Merge pull request #93 from apdavison/issue92

Partial fix for #92

builder/update_openminds.py

@@ -707,31 +707,38 @@ def get_type(prop):
         if linked:
             linked_from = linked[self._schema_payload["_type"]]
             for reverse_link_name in linked_from:
-                unique_forward_link_names = set(linked_from[reverse_link_name][0])
+                unique_forward_iris = set(linked_from[reverse_link_name][0])
                 types_str = [generate_class_name(iri) for iri in linked_from[reverse_link_name][2]]
-                if len(unique_forward_link_names) == 1:
-                    (forward_link_name,) = unique_forward_link_names
-                    (forward_link_name_plural,) = set(linked_from[reverse_link_name][1])
-                    _forward_link_name_python = generate_python_name(forward_link_name_plural)
-                    iri = f"^vocab:{forward_link_name}"
-                    doc = f"reverse of '{forward_link_name}'"  # use _plural?
+                if len(unique_forward_iris) == 1:
+                    (forward_iri,) = unique_forward_iris
+                    forward_link_names = set(linked_from[reverse_link_name][1])
+                    if len(forward_link_names) == 1:
+                        (forward_link_name,) = forward_link_names
+                    else:
+                        forward_link_name = sorted(forward_link_names)[0]
+                        print(f"Multiple forward link names found: {forward_link_names}, using {forward_link_name}")
+                    # if "FileRepository" in self._schema_payload["_type"]:
+                    #     breakpoint()
+                    _forward_link_name_python = generate_python_name(forward_link_name)
+                    iri = f"^vocab:{forward_iri}"
+                    doc = f"reverse of '{_forward_link_name_python}'"
                     types_str = sorted(types_str)
                     if len(types_str) == 1:
                         types_str = f'"{types_str[0]}"'
                 else:
                     backwards_compatible = True
                     if backwards_compatible:
-                        forward_link_name = sorted(set(linked_from[reverse_link_name][0]))
-                        forward_link_name_plural = sorted(set(linked_from[reverse_link_name][1]))
+                        forward_iri = sorted(set(linked_from[reverse_link_name][0]))
+                        forward_link_name = sorted(set(linked_from[reverse_link_name][1]))
                         types_str = sorted(types_str)
                     else:
                         # this is a better solution, since we keep the match between types and names
                         # in the order of the lists, but is not backwards compatible
-                        forward_link_name = linked_from[reverse_link_name][0]
-                        forward_link_name_plural = linked_from[reverse_link_name][1]
-                    _forward_link_name_python = [generate_python_name(name) for name in forward_link_name_plural]
-                    iri = [f"^vocab:{name}" for name in forward_link_name]
-                    doc = "reverse of " + ", ".join(name for name in forward_link_name)  # use _plural?
+                        forward_iri = linked_from[reverse_link_name][0]
+                        forward_link_name = linked_from[reverse_link_name][1]
+                    _forward_link_name_python = [generate_python_name(name) for name in forward_link_name]
+                    iri = [f"^vocab:{part}" for part in forward_iri]
+                    doc = "reverse of " + ", ".join(name for name in _forward_link_name_python)
                 reverse_name_python = generate_python_name(reverse_link_name)
                 if reverse_name_python in forward_property_names:
                     if reverse_name_python in conflict_resolution:
@@ -821,12 +828,15 @@ def get_edges(self):
                 reverse_link_name = prop["nameForReverseLink"]
                 if reverse_link_name is None:
                     reverse_link_name = reverse_name_map[prop["name"]]
+                allow_multiple = prop.get("type", "") == "array"
                 linked[lnk] = (
                     self._schema_payload["_type"],
-                    prop["name"],
-                    prop["namePlural"],
+                    prop["name"],  # property name
+                    prop["namePlural"] if allow_multiple else prop["name"],  # forward link name
                     reverse_link_name,
                 )  # linked from (cls, prop name, prop name plural, reverse name)
+                # if self._schema_payload["_type"].endswith("File"):
+                #     breakpoint()
         return embedded, linked
 
 
@@ -845,16 +855,16 @@ def main(openminds_root, ignore=[]):
     for schema_file_path in schema_file_paths:
         embedded_in, linked_from = FairgraphClassBuilder(schema_file_path, openminds_root, target_path).get_edges()
         embedded.update(embedded_in)
-        for openminds_type, (link_type, property_name, property_name_plural, reverse_name) in linked_from.items():
+        for openminds_type, (link_type, property_name, forward_name, reverse_name) in linked_from.items():
             if link_type not in embedded:
                 if isinstance(reverse_name, dict):
                     reverse_name = reverse_name[link_type]
                 if reverse_name in linked[openminds_type]:
                     linked[openminds_type][reverse_name][0].append(property_name)
-                    linked[openminds_type][reverse_name][1].append(property_name_plural)
+                    linked[openminds_type][reverse_name][1].append(forward_name)
                     linked[openminds_type][reverse_name][2].append(link_type)
                 else:
-                    linked[openminds_type][reverse_name] = ([property_name], [property_name_plural], [link_type])
+                    linked[openminds_type][reverse_name] = ([property_name], [forward_name], [link_type])
     conflicts = set(linked).intersection(embedded)
     if conflicts:
         print(f"Found schema(s) that are both linked and embedded: {conflicts}")

fairgraph/openminds/chemicals/chemical_mixture.py

@@ -62,9 +62,9 @@ class ChemicalMixture(KGObject):
             "composes",
             ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"],
             ["^vocab:insulatorMaterial", "^vocab:material"],
-            reverse=["insulator_materials", "materials"],
+            reverse=["insulator_material", "material"],
             multiple=True,
-            doc="reverse of insulatorMaterial, material",
+            doc="reverse of insulator_material, material",
         ),
         Property(
             "used_in",
@@ -75,9 +75,9 @@ class ChemicalMixture(KGObject):
                 "openminds.specimen_prep.TissueSampleSlicing",
             ],
             ["^vocab:cultureMedium", "^vocab:pipetteSolution", "^vocab:tissueBathSolution"],
-            reverse=["culture_media", "pipette_solutions", "tissue_bath_solutions"],
+            reverse=["culture_medium", "pipette_solution", "tissue_bath_solution"],
             multiple=True,
-            doc="reverse of cultureMedium, pipetteSolution, tissueBathSolution",
+            doc="reverse of culture_medium, pipette_solution, tissue_bath_solution",
         ),
     ]
     existence_query_properties = ("has_parts", "type")

fairgraph/openminds/chemicals/chemical_substance.py

@@ -55,17 +55,17 @@ class ChemicalSubstance(KGObject):
             "composes",
             ["openminds.ephys.Electrode", "openminds.ephys.ElectrodeArray", "openminds.ephys.Pipette"],
             ["^vocab:insulatorMaterial", "^vocab:material"],
-            reverse=["insulator_materials", "materials"],
+            reverse=["insulator_material", "material"],
             multiple=True,
-            doc="reverse of insulatorMaterial, material",
+            doc="reverse of insulator_material, material",
         ),
         Property(
             "labels",
             "openminds.ephys.PipetteUsage",
             "^vocab:labelingCompound",
-            reverse="labeling_compounds",
+            reverse="labeling_compound",
             multiple=True,
-            doc="reverse of 'labelingCompound'",
+            doc="reverse of 'labeling_compound'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/chemicals/product_source.py

@@ -50,9 +50,9 @@ class ProductSource(KGObject):
             "is_source_of",
             ["openminds.chemicals.ChemicalMixture", "openminds.chemicals.ChemicalSubstance"],
             "^vocab:productSource",
-            reverse="product_sources",
+            reverse="product_source",
             multiple=True,
-            doc="reverse of 'productSource'",
+            doc="reverse of 'product_source'",
         ),
     ]
     existence_query_properties = ("product_name", "provider")

fairgraph/openminds/computation/data_analysis.py

@@ -183,15 +183,15 @@ class DataAnalysis(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/data_copy.py

@@ -179,15 +179,15 @@ class DataCopy(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/environment.py

@@ -68,7 +68,7 @@ class Environment(KGObject):
                 "openminds.computation.Visualization",
             ],
             "^vocab:environment",
-            reverse="environments",
+            reverse="environment",
             multiple=True,
             doc="reverse of 'environment'",
         ),

fairgraph/openminds/computation/generic_computation.py

@@ -181,15 +181,15 @@ class GenericComputation(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/launch_configuration.py

@@ -57,9 +57,9 @@ class LaunchConfiguration(KGObject):
                 "openminds.computation.Visualization",
             ],
             "^vocab:launchConfiguration",
-            reverse="launch_configurations",
+            reverse="launch_configuration",
             multiple=True,
-            doc="reverse of 'launchConfiguration'",
+            doc="reverse of 'launch_configuration'",
         ),
     ]
     existence_query_properties = ("executable", "name")

fairgraph/openminds/computation/local_file.py

@@ -80,15 +80,15 @@ class LocalFile(KGObject):
             "^vocab:output",
             reverse="outputs",
             multiple=True,
-            doc="reverse of 'output'",
+            doc="reverse of 'outputs'",
         ),
         Property(
             "is_used_to_group",
             "openminds.core.FileBundle",
             "^vocab:groupedBy",
             reverse="grouped_by",
             multiple=True,
-            doc="reverse of 'groupedBy'",
+            doc="reverse of 'grouped_by'",
         ),
     ]
     existence_query_properties = ("name", "path")

fairgraph/openminds/computation/model_validation.py

@@ -179,15 +179,15 @@ class ModelValidation(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/optimization.py

@@ -182,15 +182,15 @@ class Optimization(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/simulation.py

@@ -182,15 +182,15 @@ class Simulation(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/software_agent.py

@@ -57,7 +57,7 @@ class SoftwareAgent(KGObject):
             "^vocab:performedBy",
             reverse="performed_by",
             multiple=True,
-            doc="reverse of 'performedBy'",
+            doc="reverse of 'performed_by'",
         ),
         Property(
             "started",
@@ -74,7 +74,7 @@ class SoftwareAgent(KGObject):
             "^vocab:startedBy",
             reverse="started_by",
             multiple=True,
-            doc="reverse of 'startedBy'",
+            doc="reverse of 'started_by'",
         ),
     ]
     existence_query_properties = ("name", "software")

fairgraph/openminds/computation/validation_test.py

@@ -149,7 +149,7 @@ class ValidationTest(KGObject):
             "^vocab:hasPart",
             reverse="has_parts",
             multiple=True,
-            doc="reverse of 'hasPart'",
+            doc="reverse of 'has_parts'",
         ),
         Property(
             "learning_resources",

fairgraph/openminds/computation/validation_test_version.py

@@ -304,31 +304,31 @@ class ValidationTestVersion(KGObject):
             "^vocab:input",
             reverse="inputs",
             multiple=True,
-            doc="reverse of 'input'",
+            doc="reverse of 'inputs'",
         ),
         Property(
             "is_old_version_of",
             "openminds.computation.ValidationTestVersion",
             "^vocab:isNewVersionOf",
             reverse="is_new_version_of",
             multiple=True,
-            doc="reverse of 'isNewVersionOf'",
+            doc="reverse of 'is_new_version_of'",
         ),
         Property(
             "is_part_of",
             ["openminds.core.Project", "openminds.core.ResearchProductGroup"],
             "^vocab:hasPart",
             reverse="has_parts",
             multiple=True,
-            doc="reverse of 'hasPart'",
+            doc="reverse of 'has_parts'",
         ),
         Property(
             "is_version_of",
             "openminds.computation.ValidationTest",
             "^vocab:hasVersion",
             reverse="has_versions",
             multiple=True,
-            doc="reverse of 'hasVersion'",
+            doc="reverse of 'has_versions'",
         ),
         Property(
             "learning_resources",

fairgraph/openminds/computation/visualization.py

@@ -181,15 +181,15 @@ class Visualization(KGObject):
             "^vocab:wasInformedBy",
             reverse="was_informed_by",
             multiple=True,
-            doc="reverse of 'wasInformedBy'",
+            doc="reverse of 'was_informed_by'",
         ),
         Property(
             "is_part_of",
             "openminds.computation.WorkflowExecution",
             "^vocab:stage",
             reverse="stages",
             multiple=True,
-            doc="reverse of 'stage'",
+            doc="reverse of 'stages'",
         ),
     ]
     existence_query_properties = ("lookup_label",)

fairgraph/openminds/computation/workflow_recipe.py

@@ -99,7 +99,7 @@ class WorkflowRecipe(KGObject):
             "^vocab:hasPart",
             reverse="has_parts",
             multiple=True,
-            doc="reverse of 'hasPart'",
+            doc="reverse of 'has_parts'",
         ),
         Property(
             "learning_resources",