lx-dtypes 0.1.1__py3-none-any.whl

lx_dtypes/conftest.py

@@ -0,0 +1,245 @@
+from lx_dtypes.models.base.app_base_model.test_fixtures import (
+    app_base_model_data_dict_fixture,
+    app_base_model_names_uuid_tags_data_dict_fixture,
+    app_base_model_names_uuid_tags_pydantic_fixture,
+    app_base_model_pydantic_fixture,
+    app_base_model_uuid_tags_data_dict_fixture,
+    app_base_model_uuid_tags_pydantic_fixture,
+)
+from lx_dtypes.models.interface.test_fixtures import (
+    db_interface_fixture,
+    knowledge_base_fixture,
+    ledger_fixture,
+    lx_knowledge_base,
+)
+from lx_dtypes.models.interface.test_fixtures.dataloader import (
+    empty_data_loader,
+    initialized_demo_kb_config,
+    uninitialized_demo_kb_config,
+    yaml_data_loader,
+)
+from lx_dtypes.models.interface.test_fixtures.names import demo_kb_config_name
+from lx_dtypes.models.interface.test_fixtures.paths import (
+    log_dir,
+    sample_citations_yaml_filepath,
+    sample_classification_choices_yaml_filepath,
+    sample_classifications_yaml_filepath,
+    sample_examination_types_yaml_filepath,
+    sample_examinations_yaml_filepath,
+    sample_findings_yaml_filepath,
+    sample_indications_yaml_filepath,
+    sample_information_source_yaml_filepath,
+    sample_interventions_yaml_filepath,
+    yaml_repo_dirs,
+)
+from lx_dtypes.models.interface.test_fixtures.star_upper_gi.dataloader import (
+    star_ugi_initialized_kb_config,
+    star_ugi_knowledge_base,
+    star_ugi_yaml_data_loader,
+)
+from lx_dtypes.models.knowledge_base.citation.test_fixtures import (
+    citation_fixture,
+    django_citation_fixture,
+)
+from lx_dtypes.models.knowledge_base.classification.test_fixtures import (
+    classification_fixture,
+    classification_type_fixture,
+    django_classification_fixture,
+    django_classification_type_fixture,
+)
+from lx_dtypes.models.knowledge_base.classification_choice.test_fixtures import (
+    classification_choice_fixture,
+    django_classification_choice_fixture,
+)
+from lx_dtypes.models.knowledge_base.classification_choice_descriptor.test_fixtures import (
+    classification_choice_descriptor_fixture,
+    django_classification_choice_descriptor_fixture,
+)
+from lx_dtypes.models.knowledge_base.examination.test_fixtures import (
+    django_examination_fixture,
+    django_examination_type_fixture,
+    examination_fixture,
+    examination_type_fixture,
+)
+from lx_dtypes.models.knowledge_base.finding.test_fixtures import (
+    django_finding_fixture,
+    django_finding_type_fixture,
+    finding_fixture,
+    finding_type_fixture,
+)
+from lx_dtypes.models.knowledge_base.indication.test_fixtures import (
+    django_indication_fixture,
+    django_indication_type_fixture,
+    indication_fixture,
+    indication_type_fixture,
+)
+from lx_dtypes.models.knowledge_base.intervention.test_fixtures import (
+    django_intervention_fixture,
+    django_intervention_type_fixture,
+    intervention_fixture,
+    intervention_type_fixture,
+)
+from lx_dtypes.models.knowledge_base.unit.test_fixtures import (
+    django_unit_fixture,
+    django_unit_type_fixture,
+    unit_fixture,
+    unit_type_fixture,
+)
+from lx_dtypes.models.ledger.center.test_fixtures import (
+    center_fixture,
+    django_center_fixture,
+)
+from lx_dtypes.models.ledger.p_examination.test_fixtures import (
+    django_p_examination_fixture,
+    django_populated_p_examination_fixture,
+    p_examination_fixture,
+)
+from lx_dtypes.models.ledger.p_finding.test_fixtures import (
+    django_p_finding_fixture,
+    django_populated_p_finding_fixture,
+    p_finding_fixture,
+)
+from lx_dtypes.models.ledger.p_finding_classification_choice.test_fixtures import (
+    django_p_finding_classification_choice_fixture,
+    django_populated_p_finding_classification_choice_fixture,
+    p_finding_classification_choice_fixture,
+)
+from lx_dtypes.models.ledger.p_finding_classification_choice_descriptor.test_fixtures import (
+    django_p_finding_classification_choice_descriptor_fixture,
+    p_finding_classification_choice_descriptor_fixture,
+)
+from lx_dtypes.models.ledger.p_finding_classifications.test_fixtures import (
+    django_p_finding_classifications_fixture,
+    django_populated_p_finding_classifications_fixture,
+    p_finding_classifications_fixture,
+)
+from lx_dtypes.models.ledger.p_indication.test_fixtures import (
+    django_p_indication_fixture,
+    p_indication_fixture,
+)
+from lx_dtypes.models.ledger.p_intervention.test_fixtures import (
+    django_p_finding_intervention_fixture,
+    p_finding_intervention_fixture,
+)
+from lx_dtypes.models.ledger.p_interventions.test_fixtures import (
+    django_p_finding_interventions_fixture,
+    django_populated_p_finding_interventions_fixture,
+    p_finding_interventions_fixture,
+)
+from lx_dtypes.models.ledger.patient.test_fixtures import (
+    django_patient_fixture,
+    patient_fixture,
+)
+
+__all__ = [
+    # App Base Model Fixtures
+    "app_base_model_data_dict_fixture",
+    "app_base_model_uuid_tags_data_dict_fixture",
+    "app_base_model_names_uuid_tags_data_dict_fixture",
+    "app_base_model_pydantic_fixture",
+    "app_base_model_uuid_tags_pydantic_fixture",
+    "app_base_model_names_uuid_tags_pydantic_fixture",
+    # Citation Fixtures
+    "citation_fixture",
+    "django_citation_fixture",
+    # Classification Fixtures
+    "classification_fixture",
+    "classification_type_fixture",
+    "django_classification_fixture",
+    "django_classification_type_fixture",
+    # Classification Choice Fixtures
+    "classification_choice_fixture",
+    "django_classification_choice_fixture",
+    # Classification Choice Descriptor Fixtures
+    "classification_choice_descriptor_fixture",
+    "django_classification_choice_descriptor_fixture",
+    # Examination Fixtures
+    "examination_fixture",
+    "examination_type_fixture",
+    "django_examination_fixture",
+    "django_examination_type_fixture",
+    # Finding Fixtures
+    "finding_fixture",
+    "finding_type_fixture",
+    "django_finding_fixture",
+    "django_finding_type_fixture",
+    # Indication Fixtures
+    "indication_fixture",
+    "indication_type_fixture",
+    "django_indication_fixture",
+    "django_indication_type_fixture",
+    # Intervention Fixtures
+    "intervention_fixture",
+    "intervention_type_fixture",
+    "django_intervention_fixture",
+    "django_intervention_type_fixture",
+    # Unit Fixtures
+    "unit_type_fixture",
+    "unit_fixture",
+    "django_unit_type_fixture",
+    "django_unit_fixture",
+    # db Interface Fixtures
+    "db_interface_fixture",
+    "knowledge_base_fixture",
+    "ledger_fixture",
+    # Path Fixtures
+    "yaml_repo_dirs",
+    "log_dir",
+    "sample_citations_yaml_filepath",
+    "sample_classifications_yaml_filepath",
+    "sample_classification_choices_yaml_filepath",
+    "sample_examinations_yaml_filepath",
+    "sample_examination_types_yaml_filepath",
+    "sample_findings_yaml_filepath",
+    "sample_indications_yaml_filepath",
+    "sample_interventions_yaml_filepath",
+    "sample_information_source_yaml_filepath",
+    # Names
+    "demo_kb_config_name",
+    # YAML Dataloader
+    "empty_data_loader",
+    "initialized_demo_kb_config",
+    "uninitialized_demo_kb_config",
+    "yaml_data_loader",
+    # lx Knowledge Base Fixtures
+    "lx_knowledge_base",
+    ########### Ledger Fixtures ###########
+    "center_fixture",
+    "django_center_fixture",
+    # Patient Examination Fixtures
+    "p_examination_fixture",
+    "django_p_examination_fixture",
+    "django_populated_p_examination_fixture",
+    # Patient Finding Fixtures
+    "p_finding_fixture",
+    "django_p_finding_fixture",
+    "django_populated_p_finding_fixture",
+    # Patient Indication Fixtures
+    "p_indication_fixture",
+    "django_p_indication_fixture",
+    # Patient Interventions fixtures
+    "p_finding_interventions_fixture",
+    "django_p_finding_interventions_fixture",
+    "django_populated_p_finding_interventions_fixture",
+    # Patient Finding Intervention Fixtures
+    "p_finding_intervention_fixture",
+    "django_p_finding_intervention_fixture",
+    # Patient Finding Classifications Fixtures
+    "p_finding_classifications_fixture",
+    "django_p_finding_classifications_fixture",
+    "django_populated_p_finding_classifications_fixture",
+    # Patient Finding Classification Choice Fixtures
+    "p_finding_classification_choice_fixture",
+    "django_p_finding_classification_choice_fixture",
+    "django_populated_p_finding_classification_choice_fixture",
+    # Patient Finding Classification Choice Descriptor Fixtures
+    "p_finding_classification_choice_descriptor_fixture",
+    "django_p_finding_classification_choice_descriptor_fixture",
+    # Patient Fixtures
+    "patient_fixture",
+    "django_patient_fixture",
+    # STAR UGI
+    "star_ugi_yaml_data_loader",
+    "star_ugi_initialized_kb_config",
+    "star_ugi_knowledge_base",
+]

lx_dtypes/data/README.md

@@ -0,0 +1,49 @@
+# Knowledge Base Data
+This directory bundles the canonical data modules that ship with LX data models. Every subdirectory that contains a `config.yaml` is a loadable module and can declare dependencies on siblings so the loader can resolve an ordered data graph.
+
+*Content*
+- [1. Module Overview](#1-module-overview)
+- [2. Detailed Module Notes](#2-detailed-module-notes)
+- [3. Extending Or Overriding](#3-extending-or-overriding)
+
+## 1. Module Overview
+| Module Path | Purpose | Key Data | Depends On |
+| --- | --- | --- | --- |
+| `sample_knowledge_base/` | Top-level package that mirrors the current working knowledge base. Aggregates all core modules through `modules` field. | Pulls in everything below; no direct data files. | `information_source_data`, `citations`, `lx_utils`, `lx_hardware`, `example_terminology` |
+| `information_source_data/` | Seeds canonical information sources so downstream modules can reference consistent IDs. | `data/unknown.yaml`. | None |
+| `citations/` | Bibliography references shared across models. | `data/sample_references.yaml`, `sample_references.bib`. | None |
+| `lx_utils/` | Cross-cutting utility enumerations (genders, tags, units, etc.). | Nested `gender/`, `tag/`, `unit/` submodules each with `default.yaml`. | `information_source_data` |
+| `lx_hardware/` | Placeholder hardware knowledge base; currently empty but structured for overrides. | Declares empty `files`/`dirs`. | `lx_utils` |
+| `terminology/` (`example_terminology`) | Grouping module that wires up the clinical terminology stack. | Delegates to `lx_*` submodules listed below. | None |
+| `terminology/lx_units/` | Canonical units referenced by descriptors. | `data/`. | None |
+| `terminology/lx_descriptors/` | Descriptor vocabulary with localized labels and metadata. | `data/`. | `lx_units` |
+| `terminology/lx_classification_choices/` | Atomic choices used by classifications. | `data/`. | `lx_descriptors` |
+| `terminology/lx_classifications/` | Classification definitions and types. | `data/`, `classification_types/`. | `lx_classification_choices` |
+| `terminology/lx_interventions/` | Intervention catalog and type data. | `data/`, `intervention_types/`. | None |
+| `terminology/lx_findings/` | Finding catalog plus finding/former_event/type folders. | `data/`, `finding_types/`, `former_events/`. | `lx_classifications` |
+| `terminology/lx_indications/` | Indication catalog plus types. | `data/`, `indication_types/`. | `lx_interventions`, `lx_classifications` |
+| `terminology/lx_examinations/` | Examination definitions that stitch findings, indications, interventions. | `data/`. | `lx_findings`, `lx_indications`, `lx_interventions` |
+| `logs/` | Golden log snapshots for tests, grouped by suite. | `tests/` with dated YAML logs, `scripts/` placeholder. | None (test fixture only) |
+| `endoreg/` | Placeholder for center-specific overrides. | Empty `center/` folder. | None |
+| `mock/` | Reserved for ad-hoc mock data during development. | Currently empty. | None |
+
+The dependency column mirrors the `depends_on` stanza in each module's `config.yaml`. Load order is depth-first according to those relationships, so higher-level packs such as `sample_knowledge_base` or `example_terminology` are thin orchestrators.
+
+## 2. Detailed Module Notes
+- **Configuration contracts**: Every module root carries a `config.yaml` that at minimum defines `name`, `version`, and optional `modules`, `depends_on`, and `data` entries. Relative `data.dirs` paths are resolved from the module directory, and folders are scanned recursively in ascending filename order.
+- **Sample knowledge base**: `sample_knowledge_base/config.yaml` lists the exact module order used in tests. Add custom modules by appending to its `modules` array or by creating a new top-level module that depends on this one.
+- **Utility submodules**: Under `lx_utils/`, each child (`gender`, `tag`, `unit`) is an independent module so that downstream packs can cherry-pick only the enumerations they need. Their `config.yaml` files omit `depends_on` unless coupling is required.
+- **Terminology stack**: `terminology/config.yaml` introduces the alias `example_terminology`, which subsequently imports the six `lx_*` terminology modules. This indirection allows you to swap entire terminology bundles by changing a single module reference.
+- **Logs as fixtures**: The `logs/tests/` tree stores YAML exports generated by the automated suites (`TestKnowledgebaseBaseModel`, `TestLogWriter`, `TestParser`, etc.). While not consumed by the knowledge base loader, keeping them under `data/` simplifies packaging when fixtures must accompany deployments.
+- **Placeholders**: `endoreg/` and `mock/` intentionally ship empty so integrators can copy the directory layout when creating client-specific overrides without touching the shared modules.
+
+## 3. Extending Or Overriding
+To extend this corpus, create a new module directory beside the existing ones:
+
+1. Add a `config.yaml` that declares `depends_on` entries for every module you need (for instance, `$new_module` might depend on `sample_knowledge_base`).
+2. Point `data.dirs` at the folders that contain your YAML payloads. Use the same folder conventions (`data/`, `*_types/`, etc.) to stay compatible with the loader.
+3. Register the module by either
+	- referencing it from another module's `modules` array (e.g., append to `sample_knowledge_base/config.yaml`), or
+	- loading it explicitly when constructing the knowledge base in code.
+
+Because dependencies are DAG-based and processed in order, later modules can override IDs defined by earlier ones. For example, placing `$custom_findings` after `terminology/lx_findings` allows you to tweak a subset of findings without copying the entire catalog.

lx_dtypes/data/citations/config.yaml

@@ -0,0 +1,7 @@
+name: citations
+description: "Bibliographic references for LX data models"
+version: 0.1.0
+modules: []
+data:
+  dirs:
+    - ./data