Merge cf3e623 into da7c035

WDL/CLI.py

@@ -428,7 +428,7 @@ def runner(
         (k, kwargs[k]) for k in ["copy_input_files", "run_dir", "runtime_cpu_max", "as_me"]
     )
     if runtime_memory_max:
-        run_kwargs["runtime_memory_max"] = parse_byte_size(runtime)
+        run_kwargs["runtime_memory_max"] = parse_byte_size(runtime_memory_max)
     if runtime_defaults:
         if runtime_defaults.lstrip()[0] == "{":
             run_kwargs["runtime_defaults"] = json.loads(runtime_defaults)
@@ -943,7 +943,7 @@ def cromwell(
 
     # launch Cromwell
     jarpath = ensure_cromwell_jar(jarfile)
-    cromwell_cmd = ["java", "-DLOG_LEVEL=warn", "-DLOG_MODE=pretty"]
+    cromwell_cmd = ["java", "-DLOG_LEVEL=info", "-DLOG_MODE=pretty"]
     cromwell_cmd.extend([config_setting] if config_setting else [])
     cromwell_cmd.extend(
         [

WDL/Expr.py

@@ -300,7 +300,9 @@ def _eval(
         if isinstance(v, Value.String):
             return v
         if isinstance(v, Value.Array):
-            return Value.String(self.options["sep"].join(str(item.value) for item in v.value))
+            return Value.String(
+                self.options["sep"].join(item.coerce(Type.String()).value for item in v.value)
+            )
         if v == Value.Boolean(True) and "true" in self.options:
             return Value.String(self.options["true"])
         if v == Value.Boolean(False) and "false" in self.options:

WDL/Value.py

@@ -295,10 +295,11 @@ def coerce(self, desired_type: Optional[Type.Base] = None) -> Base:
         if desired_type and not desired_type.optional and not isinstance(desired_type, Type.Any):
             # normally the typechecker should prevent this, but it might have
             # had check_quant=False
+            if isinstance(desired_type, Type.String):
+                return String("", self.expr)
             if self.expr:
                 raise Error.NullValue(self.expr)
-            else:
-                raise Error.InputError("'None' for non-optional input/declaration")
+            raise Error.InputError("'None' for non-optional input/declaration")
         return self
 
     @property

tests/test_5stdlib.py

@@ -409,13 +409,15 @@ def test_concat(self):
                 echo ~{foo + none + bar}
                 echo ~{foo + bar + none}
                 echo ~{foo + bar + i_none}
+                echo ~{sep='::' [foo,bar,none]}
+                echo ~{sep='::' [foo,none,bar]}
             }
             output {
                 String s = read_string(stdout())
             }
         }
         """)
-        self.assertEqual(outputs["s"], "foobar\nfoobar42\n\n\n\n\n")
+        self.assertEqual(outputs["s"], "foobar\nfoobar42\n\n\n\n\n\nfoo::bar::\nfoo::::bar")
 
     def test_read(self):
         with open(os.path.join(self._dir, "strings.txt"), "w") as outfile: