Merge remote-tracking branch 'upstream/release_24.1' into dev

.github/workflows/build_client.yaml

@@ -32,5 +32,7 @@ jobs:
           path: 'galaxy root/static'
       - name: Build client
         if: steps.cache.outputs.cache-hit != 'true'
+        env:
+          GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR: 1
         run: make client
         working-directory: 'galaxy root'

.gitignore

@@ -167,14 +167,14 @@ packages/*/*.egg-info
 config/plugins/**/static/dist
 config/plugins/**/static/script.js
 config/plugins/**/static/main.css
+config/plugins/**/static/script.css
 config/plugins/**/static/plugin_build_hash.txt
 config/plugins/**/static/*.map
 
 # Viz-specific build artifacts to ignore (until these are removed from codebase)
 config/plugins/visualizations/annotate_image/static/jquery.contextMenu.css
 config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
-config/plugins/visualizations/h5web/static/script.css
-config/plugins/visualizations/tiffviewer/static/script.css
+config/plugins/visualizations/scatterplot/static/scatterplot.js
 
 # CWL conformance tests
 lib/galaxy_test/api/cwl/test_cwl_conformance_v1_?.py

Makefile

@@ -13,10 +13,12 @@ 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'
 YARN := $(shell $(IN_VENV) command -v yarn 2> /dev/null)
 YARN_INSTALL_OPTS=--network-timeout 300000 --check-files
+# Default to not fail on error, set to 1 to fail client builds on a plugin error.
+GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR?=0
 # Respect predefined NODE_OPTIONS, otherwise set maximum heap size low for
 # compatibility with smaller machines.
 NODE_OPTIONS ?= --max-old-space-size=3072
-NODE_ENV = env NODE_OPTIONS=$(NODE_OPTIONS)
+NODE_ENV = env NODE_OPTIONS=$(NODE_OPTIONS) GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR=$(GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR)	
 CWL_TARGETS := test/functional/tools/cwl_tools/v1.0/conformance_tests.yaml \
 	test/functional/tools/cwl_tools/v1.1/conformance_tests.yaml \
 	test/functional/tools/cwl_tools/v1.2/conformance_tests.yaml \

client/gulpfile.js

@@ -27,16 +27,17 @@ const STATIC_PLUGIN_BUILD_IDS = [
     "msa",
     "mvpapp",
     "ngl",
+    "nora",
     "nvd3/nvd3_bar",
     "openlayers",
     "openseadragon",
     "PCA_3Dplot",
     "phylocanvas",
     "pv",
-    "nora",
-    "venn",
+    "scatterplot",
     "tiffviewer",
     "ts_visjs",
+    "venn",
 ];
 const DIST_PLUGIN_BUILD_IDS = ["new_user"];
 const PLUGIN_BUILD_IDS = Array.prototype.concat(DIST_PLUGIN_BUILD_IDS, STATIC_PLUGIN_BUILD_IDS);
@@ -56,6 +57,11 @@ const PATHS = {
     },
 };
 
+const failOnError =
+    process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR && process.env.GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR !== "0"
+        ? true
+        : false;
+
 PATHS.pluginBaseDir =
     (process.env.GALAXY_PLUGIN_PATH && process.env.GALAXY_PLUGIN_PATH !== "None"
         ? process.env.GALAXY_PLUGIN_PATH
@@ -186,6 +192,13 @@ function buildPlugins(callback, forceRebuild) {
                 console.error(
                     `Error building ${pluginName}, not saving build state.  Please report this issue to the Galaxy Team.`
                 );
+                if (failOnError) {
+                    // Fail on error.
+                    console.error(
+                        "Failing build due to GALAXY_PLUGIN_BUILD_FAIL_ON_ERROR being set, see error(s) above."
+                    );
+                    process.exit(1);
+                }
             }
         }
     });

config/plugins/visualizations/annotate_image/package.json

@@ -8,18 +8,18 @@
     ],
     "license": "AFL-3.0",
     "dependencies": {
-        "babel-preset-env": "^1.6.1",
-        "backbone": "^1.3.3",
         "jquery": "^3.3.1",
         "jquery-contextmenu": "^2.7.1",
         "jquery.ui.position": "^1.11.4",
         "paper": "^0.12.3",
-        "parcel-bundler": "^1.4.1",
         "underscore": "^1.8.3"
     },
+    "devDependencies": {
+        "parcel": "2.12.0"
+    },
     "scripts": {
         "build": "yarn build-css && yarn build-js",
         "build-css": "cp 'node_modules/jquery-contextmenu/dist/jquery.contextMenu.css' 'static/'",
-        "build-js": "parcel build src/script.js -d static --no-source-maps"
+        "build-js": "parcel build src/script.js --dist-dir static"
     }
 }

config/plugins/visualizations/annotate_image/src/jq-loader.js

@@ -0,0 +1,3 @@
+import jquery from "jquery";
+
+export default window.$ = window.jQuery = jquery;