Make upload tool python3 compatible

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -129,6 +129,6 @@ vine==1.1.4
 warlock==1.2.0
 wcwidth==0.1.7; sys_platform != 'win32'
 webencodings==0.5.1
-webob==1.4.2
+webob==1.8.2
 whoosh==2.7.4
 wrapt==1.10.11

lib/galaxy/tools/actions/upload_common.py

@@ -372,7 +372,7 @@ def _chown(path):
             if link_data_only == 'copy_files' and trans.app.config.external_chown_script:
                 _chown(uploaded_dataset.path)
         tool_params.append(params)
-    with tempfile.NamedTemporaryFile(prefix='upload_params_', delete=False) as fh:
+    with tempfile.NamedTemporaryFile(mode="w", prefix='upload_params_', delete=False) as fh:
         json_file_path = fh.name
         dump(tool_params, fh)
     return json_file_path

lib/galaxy/tools/parameters/dynamic_options.py

@@ -470,7 +470,7 @@ def load_from_parameter(from_parameter, transform_lines=None):
             for field in from_parameter.split('.'):
                 obj = getattr(obj, field)
             if transform_lines:
-                obj = eval(transform_lines)
+                obj = eval(transform_lines, globals(), locals())
             return self.parse_file_fields(obj)
         self.tool_param = tool_param
         self.columns = {}

lib/galaxy/web/framework/base.py

@@ -12,7 +12,7 @@
 import types
 
 import routes
-import webob
+import webob.exc
 # We will use some very basic HTTP/wsgi utilities from the paste library
 from paste import httpexceptions
 from paste.request import get_cookies
@@ -459,7 +459,7 @@ def wsgi_status(self):
         Return status line in format appropriate for WSGI `start_response`
         """
         if isinstance(self.status, int):
-            exception = httpexceptions.get_exception(self.status)
+            exception = webob.exc.status_map.get(self.status)
             return "%d %s" % (exception.code, exception.title)
         else:
             return self.status

tools/data_source/upload.py

@@ -13,10 +13,13 @@
 
 from six.moves.urllib.request import urlopen
 
-from galaxy import util
 from galaxy.datatypes import sniff
 from galaxy.datatypes.registry import Registry
 from galaxy.datatypes.upload_util import handle_upload, UploadProblemException
+from galaxy.util import (
+    bunch,
+    unicodify
+)
 
 assert sys.version_info[:2] >= (2, 7)
 
@@ -36,9 +39,9 @@ def file_err(msg, dataset):
 
 
 def safe_dict(d):
-    """Recursively clone json structure with UTF-8 dictionary keys."""
+    """Recursively clone JSON structure with unicode dictionary keys."""
     if isinstance(d, dict):
-        return dict([(k.encode('utf-8'), safe_dict(v)) for k, v in d.items()])
+        return dict([(unicodify(k), safe_dict(v)) for k, v in d.items()])
     elif isinstance(d, list):
         return [safe_dict(x) for x in d]
     else:
@@ -172,7 +175,7 @@ def add_composite_file(dataset, output_path, files_path):
     if dataset.composite_files:
         os.mkdir(files_path)
         for name, value in dataset.composite_files.items():
-            value = util.bunch.Bunch(**value)
+            value = bunch.Bunch(**value)
             if dataset.composite_file_paths[value.name] is None and not value.optional:
                 raise UploadProblemException('A required composite data file was not provided (%s)' % name)
             elif dataset.composite_file_paths[value.name] is not None:
@@ -251,7 +254,7 @@ def __main__():
 
     metadata = []
     for dataset in datasets:
-        dataset = util.bunch.Bunch(**safe_dict(dataset))
+        dataset = bunch.Bunch(**safe_dict(dataset))
         try:
             output_path = output_paths[int(dataset.dataset_id)][0]
         except Exception: