secfiles DSL fix & refresh from 1.2.1_proposed

mr-c · mr-c · commit 99b4c666bcdb · 2021-10-20T14:35:40.000+02:00
diff --git a/cwl_utils/parser/cwl_v1_1.py b/cwl_utils/parser/cwl_v1_1.py
@@ -2,13 +2,13 @@
 # This file was autogenerated using schema-salad-tool --codegen=python
 # The code itself is released under the Apache 2.0 license and the help text is
 # subject to the license of the original schema.
-from abc import ABC, abstractmethod
 import copy
 import os
 import pathlib
 import re
 import tempfile
 import uuid as _uuid__  # pylint: disable=unused-import # noqa: F401
+from abc import ABC, abstractmethod
 from io import StringIO
 from typing import (
     Any,
@@ -337,6 +337,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                                 d
                             )
                         )
+                    r.append(new_dict)
 
                 else:
                     raise ValidationException(
@@ -360,6 +361,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                         doc
                     )
                 )
+            r.append(new_dict)
 
         elif isinstance(doc, str):
             if doc.endswith("?"):
diff --git a/cwl_utils/parser/cwl_v1_2.py b/cwl_utils/parser/cwl_v1_2.py
@@ -2,13 +2,13 @@
 # This file was autogenerated using schema-salad-tool --codegen=python
 # The code itself is released under the Apache 2.0 license and the help text is
 # subject to the license of the original schema.
-from abc import ABC, abstractmethod
 import copy
 import os
 import pathlib
 import re
 import tempfile
 import uuid as _uuid__  # pylint: disable=unused-import # noqa: F401
+from abc import ABC, abstractmethod
 from io import StringIO
 from typing import (
     Any,
@@ -337,6 +337,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                                 d
                             )
                         )
+                    r.append(new_dict)
 
                 else:
                     raise ValidationException(
@@ -360,6 +361,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                         doc
                     )
                 )
+            r.append(new_dict)
 
         elif isinstance(doc, str):
             if doc.endswith("?"):
@@ -1112,7 +1114,7 @@ def fromDoc(
         try:
             items = load_field(
                 _doc.get("items"),
-                uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2,
+                typedsl_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_2,
                 baseuri,
                 loadingOptions,
             )
@@ -1174,9 +1176,9 @@ def save(
         for ef in self.extension_fields:
             r[prefix_url(ef, self.loadingOptions.vocab)] = self.extension_fields[ef]
         if self.items is not None:
-            u = save_relative_uri(self.items, base_url, False, 2, relative_uris)
-            if u:
-                r["items"] = u
+            r["items"] = save(
+                self.items, top=False, base_url=base_url, relative_uris=relative_uris
+            )
         if self.type is not None:
             r["type"] = save(
                 self.type, top=False, base_url=base_url, relative_uris=relative_uris
@@ -2811,7 +2813,7 @@ def fromDoc(
         try:
             items = load_field(
                 _doc.get("items"),
-                uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2,
+                typedsl_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_2,
                 baseuri,
                 loadingOptions,
             )
@@ -2916,9 +2918,9 @@ def save(
             if u:
                 r["name"] = u
         if self.items is not None:
-            u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
-            if u:
-                r["items"] = u
+            r["items"] = save(
+                self.items, top=False, base_url=self.name, relative_uris=relative_uris
+            )
         if self.type is not None:
             r["type"] = save(
                 self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -3679,7 +3681,7 @@ def fromDoc(
         try:
             items = load_field(
                 _doc.get("items"),
-                uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2,
+                typedsl_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_2,
                 baseuri,
                 loadingOptions,
             )
@@ -3784,9 +3786,9 @@ def save(
             if u:
                 r["name"] = u
         if self.items is not None:
-            u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
-            if u:
-                r["items"] = u
+            r["items"] = save(
+                self.items, top=False, base_url=self.name, relative_uris=relative_uris
+            )
         if self.type is not None:
             r["type"] = save(
                 self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -5966,7 +5968,7 @@ def fromDoc(
         try:
             items = load_field(
                 _doc.get("items"),
-                uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2,
+                typedsl_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_2,
                 baseuri,
                 loadingOptions,
             )
@@ -6092,9 +6094,9 @@ def save(
             if u:
                 r["name"] = u
         if self.items is not None:
-            u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
-            if u:
-                r["items"] = u
+            r["items"] = save(
+                self.items, top=False, base_url=self.name, relative_uris=relative_uris
+            )
         if self.type is not None:
             r["type"] = save(
                 self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -6905,7 +6907,7 @@ def fromDoc(
         try:
             items = load_field(
                 _doc.get("items"),
-                uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2,
+                typedsl_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_2,
                 baseuri,
                 loadingOptions,
             )
@@ -7012,9 +7014,9 @@ def save(
             if u:
                 r["name"] = u
         if self.items is not None:
-            u = save_relative_uri(self.items, self.name, False, 2, relative_uris)
-            if u:
-                r["items"] = u
+            r["items"] = save(
+                self.items, top=False, base_url=self.name, relative_uris=relative_uris
+            )
         if self.type is not None:
             r["type"] = save(
                 self.type, top=False, base_url=self.name, relative_uris=relative_uris
@@ -14699,12 +14701,6 @@ def save(
 typedsl_enum_d961d79c225752b9fadb617367615ab176b47d77Loader_2 = _TypeDSLLoader(
     enum_d961d79c225752b9fadb617367615ab176b47d77Loader, 2
 )
-uri_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
-    union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype_or_array_of_union_of_PrimitiveTypeLoader_or_RecordSchemaLoader_or_EnumSchemaLoader_or_ArraySchemaLoader_or_strtype,
-    False,
-    True,
-    2,
-)
 enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader = _EnumLoader(("array",))
 typedsl_enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader_2 = _TypeDSLLoader(
     enum_d062602be0b4b8fd33e69e29a841317b6ab665bcLoader, 2
@@ -14834,12 +14830,6 @@ def save(
 idmap_fields_union_of_None_type_or_array_of_InputRecordFieldLoader = _IdMapLoader(
     union_of_None_type_or_array_of_InputRecordFieldLoader, "name", "type"
 )
-uri_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
-    union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_InputRecordSchemaLoader_or_InputEnumSchemaLoader_or_InputArraySchemaLoader_or_strtype,
-    False,
-    True,
-    2,
-)
 union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype = _UnionLoader(
     (
         CWLTypeLoader,
@@ -14876,12 +14866,6 @@ def save(
 idmap_fields_union_of_None_type_or_array_of_OutputRecordFieldLoader = _IdMapLoader(
     union_of_None_type_or_array_of_OutputRecordFieldLoader, "name", "type"
 )
-uri_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
-    union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_OutputRecordSchemaLoader_or_OutputEnumSchemaLoader_or_OutputArraySchemaLoader_or_strtype,
-    False,
-    True,
-    2,
-)
 union_of_None_type_or_Any_type = _UnionLoader(
     (
         None_type,
@@ -15082,12 +15066,6 @@ def save(
         union_of_None_type_or_array_of_CommandInputRecordFieldLoader, "name", "type"
     )
 )
-uri_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
-    union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype,
-    False,
-    True,
-    2,
-)
 union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype = _UnionLoader(
     (
         CWLTypeLoader,
@@ -15132,12 +15110,6 @@ def save(
         union_of_None_type_or_array_of_CommandOutputRecordFieldLoader, "name", "type"
     )
 )
-uri_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_False_True_2 = _URILoader(
-    union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandOutputRecordSchemaLoader_or_CommandOutputEnumSchemaLoader_or_CommandOutputArraySchemaLoader_or_strtype,
-    False,
-    True,
-    2,
-)
 union_of_CWLTypeLoader_or_stdinLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype_or_array_of_union_of_CWLTypeLoader_or_CommandInputRecordSchemaLoader_or_CommandInputEnumSchemaLoader_or_CommandInputArraySchemaLoader_or_strtype = _UnionLoader(
     (
         CWLTypeLoader,

Original file line number	Diff line number	Diff line change
`@@ -2,13 +2,13 @@`
`2`	`2`	`# This file was autogenerated using schema-salad-tool --codegen=python`
`3`	`3`	`# The code itself is released under the Apache 2.0 license and the help text is`
`4`	`4`	`# subject to the license of the original schema.`
`5`		`-from abc import ABC, abstractmethod`
`6`	`5`	`import copy`
`7`	`6`	`import os`
`8`	`7`	`import pathlib`
`9`	`8`	`import re`
`10`	`9`	`import tempfile`
`11`	`10`	`import uuid as _uuid__ # pylint: disable=unused-import # noqa: F401`
	`11`	`+from abc import ABC, abstractmethod`
`12`	`12`	`from io import StringIO`
`13`	`13`	`from typing import (`
`14`	`14`	`Any,`
`@@ -337,6 +337,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):`
`337`	`337`	`d`
`338`	`338`	`)`
`339`	`339`	`)`
	`340`	`+ r.append(new_dict)`
`340`	`341`
`341`	`342`	`else:`
`342`	`343`	`raise ValidationException(`
`@@ -360,6 +361,7 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):`
`360`	`361`	`doc`
`361`	`362`	`)`
`362`	`363`	`)`
	`364`	`+ r.append(new_dict)`
`363`	`365`
`364`	`366`	`elif isinstance(doc, str):`
`365`	`367`	`if doc.endswith("?"):`