Fix mypy errors in docs/examples/

Also:
- Update examples to use the ``invoke()`` method instead of the
  removed ``run()``.
- Use ``requests`` instead of ``scripts/api/common.py`` from Galaxy.

CHANGELOG.md

@@ -4,6 +4,9 @@
   ``GalaxyClient``, ``GalaxyInstance`` and ``ToolShedInstance`` classes are now
   keyword-only.
 
+* Classes defined in ``bioblend.galaxy.objects.wrappers`` are no more
+  re-exported by ``bioblend.galaxy.objects``.
+
 ### BioBlend v1.2.0 - 2023-06-30
 
 * Dropped support for Galaxy releases 17.09-19.01. Added support for Galaxy

bioblend/galaxy/objects/__init__.py

@@ -1,2 +1,3 @@
 from .galaxy_instance import GalaxyInstance  # noqa: F401
-from .wrappers import *  # noqa: F401,F403
+
+__all__ = ("GalaxyInstance",)

bioblend/galaxy/objects/wrappers.py

@@ -1827,6 +1827,8 @@ class DatasetContainerPreview(Wrapper):
         "deleted",
         "name",
     )
+    deleted: bool
+    name: str
 
 
 class LibraryPreview(DatasetContainerPreview):
@@ -1872,6 +1874,12 @@ class WorkflowPreview(Wrapper):
         "show_in_tool_panel",
         "tags",
     )
+    deleted: bool
+    name: str
+    owner: str
+    published: bool
+    show_in_tool_panel: bool
+    tags: List[str]
 
 
 class InvocationPreview(Wrapper):
@@ -1884,7 +1892,6 @@ class InvocationPreview(Wrapper):
 
     BASE_ATTRS = Wrapper.BASE_ATTRS + (
         "history_id",
-        "id",
         "state",
         "update_time",
         "uuid",

docs/examples/objects/common.py

@@ -1,4 +1,12 @@
-def get_one(iterable):
+from typing import (
+    Iterable,
+    TypeVar,
+)
+
+T = TypeVar("T")
+
+
+def get_one(iterable: Iterable[T]) -> T:
     seq = list(iterable)
     assert len(seq) == 1
     return seq[0]

docs/examples/objects/small.py

@@ -42,13 +42,15 @@
 history_name = "get_col output"
 params = {"Cut1": {"columnList": "c2"}}
 print(f"Running workflow: {wf.name} [{wf.id}]")
-outputs, out_hist = wf.run(input_map, history_name, params=params, wait=True)
+inv = wf.invoke(input_map, params=params, history=history_name, inputs_by="name")
+out_hist = gi.histories.get(inv.history_id)
+inv.wait()
 print("Job has finished")
 assert out_hist.name == history_name
 print(f"Output history: {out_hist.name} [{out_hist.id}]")
 
 # Save results to local disk
-out_ds = get_one([_ for _ in outputs if _.name == "Cut on data 1"])
-with tempfile.NamedTemporaryFile(prefix="bioblend_", delete=False) as f:
-    out_ds.download(f)
+out_ds = get_one(out_hist.get_datasets(name="Cut on data 1"))
+with tempfile.NamedTemporaryFile(prefix="bioblend_", delete=False) as tmp_f:
+    out_ds.download(tmp_f)
 print(f'Output downloaded to "{f.name}"')

docs/examples/objects/w2_bacterial_reseq.py

@@ -56,7 +56,8 @@
 
 # Run the workflow on a new history with the selected datasets as inputs
 
-outputs, out_hist = iw.run(input_map, h, params=params)
+inv = iw.invoke(input_map, params=params, history=h, inputs_by="name")
+out_hist = gi.histories.get(inv.history_id)
 assert out_hist.name == history_name
 
 print(f"Running workflow: {iw.name} [{iw.id}]")

docs/examples/objects/w3_bacterial_denovo.py

@@ -1,6 +1,10 @@
 import json
 import os
 import sys
+from typing import (
+    Any,
+    Dict,
+)
 
 from common import get_one  # noqa:I100,I201
 
@@ -51,7 +55,7 @@
 lengths = {"19", "23", "29"}
 ws_ids = iw.tool_labels_to_ids["velveth"]
 assert len(ws_ids) == len(lengths)
-params = {id_: {"hash_length": v} for id_, v in zip(ws_ids, lengths)}
+params: Dict[str, Any] = {id_: {"hash_length": v} for id_, v in zip(ws_ids, lengths)}
 
 # Set the "ins_length" runtime parameter to the same value for the 3
 # "velvetg" steps
@@ -70,7 +74,8 @@
 
 # Run the workflow on a new history with the selected datasets as inputs
 
-outputs, out_hist = iw.run(input_map, h, params=params)
+inv = iw.invoke(input_map, params=params, history=h, inputs_by="name")
+out_hist = gi.histories.get(inv.history_id)
 assert out_hist.name == history_name
 
 print(f"Running workflow: {iw.name} [{iw.id}]")

docs/examples/objects/w5_galaxy_api.py

@@ -2,61 +2,59 @@
 import os
 import sys
 
+import requests
+
 # This example, provided for comparison with w5_metagenomics.py,
 # contains the code required to run the metagenomics workflow
 # *without* BioBlend.
 
 URL = os.getenv("GALAXY_URL", "https://orione.crs4.it").rstrip("/")
 API_URL = f"{URL}/api"
-API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
-if API_KEY == "YOUR_API_KEY":
+API_KEY = os.getenv("GALAXY_API_KEY")
+if not API_KEY:
     sys.exit("API_KEY not set, see the README.txt file")
-
-# Clone the galaxy git repository and replace
-# YOUR_GALAXY_PATH with the clone's local path in the following code, e.g.:
-#   cd /tmp
-#   git clone https://github.com/galaxyproject/galaxy
-#   GALAXY_PATH = '/tmp/galaxy'
-
-GALAXY_PATH = "YOUR_GALAXY_PATH"
-sys.path.insert(1, os.path.join(GALAXY_PATH, "scripts/api"))
-import common  # noqa: E402,I100,I202
+headers = {"Content-Type": "application/json", "x-api-key": API_KEY}
 
 # Select "W5 - Metagenomics" from published workflows
 
 workflow_name = "W5 - Metagenomics"
-workflows = common.get(API_KEY, f"{API_URL}/workflows?show_published=True")
-w = [_ for _ in workflows if _["published"] and _["name"] == workflow_name]
-assert len(w) == 1
-w = w[0]
+r = requests.get(f"{API_URL}/workflows", params={"show_published": True}, headers=headers)
+workflows = r.json()
+filtered_workflows = [_ for _ in workflows if _["published"] and _["name"] == workflow_name]
+assert len(filtered_workflows) == 1
+w = filtered_workflows[0]
 
 # Import the workflow to user space
 
 data = {"workflow_id": w["id"]}
-iw = common.post(API_KEY, f"{API_URL}/workflows/import", data)
-iw_details = common.get(API_KEY, f"{API_URL}/workflows/{iw['id']}")
+r = requests.post(f"{API_URL}/workflows/import", data=json.dumps(data), headers=headers)
+iw = r.json()
+r = requests.get(f"{API_URL}/workflows/{iw['id']}", headers=headers)
+iw_details = r.json()
 
 # Select the "Orione SupMat" library
 
 library_name = "Orione SupMat"
-libraries = common.get(API_KEY, f"{API_URL}/libraries")
+r = requests.get(f"{API_URL}/libraries", headers=headers)
+libraries = r.json()
 filtered_libraries = [_ for _ in libraries if _["name"] == library_name]
 assert len(filtered_libraries) == 1
 library = filtered_libraries[0]
 
 # Select the "/Metagenomics/MetagenomicsDataset.fq" dataset
 
 ds_name = "/Metagenomics/MetagenomicsDataset.fq"
-contents = common.get(API_KEY, f"{API_URL}/libraries/{library['id']}/contents")
-ld = [_ for _ in contents if _["type"] == "file" and _["name"] == ds_name]
-assert len(ld) == 1
-ld = ld[0]
+r = requests.get(f"{API_URL}/libraries/{library['id']}/contents", headers=headers)
+contents = r.json()
+filtered_contents = [_ for _ in contents if _["type"] == "file" and _["name"] == ds_name]
+assert len(filtered_contents) == 1
+ld = filtered_contents[0]
 
 # Select the blastn step
 
-ws = [_ for _ in iw_details["steps"].values() if _["tool_id"] and "blastn" in _["tool_id"]]
-assert len(ws) == 1
-ws = ws[0]
+filtered_wf_steps = [_ for _ in iw_details["steps"].values() if _["tool_id"] and "blastn" in _["tool_id"]]
+assert len(filtered_wf_steps) == 1
+ws = filtered_wf_steps[0]
 tool_id = ws["tool_id"]
 
 # Get (a copy of) the parameters dict for the selected step
@@ -78,7 +76,8 @@
 input_step_id = iw_details["inputs"].keys()[0]
 data["ds_map"] = {input_step_id: {"src": "ld", "id": ld["id"]}}
 data["history"] = history_name
-r_dict = common.post(API_KEY, f"{API_URL}/workflows", data)
+r = requests.post(f"{API_URL}/workflows", data=json.dumps(data), headers=headers)
+r_dict = r.json()
 
 print(f"Running workflow: {iw['name']} [{iw['id']}]")
 print(f"Output history: {history_name} [{r_dict['history']}]")

docs/examples/objects/w5_metagenomics.py

@@ -52,7 +52,8 @@
 
 params = {tool_id: {"db_opts": json.loads(ws_parameters["db_opts"])}}
 params[tool_id]["db_opts"]["database"] = "16SMicrobial-20131106"
-outputs, out_hist = iw.run(input_map, h, params=params)
+inv = iw.invoke(input_map, params=params, history=h, inputs_by="name")
+out_hist = gi.histories.get(inv.history_id)
 assert out_hist.name == history_name
 
 print(f"Running workflow: {iw.name} [{iw.id}]")

tox.ini

@@ -21,7 +21,7 @@ commands =
     flake8 .
     black --check --diff .
     isort --check --diff .
-    mypy bioblend/
+    mypy bioblend/ docs/examples/
 deps =
     black
     flake8