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["psycopg2-binary"] [metadata] lock-version = "2.1" python-versions = "^3.9" -content-hash = "6875551e277cc703a124e57f84d0fa65ba60e8a77f619f1e5786e6bd4d498b85" +content-hash = "36592b2404117e8f8e38e7c1b6b170def08c65c362e74c4e35bfd190d8a9225b" diff --git a/pyproject.toml b/pyproject.toml index a481bf9..9533229 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -32,7 +32,7 @@ packages = [ [tool.poetry.dependencies] python = "^3.9" -linkml = "^1.7.4" +linkml = "^1.9.1" pandas = ">=1.3.5" python-dateutil = ">=2.8.2" quantulum3 = ">=0.7.9" @@ -45,8 +45,8 @@ oaklib = ">=0.5.25" pandera = ">=0.12.0" tomlkit = ">=0.11.4" inflect = ">=6.0.0" -schemasheets = ">=0.1.24" -linkml-runtime = "^1.7.2" +schemasheets = "^0.4.0" +linkml-runtime = "^1.9.2" duckdb = { version = "^0.10.1", optional = true } click = "^8.1.7" deprecated = "^1.2.15" diff --git a/schema_automator/annotators/schema_annotator.py b/schema_automator/annotators/schema_annotator.py index 514301a..a305419 100644 --- a/schema_automator/annotators/schema_annotator.py +++ b/schema_automator/annotators/schema_annotator.py @@ -1,12 +1,13 @@ import click import logging +import re import yaml from dataclasses import dataclass from typing import List, Union, Iterator from linkml_runtime.linkml_model import SchemaDefinition, Element, PermissibleValue, ClassDefinition, SlotDefinition from linkml_runtime.utils.metamodelcore import Curie -from linkml_runtime.utils.schemaview import SchemaView, re, EnumDefinition +from linkml_runtime.utils.schemaview import SchemaView, EnumDefinition from oaklib import BasicOntologyInterface from oaklib.datamodels.search import SearchConfiguration from oaklib.datamodels.text_annotator import TextAnnotation diff --git a/schema_automator/importers/jsonschema_import_engine.py b/schema_automator/importers/jsonschema_import_engine.py index 98d571f..fec8629 100644 --- a/schema_automator/importers/jsonschema_import_engine.py +++ b/schema_automator/importers/jsonschema_import_engine.py @@ -101,7 +101,7 @@ def import_project(self, import_directory: str, export_directory: str, match_suf if rng in schema.classes: # no need to self-import continue - import_module_name = class_name_to_module_map[rng] + import_module_name = rel + class_name_to_module_map[rng] if import_module_name not in schema.imports: logging.info(f"Adding import to {import_module_name} in {schema.name} for {rng}") schema.imports.append(import_module_name)