Merge branch 'release_18.01' into release_18.05

lib/galaxy/tools/__init__.py

@@ -1871,6 +1871,7 @@ def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
         if self.input_translator:
             self.input_translator.translate(params)
 
+        set_dataset_matcher_factory(request_context, self)
         # create tool state
         state_inputs = {}
         state_errors = {}
@@ -1879,7 +1880,6 @@ def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
         # create tool model
         tool_model = self.to_dict(request_context)
         tool_model['inputs'] = []
-        set_dataset_matcher_factory(request_context, self, state_inputs)
         self.populate_model(request_context, self.inputs, state_inputs, tool_model['inputs'])
         unset_dataset_matcher_factory(request_context)
 

lib/galaxy/tools/parameters/dataset_matcher.py

@@ -5,8 +5,8 @@
 log = getLogger(__name__)
 
 
-def set_dataset_matcher_factory(trans, tool, param_values):
-    trans.dataset_matcher_factory = DatasetMatcherFactory(trans, tool, param_values)
+def set_dataset_matcher_factory(trans, tool):
+    trans.dataset_matcher_factory = DatasetMatcherFactory(trans, tool)
 
 
 def unset_dataset_matcher_factory(trans):
@@ -21,7 +21,7 @@ def get_dataset_matcher_factory(trans):
 class DatasetMatcherFactory(object):
     """"""
 
-    def __init__(self, trans, tool=None, param_values=None):
+    def __init__(self, trans, tool=None):
         self._trans = trans
         self._tool = tool
         self._data_inputs = []
@@ -32,8 +32,9 @@ def __init__(self, trans, tool=None, param_values=None):
             valid_input_states = galaxy.model.Dataset.valid_input_states
         self.valid_input_states = valid_input_states
         can_process_summary = False
-        if tool is not None and param_values is not None:
-            self._collect_data_inputs(tool, param_values)
+        if tool is not None:
+            for input in tool.inputs.values():
+                self._collect_data_inputs(input)
 
             require_public = self._tool and self._tool.tool_type == 'data_destination'
             if not require_public and self._data_inputs:
@@ -62,15 +63,17 @@ def matches_format(self, hda_extension, format):
 
         return formats[format]
 
-    def _collect_data_inputs(self, tool, param_values):
-        def visitor(input, value, prefix, parent=None, **kwargs):
-            type_name = type(input).__name__
-            if "DataToolParameter" in type_name:
-                self._data_inputs.append(input)
-            elif "DataCollectionToolParameter" in type_name:
-                self._data_inputs.append(input)
-
-        tool.visit_inputs(param_values, visitor)
+    def _collect_data_inputs(self, input):
+        type_name = input.type
+        if type_name == "repeat" or type_name == "upload_dataset" or type_name == "section":
+            for child_input in input.inputs.values():
+                self._collect_data_inputs(child_input)
+        elif type_name == "conditional":
+            for case in input.cases:
+                for child_input in case.inputs.values():
+                    self._collect_data_inputs(child_input)
+        elif type_name == "data" or type_name == "data_collection":
+            self._data_inputs.append(input)
 
     def dataset_matcher(self, param, other_values):
         return DatasetMatcher(self, self._trans, param, other_values)

lib/galaxy/util/permutations.py

@@ -83,7 +83,8 @@ def __extend_with_matched_combos(single_inputs, multi_inputs):
         if multi_input_key == first_multi_input_key:
             continue
         if len(multi_input_values) != len(first_multi_value):
-            raise InputMatchedException()
+            raise InputMatchedException("Received %d inputs for '%s' and %d inputs for '%s', these should be of equal length" %
+                                        (len(multi_input_values), multi_input_key, len(first_multi_value), first_multi_input_key))
 
         for index, value in enumerate(multi_input_values):
             matched_multi_inputs[index][multi_input_key] = value

scripts/grt/export.py

@@ -69,7 +69,7 @@ def __init__(self, sanitization_config, model, sa_session):
             self.sanitization_config['tool_params'] = {}
 
     def blacklisted_tree(self, path):
-        if path.lstrip('.') in self.sanitization_config['tool_params'][self.tool_id]:
+        if self.tool_id in self.sanitization_config['tool_params'] and path.lstrip('.') in self.sanitization_config['tool_params'][self.tool_id]:
             return True
         return False
 
@@ -79,21 +79,23 @@ def sanitize_data(self, tool_id, key, value):
             return 'null'
         # Thus, all tools below here are not blacklisted at the top level.
 
-        # If it isn't in tool_params, there are no keys being sanitized for
-        # this tool so we can return quickly without parsing.
-        if tool_id not in self.sanitization_config['tool_params']:
-            return value
-
         # If the key is listed precisely (not a sub-tree), we can also return slightly more quickly.
-        if key in self.sanitization_config['tool_params'][tool_id]:
+        if tool_id in self.sanitization_config['tool_params'] and key in self.sanitization_config['tool_params'][tool_id]:
             return 'null'
 
         # If the key isn't a prefix for any of the keys being sanitized, then this is safe.
-        if not any(san_key.startswith(key) for san_key in self.sanitization_config['tool_params'][tool_id]):
+        if tool_id in self.sanitization_config['tool_params'] and not any(san_key.startswith(key) for san_key in self.sanitization_config['tool_params'][tool_id]):
             return value
 
         # Slow path.
-        unsanitized = {key: json.loads(value)}
+        if isinstance(value, str):
+            try:
+                unsanitized = {key: json.loads(value)}
+            except ValueError:
+                unsanitized = {key: value}
+        else:
+            unsanitized = {key: value}
+
         self.tool_id = tool_id
         return json.dumps(self._sanitize_value(unsanitized))
 
@@ -117,7 +119,8 @@ def _file_dict(self, data):
             self.filesize_cache[data['id']] = data
             return data
         else:
-            raise Exception("Cannot handle {src} yet".format(data))
+            logging.warning("Cannot handle {src} yet".format(data))
+            return data
 
     def _sanitize_dict(self, unsanitized_dict, path=""):
         # if it is a file dictionary, handle specially.