Merge pull request #6737 from nsoranzo/release_18.05_revert_6707

[18.05] Decode tool id and version in the client, not in the API 

client/galaxy/scripts/apps/analysis.js

 import $ from "jquery";
 import "bootstrap";
 import * as _ from "underscore";
+import decodeUriComponent from "decode-uri-component";
 import GalaxyApp from "galaxy";
 import Router from "layout/router";
 import ToolPanel from "./panels/tool-panel";
@@ -314,7 +315,12 @@ window.app = function app(options, bootstrapped) {
         /** load the center panel with a tool form described by the given params obj */
         _loadToolForm: function(params) {
             //TODO: load tool form code async
-            params.id = decodeURIComponent(params.tool_id);
+            if (params.tool_id) {
+                params.id = decodeUriComponent(params.tool_id);
+            }
+            if (params.version) {
+                params.version = decodeUriComponent(params.version);
+            }
             this.page.display(new ToolForm.View(params));
         },
 

client/package.json

@@ -20,6 +20,7 @@
     "bootstrap-tour": "https://github.com/sorich87/bootstrap-tour.git#6a1028fb562f9aa68c451f0901f8cfeb43cad140",
     "bootstrap-vue": "^2.0.0-rc.8",
     "d3": "3",
+    "decode-uri-component": "^0.2.0",
     "font-awesome": "^4.7.0",
     "gulp-sass": "^3.1.0",
     "handsontable": "^2.0.0",

lib/galaxy/webapps/galaxy/api/tools.py

 import logging
 from json import dumps
 
-from six.moves.urllib.parse import unquote
-
 import galaxy.queue_worker
 from galaxy import exceptions, managers, util, web
 from galaxy.managers.collections_util import dictify_dataset_collection_instance
@@ -512,9 +510,6 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin):
     # -- Helper methods --
     #
     def _get_tool(self, id, tool_version=None, user=None):
-        id = unquote(id)
-        if tool_version:
-            tool_version = unquote(tool_version)
         tool = self.app.toolbox.get_tool(id, tool_version)
         if not tool:
             raise exceptions.ObjectNotFound("Could not find tool with id '%s'." % id)

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -9,7 +9,6 @@ import os
 
 import requests
 from markupsafe import escape
-from six.moves.urllib.parse import unquote
 from sqlalchemy import desc, false, or_, true
 from sqlalchemy.orm import joinedload
 
@@ -545,15 +544,6 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
     #
     # -- Helper methods --
     #
-    def _get_tool(self, id, tool_version=None, user=None):
-        id = unquote(id)
-        if tool_version:
-            tool_version = unquote(tool_version)
-        tool = self.app.toolbox.get_tool(id, tool_version)
-        if not tool or not tool.allow_user_access(user):
-            raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id)
-        return tool
-
     def __api_import_from_archive(self, trans, archive_data, source=None):
         try:
             data = json.loads(archive_data)

scripts/plugin_staging.py

+from __future__ import print_function
+
 import glob
 import os
 import shutil
@@ -9,16 +11,20 @@ def link_up_static(f):
     src = os.path.join(GXY_ROOT, 'config/plugins', f)
     dest = os.path.join(GXY_ROOT, 'static/plugins', f)
     dest_parent = os.path.abspath(os.path.join(dest, os.pardir))
-    if os.path.exists(dest):
+    if os.path.lexists(dest):
         # We have to clear out the old staged or linked static to relink.
         if os.path.islink(dest):
-            os.unlink(dest)
+            os.remove(dest)
         else:
             shutil.rmtree(dest)
     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:
+        print("Error symlinking '%s' to '%s'" % (src, dest))
+        raise
 
 
 if __name__ == "__main__":