update contents per further review

- fix is_hidden always returning True on nonexistent files
- create hidden dir fails with 400
- don't read binary files twice
- logging improvements
- dialog on invalid notebook upload
- warn about disabled `--save`

IPython/html/notebookapp.py

@@ -265,6 +265,11 b" flags['no-mathjax']=("
     """
 )
 
+# Add notebook manager flags
+flags.update(boolean_flag('script', 'FileContentsManager.save_script',
+               'DEPRECATED, IGNORED',
+               'DEPRECATED, IGNORED'))
+
 aliases = dict(base_aliases)
 
 aliases.update({

IPython/html/services/contents/filemanager.py

@@ -17,20 +17,27 b' from IPython.utils.path import ensure_dir_exists'
 from IPython.utils.traitlets import Unicode, Bool, TraitError
 from IPython.utils.py3compat import getcwd
 from IPython.utils import tz
-from IPython.html.utils import is_hidden, to_os_path
+from IPython.html.utils import is_hidden, to_os_path, url_path_join
 
 
 class FileContentsManager(ContentsManager):
 
     root_dir = Unicode(getcwd(), config=True)
 
+    save_script = Bool(False, config=True, help='DEPRECATED, IGNORED')
+    def _save_script_changed(self):
+        self.log.warn("""
+        Automatically saving notebooks as scripts has been removed.
+        Use `ipython nbconvert --to python [notebook]` instead.
+        """)
+
     def _root_dir_changed(self, name, old, new):
         """Do a bit of validation of the root_dir."""
         if not os.path.isabs(new):
             # If we receive a non-absolute path, make it absolute.
             self.root_dir = os.path.abspath(new)
             return
-        if not os.path.exists(new) or not os.path.isdir(new):
+        if not os.path.isdir(new):
             raise TraitError("%r is not a directory" % new)
 
     checkpoint_dir = Unicode('.ipynb_checkpoints', config=True,
@@ -70,7 +77,7 b' class FileContentsManager(ContentsManager):'
             API path to be evaluated relative to root_dir.
         """
         if name is not None:
-            path = path + '/' + name
+            path = url_path_join(path, name)
         return to_os_path(path, self.root_dir)
 
     def path_exists(self, path):
@@ -177,11 +184,15 b' class FileContentsManager(ContentsManager):'
         """
         os_path = self._get_os_path(name, path)
 
+        four_o_four = u'directory does not exist: %r' % os_path
+
         if not os.path.isdir(os_path):
-            raise web.HTTPError(404, u'directory does not exist: %r' % os_path)
+            raise web.HTTPError(404, four_o_four)
         elif is_hidden(os_path, self.root_dir):
-            self.log.info("Refusing to serve hidden directory, via 404 Error")
-            raise web.HTTPError(404, u'directory does not exist: %r' % os_path)
+            self.log.info("Refusing to serve hidden directory %r, via 404 Error",
+                os_path
+            )
+            raise web.HTTPError(404, four_o_four)
 
         if name is None:
             if '/' in path:
@@ -212,14 +223,13 b' class FileContentsManager(ContentsManager):'
         model['type'] = 'file'
         if content:
             os_path = self._get_os_path(name, path)
+            with io.open(os_path, 'rb') as f:
+                bcontent = f.read()
             try:
-                with io.open(os_path, 'r', encoding='utf-8') as f:
-                    model['content'] = f.read()
+                model['content'] = bcontent.decode('utf8')
             except UnicodeError as e:
-                with io.open(os_path, 'rb') as f:
-                    bcontent = f.read()
-                    model['content'] = base64.encodestring(bcontent).decode('ascii')
-                    model['format'] = 'base64'
+                model['content'] = base64.encodestring(bcontent).decode('ascii')
+                model['format'] = 'base64'
             else:
                 model['format'] = 'text'
         return model
@@ -307,10 +317,14 b' class FileContentsManager(ContentsManager):'
 
     def _save_directory(self, os_path, model, name='', path=''):
         """create a directory"""
+        if is_hidden(os_path, self.root_dir):
+            raise web.HTTPError(400, u'Cannot create hidden directory %r' % os_path)
         if not os.path.exists(os_path):
             os.mkdir(os_path)
         elif not os.path.isdir(os_path):
             raise web.HTTPError(400, u'Not a directory: %s' % (os_path))
+        else:
+            self.log.debug("Directory %r already exists", os_path)
 
     def save(self, model, name='', path=''):
         """Save the file model and return the model with no content."""
@@ -372,7 +386,7 b' class FileContentsManager(ContentsManager):'
         if os.path.isdir(os_path):
             listing = os.listdir(os_path)
             # don't delete non-empty directories (checkpoints dir doesn't count)
-            if listing and listing != ['.ipynb_checkpoints']:
+            if listing and listing != [self.checkpoint_dir]:
                 raise web.HTTPError(400, u'Directory %s not empty' % os_path)
         elif not os.path.isfile(os_path):
             raise web.HTTPError(404, u'File does not exist: %s' % os_path)

IPython/html/services/contents/tests/test_contents_api.py

@@ -303,6 +303,10 b' class APITest(NotebookTestBase):'
         resp = self.api.mkdir(u'New ∂ir', path=u'å b')
         self._check_created(resp, u'New ∂ir', u'å b', type='directory')
 
+    def test_mkdir_hidden_400(self):
+        with assert_http_error(400):
+            resp = self.api.mkdir(u'.hidden', path=u'å b')
+
     def test_upload_txt(self):
         body = u'ünicode téxt'
         model = {

IPython/html/static/tree/js/notebooklist.js

@@ -382,7 +382,20 b' define(['
                 if (file_ext === '.ipynb') {
                     model.type = 'notebook';
                     model.format = 'json';
-                    model.content = JSON.parse(filedata);
+                    try {
+                        model.content = JSON.parse(filedata);
+                    } catch (e) {
+                        dialog.modal({
+                            title : 'Cannot upload invalid Notebook',
+                            body : "The error was: " + e,
+                            buttons : {'OK' : {
+                                'class' : 'btn-primary',
+                                click: function () {
+                                    item.remove();
+                                }
+                            }}
+                        });
+                    }
                     content_type = 'application/json';
                 } else {
                     model.type = 'file';

IPython/html/utils.py

@@ -113,6 +113,9 b" def is_hidden(abs_path, abs_root=''):"
     # check UF_HIDDEN on any location up to root
     path = abs_path
     while path and path.startswith(abs_root) and path != abs_root:
+        if not os.path.exists(path):
+            path = os.path.dirname(path)
+            continue
         try:
             # may fail on Windows junctions
             st = os.stat(path)

docs/source/whatsnew/pr/incompat-contents-service.rst

@@ -3,4 +3,4 b''
   which supports all kinds of files.
 - The Dashboard now lists all files, not just notebooks and directories.
 - The ``--script`` hook for saving notebooks to Python scripts is removed,
-  use ``ipython nbconvert --to python [notebook]`` instead.
+  use :samp:`ipython nbconvert --to python {notebook}` instead.