Merge pull request #1382 from bernt-matthias/type-comparisons

fix type comparisons

planemo/autoupdate.py

@@ -319,7 +319,7 @@ def check_tool_step(step, ts):  # return a dict with current and newest tool ver
             return {}
 
     outdated_tool_dict = {}
-    steps = wf_dict["steps"].values() if type(wf_dict["steps"]) == dict else wf_dict["steps"]
+    steps = wf_dict["steps"].values() if isinstance(wf_dict["steps"], dict) else wf_dict["steps"]
     for step in steps:
         if step.get("type", "tool") == "tool" and not step.get("run", {}).get("class") == "GalaxyWorkflow":
             outdated_tool_dict.update(check_tool_step(step, ts))

planemo/galaxy/workflows.py

@@ -300,7 +300,7 @@ def rewrite_job_file(input_file, output_file, job):
     with open(input_file) as f:
         job_contents = yaml.safe_load(f)
         for job_input, job_input_name in job_contents.items():
-            if type(job[job_input]) == dict:  # dataset or collection
+            if isinstance(job[job_input], dict):  # dataset or collection
                 job_contents[job_input] = {"class": job_input_name["class"], "galaxy_id": job[job_input]["id"]}
             # else: presumably a parameter, no need to modify
     with open(output_file, "w") as f:

planemo/workflow_lint.py

@@ -191,12 +191,12 @@ def _lint_best_practices(path: str, lint_context: WorkflowLintContext) -> None:
     """
 
     def check_json_for_untyped_params(j):
-        values = j if type(j) == list else j.values()
+        values = j.values() if isinstance(j, dict) else j
         for value in values:
             if type(value) in [list, dict, OrderedDict]:
                 if check_json_for_untyped_params(value):
                     return True
-            elif type(value) == str:
+            elif isinstance(value, str):
                 if re.match(r"\$\{.+?\}", value):
                     return True
         return False
@@ -345,7 +345,7 @@ def _tst_input_valid(
     input_def: Dict[str, Any],
     lint_context: WorkflowLintContext,
 ) -> bool:
-    if type(input_def) == dict:  # else assume it is a parameter
+    if isinstance(input_def, dict):  # else assume it is a parameter
         clazz = input_def.get("class")
         if clazz == "File":
             input_path = input_def.get("path")