cognite-neat 0.88.1__py3-none-any.whl → 0.88.2__py3-none-any.whl
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- cognite/neat/_version.py +1 -1
- cognite/neat/exceptions.py +2 -2
- cognite/neat/graph/loaders/_base.py +4 -4
- cognite/neat/graph/loaders/_rdf2asset.py +12 -14
- cognite/neat/graph/loaders/_rdf2dms.py +14 -10
- cognite/neat/issues/__init__.py +16 -0
- cognite/neat/{issues.py → issues/_base.py} +73 -5
- cognite/neat/issues/errors/external.py +21 -0
- cognite/neat/issues/errors/properties.py +75 -0
- cognite/neat/issues/errors/resources.py +123 -0
- cognite/neat/issues/errors/schema.py +0 -0
- cognite/neat/{rules/issues → issues}/formatters.py +9 -9
- cognite/neat/issues/neat_warnings/__init__.py +2 -0
- cognite/neat/issues/neat_warnings/identifier.py +27 -0
- cognite/neat/issues/neat_warnings/models.py +22 -0
- cognite/neat/issues/neat_warnings/properties.py +77 -0
- cognite/neat/issues/neat_warnings/resources.py +125 -0
- cognite/neat/rules/exporters/_rules2dms.py +3 -2
- cognite/neat/rules/exporters/_validation.py +2 -2
- cognite/neat/rules/importers/__init__.py +7 -3
- cognite/neat/rules/importers/_base.py +3 -3
- cognite/neat/rules/importers/_dms2rules.py +39 -18
- cognite/neat/rules/importers/_dtdl2rules/dtdl_converter.py +44 -53
- cognite/neat/rules/importers/_dtdl2rules/dtdl_importer.py +6 -5
- cognite/neat/rules/importers/_rdf/__init__.py +0 -0
- cognite/neat/rules/importers/_rdf/_imf2rules/__init__.py +3 -0
- cognite/neat/rules/importers/_rdf/_imf2rules/_imf2classes.py +82 -0
- cognite/neat/rules/importers/_rdf/_imf2rules/_imf2metadata.py +34 -0
- cognite/neat/rules/importers/_rdf/_imf2rules/_imf2properties.py +123 -0
- cognite/neat/rules/importers/{_owl2rules/_owl2rules.py → _rdf/_imf2rules/_imf2rules.py} +15 -11
- cognite/neat/rules/importers/{_inference2rules.py → _rdf/_inference2rules.py} +1 -1
- cognite/neat/rules/importers/_rdf/_owl2rules/_owl2classes.py +57 -0
- cognite/neat/rules/importers/_rdf/_owl2rules/_owl2metadata.py +68 -0
- cognite/neat/rules/importers/_rdf/_owl2rules/_owl2properties.py +59 -0
- cognite/neat/rules/importers/_rdf/_owl2rules/_owl2rules.py +76 -0
- cognite/neat/rules/importers/_rdf/_shared.py +586 -0
- cognite/neat/rules/importers/_spreadsheet2rules.py +1 -1
- cognite/neat/rules/importers/_yaml2rules.py +2 -1
- cognite/neat/rules/issues/__init__.py +1 -5
- cognite/neat/rules/issues/base.py +2 -21
- cognite/neat/rules/issues/dms.py +0 -134
- cognite/neat/rules/issues/spreadsheet.py +3 -3
- cognite/neat/rules/models/_types/_field.py +5 -2
- cognite/neat/rules/models/asset/_validation.py +1 -1
- cognite/neat/rules/models/dms/_schema.py +53 -30
- cognite/neat/rules/models/dms/_validation.py +2 -2
- cognite/neat/rules/models/entities.py +3 -0
- cognite/neat/rules/models/information/_validation.py +1 -1
- cognite/neat/workflows/steps/lib/current/rules_importer.py +73 -1
- cognite/neat/workflows/steps/lib/current/rules_validator.py +19 -7
- {cognite_neat-0.88.1.dist-info → cognite_neat-0.88.2.dist-info}/METADATA +1 -1
- {cognite_neat-0.88.1.dist-info → cognite_neat-0.88.2.dist-info}/RECORD +57 -42
- cognite/neat/graph/issues/loader.py +0 -104
- cognite/neat/rules/importers/_owl2rules/_owl2classes.py +0 -215
- cognite/neat/rules/importers/_owl2rules/_owl2metadata.py +0 -209
- cognite/neat/rules/importers/_owl2rules/_owl2properties.py +0 -203
- cognite/neat/rules/issues/importing.py +0 -423
- /cognite/neat/{graph/issues → issues/errors}/__init__.py +0 -0
- /cognite/neat/rules/importers/{_owl2rules → _rdf/_owl2rules}/__init__.py +0 -0
- {cognite_neat-0.88.1.dist-info → cognite_neat-0.88.2.dist-info}/LICENSE +0 -0
- {cognite_neat-0.88.1.dist-info → cognite_neat-0.88.2.dist-info}/WHEEL +0 -0
- {cognite_neat-0.88.1.dist-info → cognite_neat-0.88.2.dist-info}/entry_points.txt +0 -0
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FILTER (!bound(?name) || LANG(?name) = "" || LANGMATCHES(LANG(?name), "en"))
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35
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FILTER (!bound(?description) || LANG(?description) = "" || LANGMATCHES(LANG(?description), "en"))
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36
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}
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37
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"""
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38
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-
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39
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# create raw dataframe
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40
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-
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41
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raw_df = _parse_raw_dataframe(cast(list[tuple], list(graph.query(query.replace("en", language)))))
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42
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if raw_df.empty:
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43
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return []
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44
|
-
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45
|
-
# group values and clean up
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46
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-
processed_df = _clean_up_classes(raw_df)
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47
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-
|
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48
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# make compliant
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49
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processed_df = make_classes_compliant(processed_df)
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50
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-
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51
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# Make Parent Class list elements into string joined with comma
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52
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processed_df["Parent Class"] = processed_df["Parent Class"].apply(
|
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53
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lambda x: ", ".join(x) if isinstance(x, list) and x else None
|
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54
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-
)
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55
|
-
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56
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return processed_df.dropna(axis=0, how="all").replace(float("nan"), None).to_dict(orient="records")
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|
57
|
-
|
|
58
|
-
|
|
59
|
-
def _parse_raw_dataframe(query_results: list[tuple]) -> pd.DataFrame:
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60
|
-
df = pd.DataFrame(
|
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61
|
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query_results,
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|
62
|
-
columns=["Class", "Name", "Description", "Parent Class", "Reference", "Match", "Comment"],
|
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63
|
-
)
|
|
64
|
-
if df.empty:
|
|
65
|
-
return df
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|
66
|
-
|
|
67
|
-
# # remove NaNs
|
|
68
|
-
df.replace(np.nan, "", regex=True, inplace=True)
|
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69
|
-
|
|
70
|
-
df.Reference = df.Class
|
|
71
|
-
df.Class = df.Class.apply(lambda x: remove_namespace_from_uri(x))
|
|
72
|
-
df["Match Type"] = len(df) * [MatchType.exact]
|
|
73
|
-
df["Comment"] = len(df) * [None]
|
|
74
|
-
df["Parent Class"] = df["Parent Class"].apply(lambda x: remove_namespace_from_uri(x))
|
|
75
|
-
|
|
76
|
-
return df
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
def _clean_up_classes(df: pd.DataFrame) -> pd.DataFrame:
|
|
80
|
-
clean_list = [
|
|
81
|
-
{
|
|
82
|
-
"Class": class_,
|
|
83
|
-
"Name": group_df["Name"].unique()[0],
|
|
84
|
-
"Description": "\n".join(list(group_df.Description.unique())),
|
|
85
|
-
"Parent Class": ", ".join(list(group_df["Parent Class"].unique())),
|
|
86
|
-
"Reference": group_df["Reference"].unique()[0],
|
|
87
|
-
"Match Type": group_df["Match Type"].unique()[0],
|
|
88
|
-
"Comment": group_df["Comment"].unique()[0],
|
|
89
|
-
}
|
|
90
|
-
for class_, group_df in df.groupby("Class")
|
|
91
|
-
]
|
|
92
|
-
|
|
93
|
-
df = pd.DataFrame(clean_list)
|
|
94
|
-
|
|
95
|
-
# bring NaNs back
|
|
96
|
-
df.replace("", None, inplace=True)
|
|
97
|
-
|
|
98
|
-
# split Parent Class column back into list
|
|
99
|
-
df["Parent Class"] = df["Parent Class"].apply(lambda x: x.split(", ") if isinstance(x, str) else None)
|
|
100
|
-
|
|
101
|
-
return df
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
def make_classes_compliant(classes: pd.DataFrame) -> pd.DataFrame:
|
|
105
|
-
"""Make classes compliant.
|
|
106
|
-
|
|
107
|
-
Returns:
|
|
108
|
-
Dataframe containing compliant classes
|
|
109
|
-
|
|
110
|
-
!!! note "About the compliant classes"
|
|
111
|
-
The compliant classes are based on the OWL base ontology, but adapted to NEAT and use in CDF.
|
|
112
|
-
One thing to note is that this method would not be able to fix issues with class ids which
|
|
113
|
-
are not compliant with the CDF naming convention. For example, if a class id contains a space,
|
|
114
|
-
starts with a number, etc. This will cause issues when trying to create the class in CDF.
|
|
115
|
-
"""
|
|
116
|
-
|
|
117
|
-
# Replace empty or non-string values in "Match" column with "exact"
|
|
118
|
-
classes["Match Type"] = classes["Match Type"].fillna(MatchType.exact)
|
|
119
|
-
classes["Match Type"] = classes["Match Type"].apply(
|
|
120
|
-
lambda x: MatchType.exact if not isinstance(x, str) or len(x) == 0 else x
|
|
121
|
-
)
|
|
122
|
-
|
|
123
|
-
# Replace empty or non-string values in "Comment" column with a default value
|
|
124
|
-
classes["Comment"] = classes["Comment"].fillna("Imported from Ontology by NEAT")
|
|
125
|
-
classes["Comment"] = classes["Comment"].apply(
|
|
126
|
-
lambda x: "Imported from Ontology by NEAT" if not isinstance(x, str) or len(x) == 0 else x
|
|
127
|
-
)
|
|
128
|
-
|
|
129
|
-
# Add _object_property_class, _data_type_property_class, _thing_class to the dataframe
|
|
130
|
-
classes = pd.concat(
|
|
131
|
-
[classes, pd.DataFrame([_object_property_class(), _data_type_property_class(), _thing_class()])],
|
|
132
|
-
ignore_index=True,
|
|
133
|
-
)
|
|
134
|
-
|
|
135
|
-
# Reduce length of elements in the "Description" column to 1024 characters
|
|
136
|
-
classes["Description"] = classes["Description"].apply(lambda x: x[:1024] if isinstance(x, str) else None)
|
|
137
|
-
|
|
138
|
-
# Add missing parent classes to the dataframe
|
|
139
|
-
classes = pd.concat(
|
|
140
|
-
[classes, pd.DataFrame(_add_parent_class(classes))],
|
|
141
|
-
ignore_index=True,
|
|
142
|
-
)
|
|
143
|
-
|
|
144
|
-
return classes
|
|
145
|
-
|
|
146
|
-
|
|
147
|
-
def _object_property_class() -> dict:
|
|
148
|
-
return {
|
|
149
|
-
"Class": "ObjectProperty",
|
|
150
|
-
"Name": None,
|
|
151
|
-
"Description": "The class of object properties.",
|
|
152
|
-
"Parent Class": None,
|
|
153
|
-
"Reference": OWL.ObjectProperty,
|
|
154
|
-
"Match Type": MatchType.exact,
|
|
155
|
-
"Comment": "Added by NEAT based on owl:ObjectProperty but adapted to NEAT and use in CDF.",
|
|
156
|
-
}
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
def _data_type_property_class() -> dict:
|
|
160
|
-
return {
|
|
161
|
-
"Class": "DatatypeProperty",
|
|
162
|
-
"Name": None,
|
|
163
|
-
"Description": "The class of data properties.",
|
|
164
|
-
"Parent Class": None,
|
|
165
|
-
"Reference": OWL.DatatypeProperty,
|
|
166
|
-
"Match Type": MatchType.exact,
|
|
167
|
-
"Comment": "Added by NEAT based on owl:DatatypeProperty but adapted to NEAT and use in CDF.",
|
|
168
|
-
}
|
|
169
|
-
|
|
170
|
-
|
|
171
|
-
def _thing_class() -> dict:
|
|
172
|
-
return {
|
|
173
|
-
"Class": "Thing",
|
|
174
|
-
"Name": None,
|
|
175
|
-
"Description": "The class of holding class individuals.",
|
|
176
|
-
"Parent Class": None,
|
|
177
|
-
"Reference": OWL.Thing,
|
|
178
|
-
"Match Type": MatchType.exact,
|
|
179
|
-
"Comment": (
|
|
180
|
-
"Added by NEAT. "
|
|
181
|
-
"Imported from OWL base ontology, it is meant for use as a default"
|
|
182
|
-
" value type for object properties which miss a declared range."
|
|
183
|
-
),
|
|
184
|
-
}
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
def _add_parent_class(df: pd.DataFrame) -> list[dict]:
|
|
188
|
-
parent_set = {
|
|
189
|
-
item
|
|
190
|
-
for sublist in df["Parent Class"].tolist()
|
|
191
|
-
if sublist
|
|
192
|
-
for item in sublist
|
|
193
|
-
if item != "" and item is not None
|
|
194
|
-
}
|
|
195
|
-
class_set = set(df["Class"].tolist())
|
|
196
|
-
|
|
197
|
-
rows = []
|
|
198
|
-
for missing_parent_class in parent_set.difference(class_set):
|
|
199
|
-
rows += [
|
|
200
|
-
{
|
|
201
|
-
"Class": missing_parent_class,
|
|
202
|
-
"Name": None,
|
|
203
|
-
"Description": None,
|
|
204
|
-
"Parent Class": None,
|
|
205
|
-
"Reference": None,
|
|
206
|
-
"Match Type": None,
|
|
207
|
-
"Comment": (
|
|
208
|
-
"Added by NEAT. "
|
|
209
|
-
"This is a parent class that is missing in the ontology. "
|
|
210
|
-
"It is added by NEAT to make the ontology compliant with CDF."
|
|
211
|
-
),
|
|
212
|
-
}
|
|
213
|
-
]
|
|
214
|
-
|
|
215
|
-
return rows
|