Merge branch 'upstream/pr-5553' into usegalaxy

.ci/check_py3_compatibility.sh

@@ -7,15 +7,16 @@ else
 fi
 
 export ACK_OPTIONS=" --type python \
---ignore-dir=.git/ \
---ignore-dir=.tox/ \
---ignore-dir=.venv/ \
---ignore-dir=client/node_modules/ \
---ignore-dir=database/ \
---ignore-dir=doc/build/ \
---ignore-dir=eggs/ \
---ignore-dir=static/maps/ \
---ignore-dir=static/scripts/"
+--ignore-dir=.git \
+--ignore-dir=.tox \
+--ignore-dir=.venv \
+--ignore-dir=.venv3 \
+--ignore-dir=client/node_modules \
+--ignore-dir=database \
+--ignore-dir=doc/build \
+--ignore-dir=eggs \
+--ignore-dir=static/maps \
+--ignore-dir=static/scripts"
 
 PYTHON2_ONLY_MODULES="__builtin__ _winreg BaseHTTPServer CGIHTTPServer \
 ConfigParser Cookie cookielib copy_reg cPickle cStringIO Dialog dummy_thread \

.ci/flake8_blacklist.txt

@@ -1,8 +1,12 @@
-.venv/
-.tox/
-client/node_modules/
-database/
+.git
+.tox
+.venv
+.venv3
+client/node_modules
+database
+doc/build
 doc/source/conf.py
-eggs/
+eggs
 lib/galaxy/util/jstree.py
-lib/galaxy/web/proxy/js/node_modules/
+static/maps
+static/scripts

.ci/flake8_wrapper.sh

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

.ci/flake8_wrapper_docstrings.sh

@@ -15,7 +15,7 @@ args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
 
 if [ "$1" = "--include" ];
 then
-    flake8 $args `paste .ci/flake8_docstrings_include_list.txt`
+    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_blacklist.txt) .
 fi

.ci/jenkins/selenium-compose/run_tests.sh

@@ -23,8 +23,8 @@ find test -iname '*pyc' -exec rm -rf {} \;
 pip install docker-compose
 
 # TODO: Let docker-compose pick these at random.
-export GALAXY_PORT=`python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
-export SELENIUM_PORT=`python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
+export GALAXY_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
+export SELENIUM_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
 
 export TARGET_ROOT=`pwd`
 export TARGET_PATH=/galaxy

.gitignore

@@ -7,6 +7,7 @@ scripts/scramble/archives
 
 # Python virtualenv
 .venv
+.venv3
 
 # Database stuff
 database/beaker_sessions
@@ -123,9 +124,8 @@ tool-data/shared/jars/
 sprite-*.less
 
 # JS, Local node_modules, and bower_components directories
-static/scripts/bundled/[0-9]*
+static/scripts
 static/maps
-static/scripts/bundled/*.map
 node_modules
 bower_components
 client/galaxy/scripts/libs/*

.travis.yml

@@ -8,13 +8,13 @@ env:
   - TOX_ENV=py27-lint
   - TOX_ENV=py27-unit
   - TOX_ENV=qunit
-  - TOX_ENV=first_startup
-  - TOX_ENV=py27-lint-docstring-include-list
-  - TOX_ENV=check-python-dependencies
+  - TOX_ENV=py27-first_startup
+  - TOX_ENV=py27-lint_docstring_include_list
+  - TOX_ENV=check_python_dependencies
 
 matrix:
   include:
-    - env: TOX_ENV=validate-test-tools
+    - env: TOX_ENV=validate_test_tools
       addons:
         apt:
           packages:
@@ -25,12 +25,19 @@ matrix:
           packages:
             - ack-grep
   allow_failures:
-  - env: TOX_ENV=check-python-dependencies
+    - env: TOX_ENV=check_python_dependencies
 
 
 install:
+  - set -e
   - pip install tox
-  - if [ "$TOX_ENV" == "first_startup" ]; then bash -c "bash scripts/common_startup.sh && wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite && mv db_gx_rev_0127.sqlite database/universe.sqlite && bash manage_db.sh -c ./config/galaxy.yml.sample upgrade"; fi
+  - |
+    if [ "$TOX_ENV" == "py27-first_startup" ]; then
+        sh scripts/common_startup.sh
+        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
+        mv db_gx_rev_0127.sqlite database/universe.sqlite
+        sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
+    fi
 
 script: tox -e $TOX_ENV
 

Makefile

@@ -17,7 +17,6 @@ DOC_SOURCE_DIR=$(DOCS_DIR)/source
 SLIDESHOW_DIR=$(DOC_SOURCE_DIR)/slideshow
 OPEN_RESOURCE=bash -c 'open $$0 || xdg-open $$0'
 SLIDESHOW_TO_PDF?=bash -c 'docker run --rm -v `pwd`:/cwd astefanutti/decktape /cwd/$$0 /cwd/`dirname $$0`/`basename -s .html $$0`.pdf'
-CLIENT_COMMIT_WARNING="Please remember to 'make client-production' when finished developing, before a commit!"
 YARN := $(shell command -v yarn 2> /dev/null)
 
 all: help
@@ -72,9 +71,6 @@ tool-shed-config-convert-dry-run: ## convert old style tool shed ini to yaml (dr
 tool-shed-config-convert: ## convert old style tool shed ini to yaml
 	$(CONFIG_MANAGE) convert tool_shed
 
-tool-shed-config-rebuild-sample: ## Rebuild sample tool shed yaml file from schema
-	$(CONFIG_MANAGE) build_sample_yaml tool_shed --add-comments
-
 reports-config-validate: ## validate reports YAML configuration file
 	$(CONFIG_MANAGE) validate reports
 
@@ -84,15 +80,9 @@ reports-config-convert-dry-run: ## convert old style reports ini to yaml (dry ru
 reports-config-convert: ## convert old style reports ini to yaml
 	$(CONFIG_MANAGE) convert reports
 
-reports-config-rebuild-sample: ## Rebuild sample reports yaml file from schema
-	$(CONFIG_MANAGE) build_sample_yaml reports --add-comments
-
 reports-config-lint: ## lint reports YAML configuration file
 	$(CONFIG_MANAGE) lint reports
 
-reports-config-rebuild-rst: ## Rebuild sample reports RST docs
-	$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
-
 config-validate: ## validate galaxy YAML configuration file
 	$(CONFIG_MANAGE) validate galaxy
 
@@ -102,15 +92,16 @@ config-convert-dry-run: ## convert old style galaxy ini to yaml (dry run)
 config-convert: ## convert old style galaxy ini to yaml
 	$(CONFIG_MANAGE) convert galaxy
 
-config-rebuild-sample: ## Rebuild sample galaxy yaml file from schema
+config-rebuild: ## Rebuild all sample YAML and RST files from config schema
 	$(CONFIG_MANAGE) build_sample_yaml galaxy --add-comments
+	$(CONFIG_MANAGE) build_rst galaxy > doc/source/admin/galaxy_options.rst
+	$(CONFIG_MANAGE) build_sample_yaml reports --add-comments
+	$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
+	$(CONFIG_MANAGE) build_sample_yaml tool_shed --add-comments
 
 config-lint: ## lint galaxy YAML configuration file
 	$(CONFIG_MANAGE) lint galaxy
 
-config-rebuild-rst: ## Rebuild sample galaxy RST docs
-	$(CONFIG_MANAGE) build_rst galaxy > doc/source/admin/galaxy_options.rst
-
 release-ensure-upstream: ## Ensure upstream branch for release commands setup
 ifeq (shell git remote -v | grep $(RELEASE_UPSTREAM), )
 	git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git
@@ -156,7 +147,6 @@ endif
 
 client: node-deps ## Rebuild client-side artifacts for local development.
 	cd client && yarn run build
-	@echo $(CLIENT_COMMIT_WARNING)
 
 client-production: node-deps ## Rebuild client-side artifacts for a production deployment (or committing to the repository).
 	cd client && yarn run build-production
@@ -169,7 +159,6 @@ client-format: node-deps ## Reformat client code
 
 client-watch: node-deps ## A useful target for parallel development building.
 	cd client && yarn run watch
-	@echo $(CLIENT_COMMIT_WARNING)
 
 client-test: client ## Run qunit tests via Karma
 	cd client && yarn run test

client/galaxy/scripts/apps/analysis.js

@@ -21,6 +21,7 @@ import Utils from "utils/utils";
 import Ui from "mvc/ui/ui-misc";
 import DatasetError from "mvc/dataset/dataset-error";
 import DatasetEditAttributes from "mvc/dataset/dataset-edit-attributes";
+import Visualization from "mvc/visualization/visualization-view";
 import Citations from "components/Citations.vue";
 import Vue from "vue";
 
@@ -52,6 +53,8 @@ window.app = function app(options, bootstrapped) {
             "(/)pages(/)edit(/)": "show_pages_edit",
             "(/)pages(/)(:action_id)": "show_pages",
             "(/)visualizations(/)edit(/)": "show_visualizations_edit",
+            "(/)visualizations/show/(:visualization_id)": "show_visualizations_client",
+            "(/)visualizations/dataset_id=(:dataset_id)": "show_visualizations_selector",
             "(/)visualizations/(:action_id)": "show_visualizations",
             "(/)workflows/import_workflow": "show_import_workflow",
             "(/)workflows/run(/)": "show_run",
@@ -113,6 +116,14 @@ window.app = function app(options, bootstrapped) {
             );
         },
 
+        show_visualizations_selector: function(dataset_id) {
+            this.page.display(
+                new Visualization.View({
+                    dataset_id: dataset_id
+                })
+            );
+        },
+
         show_workflows_published: function() {
             this.page.display(
                 new GridView({
@@ -302,6 +313,10 @@ window.app = function app(options, bootstrapped) {
 
     // render and start the router
     $(() => {
+        options.config = _.extend(options.config, {
+            hide_panels: Galaxy.params.hide_panels,
+            hide_masthead: Galaxy.params.hide_masthead
+        });
         Galaxy.page = new Page.View(
             _.extend(options, {
                 Left: ToolPanel,

client/galaxy/scripts/apps/chart.js

@@ -0,0 +1,20 @@
+import * as _ from "libs/underscore";
+import Client from "mvc/visualization/chart/chart-client";
+import Datasets from "mvc/visualization/chart/utilities/datasets";
+import Series from "mvc/visualization/chart/utilities/series";
+import Jobs from "mvc/visualization/chart/utilities/jobs";
+
+window.bundleEntries = window.bundleEntries || {};
+
+export const bundleEntries = {
+    chart: function(options) {
+        return new Client(options);
+    },
+    chartUtilities: {
+        Datasets: Datasets,
+        Jobs: Jobs,
+        Series: Series
+    }
+};
+
+_.extend(window.bundleEntries, bundleEntries);

client/galaxy/scripts/galaxy.js

@@ -5,6 +5,9 @@ import userModel from "mvc/user/user-model";
 import metricsLogger from "utils/metrics-logger";
 import addLogging from "utils/add-logging";
 import localize from "utils/localization";
+
+/* global $ */
+
 // TODO: move into a singleton pattern and have dependents import Galaxy
 // ============================================================================
 /** Base galaxy client-side application.
@@ -70,6 +73,9 @@ GalaxyApp.prototype._init = function __init(options, bootstrapped) {
     self._initUser(options.user || {});
     self.debug("GalaxyApp.user: ", self.user);
 
+    self._initUserLocale();
+    self.debug("currentLocale: ", sessionStorage.getItem("currentLocale"));
+
     self._setUpListeners();
     self.trigger("ready", self);
 
@@ -171,6 +177,37 @@ GalaxyApp.prototype._initLocale = function _initLocale(options) {
     return self;
 };
 
+/** add the localize fn to this object and the window namespace (as '_l') */
+GalaxyApp.prototype._initUserLocale = function _initUserLocale(options) {
+    var self = this;
+
+    // Choose best locale
+    var global_locale = self.config.default_locale ? self.config.default_locale.toLowerCase() : false;
+
+    var extra_user_preferences = {};
+    if (self.user && self.user.attributes.preferences && "extra_user_preferences" in self.user.attributes.preferences) {
+        extra_user_preferences = JSON.parse(self.user.attributes.preferences.extra_user_preferences);
+    }
+
+    var user_locale =
+        "localization|locale" in extra_user_preferences
+            ? extra_user_preferences["localization|locale"].toLowerCase()
+            : false;
+
+    if (user_locale == "auto") {
+        user_locale = false;
+    }
+
+    var nav_locale =
+        typeof navigator === "undefined"
+            ? "__root"
+            : (navigator.language || navigator.userLanguage || "__root").toLowerCase();
+
+    let locale = user_locale || global_locale || nav_locale;
+
+    sessionStorage.setItem("currentLocale", locale);
+};
+
 /** set up the current user as a Backbone model (mvc/user/user-model) */
 GalaxyApp.prototype._initUser = function _initUser(userJSON) {
     var self = this;