wip

extensions/sand_drepr/pyproject.toml

@@ -0,0 +1,15 @@
+[tool.poetry]
+name = "sand-drepr"
+version = "1.0.0"
+description = "SAND & DRepr Integration"
+authors = ["Binh Vu <[email protected]>"]
+license = "MIT"
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "3.9"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

extensions/sand_drepr/sand_drepr/dreprmodel.py

@@ -0,0 +1,165 @@
+from __future__ import annotations
+
+from collections import defaultdict
+from io import BytesIO, StringIO
+from typing import List, Mapping, Set
+
+import orjson
+import sm.outputs.semantic_model as O
+from dependency_injector.wiring import Provide, inject
+from drepr.engine import MemoryOutput, OutputFormat, ResourceDataString, execute
+from drepr.models import (
+    AlignedStep,
+    Attr,
+    CSVProp,
+    DRepr,
+    IndexExpr,
+    Path,
+    PMap,
+    Preprocessing,
+    PreprocessingType,
+    RangeAlignment,
+    RangeExpr,
+    Resource,
+    ResourceType,
+)
+from kgdata.misc.resource import RDFResource
+from rdflib import RDF, Graph, URIRef
+from sand_drepr.semanticmodel import get_drepr_sm, get_entity_data_nodes
+from slugify import slugify
+from sm.misc.funcs import assert_not_null
+from sm.namespaces.prelude import KnowledgeGraphNamespace
+
+from sand.config import AppConfig
+from sand.extension_interface.export import IExport
+from sand.extensions.export.drepr.resources import (
+    get_entity_resource,
+    get_table_resource,
+)
+from sand.extensions.export.drepr.transformation import (
+    get_transformation,
+    has_transformation,
+)
+from sand.helpers.namespace import NamespaceService
+from sand.models.ontology import OntProperty, OntPropertyAR, OntPropertyDataType
+from sand.models.table import Table, TableRow
+
+
+def get_drepr_model(
+    table_columns: list[str],
+    table_size: int,
+    sm: O.SemanticModel,
+    kgns: KnowledgeGraphNamespace,
+    kgns_prefixes: dict[str, str],
+    ontprop_ar: Mapping[str, OntProperty],
+    ident_props: list[str],
+) -> DRepr:
+    """Create a D-REPR model of the dataset.
+
+    Args:
+        table_columns: list of column names
+        table_size: number of rows in the table (exclude header)
+        sm: the semantic model we want to convert
+        kgns: the knowledge graph namespace
+        kgns_prefixes: the prefixes of the knowledge graph namespace
+        ontprop_ar: mapping from the id to ontology property
+        ident_props: list of properties that telling a data node contains entities (e.g., rdfs:label)
+    """
+    columns = [slugify(c).replace("-", "_") for c in table_columns]
+    get_attr_id = lambda ci: f"{ci}__{columns[ci]}"
+    get_ent_attr_id = lambda ci: f"{ci}__ent__{columns[ci]}"
+    ent_dnodes = get_entity_data_nodes(sm, ident_props)
+
+    attrs = [
+        Attr(
+            id=get_attr_id(ci),
+            resource_id="table",
+            path=Path(
+                steps=[
+                    RangeExpr(start=1, end=table_size + 1, step=1),
+                    IndexExpr(val=ci),
+                ]
+            ),
+            missing_values=[""],
+        )
+        for ci in range(len(table_columns))
+    ]
+    attrs += [
+        Attr(
+            id=get_ent_attr_id(node.col_index),
+            resource_id="entity",
+            path=Path(
+                steps=[
+                    RangeExpr(start=1, end=table_size + 1, step=1),
+                    IndexExpr(val=node.col_index),
+                ]
+            ),
+            missing_values=[""],
+        )
+        for node in ent_dnodes
+    ]
+
+    dsm = get_drepr_sm(
+        sm=sm,
+        kgns=kgns,
+        kgns_prefixes=kgns_prefixes,
+        ontprop_ar=ontprop_ar,
+        ident_props=ident_props,
+        get_attr_id=get_attr_id,
+        get_ent_attr_id=get_ent_attr_id,
+    )
+
+    datatype_transformations = []
+    for node in sm.nodes():
+        if not isinstance(node, O.DataNode):
+            continue
+
+        datatypes: Set[OntPropertyDataType] = {
+            assert_not_null(ontprop_ar[kgns.uri_to_id(inedge.abs_uri)]).datatype
+            for inedge in sm.in_edges(node.id)
+        }
+        datatype = list(datatypes)[0] if len(datatypes) == 1 else None
+        if datatype is None or not has_transformation(datatype):
+            continue
+        datatype_transformations.append(
+            Preprocessing(
+                type=PreprocessingType.pmap,
+                value=PMap(
+                    resource_id="table",
+                    path=Path(
+                        steps=[
+                            RangeExpr(start=1, end=table_size + 1, step=1),
+                            IndexExpr(val=node.col_index),
+                        ]
+                    ),
+                    code=get_transformation(datatype),
+                    change_structure=False,
+                ),
+            )
+        )
+
+    return DRepr(
+        resources=[
+            Resource(id="table", type=ResourceType.CSV, prop=CSVProp()),
+            Resource(id="entity", type=ResourceType.CSV, prop=CSVProp()),
+        ],
+        preprocessing=datatype_transformations,
+        attrs=attrs,
+        aligns=[
+            RangeAlignment(
+                source=get_attr_id(0),
+                target=get_attr_id(ci),
+                aligned_steps=[AlignedStep(source_idx=0, target_idx=0)],
+            )
+            for ci in range(1, len(table_columns))
+        ]
+        + [
+            RangeAlignment(
+                source=get_attr_id(0),
+                target=get_ent_attr_id(node.col_index),
+                aligned_steps=[AlignedStep(source_idx=0, target_idx=0)],
+            )
+            for node in ent_dnodes
+        ],
+        sm=dsm,
+    )