Add type annotations, some small fixes

bioblend/_tests/TestGalaxyObjects.py

@@ -187,7 +187,18 @@ def test_kwargs(self):
             w.parent = 0
 
 
-class TestWorkflow(unittest.TestCase):
+@test_util.skip_unless_galaxy()
+class GalaxyObjectsTestBase(unittest.TestCase):
+    gi: galaxy_instance.GalaxyInstance
+
+    @classmethod
+    def setUpClass(cls):
+        galaxy_key = os.environ["BIOBLEND_GALAXY_API_KEY"]
+        galaxy_url = os.environ["BIOBLEND_GALAXY_URL"]
+        cls.gi = galaxy_instance.GalaxyInstance(galaxy_url, galaxy_key)
+
+
+class TestWorkflow(GalaxyObjectsTestBase):
     def setUp(self):
         self.wf = wrappers.Workflow(SAMPLE_WF_DICT)
 
@@ -236,8 +247,10 @@ def test_taint(self):
         self.assertTrue(self.wf.is_modified)
 
     def test_input_map(self):
-        hda = wrappers.HistoryDatasetAssociation({"id": "hda_id"}, container="mock_history")
-        ldda = wrappers.LibraryDatasetDatasetAssociation({"id": "ldda_id"}, container="mock_library")
+        history = wrappers.History({}, gi=self.gi)
+        library = wrappers.Library({}, gi=self.gi)
+        hda = wrappers.HistoryDatasetAssociation({"id": "hda_id"}, container=history, gi=self.gi)
+        ldda = wrappers.LibraryDatasetDatasetAssociation({"id": "ldda_id"}, container=library, gi=self.gi)
         input_map = self.wf._convert_input_map({"0": hda, "1": ldda, "2": {"id": "hda2_id", "src": "hda"}})
         self.assertEqual(
             input_map,
@@ -249,20 +262,12 @@ def test_input_map(self):
         )
 
 
-@test_util.skip_unless_galaxy()
-class GalaxyObjectsTestBase(unittest.TestCase):
-    def setUp(self):
-        galaxy_key = os.environ["BIOBLEND_GALAXY_API_KEY"]
-        galaxy_url = os.environ["BIOBLEND_GALAXY_URL"]
-        self.gi = galaxy_instance.GalaxyInstance(galaxy_url, galaxy_key)
-
-
 @test_util.skip_unless_galaxy("release_19.09")
 class TestInvocation(GalaxyObjectsTestBase):
     @classmethod
     def setUpClass(cls):
-        super().setUp(cls)
-        cls.inv = wrappers.Invocation(SAMPLE_INV_DICT)
+        super().setUpClass()
+        cls.inv = wrappers.Invocation(SAMPLE_INV_DICT, gi=cls.gi)
         with open(SAMPLE_FN) as f:
             cls.workflow = cls.gi.workflows.import_new(f.read())
         path_pause = test_util.get_abspath(os.path.join("data", "test_workflow_pause.ga"))
@@ -394,7 +399,7 @@ def _obj_invoke_workflow(self):
 class TestObjInvocationClient(GalaxyObjectsTestBase):
     @classmethod
     def setUpClass(cls):
-        super().setUp(cls)
+        super().setUpClass()
         with open(SAMPLE_FN) as f:
             cls.workflow = cls.gi.workflows.import_new(f.read())
         cls.history = cls.gi.histories.create(name="TestGalaxyObjInvocationClient")

bioblend/galaxy/client.py

@@ -6,6 +6,7 @@
 """
 
 import time
+import typing
 from typing import Optional
 
 import requests
@@ -16,10 +17,14 @@
 # ConnectionError class was originally defined here
 from bioblend import ConnectionError  # noqa: I202
 
+if typing.TYPE_CHECKING:
+    from bioblend.galaxy import GalaxyInstance
+
 
 class Client:
     # The `module` attribute needs to be defined in subclasses
     module: str
+    gi: "GalaxyInstance"
 
     # Class variables that configure GET request retries.  Note that since these
     # are class variables their values are shared by all Client instances --
@@ -69,7 +74,7 @@ def set_get_retry_delay(cls, value):
         cls._get_retry_delay = value
         return cls
 
-    def __init__(self, galaxy_instance):
+    def __init__(self, galaxy_instance: "GalaxyInstance"):
         """
         A generic Client interface defining the common fields.
 

bioblend/galaxy/objects/client.py

@@ -6,6 +6,7 @@
 """
 import abc
 import json
+import typing
 from collections.abc import (
     Mapping,
     Sequence,
@@ -15,9 +16,12 @@
 import bioblend
 from . import wrappers
 
+if typing.TYPE_CHECKING:
+    from .galaxy_instance import GalaxyInstance
+
 
 class ObjClient(abc.ABC):
-    def __init__(self, obj_gi):
+    def __init__(self, obj_gi: "GalaxyInstance"):
         self.obj_gi = obj_gi
         self.gi = self.obj_gi.gi
         self.log = bioblend.log
@@ -100,6 +104,13 @@ def _get_container(self, id_, ctype):
         c_infos = [ctype.CONTENT_INFO_TYPE(_) for _ in c_infos]
         return ctype(cdict, content_infos=c_infos, gi=self.obj_gi)
 
+    @abc.abstractmethod
+    def get(self, id_: str) -> wrappers.DatasetContainer:
+        """
+        Retrieve the dataset corresponding to the given id.
+        """
+        pass
+
 
 class ObjLibraryClient(ObjDatasetContainerClient):
     """
@@ -120,7 +131,7 @@ def create(self, name, description=None, synopsis=None):
         lib_info = self._get_dict("create_library", res)
         return self.get(lib_info["id"])
 
-    def get(self, id_):
+    def get(self, id_) -> wrappers.Library:
         """
         Retrieve the data library corresponding to the given id.
 
@@ -188,7 +199,7 @@ def create(self, name=None):
         hist_info = self._get_dict("create_history", res)
         return self.get(hist_info["id"])
 
-    def get(self, id_):
+    def get(self, id_) -> wrappers.History:
         """
         Retrieve the history corresponding to the given id.
 
@@ -279,7 +290,7 @@ def import_shared(self, id_):
         wf_info = self.gi.workflows.import_shared_workflow(id_)
         return self.get(wf_info["id"])
 
-    def get(self, id_):
+    def get(self, id_) -> wrappers.Workflow:
         """
         Retrieve the workflow corresponding to the given id.
 
@@ -349,7 +360,7 @@ def get_previews(self) -> List[wrappers.InvocationPreview]:
         :param: previews of invocations
         """
         inv_list = self.gi.invocations.get_invocations()
-        return [wrappers.InvocationPreview(inv_dict, self.obj_gi) for inv_dict in inv_list]
+        return [wrappers.InvocationPreview(inv_dict, gi=self.obj_gi) for inv_dict in inv_list]
 
     def list(self, workflow=None, history=None, include_terminal=True, limit=None) -> List[wrappers.Invocation]:
         """
@@ -390,7 +401,7 @@ class ObjToolClient(ObjClient):
     Interacts with Galaxy tools.
     """
 
-    def get(self, id_, io_details=False, link_details=False):
+    def get(self, id_, io_details=False, link_details=False) -> wrappers.Tool:
         """
         Retrieve the tool corresponding to the given id.
 
@@ -454,7 +465,7 @@ class ObjJobClient(ObjClient):
     Interacts with Galaxy jobs.
     """
 
-    def get(self, id_, full_details=False):
+    def get(self, id_, full_details=False) -> wrappers.Job:
         """
         Retrieve the job corresponding to the given id.
 
@@ -488,7 +499,7 @@ class ObjDatasetClient(ObjClient):
     Interacts with Galaxy datasets.
     """
 
-    def get(self, id_: str, hda_ldda: str = "hda"):
+    def get(self, id_: str, hda_ldda: str = "hda") -> wrappers.Dataset:
         """
         Retrieve the dataset corresponding to the given id.
 
@@ -522,7 +533,7 @@ class ObjDatasetCollectionClient(ObjClient):
     Interacts with Galaxy dataset collections.
     """
 
-    def get(self, id_: str):
+    def get(self, id_: str) -> wrappers.HistoryDatasetCollectionAssociation:
         """
         Retrieve the dataset collection corresponding to the given id.