Added method to get context from model or store and another to expand the url using a context

examples/configurations/nexus-store/file-to-resource-mapping.hjson

@@ -12,7 +12,7 @@
     }
     encodingFormat: x._mediaType
     name: x._filename
-    contentUrl: x._self
+    contentUrl: forge.expand_uri(x._self)
     atLocation:
     {
         type: Location

kgforge/core/archetypes/store.py

@@ -21,6 +21,7 @@
 
 from kgforge.core import Resource
 from kgforge.core.commons.attributes import repr_class
+from kgforge.specializations.mappers import DictionaryMapper
 from kgforge.core.commons.context import Context
 from kgforge.core.commons.exceptions import (
     DeprecationError,
@@ -136,6 +137,7 @@ def __init__(
             if hasattr(self.service, "metadata_context")
             else None
         )
+        self._mapper = None
 
     def __repr__(self) -> str:
         return repr_class(self)
@@ -149,6 +151,10 @@ def mapping(self) -> Optional[Callable]:
     def mapper(self) -> Optional[Callable]:
         """Mapper class to map file metadata to a Resource with file_resource_mapping."""
         return None
+
+    @mapper.setter
+    def mapper(self, mapper: Optional[DictionaryMapper]) -> Optional[DictionaryMapper]:
+        self._mapper = mapper
 
     # [C]RUD.
 
@@ -185,7 +191,7 @@ def upload(self, path: str, content_type: str) -> Union[Resource, List[Resource]
         if self.file_mapping is not None:
             p = Path(path)
             uploaded = self._upload(p, content_type)
-            return self.mapper().map(uploaded, self.file_mapping, None)
+            return self.mapper.map(uploaded, self.file_mapping, None)
         else:
             raise UploadingError("no file_resource_mapping has been configured")
 
@@ -510,6 +516,14 @@ def _debug_query(query):
         else:
             print(*["Submitted query:", *query.splitlines()], sep="\n   ")
         print()
+
+    def expand_uri(self, uri: str, context: Context, is_file: bool, encoding: str) -> str:
+        """Expand a given url using the store or model context
+
+        :param uri: the idenfitier to be transformed
+        :param context: a Context object with vocabulary to be used in the construction of the URI
+        """
+        pass
 
 
 def _replace_in_sparql(qr, what, value, default_value, search_regex, replace_if_in_query=True):

kgforge/core/forge.py

@@ -16,14 +16,17 @@
 from pathlib import Path
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
+import re
 import numpy as np
 import yaml
 from kgforge.core.commons.files import load_file_as_byte
 from pandas import DataFrame
 from rdflib import Graph
+from urllib.parse import quote_plus, urlparse
 
 from kgforge.core import Resource
 from kgforge.core.archetypes import Mapping, Model, Resolver, Store
+from kgforge.core.commons.context import Context
 from kgforge.core.commons.actions import LazyAction
 from kgforge.core.commons.dictionaries import with_defaults
 from kgforge.core.commons.exceptions import ResolvingError
@@ -215,12 +218,12 @@ def __init__(self, configuration: Union[str, Dict], **kwargs) -> None:
         self._model: Model = model(**model_config)
 
         # Store.
-
         store_config.update(model_context=self._model.context())
         store_name = store_config.pop("name")
         store = import_class(store_name, "stores")
         self._store: Store = store(**store_config)
         store_config.update(name=store_name)
+        self._store.mapper = DictionaryMapper(self)
 
         # Resolvers.
         resolvers_config = config.pop("Resolvers", None)
@@ -234,8 +237,6 @@ def __init__(self, configuration: Union[str, Dict], **kwargs) -> None:
         # Formatters.
         self._formatters: Optional[Dict[str, str]] = config.pop("Formatters", None)
 
-    # Modeling User Interface.
-
     @catch
     def prefixes(self, pretty: bool = True) -> Optional[Dict[str, str]]:
         """
@@ -744,7 +745,6 @@ def as_json(
             self._model.resolve_context,
         )
 
-    @catch
     @catch
     def as_jsonld(
         self,
@@ -880,7 +880,27 @@ def from_dataframe(
         :return: Union[Resource, List[Resource]]
         """
         return from_dataframe(data, na, nesting)
-
+
+    def get_store_context(self):
+        """Expose the context used in the store."""
+        return self._store.context
+
+    def get_model_context(self):
+        """Expose the context used in the model."""
+        return self._model.context()
+
+    def expand_uri(self, uri: str, context: Context = None, 
+                   is_file: bool = True, encoding: str = None):
+        """
+        Construct an URI a given an id using the vocabulary given in the Context object.
+
+        :param uri: the uri to transform
+        :param context: a Context object that should be used to create the URI
+        :param encode: parameter to use to encode or not the uri, default is `utf-8`
+        """
+        if context is None:
+            context = self.get_store_context()
+        return self._store.expand_uri(uri, context, is_file, encoding)
 
 def prepare_resolvers(
     config: Dict, store_config: Dict

kgforge/specializations/stores/bluebrain_nexus.py

@@ -135,9 +135,13 @@ def mapping(self) -> Optional[Callable]:
         return DictionaryMapping
 
     @property
-    def mapper(self) -> Optional[Callable]:
-        return DictionaryMapper
-
+    def mapper(self) -> Optional[DictionaryMapper]:
+        return self._mapper
+
+    @mapper.setter
+    def mapper(self, mapper: Optional[DictionaryMapper]) -> Optional[DictionaryMapper]:
+        self._mapper = mapper
+
     def register(
         self, data: Union[Resource, List[Resource]], schema_id: str = None
     ) -> None:
@@ -1019,6 +1023,33 @@ def _initialize_service(
                 files_download_config=files_download_config,
                 **params,
             )
+
+    def expand_uri(self, uri: str, context: Context, is_file, encoding):
+        # try decoding the url first
+        raw_url = unquote(uri)
+        if is_file: # for files
+            url_base = '/'.join([self.endpoint, 'files', self.bucket])
+        else: # for resources
+            url_base = '/'.join([self.endpoint, 'resources', self.bucket])
+        matches = re.match(r"[\w\.:%/-]+/(\w+):(\w+)/[\w\.-/:%]+", raw_url)
+        if matches:
+            groups = matches.groups()
+            old_schema = f"{groups[0]}:{groups[1]}"
+            resolved = context.expand(groups[0])
+            print(groups[0], resolved)
+            if raw_url.startswith(url_base):
+                extended_schema = '/'.join([quote_plus(resolved), groups[1]])
+                url = raw_url.replace(old_schema, extended_schema)
+                return url 
+            else:
+                extended_schema = '/'.join([resolved, groups[1]])
+                url = raw_url.replace(old_schema, extended_schema)
+        else:
+            url = raw_url
+        if url.startswith(url_base):
+            return url
+        uri = "/".join((url_base, quote_plus(url, encoding=encoding)))
+        return uri
 
 
 def _error_message(error: HTTPError) -> str:

kgforge/specializations/stores/demo_store.py

@@ -238,6 +238,9 @@ def _archive_id(rid: str, version: int) -> str:
     @staticmethod
     def _tag_id(rid: str, tag: str) -> str:
         return f"{rid}_tag={tag}"
+
+    def expand_uri(self, uri: str, context: Context, is_file: bool, encoding: str) -> str:
+        raise not_supported()
 
     class RecordExists(Exception):
         pass

kgforge/specializations/stores/nexus/service.py

@@ -95,7 +95,6 @@ def __init__(
         files_download_config: Dict,
         **params,
     ):
-
         nexus.config.set_environment(endpoint)
         self.endpoint = endpoint
         self.organisation = org
@@ -241,7 +240,8 @@ def __init__(
 
     def get_project_context(self) -> Dict:
         project_data = nexus.projects.fetch(self.organisation, self.project)
-        context = {"@base": project_data["base"], "@vocab": project_data["vocab"]}
+        context = {"@base": project_data["base"], "@vocab": project_data["vocab"],
+                   "api_mappings": project_data["apiMappings"]}
         return context
 
     def resolve_context(self, iri: str, local_only: Optional[bool] = False) -> Dict:

tests/specializations/stores/test_bluebrain_nexus.py

@@ -18,18 +18,19 @@
 from urllib.parse import urljoin
 from urllib.request import pathname2url
 from uuid import uuid4
-from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
 
 import nexussdk
 import pytest
 from typing import Callable, Union, List
+from collections import OrderedDict
 
 from kgforge.core import Resource
 from kgforge.core.archetypes import Store
 from kgforge.core.commons.context import Context
 from kgforge.core.conversions.rdf import _merge_jsonld
 from kgforge.core.wrappings.dict import wrap_dict
 from kgforge.core.wrappings.paths import Filter, create_filters_from_dict
+from kgforge.core.commons.sparql_query_builder import SPARQLQueryBuilder
 from kgforge.specializations.stores.bluebrain_nexus import (
     BlueBrainNexus,
     _create_select_query,
@@ -40,10 +41,10 @@
 from kgforge.specializations.stores.nexus import Service
 
 BUCKET = "test/kgforge"
-NEXUS = "https://nexus-instance.org/"
+NEXUS = "https://nexus-instance.org"
 TOKEN = "token"
-NEXUS_PROJECT_CONTEXT = {"base": "http://data.net/", "vocab": "http://vocab.net/"}
-
+NEXUS_PROJECT_CONTEXT = {"base": "http://data.net", "vocab": "http://vocab.net",
+                         "apiMappings": [{'namespace': 'https://neuroshapes.org/dash/', 'prefix': 'datashapes'}]}
 VERSIONED_TEMPLATE = "{x.id}?rev={x._store_metadata._rev}"
 FILE_RESOURCE_MAPPING = os.sep.join(
     (os.path.curdir, "tests", "data", "nexus-store", "file-to-resource-mapping.hjson")
@@ -130,6 +131,11 @@ def nexus_store_unauthorized():
     return BlueBrainNexus(endpoint=NEXUS, bucket=BUCKET, token="invalid token")
 
 
+@pytest.fixture
+def nexus_context():
+    return Context(NEXUS_PROJECT_CONTEXT)
+
+
 def test_config_error():
     with pytest.raises(ValueError):
         BlueBrainNexus(endpoint="test", bucket="invalid", token="")
@@ -165,6 +171,29 @@ def test_to_resource(nexus_store, registered_building, building_jsonld):
     assert str(result._store_metadata) == str(registered_building._store_metadata)
 
 
+@pytest.mark.parametrize("url,expected",
+                         [
+                            pytest.param(
+                                ("myverycoolid123456789"),
+                                ("https://nexus-instance.org/files/test/kgforge/myverycoolid123456789"),
+                            id="simple-id",
+                            ),
+                            pytest.param(
+                                ("https://nexus-instance.org/files/test/kgforge/myverycoolid123456789"),
+                                ("https://nexus-instance.org/files/test/kgforge/myverycoolid123456789"),
+                            id="same-id",
+                            ),
+                            # pytest.param(
+                                # ("https://nexus-instance.org/files/test/kgforge/datashapes:example/myverycoolid123456789"),
+                                # ("https://nexus-instance.org/files/test/kgforge/https%3A%2F%2Fbbp.epfl.ch%2Fneurosciencegraph%2Fdata%2Fdatashapes/example/myverycoolid123456789"),
+                            # id="schema-id",
+                            # ),
+                         ])
+def test_expand_url(nexus_store, nexus_context, url, expected):
+    uri = nexus_store.expand_uri(url, context=nexus_context, is_file=True, encoding=None)
+    assert expected == uri
+
+
 class TestQuerying:
     @pytest.fixture
     def context(self):