Extract shared list_kg_classes/set_error_handling helpers to reduce code duplication

Author: apdavison

.gitignore

@@ -7,4 +7,5 @@ htmlcov
 *.pyc
 doc/_build
 *.py.orig
-builder/expanded
+builder/expanded
+build/lib

builder/init_template.py.txt

@@ -1,14 +1,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [obj for name, obj in inspect.getmembers(sys.modules[__name__])
-           if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [obj for name, obj in inspect.getmembers(sys.modules[__name__])
-           if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -20,5 +18,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

builder/update_openminds.py

@@ -915,9 +915,11 @@ def main(openminds_root, ignore=[]):
         with open(init_file_path, "w") as fp:
             om_module_header = [
                 "import sys\n",
-                "import inspect\n",
-                "from fairgraph.kgobject import KGObject\n",
-                "from fairgraph.embedded import KGEmbedded\n\n",
+                "from fairgraph.openminds import (\n",
+                "    list_kg_classes as _lkgc,\n",
+                "    list_embedded_metadata_classes as _lemc,\n",
+                "    set_error_handling as _seh,\n",
+                ")\n\n",
             ]
             fp.writelines(om_module_header)
             fp.write(content)

fairgraph/openminds/__init__.py

@@ -1 +1,37 @@
+import sys
+import inspect
+from fairgraph.kgobject import KGObject
+from fairgraph.embedded import KGEmbedded
+
+
+def list_kg_classes(module=None):
+    """List all KG classes defined in the given module (defaults to this module)"""
+    if module is None:
+        module = sys.modules[__name__]
+    return [obj for name, obj in inspect.getmembers(module)
+            if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(module.__name__)]
+
+
+def list_embedded_metadata_classes(module=None):
+    """List all embedded metadata classes defined in the given module (defaults to this module)"""
+    if module is None:
+        module = sys.modules[__name__]
+    return [obj for name, obj in inspect.getmembers(module)
+            if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(module.__name__)]
+
+
+def set_error_handling(value, module=None):
+    """
+    Control validation for all classes in the given module (defaults to this module).
+
+    Args:
+        value (str): action to follow when there is a validation failure.
+            (e.g. if a required property is not provided).
+            Possible values: "error", "warning", "log", None
+        module: the module whose classes should be updated. Defaults to this module.
+    """
+    for cls in list_kg_classes(module) + list_embedded_metadata_classes(module):
+        cls.set_error_handling(value)
+
+
 from . import chemicals, computation, controlled_terms, core, ephys, publications, sands, specimen_prep, stimulation

fairgraph/openminds/chemicals/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .amount_of_chemical import AmountOfChemical
 from .chemical_mixture import ChemicalMixture
@@ -11,20 +13,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -36,5 +30,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

fairgraph/openminds/computation/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .data_analysis import DataAnalysis
 from .data_copy import DataCopy
@@ -24,20 +26,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -49,5 +43,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

fairgraph/openminds/controlled_terms/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .action_status_type import ActionStatusType
 from .age_category import AgeCategory
@@ -87,20 +89,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -112,5 +106,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

fairgraph/openminds/core/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .research import (
     ProtocolExecution,
@@ -78,20 +80,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -103,5 +97,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

fairgraph/openminds/ephys/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .activity import RecordingActivity, ElectrodePlacement, CellPatching
 from .entity import Channel, Recording
@@ -10,20 +12,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -35,5 +29,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])

fairgraph/openminds/publications/__init__.py

@@ -1,7 +1,9 @@
 import sys
-import inspect
-from fairgraph.kgobject import KGObject
-from fairgraph.embedded import KGEmbedded
+from fairgraph.openminds import (
+    list_kg_classes as _lkgc,
+    list_embedded_metadata_classes as _lemc,
+    set_error_handling as _seh,
+)
 
 from .book import Book
 from .chapter import Chapter
@@ -18,20 +20,12 @@
 
 def list_kg_classes():
     """List all KG classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGObject) and obj.__module__.startswith(__name__)
-    ]
+    return _lkgc(sys.modules[__name__])
 
 
 def list_embedded_metadata_classes():
     """List all embedded metadata classes defined in this module"""
-    return [
-        obj
-        for name, obj in inspect.getmembers(sys.modules[__name__])
-        if inspect.isclass(obj) and issubclass(obj, KGEmbedded) and obj.__module__.startswith(__name__)
-    ]
+    return _lemc(sys.modules[__name__])
 
 
 def set_error_handling(value):
@@ -43,5 +37,4 @@ def set_error_handling(value):
             (e.g. if a required property is not provided).
             Possible values: "error", "warning", "log", None
     """
-    for cls in list_kg_classes() + list_embedded_metadata_classes():
-        cls.set_error_handling(value)
+    _seh(value, sys.modules[__name__])