pyupgrade for Python 3.6

Author: mr-c

cwl_flask.py

@@ -16,7 +16,7 @@
 
 class Job(threading.Thread):
     def __init__(self, jobid, path, inputobj):
-        super(Job, self).__init__()
+        super().__init__()
         self.jobid = jobid
         self.path = path
         self.inputobj = inputobj
@@ -108,7 +108,7 @@ def jobcontrol(jobid):
 
 
 def logspooler(job):
-    with open(job.logname, "r") as f:
+    with open(job.logname) as f:
         while True:
             r = f.read(4096)
             if r:

setup.py

@@ -20,7 +20,7 @@
     url="https://github.com/common-workflow-language/cwltool-service",
     download_url="https://github.com/common-workflow-language/cwltool-service",
     license="Apache 2.0",
-    python_requires="~=3.5",
+    python_requires="~=3.6",
     setup_requires=["pytest-runner"],
     tests_require=["pytest"],
     packages=["wes_service", "wes_client"],
@@ -53,6 +53,7 @@
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
         "Topic :: Software Development :: Libraries :: Python Modules",
     ],
 )

wes_client/util.py

@@ -196,7 +196,7 @@ def wes_reponse(postresult):
     return json.loads(postresult.text)
 
 
-class WESClient(object):
+class WESClient:
     def __init__(self, service):
         self.auth = service["auth"]
         self.proto = service["proto"]
@@ -216,7 +216,7 @@ def get_service_info(self):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get(
-            "%s://%s/ga4gh/wes/v1/service-info" % (self.proto, self.host),
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/service-info",
             headers=self.auth,
         )
         return wes_reponse(postresult)
@@ -234,7 +234,7 @@ def list_runs(self):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get(
-            "%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host), headers=self.auth
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/runs", headers=self.auth
         )
         return wes_reponse(postresult)
 
@@ -254,7 +254,7 @@ def run(self, wf, jsonyaml, attachments):
         attachments = list(expand_globs(attachments))
         parts = build_wes_request(wf, jsonyaml, attachments)
         postresult = requests.post(
-            "%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/runs",
             files=parts,
             headers=self.auth,
         )
@@ -271,7 +271,7 @@ def cancel(self, run_id):
         :return: The body of the delete result as a dictionary.
         """
         postresult = requests.post(
-            "%s://%s/ga4gh/wes/v1/runs/%s/cancel" % (self.proto, self.host, run_id),
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/runs/{run_id}/cancel",
             headers=self.auth,
         )
         return wes_reponse(postresult)
@@ -287,7 +287,7 @@ def get_run_log(self, run_id):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get(
-            "%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/runs/{run_id}",
             headers=self.auth,
         )
         return wes_reponse(postresult)
@@ -303,7 +303,7 @@ def get_run_status(self, run_id):
         :return: The body of the get result as a dictionary.
         """
         postresult = requests.get(
-            "%s://%s/ga4gh/wes/v1/runs/%s/status" % (self.proto, self.host, run_id),
+            f"{self.proto}://{self.host}/ga4gh/wes/v1/runs/{run_id}/status",
             headers=self.auth,
         )
         return wes_reponse(postresult)

wes_client/wes_client_main.py

@@ -71,7 +71,7 @@ def main(argv=sys.argv[1:]):
 
     if args.version:
         pkg = pkg_resources.require("wes_service")
-        print(u"%s %s" % (sys.argv[0], pkg[0].version))
+        print(f"{sys.argv[0]} {pkg[0].version}")
         exit(0)
 
     auth = {}

wes_service/arvados_wes.py

@@ -175,7 +175,7 @@ def invoke_cwl_runner(
 
                 self.log_for_run(
                     cr_uuid,
-                    "Contents of %s:\n%s" % (tempdir, msg),
+                    f"Contents of {tempdir}:\n{msg}",
                     env["ARVADOS_API_TOKEN"],
                 )
 
@@ -367,7 +367,7 @@ def GetRunLog(self, run_id):
 
                 def keepref(d):
                     if isinstance(d, dict) and "location" in d:
-                        d["location"] = "%sc=%s/_/%s" % (
+                        d["location"] = "{}c={}/_/{}".format(
                             api._resourceDesc["keepWebServiceUrl"],
                             c.portable_data_hash(),
                             d["location"],
@@ -395,12 +395,12 @@ def log_object(cr):
                 "exit_code": containerlog["exit_code"] or 0,
             }
             if containerlog["log"]:
-                r["stdout_keep"] = "%sc=%s/_/%s" % (
+                r["stdout_keep"] = "{}c={}/_/{}".format(
                     api._resourceDesc["keepWebServiceUrl"],
                     containerlog["log"],
                     "stdout.txt",
                 )  # NOQA
-                r["stderr_keep"] = "%sc=%s/_/%s" % (
+                r["stderr_keep"] = "{}c={}/_/{}".format(
                     api._resourceDesc["keepWebServiceUrl"],
                     containerlog["log"],
                     "stderr.txt",

wes_service/cwl_runner.py

@@ -6,9 +6,9 @@
 from wes_service.util import WESBackend
 
 
-class Workflow(object):
+class Workflow:
     def __init__(self, run_id):
-        super(Workflow, self).__init__()
+        super().__init__()
         self.run_id = run_id
         self.workdir = os.path.join(os.getcwd(), "workflows", self.run_id)
         self.outdir = os.path.join(self.workdir, "outdir")
@@ -94,7 +94,7 @@ def getstate(self):
             with open(exitcode_file) as f:
                 exit_code = int(f.read())
         elif os.path.exists(pid_file):
-            with open(pid_file, "r") as pid:
+            with open(pid_file) as pid:
                 pid = int(pid.read())
             try:
                 (_pid, exit_status) = os.waitpid(pid, os.WNOHANG)
@@ -122,16 +122,16 @@ def getstatus(self):
     def getlog(self):
         state, exit_code = self.getstate()
 
-        with open(os.path.join(self.workdir, "request.json"), "r") as f:
+        with open(os.path.join(self.workdir, "request.json")) as f:
             request = json.load(f)
 
-        with open(os.path.join(self.workdir, "stderr"), "r") as f:
+        with open(os.path.join(self.workdir, "stderr")) as f:
             stderr = f.read()
 
         outputobj = {}
         if state == "COMPLETE":
             output_path = os.path.join(self.workdir, "cwl.output.json")
-            with open(output_path, "r") as outputtemp:
+            with open(output_path) as outputtemp:
                 outputobj = json.load(outputtemp)
 
         return {

wes_service/toil_wes.py

@@ -12,15 +12,15 @@
 logging.basicConfig(level=logging.INFO)
 
 
-class ToilWorkflow(object):
+class ToilWorkflow:
     def __init__(self, run_id):
         """
         Represents a toil workflow.
 
         :param str run_id: A uuid string.  Used to name the folder that contains
             all of the files containing this particular workflow instance's information.
         """
-        super(ToilWorkflow, self).__init__()
+        super().__init__()
         self.run_id = run_id
 
         self.workdir = os.path.join(os.getcwd(), "workflows", self.run_id)
@@ -135,17 +135,17 @@ def cancel(self):
 
     def fetch(self, filename):
         if os.path.exists(filename):
-            with open(filename, "r") as f:
+            with open(filename) as f:
                 return f.read()
         return ""
 
     def getlog(self):
         state, exit_code = self.getstate()
 
-        with open(self.request_json, "r") as f:
+        with open(self.request_json) as f:
             request = json.load(f)
 
-        with open(self.jobstorefile, "r") as f:
+        with open(self.jobstorefile) as f:
             self.jobstore = f.read()
 
         stderr = self.fetch(self.errfile)
@@ -269,7 +269,7 @@ def getstate(self):
 
         # TODO: Query with "toil status"
         completed = False
-        with open(self.errfile, "r") as f:
+        with open(self.errfile) as f:
             for line in f:
                 if "Traceback (most recent call last)" in line:
                     logging.info("Workflow " + self.run_id + ": EXECUTOR_ERROR")

wes_service/util.py

@@ -18,7 +18,7 @@ def visit(d, op):
             visit(i, op)
 
 
-class WESBackend(object):
+class WESBackend:
     """Stores and retrieves options.  Intended to be inherited."""
 
     def __init__(self, opts):
@@ -64,7 +64,7 @@ def collect_attachments(self, run_id=None):
                             os.makedirs(os.path.dirname(dest))
                         self.log_for_run(
                             run_id,
-                            "Staging attachment '%s' to '%s'" % (v.filename, dest),
+                            f"Staging attachment '{v.filename}' to '{dest}'",
                         )
                         v.save(dest)
                         has_attachments = True
@@ -77,7 +77,7 @@ def collect_attachments(self, run_id=None):
                     else:
                         body[k] = v.read().decode()
             except Exception as e:
-                raise ValueError("Error reading parameter '%s': %s" % (k, e))
+                raise ValueError(f"Error reading parameter '{k}': {e}")
         for k, ls in connexion.request.form.lists():
             try:
                 for v in ls:
@@ -88,7 +88,7 @@ def collect_attachments(self, run_id=None):
                     else:
                         body[k] = v
             except Exception as e:
-                raise ValueError("Error reading parameter '%s': %s" % (k, e))
+                raise ValueError(f"Error reading parameter '{k}': {e}")
 
         if "workflow_url" in body:
             if ":" not in body["workflow_url"]:

wes_service/wes_service_main.py

@@ -19,7 +19,7 @@ def setup(args=None):
     configfile = "config.yml"
     if os.path.isfile(configfile):
         logging.info("Loading %s", configfile)
-        with open(configfile, "r") as f:
+        with open(configfile) as f:
             config = ruamel.yaml.safe_load(f)
         for c in config:
             setattr(args, c, config[c])
@@ -69,7 +69,7 @@ def main(argv=sys.argv[1:]):
 
     if args.version:
         pkg = pkg_resources.require("wes_service")
-        print(u"%s %s" % (sys.argv[0], pkg[0].version))
+        print(f"{sys.argv[0]} {pkg[0].version}")
         exit(0)
 
     app = setup(args)