Drop "Atomic" types in favor of recursive typedefs

common-workflow-language · Nov 15, 2023 · 641de7a · 641de7a
1 parent 1e35dc4
commit 641de7a
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Showing 4 changed files with 17 additions and 33 deletions.
diff --git a/cwltool/checker.py b/cwltool/checker.py
@@ -21,7 +21,7 @@
 from .errors import WorkflowException
 from .loghandler import _logger
 from .process import shortname
-from .utils import CWLObjectType, CWLOutputAtomType, CWLOutputType, SinkType, aslist
+from .utils import CWLObjectType, CWLOutputType, SinkType, aslist
 
 
 def _get_type(tp):
@@ -90,8 +90,8 @@ def can_assign_src_to_sink(src: SinkType, sink: Optional[SinkType], strict: bool
             return False
         if src["type"] == "array" and sink["type"] == "array":
             return can_assign_src_to_sink(
-                cast(MutableSequence[CWLOutputAtomType], src["items"]),
-                cast(MutableSequence[CWLOutputAtomType], sink["items"]),
+                cast(MutableSequence[CWLOutputType], src["items"]),
+                cast(MutableSequence[CWLOutputType], sink["items"]),
                 strict,
             )
         if src["type"] == "record" and sink["type"] == "record":

diff --git a/cwltool/main.py b/cwltool/main.py
@@ -105,7 +105,6 @@
 from .utils import (
     DEFAULT_TMP_PREFIX,
     CWLObjectType,
-    CWLOutputAtomType,
     CWLOutputType,
     HasReqsHints,
     adjustDirObjs,
@@ -289,7 +288,7 @@ def realize_input_schema(
                 _, input_type_name = entry["type"].split("#")
                 if input_type_name in schema_defs:
                     entry["type"] = cast(
-                        CWLOutputAtomType,
+                        CWLOutputType,
                         realize_input_schema(
                             cast(
                                 MutableSequence[Union[str, CWLObjectType]],
@@ -300,29 +299,29 @@ def realize_input_schema(
                     )
             if isinstance(entry["type"], MutableSequence):
                 entry["type"] = cast(
-                    CWLOutputAtomType,
+                    CWLOutputType,
                     realize_input_schema(
                         cast(MutableSequence[Union[str, CWLObjectType]], entry["type"]),
                         schema_defs,
                     ),
                 )
             if isinstance(entry["type"], Mapping):
                 entry["type"] = cast(
-                    CWLOutputAtomType,
+                    CWLOutputType,
                     realize_input_schema([cast(CWLObjectType, entry["type"])], schema_defs),
                 )
             if entry["type"] == "array":
                 items = entry["items"] if not isinstance(entry["items"], str) else [entry["items"]]
                 entry["items"] = cast(
-                    CWLOutputAtomType,
+                    CWLOutputType,
                     realize_input_schema(
                         cast(MutableSequence[Union[str, CWLObjectType]], items),
                         schema_defs,
                     ),
                 )
             if entry["type"] == "record":
                 entry["fields"] = cast(
-                    CWLOutputAtomType,
+                    CWLOutputType,
                     realize_input_schema(
                         cast(MutableSequence[Union[str, CWLObjectType]], entry["fields"]),
                         schema_defs,
@@ -612,7 +611,7 @@ def loadref(base: str, uri: str) -> Union[CommentedMap, CommentedSeq, str, None]
         nestdirs=nestdirs,
     )
     if sfs is not None:
-        deps["secondaryFiles"] = cast(MutableSequence[CWLOutputAtomType], mergedirs(sfs))
+        deps["secondaryFiles"] = cast(MutableSequence[CWLOutputType], mergedirs(sfs))
 
     return deps
 

diff --git a/cwltool/process.py b/cwltool/process.py
@@ -61,7 +61,6 @@
 from .update import INTERNAL_VERSION, ORDERED_VERSIONS, ORIGINAL_CWLVERSION
 from .utils import (
     CWLObjectType,
-    CWLOutputAtomType,
     CWLOutputType,
     HasReqsHints,
     JobsGeneratorType,
@@ -1146,7 +1145,7 @@ def mergedirs(
     for e in ents.values():
         if e["class"] == "Directory" and "listing" in e:
             e["listing"] = cast(
-                MutableSequence[CWLOutputAtomType],
+                MutableSequence[CWLOutputType],
                 mergedirs(cast(List[CWLObjectType], e["listing"])),
             )
     r.extend(ents.values())
@@ -1206,7 +1205,7 @@ def scandeps(
                     deps["listing"] = doc["listing"]
                 if doc["class"] == "File" and "secondaryFiles" in doc:
                     deps["secondaryFiles"] = cast(
-                        CWLOutputAtomType,
+                        CWLOutputType,
                         scandeps(
                             base,
                             cast(
@@ -1290,7 +1289,7 @@ def scandeps(
                         )
                         if sf:
                             deps2["secondaryFiles"] = cast(
-                                MutableSequence[CWLOutputAtomType], mergedirs(sf)
+                                MutableSequence[CWLOutputType], mergedirs(sf)
                             )
                         if nestdirs:
                             deps2 = nestdir(base, deps2)

diff --git a/cwltool/utils.py b/cwltool/utils.py
@@ -67,27 +67,14 @@
 
 processes_to_kill: Deque["subprocess.Popen[str]"] = collections.deque()
 
-CWLOutputAtomType = Union[
-    None,
-    bool,
-    str,
-    int,
-    float,
-    MutableSequence[
-        Union[None, bool, str, int, float, MutableSequence[Any], MutableMapping[str, Any]]
-    ],
-    MutableMapping[
-        str,
-        Union[None, bool, str, int, float, MutableSequence[Any], MutableMapping[str, Any]],
-    ],
-]
 CWLOutputType = Union[
+    None,
     bool,
     str,
     int,
     float,
-    MutableSequence[CWLOutputAtomType],
-    MutableMapping[str, CWLOutputAtomType],
+    MutableSequence["CWLOutputType"],
+    MutableMapping[str, "CWLOutputType"],
 ]
 CWLObjectType = MutableMapping[str, Optional[CWLOutputType]]
 """Typical raw dictionary found in lightly parsed CWL."""
@@ -103,8 +90,7 @@
 DirectoryType = TypedDict(
     "DirectoryType", {"class": str, "listing": List[CWLObjectType], "basename": str}
 )
-JSONAtomType = Union[Dict[str, Any], List[Any], str, int, float, bool, None]
-JSONType = Union[Dict[str, JSONAtomType], List[JSONAtomType], str, int, float, bool, None]
+JSONType = Union[Dict[str, "JSONType"], List["JSONType"], str, int, float, bool, None]
 
 
 class WorkflowStateItem(NamedTuple):
@@ -297,7 +283,7 @@ def get_listing(fs_access: "StdFsAccess", rec: CWLObjectType, recursive: bool =
         return
     if "listing" in rec:
         return
-    listing: List[CWLOutputAtomType] = []
+    listing: List[CWLOutputType] = []
     loc = cast(str, rec["location"])
     for ld in fs_access.listdir(loc):
         parse = urllib.parse.urlparse(ld)