ActionMapperRefactor: path -> source dict.

pulsar/client/action_mapper.py

@@ -104,46 +104,46 @@ class FileActionMapper(object):
     ...     return mapper
     >>> mapper = mapper_for(default_action='none', config_contents=json_string)
     >>> # Test first config line above, implicit path prefix mapper
-    >>> action = mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')
+    >>> action = mapper.action({'path': '/opt/galaxy/tools/filters/catWrapper.py'}, 'input')
     >>> action.action_type == u'none'
     True
     >>> action.staging_needed
     False
     >>> # Test another (2nd) mapper, this one with a different action
-    >>> action = mapper.action('/galaxy/data/files/000/dataset_1.dat', 'input')
+    >>> action = mapper.action({'path': '/galaxy/data/files/000/dataset_1.dat'}, 'input')
     >>> action.action_type == u'transfer'
     True
     >>> action.staging_needed
     True
     >>> # Always at least copy work_dir outputs.
-    >>> action = mapper.action('/opt/galaxy/database/working_directory/45.sh', 'workdir')
+    >>> action = mapper.action({'path': '/opt/galaxy/database/working_directory/45.sh'}, 'workdir')
     >>> action.action_type == u'copy'
     True
     >>> action.staging_needed
     True
     >>> # Test glob mapper (matching test)
-    >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam', 'input').action_type == u'copy'
+    >>> mapper.action({'path': '/cool/bamfiles/projectABC/study1/patient3.bam'}, 'input').action_type == u'copy'
     True
     >>> # Test glob mapper (non-matching test)
-    >>> mapper.action('/cool/bamfiles/projectABC/study1/patient3.bam.bai', 'input').action_type == u'none'
+    >>> mapper.action({'path': '/cool/bamfiles/projectABC/study1/patient3.bam.bai'}, 'input').action_type == u'none'
     True
     >>> # Regex mapper test.
-    >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'input').action_type == u'copy'
+    >>> mapper.action({'path': '/old/galaxy/data/dataset_10245.dat'}, 'input').action_type == u'copy'
     True
     >>> # Doesn't map unstructured paths by default
-    >>> mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'none'
+    >>> mapper.action({'path': '/old/galaxy/data/dataset_10245.dat'}, 'unstructured').action_type == u'none'
     True
     >>> input_only_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \
       {"path": "/", "action": "transfer", "path_types": "input"} \
     ] }''')
-    >>> input_only_mapper.action('/dataset_1.dat', 'input').action_type == u'transfer'
+    >>> input_only_mapper.action({'path': '/dataset_1.dat'}, 'input').action_type == u'transfer'
     True
-    >>> input_only_mapper.action('/dataset_1.dat', 'output').action_type == u'none'
+    >>> input_only_mapper.action({'path': '/dataset_1.dat'}, 'output').action_type == u'none'
     True
     >>> unstructured_mapper = mapper_for(default_action="none", config_contents=r'''{"paths": [ \
       {"path": "/", "action": "transfer", "path_types": "*any*"} \
     ] }''')
-    >>> unstructured_mapper.action('/old/galaxy/data/dataset_10245.dat', 'unstructured').action_type == u'transfer'
+    >>> unstructured_mapper.action({'path': '/old/galaxy/data/dataset_10245.dat'}, 'unstructured').action_type == u'transfer'
     True
     """
 
@@ -161,7 +161,8 @@ class FileActionMapper(object):
         self.mappers = mappers_from_dicts(config.get("paths", []))
         self.files_endpoint = config.get("files_endpoint", None)
 
-    def action(self, path, type, mapper=None):
+    def action(self, source, type, mapper=None):
+        path = source["path"]
         mapper = self.__find_mapper(path, type, mapper)
         action_class = self.__action_class(path, type, mapper)
         file_lister = DEFAULT_FILE_LISTER

pulsar/client/path_mapper.py

@@ -60,7 +60,7 @@ class PathMapper(object):
 
     def check_for_arbitrary_rewrite(self, local_path):
         path = str(local_path)  # Use false_path if needed.
-        action = self.action_mapper.action(path, path_type.UNSTRUCTURED)
+        action = self.action_mapper.action({"path": path}, path_type.UNSTRUCTURED)
         if not action.staging_needed:
             return action.path_rewrite(self.path_helper), []
         unique_names = action.unstructured_map()
@@ -72,7 +72,7 @@ class PathMapper(object):
         """ Return remote path of this file (if staging is required) else None.
         """
         path = str(dataset_path)  # Use false_path if needed.
-        action = self.action_mapper.action(path, dataset_path_type)
+        action = self.action_mapper.action({"path": path}, dataset_path_type)
         if action.staging_needed:
             if name is None:
                 name = os.path.basename(path)

pulsar/client/staging/down.py

@@ -135,7 +135,7 @@ class ResultsCollector(object):
         # path.
         collected = False
         with self.exception_tracker():
-            action = self.action_mapper.action(path, output_type)
+            action = self.action_mapper.action({"path": path}, output_type)
             if self._collect_output(output_type, action, name):
                 collected = True
 

pulsar/client/staging/up.py

@@ -197,7 +197,7 @@ class FileStager(object):
                 if path not in referenced_arbitrary_path_mappers:
                     referenced_arbitrary_path_mappers[path] = mapper
         for path, mapper in referenced_arbitrary_path_mappers.items():
-            action = self.action_mapper.action(path, path_type.UNSTRUCTURED, mapper)
+            action = self.action_mapper.action({"path": path}, path_type.UNSTRUCTURED, mapper)
             unstructured_map = action.unstructured_map(self.path_helper)
             self.arbitrary_files.update(unstructured_map)
 
@@ -501,7 +501,7 @@ class TransferTracker(object):
             self.job_inputs.rewrite_paths(local_path, remote_path)
 
     def __action(self, path, type):
-        return self.action_mapper.action(path, type)
+        return self.action_mapper.action({"path": path}, type)
 
 
 def _read(path):

test/action_mapper_test.py

@@ -9,7 +9,7 @@ def test_endpoint_validation():
     mapper = FileActionMapper(client)
     exception_found = False
     try:
-        mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')
+        mapper.action({'path': '/opt/galaxy/tools/filters/catWrapper.py'}, 'input')
     except Exception as e:
         exception_found = True
         assert "files_endpoint" in str(e)
@@ -21,7 +21,7 @@ def test_ssh_key_validation():
     mapper = FileActionMapper(client)
     exception_found = False
     try:
-        mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')
+        mapper.action({'path': '/opt/galaxy/tools/filters/catWrapper.py'}, 'input')
     except Exception as e:
         exception_found = True
         assert "ssh_key" in str(e)
@@ -31,7 +31,7 @@ def test_ssh_key_validation():
 def test_ssh_key_defaults():
     client = _client("remote_rsync_transfer")
     mapper = FileActionMapper(client)
-    action = mapper.action('/opt/galaxy/tools/filters/catWrapper.py', 'input')
+    action = mapper.action({'path': '/opt/galaxy/tools/filters/catWrapper.py'}, 'input')
     action.to_dict()
 
 

test/path_mapper_test.py

@@ -75,7 +75,7 @@ class TestActionMapper(object):
         if not staging_needed:
             self._action.path_rewrite = lambda path: None
 
-    def action(self, path, type):
-        assert self.expected_path == path
+    def action(self, source, type):
+        assert self.expected_path == source["path"]
         assert self.expected_type == type
         return self._action