add Object getattr for #287

solvebio/cli/data.py

@@ -14,6 +14,9 @@
 
 from solvebio import Vault
 from solvebio import Object
+from solvebio import Dataset
+from solvebio import DatasetImport
+from solvebio import DatasetTemplate
 from solvebio.utils.files import check_gzip_path
 from solvebio.errors import SolveError
 from solvebio.errors import NotFoundError
@@ -157,11 +160,11 @@ def _create_template_from_file(template_file, dry_run=False):
             sys.exit(1)
 
     if dry_run:
-        template = solvebio.DatasetTemplate(**template_json)
+        template = DatasetTemplate(**template_json)
         print("A new dataset template will be created from: {0}"
               .format(template_file))
     else:
-        template = solvebio.DatasetTemplate.create(**template_json)
+        template = DatasetTemplate.create(**template_json)
         print("A new dataset template was created with id: {0}"
               .format(template.id))
 
@@ -189,7 +192,7 @@ def create_dataset(args, template=None):
 
     try:
         # Fail if a dataset already exists.
-        solvebio.Dataset.get_by_full_path(full_path)
+        Object.get_by_full_path(full_path, assert_type='dataset')
         print('A dataset already exists at path: {0}'.format(full_path))
         sys.exit(1)
     except NotFoundError:
@@ -202,8 +205,8 @@ def create_dataset(args, template=None):
         pass
     elif args.template_id:
         try:
-            template = solvebio.DatasetTemplate.retrieve(args.template_id)
-        except solvebio.SolveError as e:
+            template = DatasetTemplate.retrieve(args.template_id)
+        except SolveError as e:
             if e.status_code != 404:
                 raise e
             print("No template with ID {0} found!".format(args.template_id))
@@ -256,7 +259,7 @@ def create_dataset(args, template=None):
             print("Metadata: {}".format(metadata))
         return
 
-    return solvebio.Dataset.get_or_create_by_full_path(
+    return Dataset.get_or_create_by_full_path(
         full_path,
         capacity=args.capacity,
         fields=fields,
@@ -394,8 +397,8 @@ def import_file(args):
 
     if args.template_id:
         try:
-            template = solvebio.DatasetTemplate.retrieve(args.template_id)
-        except solvebio.SolveError as e:
+            template = DatasetTemplate.retrieve(args.template_id)
+        except SolveError as e:
             if e.status_code != 404:
                 raise e
             print("No template with ID {0} found!".format(args.template_id))
@@ -410,7 +413,7 @@ def import_file(args):
         dataset = create_dataset(args, template=template)
     else:
         try:
-            dataset = solvebio.Dataset.get_by_full_path(full_path)
+            dataset = Object.get_by_full_path(full_path, assert_type='dataset')
         except solvebio.errors.NotFoundError:
             print("Dataset not found: {0}".format(full_path))
             print("Tip: use the --create-dataset flag "
@@ -442,7 +445,7 @@ def import_file(args):
             kwargs.update(template.import_params)
 
         # Create the import
-        import_ = solvebio.DatasetImport.create(
+        import_ = DatasetImport.create(
             dataset_id=dataset.id,
             commit_mode=args.commit_mode,
             **kwargs

solvebio/resource/dataset.py

@@ -38,6 +38,10 @@ class Dataset(CreateableAPIResource,
     def make_full_path(cls, vault_name, path, name, **kwargs):
         from solvebio import SolveError
 
+        print('[Deprecated] Warning this method has been deprecated'
+              'and will be removed in a future released.'
+              'Use self.vault_object.full_path')
+
         _client = kwargs.pop('client', None) or cls._client or client
 
         try:
@@ -69,6 +73,7 @@ def get_or_create_by_full_path(cls, full_path, **kwargs):
         from solvebio import Object
         # Assert this is a dataset
         kwargs['assert_type'] = 'dataset'
+        kwargs['object_type'] = 'dataset'
         return Object.get_or_create_by_full_path(full_path, **kwargs)
 
     def saved_queries(self, **params):

solvebio/resource/object.py

@@ -418,17 +418,27 @@ def objects(self, **params):
     def ls(self, **params):
         return self.objects(**params)
 
-    def query(self, query=None, **params):
-        """Shortcut to query the underlying Dataset object"""
-        from solvebio import Dataset
+    def __getattr__(self, name):
+        """Shortcut to access attributes of the underlying Dataset resource"""
+        from solvebio.resource import Dataset
+
+        valid_attrs = [
+            # query data
+            'query', 'lookup',
+            # transform data
+            'import_file', 'export', 'migrate',
+            # dataset meta
+            'fields', 'template', 'imports', 'commits',
+            # helpers
+            'activity', 'saved_queries'
+        ]
+        if name in valid_attrs and self.is_dataset:
+            return getattr(Dataset(self.dataset_id, client=self._client), name)
 
-        if not self.is_dataset:
-            raise SolveError(
-                "The query method can only be used by a dataset. Found a {}"
-                .format(self.object_type))
-
-        return Dataset(self.dataset_id, client=self._client).query(
-            query=query, **params)
+        try:
+            return self[name]
+        except KeyError as err:
+            raise AttributeError(*err.args)
 
     @property
     def parent(self):

solvebio/test/client_mocks.py

@@ -41,7 +41,7 @@ def solve_objects(self):
         return ExtendedList([self.create()])
 
     def update_paths(self):
-        """Sets vault_name, path and full_path"""
+        """Sets vault_name, path and full_path based on mock inputs"""
         if not self.object['vault_name']:
             self.object['vault_name'] = 'mock_vault'
 
@@ -55,6 +55,11 @@ def update_paths(self):
             self.object['full_path'] = 'solvebio:{0}:{1}'.format(
                 self.object['vault_name'], self.object['path'])
 
+    def update_dataset(self):
+        """Sets dataset_id if object is a dataset"""
+        if self.object['object_type'] == 'dataset':
+            self.object['dataset_id'] = self.object['id']
+
 
 class FakeMigrationResponse(Fake201Response):
 
@@ -122,6 +127,7 @@ def __init__(self, data):
         }
         self.object.update(data)
         self.update_paths()
+        self.update_dataset()
 
 
 class FakeDatasetResponse(Fake201Response):
@@ -220,6 +226,8 @@ def fake_object_retrieve(*args, **kwargs):
 
 
 def fake_dataset_create(*args, **kwargs):
+    # Dataset.create() is deprecated
+    print("WARNING: Your code likely wants to be using FakeObjectCreate.")
     return FakeDatasetResponse(kwargs).create()
 
 

solvebio/test/test_shortcuts.py

@@ -20,7 +20,6 @@
 from solvebio.test.client_mocks import fake_object_all
 from solvebio.test.client_mocks import fake_object_create
 from solvebio.test.client_mocks import fake_object_retrieve
-from solvebio.test.client_mocks import fake_dataset_create
 from solvebio.test.client_mocks import fake_dataset_tmpl_create
 from solvebio.test.client_mocks import fake_dataset_tmpl_retrieve
 from solvebio.test.client_mocks import fake_dataset_import_create
@@ -43,23 +42,23 @@ def setUp(self):
 
     @mock.patch('solvebio.resource.Vault.all')
     @mock.patch('solvebio.resource.Object.all')
-    @mock.patch('solvebio.resource.Dataset.create')
+    @mock.patch('solvebio.resource.Object.create')
     def test_create_dataset(self, DatasetCreate, ObjectAll, VaultAll):
-        DatasetCreate.side_effect = fake_dataset_create
+        DatasetCreate.side_effect = fake_object_create
         ObjectAll.side_effect = fake_object_all
         VaultAll.side_effect = fake_vault_all
         args = ['create-dataset', 'solvebio:test_vault:/test-dataset',
                 '--capacity', 'small']
         ds = main.main(args)
-        self.assertEqual(ds.name, 'test-dataset')
+        self.assertEqual(ds.filename, 'test-dataset')
         self.assertEqual(ds.path, '/test-dataset')
 
     @mock.patch('solvebio.resource.Vault.all')
     @mock.patch('solvebio.resource.Object.all')
-    @mock.patch('solvebio.resource.Dataset.create')
+    @mock.patch('solvebio.resource.Object.create')
     def test_create_dataset_by_filename(self, DatasetCreate, ObjectAll,
                                         VaultAll):
-        DatasetCreate.side_effect = fake_dataset_create
+        DatasetCreate.side_effect = fake_object_create
         ObjectAll.side_effect = fake_object_all
         VaultAll.side_effect = fake_vault_all
         args = [
@@ -71,7 +70,7 @@ def test_create_dataset_by_filename(self, DatasetCreate, ObjectAll,
             '--metadata', 'TEST2=tag2',
         ]
         ds = main.main(args)
-        self.assertEqual(ds.name, 'test-dataset-filename')
+        self.assertEqual(ds.filename, 'test-dataset-filename')
         self.assertEqual(ds.path, '/test-dataset-filename')
         self.assertEqual(ds.capacity, 'small')
         self.assertEqual(ds.tags, ['tag_test'])
@@ -90,13 +89,13 @@ def _validate_tmpl_fields(self, fields):
 
     @mock.patch('solvebio.resource.Vault.all')
     @mock.patch('solvebio.resource.Object.all')
-    @mock.patch('solvebio.resource.Dataset.create')
+    @mock.patch('solvebio.resource.Object.create')
     @mock.patch('solvebio.resource.DatasetTemplate.create')
     def test_create_dataset_upload_template(self, TmplCreate,
                                             DatasetCreate, ObjectAll,
                                             VaultAll):
         TmplCreate.side_effect = fake_dataset_tmpl_create
-        DatasetCreate.side_effect = fake_dataset_create
+        DatasetCreate.side_effect = fake_object_create
         ObjectAll.side_effect = fake_object_all
         VaultAll.side_effect = fake_vault_all
 
@@ -112,14 +111,14 @@ def test_create_dataset_upload_template(self, TmplCreate,
 
     @mock.patch('solvebio.resource.Vault.all')
     @mock.patch('solvebio.resource.Object.all')
-    @mock.patch('solvebio.resource.Dataset.create')
+    @mock.patch('solvebio.resource.Object.create')
     @mock.patch('solvebio.resource.DatasetTemplate.retrieve')
     @mock.patch('solvebio.resource.DatasetTemplate.create')
     def test_create_dataset_template_id(self, TmplCreate, TmplRetrieve,
                                         DatasetCreate, ObjectAll, VaultAll):
         VaultAll.side_effect = fake_vault_all
         ObjectAll.side_effect = fake_object_all
-        DatasetCreate.side_effect = fake_dataset_create
+        DatasetCreate.side_effect = fake_object_create
         TmplRetrieve.side_effect = fake_dataset_tmpl_retrieve
         TmplCreate.side_effect = fake_dataset_tmpl_create
 
@@ -145,15 +144,15 @@ def test_create_dataset_template_id(self, TmplCreate, TmplRetrieve,
     @mock.patch('solvebio.resource.Vault.all')
     @mock.patch('solvebio.resource.Object.all')
     @mock.patch('solvebio.resource.Object.upload_file')
-    @mock.patch('solvebio.resource.Dataset.create')
+    @mock.patch('solvebio.resource.Object.create')
     @mock.patch('solvebio.resource.DatasetImport.create')
-    def _test_import_file(self, args, DatasetImportCreate, DatasetCreate,
-                          ObjectCreate, ObjectAll, VaultAll, VaultLookup,
+    def _test_import_file(self, args, DatasetImportCreate, ObjectCreate,
+                          UploadFile, ObjectAll, VaultAll, VaultLookup,
                           UploadPath, TmplCreate, TmplRetrieve):
         DatasetImportCreate.side_effect = fake_dataset_import_create
-        DatasetCreate.side_effect = fake_dataset_create
-        ObjectAll.side_effect = fake_object_all
         ObjectCreate.side_effect = fake_object_create
+        UploadFile.side_effect = fake_object_create
+        ObjectAll.side_effect = fake_object_all
         VaultAll.side_effect = fake_vault_all
         UploadPath.side_effect = upload_path
         VaultLookup.side_effect = fake_vault_create
@@ -199,7 +198,7 @@ def test_import_tilde(self):
         ]:
             args = ['import', '--create-dataset', dataset_path, file_]
             imports, ds = self._test_import_file(args)
-            self.assertEqual(ds.name, 'test-dataset')
+            self.assertEqual(ds.filename, 'test-dataset')
             # should be a manifest with a single file
             self.assertEqual(len(imports[0].manifest['files']), 1)