more type checking

Makefile

@@ -23,7 +23,7 @@
 MODULE1=wes_client
 MODULE2=wes_service
 PACKAGE=wes-service
-EXTRAS=[toil,arvados]
+EXTRAS=[toil]
 
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.

cwl_flask.py

@@ -7,28 +7,32 @@
 import threading
 import time
 import copy
+import shutil
+from typing import List, Dict, Any, Generator, Tuple
+
+import werkzeug.wrappers.response
 
 app = Flask(__name__)
 
 jobs_lock = threading.Lock()
-jobs = []
+jobs: List["Job"] = []
 
 
 class Job(threading.Thread):
-    def __init__(self, jobid, path, inputobj):
+    def __init__(self, jobid: int, path: str, inputobj: bytes) -> None:
         super().__init__()
         self.jobid = jobid
         self.path = path
         self.inputobj = inputobj
         self.updatelock = threading.Lock()
         self.begin()
 
-    def begin(self):
+    def begin(self) -> None:
         loghandle, self.logname = tempfile.mkstemp()
         with self.updatelock:
             self.outdir = tempfile.mkdtemp()
             self.proc = subprocess.Popen(
-                ["cwl-runner", self.path, "-"],
+                [shutil.which("cwl-runner") or "cwl-runner", self.path, "-"],
                 stdin=subprocess.PIPE,
                 stdout=subprocess.PIPE,
                 stderr=loghandle,
@@ -44,7 +48,7 @@ def begin(self):
                 "output": None,
             }
 
-    def run(self):
+    def run(self) -> None:
         self.stdoutdata, self.stderrdata = self.proc.communicate(self.inputobj)
         if self.proc.returncode == 0:
             outobj = yaml.load(self.stdoutdata, Loader=yaml.FullLoader)
@@ -55,31 +59,31 @@ def run(self):
             with self.updatelock:
                 self.status["state"] = "Failed"
 
-    def getstatus(self):
+    def getstatus(self) -> Dict[str, Any]:
         with self.updatelock:
             return self.status.copy()
 
-    def cancel(self):
+    def cancel(self) -> None:
         if self.status["state"] == "Running":
             self.proc.send_signal(signal.SIGQUIT)
             with self.updatelock:
                 self.status["state"] = "Canceled"
 
-    def pause(self):
+    def pause(self) -> None:
         if self.status["state"] == "Running":
             self.proc.send_signal(signal.SIGTSTP)
             with self.updatelock:
                 self.status["state"] = "Paused"
 
-    def resume(self):
+    def resume(self) -> None:
         if self.status["state"] == "Paused":
             self.proc.send_signal(signal.SIGCONT)
             with self.updatelock:
                 self.status["state"] = "Running"
 
 
 @app.route("/run", methods=["POST"])
-def runworkflow():
+def runworkflow() -> werkzeug.wrappers.response.Response:
     path = request.args["wf"]
     with jobs_lock:
         jobid = len(jobs)
@@ -90,7 +94,7 @@ def runworkflow():
 
 
 @app.route("/jobs/<int:jobid>", methods=["GET", "POST"])
-def jobcontrol(jobid):
+def jobcontrol(jobid: int) -> Tuple[str, int]:
     with jobs_lock:
         job = jobs[jobid]
     if request.method == "POST":
@@ -104,10 +108,10 @@ def jobcontrol(jobid):
                 job.resume()
 
     status = job.getstatus()
-    return json.dumps(status, indent=4), 200, ""
+    return json.dumps(status, indent=4), 200
 
 
-def logspooler(job):
+def logspooler(job: Job) -> Generator[str, None, None]:
     with open(job.logname) as f:
         while True:
             r = f.read(4096)
@@ -121,18 +125,18 @@ def logspooler(job):
 
 
 @app.route("/jobs/<int:jobid>/log", methods=["GET"])
-def getlog(jobid):
+def getlog(jobid: int) -> Response:
     with jobs_lock:
         job = jobs[jobid]
     return Response(logspooler(job))
 
 
 @app.route("/jobs", methods=["GET"])
-def getjobs():
+def getjobs() -> Response:
     with jobs_lock:
         jobscopy = copy.copy(jobs)
 
-    def spool(jc):
+    def spool(jc: List[Job]) -> Generator[str, None, None]:
         yield "["
         first = True
         for j in jc:

cwltool_stream.py

@@ -4,36 +4,33 @@
 import cwltool.main
 import tempfile
 import logging
-import StringIO
+from io import StringIO
 import json
+from typing import List, Union
 
 _logger = logging.getLogger("cwltool")
 _logger.setLevel(logging.ERROR)
 
 
-def main(args=None):
-    if args is None:
-        args = sys.argv[1:]
-
+def main(args: List[str] = sys.argv[1:]) -> int:
     if len(args) == 0:
         print("Workflow must be on command line")
         return 1
 
-    parser = cwltool.main.arg_parser()
+    parser = cwltool.argparser.arg_parser()
     parsedargs = parser.parse_args(args)
 
-    a = True
+    a: Union[bool, str] = True
     while a:
-        a = True
         msg = ""
         while a and a != "\n":
             a = sys.stdin.readline()
             msg += a
 
         outdir = tempfile.mkdtemp("", parsedargs.tmp_outdir_prefix)
 
-        t = StringIO.StringIO(msg)
-        err = StringIO.StringIO()
+        t = StringIO(msg)
+        err = StringIO()
         if (
             cwltool.main.main(
                 ["--outdir=" + outdir] + args + ["-"], stdin=t, stderr=err
@@ -43,6 +40,8 @@ def main(args=None):
             sys.stdout.write(json.dumps({"cwl:error": err.getvalue()}))
         sys.stdout.write("\n\n")
         sys.stdout.flush()
+        a = True
+    return 0
 
 
 if __name__ == "__main__":

mypy-requirements.txt

@@ -1 +1,4 @@
 mypy==1.10.1
+types-PyYAML
+types-requests
+types-setuptools

mypy.ini

@@ -0,0 +1,8 @@
+[mypy]
+show_error_context = true
+show_column_numbers = true
+show_error_codes = true
+pretty = true
+strict = true
+[mypy-ruamel.*]
+ignore_errors = True

test/test_client_util.py

@@ -11,7 +11,7 @@
 
 
 class IntegrationTest(unittest.TestCase):
-    def setUp(self):
+    def setUp(self) -> None:
         dirname, filename = os.path.split(os.path.abspath(__file__))
         self.testdata_dir = dirname + "data"
         self.local = {
@@ -37,26 +37,28 @@ def setUp(self):
             "pyWithPrefix": ("3", "PY"),
         }
 
-    def tearDown(self):
+    def tearDown(self) -> None:
         unittest.TestCase.tearDown(self)
 
-    def test_expand_globs(self):
+    def test_expand_globs(self) -> None:
         """Asserts that wes_client.expand_globs() sees the same files in the cwd as 'ls'."""
         files = subprocess.check_output(["ls", "-1", "."])
 
         # python 2/3 bytestring/utf-8 compatibility
         if isinstance(files, str):
-            files = files.split("\n")
+            files2 = files.split("\n")
         else:
-            files = files.decode("utf-8").split("\n")
+            files2 = files.decode("utf-8").split("\n")
 
-        if "" in files:
-            files.remove("")
-        files = ["file://" + os.path.abspath(f) for f in files]
+        if "" in files2:
+            files2.remove("")
+        files2 = ["file://" + os.path.abspath(f) for f in files2]
         glob_files = expand_globs("*")
-        assert set(files) == glob_files, "\n" + str(set(files)) + "\n" + str(glob_files)
+        assert set(files2) == glob_files, (
+            "\n" + str(set(files2)) + "\n" + str(glob_files)
+        )
 
-    def testSupportedFormatChecking(self):
+    def testSupportedFormatChecking(self) -> None:
         """
         Check that non-wdl, -python, -cwl files are rejected.
 
@@ -75,7 +77,7 @@ def testSupportedFormatChecking(self):
                 with self.assertRaises(TypeError):
                     wf_info(location)
 
-    def testFileLocationChecking(self):
+    def testFileLocationChecking(self) -> None:
         """
         Check that the function rejects unsupported file locations.