correct permission.
+echo "Deleting galaxy user - it may not exist and this is fine."
+deluser galaxy | true
+
+: ${GALAXY_TEST_UID:-"1"}
+
+echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
+groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
+echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
+useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
+echo "Setting galaxy user password - the operation may fail."
+echo "galaxy:galaxy" | chpasswd | true
+
+virtualenv "$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; }
+
 echo "Waiting for postgres to become available"
 while ! nc -z postgres 5432;
 do
@@ -13,7 +34,7 @@ echo "Creating postgres database for Galaxy"
 createdb -w -U postgres -h postgres galaxy
 
 echo "Starting and waiting for Galaxy daemon(s)"
-GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
+sudo -E -u "#${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"

.ci/jenkins/selenium/run_tests.sh

@@ -28,6 +28,7 @@ export SELENIUM_PORT=`python -c 'import socket; s=socket.socket(); s.bind(("", 0
 
 export TARGET_ROOT=`pwd`
 export TARGET_PATH=/galaxy
+export MY_UID=$(id -u)
 
 cd $TEST_DIRECTORY
 
@@ -107,7 +108,11 @@ export GALAXY_TEST_SELENIUM_RETRIES=1
 export GALAXY_TEST_PORT="${GALAXY_PORT}"
 
 # Have Selenium access Galaxy at this URL
-export GALAXY_TEST_EXTERNAL_FROM_SELENIUM="http://galaxy:8080"
+export GALAXY_TEST_EXTERNAL_FROM_SELENIUM="http://galaxy:8080/galaxypf"
+export GALAXY_TEST_EXTERNAL="http://localhost:${GALAXY_TEST_PORT}/galaxypf"
+
+# Point tests at the Master API Key configured in the Dockerfile.
+export GALAXY_CONFIG_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53
 
 cd ../../..
 

.ci/py3_sources.txt

@@ -70,6 +70,7 @@ scripts/communication/
 scripts/data_libraries/build_whoosh_index.py
 scripts/db_shell.py
 scripts/drmaa_external_runner.py
+scripts/metagenomics/
 scripts/secret_decoder_ring.py
 test/
 tool_list.py

client/galaxy/scripts/layout/router.js

@@ -19,7 +19,7 @@ var Router = Backbone.Router.extend({
             url += url.indexOf( '?' ) == -1 ? '?' : '&';
             url += $.param( data , true );
         }
-        Galaxy.params = {};
+        Galaxy.params = data;
         this.navigate( url, { 'trigger': true } );
     },