nmdc-runtime 1.6.0__py3-none-any.whl → 1.7.0__py3-none-any.whl

{nmdc_runtime-1.6.0.dist-info → nmdc_runtime-1.7.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{nmdc_runtime-1.6.0.dist-info → nmdc_runtime-1.7.0.dist-info}/entry_points.txt

@@ -2,4 +2,3 @@
 nmdcdb-mongodump = nmdc_runtime.site.backup.nmdcdb_mongodump:main
 nmdcdb-mongoexport = nmdc_runtime.site.backup.nmdcdb_mongoexport:main
 nmdcdb-mongoimport = nmdc_runtime.site.backup.nmdcdb_mongoimport:main
-schemagen-terminusdb = nmdc_runtime.site.terminusdb.generate:cli

nmdc_runtime/site/terminusdb/generate.py

@@ -1,198 +0,0 @@
-"""
-Example usage:
-$ schemagen-terminusdb ../nmdc-schema/src/schema/nmdc.yaml \
-    > nmdc_runtime/site/terminusdb/nmdc.schema.terminusdb.json
-"""
-
-import json
-import os
-from typing import Union, TextIO, List
-
-import click
-from linkml.utils.generator import Generator, shared_arguments
-from linkml_runtime.linkml_model.meta import (
-    SchemaDefinition,
-    ClassDefinition,
-    SlotDefinition,
-)
-from linkml_runtime.utils.formatutils import camelcase, be, underscore
-
-# http://books.xmlschemata.org/relaxng/relax-CHP-19.html
-XSD_Ok = {
-    "xsd:anyURI",
-    "xsd:base64Binary",
-    "xsd:boolean",
-    "xsd:byte",
-    "xsd:date",
-    "xsd:dateTime",
-    "xsd:decimal",
-    "xsd:double",
-    "xsd:duration",
-    "xsd:ENTITIES",
-    "xsd:ENTITY",
-    "xsd:float",
-    "xsd:gDay",
-    "xsd:gMonth",
-    "xsd:gMonthDay",
-    "xsd:gYear",
-    "xsd:gYearMonth",
-    "xsd:hexBinary",
-    "xsd:ID",
-    "xsd:IDREF",
-    "xsd:IDREFS",
-    "xsd:int",
-    "xsd:integer",
-    "xsd:language",
-    "xsd:long",
-    "xsd:Name",
-    "xsd:NCName",
-    "xsd:negativeInteger",
-    "xsd:NMTOKEN",
-    "xsd:NMTOKENS",
-    "xsd:nonNegativeInteger",
-    "xsd:nonPositiveInteger",
-    "xsd:normalizedString",
-    "xsd:NOTATION",
-    "xsd:positiveInteger",
-    "xsd:short",
-    "xsd:string",
-    "xsd:time",
-    "xsd:token",
-    "xsd:unsignedByte",
-    "xsd:unsignedInt",
-    "xsd:unsignedLong",
-    "xsd:unsignedShort",
-}
-
-
-def as_list(thing) -> list:
-    return thing if isinstance(thing, list) else [thing]
-
-
-def has_field(graph: List[dict], cls: dict, field: str) -> bool:
-    if field in cls:
-        return True
-    for parent_id in as_list(cls.get("@inherits", [])):
-        parent_cls = next(
-            graph_cls for graph_cls in graph if graph_cls.get("@id") == parent_id
-        )
-        if parent_cls and has_field(graph, parent_cls, field):
-            return True
-    return False
-
-
-class TerminusdbGenerator(Generator):
-    """Generates JSON file to pass to WOQLClient.insert_document(..., graph_type="schema")`."""
-
-    generatorname = os.path.basename(__file__)
-    generatorversion = "0.1.0"
-    valid_formats = ["json"]
-    visit_all_class_slots = True
-
-    def __init__(self, schema: Union[str, TextIO, SchemaDefinition], **kwargs) -> None:
-        super().__init__(schema, **kwargs)
-        self.graph = []
-        self.cls_json = {}
-
-    def visit_schema(self, inline: bool = False, **kwargs) -> None:
-        self.graph.append(
-            {
-                "@type": "@context",
-                "@base": "https://api.microbiomedata.org/nmdcschema/ids/",
-                "@schema": "https://w3id.org/nmdc/",
-            }
-        )
-
-    def end_schema(self, **_) -> None:
-        for cls in self.graph:
-            if has_field(self.graph, cls, "id"):
-                cls["@key"] = {"@type": "Lexical", "@fields": ["id"]}
-        print(json.dumps(self.graph, indent=2))
-
-    def visit_class(self, cls: ClassDefinition) -> bool:
-        self.cls_json = {
-            "@type": "Class",
-            "@id": camelcase(cls.name),
-            "@documentation": {
-                "@comment": be(cls.description),
-                "@properties": {},
-            },
-        }
-        if cls.is_a:
-            self.cls_json["@inherits"] = camelcase(cls.is_a)
-        if cls.abstract:
-            self.cls_json["@abstract"] = []
-        return True
-
-    def end_class(self, cls: ClassDefinition) -> None:
-        self.cls_json["@id"] = cls.definition_uri.split(":")[-1].rpartition("/")[-1]
-        self.graph.append(self.cls_json)
-
-    # sounding board as solist
-    # safe space to ask questions. more of a whatsapp group.
-    # both re: business, how to structure proposals, etc.
-    # And also technical content suggestions. R data pipeline / copy/paste in Figma
-    #  - how far do you go in automation in delivery
-
-    def visit_class_slot(
-        self, cls: ClassDefinition, aliased_slot_name: str, slot: SlotDefinition
-    ) -> None:
-        if slot not in self.own_slots(cls):
-            return
-        if slot.is_usage_slot:
-            # TerminusDB does not support calling different things the same name.
-            # So, ignore usage overrides.
-            slot = self.schema.slots[aliased_slot_name]
-
-        if slot.range in self.schema.classes:
-            rng = camelcase(slot.range)
-        elif slot.range in self.schema.types:
-            # XXX Why does `linkml.utils.metamodelcore.Identifier` subclass `str`??
-            rng = str(self.schema.types[slot.range].uri)
-        else:
-            rng = "xsd:string"
-
-        # name = (
-        #     f"{cls.name} {aliased_slot_name}"
-        #     if slot.is_usage_slot
-        #     else aliased_slot_name
-        # )
-        name = slot.name
-        # TODO fork nmdc schema and make any slots NOT required in parent class
-        #  also NOT required in child classes. Can have opt-in entity validation logic in code.
-
-        # XXX MAG bin -> bin name goes to "mAGBin__bin_name", etc. Weird.
-
-        # # translate to terminusdb xsd builtins:
-        # if rng == "xsd:int":
-        #     rng = "xsd:integer"
-        # elif rng == "xsd:float":
-        #     rng = "xsd:double"
-        # elif rng == "xsd:language":
-        #     rng = "xsd:string"
-
-        if rng not in XSD_Ok and slot.range not in self.schema.classes:
-            raise Exception(
-                f"slot range for {name} must be schema class or supported xsd type. "
-                f"Range {rng} is of type {type(rng)}."
-            )
-
-        self.cls_json[underscore(name)] = rng
-        self.cls_json["@documentation"]["@properties"][
-            underscore(name)
-        ] = slot.description
-        if not slot.required:
-            self.cls_json[underscore(name)] = {"@type": "Optional", "@class": rng}
-        if slot.multivalued:  # XXX what about an required multivalued field?
-            self.cls_json[underscore(name)] = {"@type": "Set", "@class": rng}
-
-
-@shared_arguments(TerminusdbGenerator)
-@click.command()
-def cli(yamlfile, **args):
-    """Generate graphql representation of a biolink model"""
-    print(TerminusdbGenerator(yamlfile, **args).serialize(**args))
-
-
-if __name__ == "__main__":
-    cli()

nmdc_runtime/site/terminusdb/ingest.py

@@ -1,44 +0,0 @@
-import json
-from pathlib import Path
-
-from terminusdb_client import WOQLClient
-
-team = "admin"
-client = WOQLClient(f"http://localhost:6364/")
-# make sure you have put the token in environment variable
-# https://docs.terminusdb.com/v10.0/#/terminusx/get-your-api-key
-client.connect(user=team, team=team, key="root")
-
-dbid = "nmdc"
-label = "NMDC"
-description = "."
-prefixes = {
-    "@base": "terminusdb:///data/",
-    "@schema": "terminusdb:///schema#",
-    "gold": "https://gold.jgi.doe.gov/biosample?id=",
-}
-
-
-def import_schema(client):
-    # sd = get_nmdc_schema_definition()
-    # sd.source_file = f"{REPO_ROOT_DIR.parent}/nmdc-schema/src/schema/nmdc.yaml"
-    # print(sd.source_file)
-    with open(Path(__file__).parent.joinpath("nmdc.schema.terminusdb.json")) as f:
-        schema_objects = json.load(f)
-
-    client.message = "Adding NMDC Schema"
-    results = client.insert_document(schema_objects, graph_type="schema")
-    print(f"Added schema: {results}")
-
-
-if __name__ == "__main__":
-    exists = client.get_database(dbid)
-
-    if exists:
-        client.delete_database(dbid, team=team, force=True)
-
-    client.create_database(
-        dbid, team, label=label, description=description, prefixes=prefixes
-    )
-
-    import_schema(client)