parsers regen: don't modify the yaml destructively

mr-c · mr-c · commit a27c60a5e9a6 · 2022-10-18T13:03:03.000+02:00
diff --git a/cwl_utils/parser/cwl_v1_0.py b/cwl_utils/parser/cwl_v1_0.py
@@ -438,22 +438,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                         r.append({"pattern": d})
                 elif isinstance(d, dict):
                     new_dict: Dict[str, Any] = {}
-                    if "pattern" in d:
-                        new_dict["pattern"] = d.pop("pattern")
+                    dict_copy = copy.deepcopy(d)
+                    if "pattern" in dict_copy:
+                        new_dict["pattern"] = dict_copy.pop("pattern")
                     else:
                         raise ValidationException(
                             "Missing pattern in secondaryFiles specification entry: {}".format(
                                 d
                             )
                         )
                     new_dict["required"] = (
-                        d.pop("required") if "required" in d else None
+                        dict_copy.pop("required") if "required" in dict_copy else None
                     )
 
-                    if len(d):
+                    if len(dict_copy):
                         raise ValidationException(
                             "Unallowed values in secondaryFiles specification entry: {}".format(
-                                d
+                                dict_copy
                             )
                         )
                     r.append(new_dict)
@@ -464,20 +465,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                     )
         elif isinstance(doc, MutableMapping):
             new_dict = {}
-            if "pattern" in doc:
-                new_dict["pattern"] = doc.pop("pattern")
+            doc_copy = copy.deepcopy(doc)
+            if "pattern" in doc_copy:
+                new_dict["pattern"] = doc_copy.pop("pattern")
             else:
                 raise ValidationException(
                     "Missing pattern in secondaryFiles specification entry: {}".format(
                         doc
                     )
                 )
-            new_dict["required"] = doc.pop("required") if "required" in doc else None
+            new_dict["required"] = (
+                doc_copy.pop("required") if "required" in doc_copy else None
+            )
 
-            if len(doc):
+            if len(doc_copy):
                 raise ValidationException(
                     "Unallowed values in secondaryFiles specification entry: {}".format(
-                        doc
+                        doc_copy
                     )
                 )
             r.append(new_dict)
diff --git a/cwl_utils/parser/cwl_v1_1.py b/cwl_utils/parser/cwl_v1_1.py
@@ -438,22 +438,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                         r.append({"pattern": d})
                 elif isinstance(d, dict):
                     new_dict: Dict[str, Any] = {}
-                    if "pattern" in d:
-                        new_dict["pattern"] = d.pop("pattern")
+                    dict_copy = copy.deepcopy(d)
+                    if "pattern" in dict_copy:
+                        new_dict["pattern"] = dict_copy.pop("pattern")
                     else:
                         raise ValidationException(
                             "Missing pattern in secondaryFiles specification entry: {}".format(
                                 d
                             )
                         )
                     new_dict["required"] = (
-                        d.pop("required") if "required" in d else None
+                        dict_copy.pop("required") if "required" in dict_copy else None
                     )
 
-                    if len(d):
+                    if len(dict_copy):
                         raise ValidationException(
                             "Unallowed values in secondaryFiles specification entry: {}".format(
-                                d
+                                dict_copy
                             )
                         )
                     r.append(new_dict)
@@ -464,20 +465,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                     )
         elif isinstance(doc, MutableMapping):
             new_dict = {}
-            if "pattern" in doc:
-                new_dict["pattern"] = doc.pop("pattern")
+            doc_copy = copy.deepcopy(doc)
+            if "pattern" in doc_copy:
+                new_dict["pattern"] = doc_copy.pop("pattern")
             else:
                 raise ValidationException(
                     "Missing pattern in secondaryFiles specification entry: {}".format(
                         doc
                     )
                 )
-            new_dict["required"] = doc.pop("required") if "required" in doc else None
+            new_dict["required"] = (
+                doc_copy.pop("required") if "required" in doc_copy else None
+            )
 
-            if len(doc):
+            if len(doc_copy):
                 raise ValidationException(
                     "Unallowed values in secondaryFiles specification entry: {}".format(
-                        doc
+                        doc_copy
                     )
                 )
             r.append(new_dict)
diff --git a/cwl_utils/parser/cwl_v1_2.py b/cwl_utils/parser/cwl_v1_2.py
@@ -438,22 +438,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                         r.append({"pattern": d})
                 elif isinstance(d, dict):
                     new_dict: Dict[str, Any] = {}
-                    if "pattern" in d:
-                        new_dict["pattern"] = d.pop("pattern")
+                    dict_copy = copy.deepcopy(d)
+                    if "pattern" in dict_copy:
+                        new_dict["pattern"] = dict_copy.pop("pattern")
                     else:
                         raise ValidationException(
                             "Missing pattern in secondaryFiles specification entry: {}".format(
                                 d
                             )
                         )
                     new_dict["required"] = (
-                        d.pop("required") if "required" in d else None
+                        dict_copy.pop("required") if "required" in dict_copy else None
                     )
 
-                    if len(d):
+                    if len(dict_copy):
                         raise ValidationException(
                             "Unallowed values in secondaryFiles specification entry: {}".format(
-                                d
+                                dict_copy
                             )
                         )
                     r.append(new_dict)
@@ -464,20 +465,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):
                     )
         elif isinstance(doc, MutableMapping):
             new_dict = {}
-            if "pattern" in doc:
-                new_dict["pattern"] = doc.pop("pattern")
+            doc_copy = copy.deepcopy(doc)
+            if "pattern" in doc_copy:
+                new_dict["pattern"] = doc_copy.pop("pattern")
             else:
                 raise ValidationException(
                     "Missing pattern in secondaryFiles specification entry: {}".format(
                         doc
                     )
                 )
-            new_dict["required"] = doc.pop("required") if "required" in doc else None
+            new_dict["required"] = (
+                doc_copy.pop("required") if "required" in doc_copy else None
+            )
 
-            if len(doc):
+            if len(doc_copy):
                 raise ValidationException(
                     "Unallowed values in secondaryFiles specification entry: {}".format(
-                        doc
+                        doc_copy
                     )
                 )
             r.append(new_dict)

Original file line number	Diff line number	Diff line change
`@@ -438,22 +438,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):`
`438`	`438`	`r.append({"pattern": d})`
`439`	`439`	`elif isinstance(d, dict):`
`440`	`440`	`new_dict: Dict[str, Any] = {}`
`441`		`- if "pattern" in d:`
`442`		`- new_dict["pattern"] = d.pop("pattern")`
	`441`	`+ dict_copy = copy.deepcopy(d)`
	`442`	`+ if "pattern" in dict_copy:`
	`443`	`+ new_dict["pattern"] = dict_copy.pop("pattern")`
`443`	`444`	`else:`
`444`	`445`	`raise ValidationException(`
`445`	`446`	`"Missing pattern in secondaryFiles specification entry: {}".format(`
`446`	`447`	`d`
`447`	`448`	`)`
`448`	`449`	`)`
`449`	`450`	`new_dict["required"] = (`
`450`		`- d.pop("required") if "required" in d else None`
	`451`	`+ dict_copy.pop("required") if "required" in dict_copy else None`
`451`	`452`	`)`
`452`	`453`
`453`		`- if len(d):`
	`454`	`+ if len(dict_copy):`
`454`	`455`	`raise ValidationException(`
`455`	`456`	`"Unallowed values in secondaryFiles specification entry: {}".format(`
`456`		`- d`
	`457`	`+ dict_copy`
`457`	`458`	`)`
`458`	`459`	`)`
`459`	`460`	`r.append(new_dict)`
`@@ -464,20 +465,23 @@ def load(self, doc, baseuri, loadingOptions, docRoot=None):`
`464`	`465`	`)`
`465`	`466`	`elif isinstance(doc, MutableMapping):`
`466`	`467`	`new_dict = {}`
`467`		`- if "pattern" in doc:`
`468`		`- new_dict["pattern"] = doc.pop("pattern")`
	`468`	`+ doc_copy = copy.deepcopy(doc)`
	`469`	`+ if "pattern" in doc_copy:`
	`470`	`+ new_dict["pattern"] = doc_copy.pop("pattern")`
`469`	`471`	`else:`
`470`	`472`	`raise ValidationException(`
`471`	`473`	`"Missing pattern in secondaryFiles specification entry: {}".format(`
`472`	`474`	`doc`
`473`	`475`	`)`
`474`	`476`	`)`
`475`		`- new_dict["required"] = doc.pop("required") if "required" in doc else None`
	`477`	`+ new_dict["required"] = (`
	`478`	`+ doc_copy.pop("required") if "required" in doc_copy else None`
	`479`	`+ )`
`476`	`480`
`477`		`- if len(doc):`
	`481`	`+ if len(doc_copy):`
`478`	`482`	`raise ValidationException(`
`479`	`483`	`"Unallowed values in secondaryFiles specification entry: {}".format(`
`480`		`- doc`
	`484`	`+ doc_copy`
`481`	`485`	`)`
`482`	`486`	`)`
`483`	`487`	`r.append(new_dict)`