remove linting that broke the functionality of jstree module

.ci/flake8_blacklist.txt

@@ -7,6 +7,7 @@ doc/source/conf.py
 lib/galaxy/model/migrate/versions/
 lib/galaxy/model/tool_shed_install/migrate/versions/
 lib/galaxy/util/pastescript/serve.py
+lib/galaxy/util/jstree.py
 lib/galaxy/webapps/tool_shed/model/migrate/versions/
 lib/pkg_resources.py
 lib/tool_shed/

lib/galaxy/util/jstree.py

@@ -7,155 +7,156 @@
 
 
 class Node(dictobj.DictionaryObject):
-    """
-    Copyright 2012 "Grim Apps"
+  """
+  Copyright 2012 "Grim Apps"
 
-    Licensed under the Apache License, Version 2.0 (the "License");
-    you may not use this file except in compliance with the License.
-    You may obtain a copy of the License at
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
 
        http://www.apache.org/licenses/LICENSE-2.0
 
-    Unless required by applicable law or agreed to in writing, software
-    distributed under the License is distributed on an "AS IS" BASIS,
-    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-    See the License for the specific language governing permissions and
-    limitations under the License.
-
-    Helper class written by William Grim - grimwm
-    Original repo: https://github.com/grimwm/py-jstree
-    Code adjusted according to the idea of Frank Blechschmidt - FraBle
-    Thank you!
-    ************************
-    This class exists as a helper to the JSTree.  Its "jsonData" method can
-    generate sub-tree JSON without putting the logic directly into the JSTree.
-
-    This data structure is only semi-immutable.  The JSTree uses a directly
-    iterative (i.e. no stack is managed) builder pattern to construct a
-    tree out of paths.  Therefore, the children are not known in advance, and
-    we have to keep the children attribute mutable.
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.
+
+  Helper class written by William Grim - grimwm
+  Original repo: https://github.com/grimwm/py-jstree
+  Code adjusted according to the idea of Frank Blechschmidt - FraBle
+  Thank you!
+  ************************
+  This class exists as a helper to the JSTree.  Its "jsonData" method can
+  generate sub-tree JSON without putting the logic directly into the JSTree.
+
+  This data structure is only semi-immutable.  The JSTree uses a directly
+  iterative (i.e. no stack is managed) builder pattern to construct a
+  tree out of paths.  Therefore, the children are not known in advance, and
+  we have to keep the children attribute mutable.
+  """
+
+  def __init__(self, path, oid, **kwargs):
     """
-
-    def __init__(self, path, oid, **kwargs):
-        """
-        kwargs allows users to pass arbitrary information into a Node that
-        will later be output in jsonData().  It allows for more advanced
-        configuration than the default path handling that JSTree currently allows.
-        For example, users may want to pass "attr" or some other valid jsTree options.
-
-        Example:
-          >>> import jstree
-          >>> node = jstree.Node('a', None)
-          >>> print node
-          Node({'text': 'a', 'children': MutableDictionaryObject({})})
-          >>> print node.jsonData()
-          {'text': 'a'}
-
-          >>> import jstree
-          >>> node = jstree.Node('a', 1)
-          >>> print node
-          Node({'text': 'a', 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 1}), 'id': 1})
-          >>> print node.jsonData()
-          {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
-
-          >>> import jstree
-          >>> node = jstree.Node('a', 5, icon="folder", state = {'opened': True})
-          >>> print node
-          Node({'text': 'a', 'id': 5, 'state': DictionaryObject({'opened': True}), 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 5}), 'icon': 'folder'})
-          >>> print node.jsonData()
-          {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
-        """
-        super(Node, self).__init__()
-
-        children = kwargs.get('children', {})
-        if len(filter(lambda key: not isinstance(children[key], Node), children)):
-            raise TypeError(
-                "One or more children were not instances of '%s'" % Node.__name__)
-        if 'children' in kwargs:
-            del kwargs['children']
-        self._items['children'] = dictobj.MutableDictionaryObject(children)
-
-        if oid is not None:
-            li_attr = kwargs.get('li_attr', {})
-            li_attr['id'] = oid
-            kwargs['li_attr'] = li_attr
-            self._items['id'] = oid
-
-        self._items.update(dictobj.DictionaryObject(**kwargs))
-        self._items['text'] = path
-
-        def jsonData(self):
-            children = [self.children[k].jsonData() for k in sorted(self.children)]
-            output = {}
-            for k in self._items:
-                if 'children' == k:
-                    continue
-                if isinstance(self._items[k], dictobj.DictionaryObject):
-                    output[k] = self._items[k].asdict()
-                else:
-                    output[k] = self._items[k]
-            if len(children):
-                output['children'] = children
-            return output
+    kwargs allows users to pass arbitrary information into a Node that
+    will later be output in jsonData().  It allows for more advanced
+    configuration than the default path handling that JSTree currently allows.
+    For example, users may want to pass "attr" or some other valid jsTree options.
+
+    Example:
+      >>> import jstree
+      >>> node = jstree.Node('a', None)
+      >>> print node
+      Node({'text': 'a', 'children': MutableDictionaryObject({})})
+      >>> print node.jsonData()
+      {'text': 'a'}
+
+      >>> import jstree
+      >>> node = jstree.Node('a', 1)
+      >>> print node
+      Node({'text': 'a', 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 1}), 'id': 1})
+      >>> print node.jsonData()
+      {'text': 'a', 'id': 1, 'li_attr': {'id': 1}}
+
+      >>> import jstree
+      >>> node = jstree.Node('a', 5, icon="folder", state = {'opened': True})
+      >>> print node
+      Node({'text': 'a', 'id': 5, 'state': DictionaryObject({'opened': True}), 'children': MutableDictionaryObject({}), 'li_attr': DictionaryObject({'id': 5}), 'icon': 'folder'})
+      >>> print node.jsonData()
+      {'text': 'a', 'state': {'opened': True}, 'id': 5, 'li_attr': {'id': 5}, 'icon': 'folder'}
+    """
+    super(Node, self).__init__()
+
+    children = kwargs.get('children', {})
+    if len(filter(lambda key: not isinstance(children[key], Node), children)):
+      raise TypeError(
+        "One or more children were not instances of '%s'" % Node.__name__)
+    if 'children' in kwargs:
+      del kwargs['children']
+    self._items['children'] = dictobj.MutableDictionaryObject(children)
+
+    if oid is not None:
+      li_attr = kwargs.get('li_attr', {})
+      li_attr['id'] = oid
+      kwargs['li_attr'] = li_attr
+      self._items['id'] = oid
+
+    self._items.update(dictobj.DictionaryObject(**kwargs))
+    self._items['text'] = path
+
+  def jsonData(self):
+    children = [self.children[k].jsonData() for k in sorted(self.children)]
+    output = {}
+    for k in self._items:
+      if 'children' == k:
+        continue
+      if isinstance(self._items[k], dictobj.DictionaryObject):
+        output[k] = self._items[k].asdict()
+      else:
+        output[k] = self._items[k]
+    if len(children):
+      output['children'] = children
+    return output
 
 
 class JSTree(dictobj.DictionaryObject):
+  """
+  An immutable dictionary-like object that converts a list of "paths"
+  into a tree structure suitable for jQuery's jsTree.
+  """
+
+  def __init__(self, paths, **kwargs):
+    """
+    Take a list of paths and put them into a tree.  Paths with the same prefix should
+    be at the same level in the tree.
+
+    kwargs may be standard jsTree options used at all levels in the tree.  These will be outputted
+    in the JSON.
+
+    """
+    if len(filter(lambda p: not isinstance(p, Path), paths)):
+      raise TypeError(
+        "All paths must be instances of '%s'" % Path.__name__)
+
+    super(JSTree, self).__init__()
+
+    root = Node('', None, **kwargs)
+    for path in sorted(paths):
+      curr = root
+      subpaths = path.path.split(os.path.sep)
+      for i, subpath in enumerate(subpaths):
+        if subpath not in curr.children:
+          opt = copy.deepcopy(kwargs)
+          if len(subpaths) - 1 == i:
+            oid = path.id
+            opt.update(path.options) if path.options is not None else None
+          else:
+            oid = None
+          curr.children[subpath] = Node(subpath, oid, **opt)          
+          # oid = path.id if len(subpaths) - 1 == i else None
+          # curr.children[subpath] = Node(subpath, oid, **kwargs)
+        curr = curr.children[subpath]
+    self._items['_root'] = root
+
+  def pretty(self, root=None, depth=0, spacing=2):
     """
-    An immutable dictionary-like object that converts a list of "paths"
-    into a tree structure suitable for jQuery's jsTree.
+    Create a "pretty print" represenation of the tree with customized indentation at each
+    level of the tree.
     """
+    if root is None:
+      root = self._root
+    fmt = "%s%s/" if root.children else "%s%s"
+    s = fmt % (" " * depth * spacing, root.text)
+    for child in root.children:
+      child = root.children[child]
+      s += "\n%s" % self.pretty(child, depth + 1, spacing)
+    return s
+
+  def jsonData(self):
+    """
+    Returns a copy of the internal tree in a JSON-friendly format,
+    ready for consumption by jsTree.  The data is represented as a
+    list of dictionaries, each of which are our internal nodes.
 
-    def __init__(self, paths, **kwargs):
-        """
-        Take a list of paths and put them into a tree.  Paths with the same prefix should
-        be at the same level in the tree.
-
-        kwargs may be standard jsTree options used at all levels in the tree.  These will be outputted
-        in the JSON.
-
-        """
-        if len(filter(lambda p: not isinstance(p, Path), paths)):
-            raise TypeError(
-                "All paths must be instances of '%s'" % Path.__name__)
-
-        super(JSTree, self).__init__()
-
-        root = Node('', None, **kwargs)
-        for path in sorted(paths):
-            curr = root
-            subpaths = path.path.split(os.path.sep)
-            for i, subpath in enumerate(subpaths):
-                if subpath not in curr.children:
-                    opt = copy.deepcopy(kwargs)
-                    if len(subpaths) - 1 == i:
-                        oid = path.id
-                        opt.update(path.options) if path.options is not None else None
-                    else:
-                        oid = None
-                    curr.children[subpath] = Node(subpath, oid, **opt)
-                    # oid = path.id if len(subpaths) - 1 == i else None
-                    # curr.children[subpath] = Node(subpath, oid, **kwargs)
-                curr = curr.children[subpath]
-        self._items['_root'] = root
-
-    def pretty(self, root=None, depth=0, spacing=2):
-        """
-        Create a "pretty print" represenation of the tree with customized indentation at each
-        level of the tree.
-        """
-        if root is None:
-            root = self._root
-        fmt = "%s%s/" if root.children else "%s%s"
-        s = fmt % (" " * depth * spacing, root.text)
-        for child in root.children:
-            child = root.children[child]
-            s += "\n%s" % self.pretty(child, depth + 1, spacing)
-        return s
-
-    def jsonData(self):
-        """
-        Returns a copy of the internal tree in a JSON-friendly format,
-        ready for consumption by jsTree.  The data is represented as a
-        list of dictionaries, each of which are our internal nodes.
-        """
-        return [self._root.children[k].jsonData() for k in sorted(self._root.children)]
+    """
+    return [self._root.children[k].jsonData() for k in sorted(self._root.children)]