sdc-gdr2fhir 4.0.0__tar.gz

sdc_gdr2fhir-4.0.0/LICENSE

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sdc_gdr2fhir-4.0.0/NOTICE

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+Copyright 2026 Axius SDC, Inc.
+
+Licensed under the Apache License, Version 2.0.
+
+src/sdc_gdr2fhir/schemas/fhir.schema.json is the JSON schema published with HL7 FHIR Release 4 (4.0.1),
+http://hl7.org/fhir/R4/fhir.schema.json.zip, unmodified. The FHIR specification is © HL7 and licensed under Creative
+Commons "No Rights Reserved" (CC0); HL7®, HEALTH LEVEL SEVEN®, FHIR® and the FHIR® flame logo are trademarks owned by
+Health Level Seven International, registered with the United States Patent and Trademark Office. This package does
+not claim that HL7 or any of its members endorses it.
+
+The package ships no terminology content. LOINC, SNOMED CT, ICD-10-CM and NCI Thesaurus codes appear in its output, its
+mapping files and its tests only as the published models bind them and the records carry them.
+
+The test fixtures under samples/ are the published packages of the NHANES Participant and NHANES Medication models of
+the FAIR Data Demo (https://github.com/SemanticDataCharter/FAIR_Data_Demo, Apache 2.0) and a seeded sample of 200
+records of each, generated by that project from the CDC's NHANES 2017-2018 public release.

sdc_gdr2fhir-4.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: sdc-gdr2fhir
+Version: 4.0.0
+Summary: Governed Data Records as HL7 FHIR R4 Bundles, through sdc-mapper: one mapping file per model, every value reported, Exceptional Values preserved.
+Author: Axius SDC, Inc.
+License-Expression: Apache-2.0
+Project-URL: Repository, https://github.com/SemanticDataCharter/sdc-gdr2fhir
+Keywords: sdc,semantic data charter,governed data record,fhir,hl7,r4,mapping,null flavor
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: sdc-mapper<5,>=4.2
+Requires-Dist: jsonschema>=4.20
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: pyyaml>=6.0; extra == "dev"
+Requires-Dist: lxml>=5.0; extra == "dev"
+Dynamic: license-file
+
+# sdc-gdr2fhir
+
+Governed Data Records as HL7 FHIR R4 Bundles. A target mapper for
+[sdc-mapper](https://github.com/SemanticDataCharter/sdc-mapper): the core validates the record, resolves every value
+against its model and reports each one; this package says which FHIR resource and element each value goes in and
+writes the Bundle. Outbound only. Apache 2.0.
+
+**Status:** 4.0.0 in development. Models so far, from the FAIR Data Demo:
+
+| Model | ct_id | Resources | Rules |
+|---|---|---|---|
+| NHANES Participant | `xy8upneajsb8vdcmnve01g6g` | Patient, Observation, QuestionnaireResponse | 112 |
+| NHANES Medication | `epbdfmvxc3gbh5f66hhb3o2m` | Patient, MedicationStatement, QuestionnaireResponse | 18 |
+
+## Use
+
+```python
+from sdc_mapper import Engine, load_mapping
+from sdc_gdr2fhir import FHIRMapper, mapping_path
+
+result = Engine().map_record(xml, FHIRMapper(), load_mapping(mapping_path("xy8upneajsb8vdcmnve01g6g")))
+result.files["Bundle.json"]     # a FHIR R4 Bundle of type collection
+result.report                   # every value: lookup, declared or not representable; every Exceptional Value
+```
+
+Through sdc-mapper's CLI and MCP server the mapper is the target `fhir`.
+
+## The target
+
+**HL7 FHIR Release 4 (4.0.1)**, JSON. The specification is © HL7 and licensed under Creative Commons "No Rights
+Reserved" (CC0); its terms allow redistribution and implementation-related products, so long as no one claims HL7's
+endorsement and no altered specification is published as FHIR. HL7® and FHIR® are HL7's trademarks. This package
+carries the FHIR R4 JSON schema unmodified (see `NOTICE`) and ships no terminology: LOINC, SNOMED CT, ICD-10-CM and NCI
+Thesaurus codes appear only as the models bind them and the records carry them.
+
+Every Bundle this package writes is valid against the FHIR R4 JSON schema, resource by resource and as a Bundle, or is
+not written. The schema checks structure, types, required members and code patterns; it does not check FHIR's
+invariants or terminology bindings. `tests/` runs the HL7 FHIR validator (`validator_cli.jar`) too, where Java and the
+validator are installed (`FHIR_VALIDATOR_JAR`); it has not been run for this version.
+
+## Where values go
+
+Each record is one Bundle of type `collection`, identified by the record's instance id
+(`https://semanticdatacharter.com/ns/sdc4/instance`). Entry ids and `urn:uuid` fullUrls are derived from the instance
+id, so the same record gives the same bytes.
+
+- **Patient**: the respondent sequence number as an identifier, and the administrative gender.
+- **Observation**: each blood pressure reading (the vital signs blood pressure panel, LOINC 85354-9, with systolic and
+  diastolic as components, body site and status), the heart rate and each laboratory result, with the LOINC code the
+  model binds and UCUM units; smoking status, with the model's LOINC code and the answer's LOINC answer code; each
+  chronic condition indicator, with the SNOMED CT concept the model names as its subject and the Yes or No answer's
+  LOINC answer code. A condition indicator is the answer to "has a doctor ever told you", so it is an Observation of
+  the answer, not a Condition.
+- **MedicationStatement**: the NHANES generic drug code and name, the ICD-10-CM reasons, and the status from "taken in
+  the past month" (Yes is active, No not-taken).
+- **QuestionnaireResponse**: every other survey answer, an item each, linkId the component's identifier and text its
+  label; a Coding where the model binds each of the answer's values to its own code, else the answer as recorded.
+
+**Lookup or declared.** Where the model binds the code FHIR needs (a laboratory result's LOINC code, a condition's
+SNOMED CT subject, an answer's LOINC answer code, an administrative gender, an observation status), the code written
+is the model's own and the value is a **lookup**; `tools/build_mapping.py` copies those bindings from the model into
+the mapping file, and the mapper checks at run time that the code it writes is one the model binds. Which resource and
+element a value goes in is **declared**, one mapping file per model.
+
+For the 200 sample records of each model:
+
+| Model | lookup | declared | not representable |
+|---|---|---|---|
+| NHANES Participant | 9,093 (65.8% of the data values) | 4,733 | 5,400 (provenance and audit) |
+| NHANES Medication | 0 | 1,591 (100% of the data values) | 5,400 (provenance and audit) |
+
+The medication model binds its ICD-10-CM and drug code components to their code systems, not each value to a code,
+so its codes are written as the record holds them: declared.
+
+## Exceptional Values: every one preserved
+
+FHIR is the target that can say what an Exceptional Value says. Where the data-absent-reason code system
+(`http://terminology.hl7.org/CodeSystem/data-absent-reason`) has the concept, an Observation's (or component's) value
+is replaced by `dataAbsentReason`, and any other element carries the data-absent-reason extension. The null flavors
+data-absent-reason has no concept for are written exactly from v3 NullFlavor
+(`http://terminology.hl7.org/CodeSystem/v3-NullFlavor`), as the `iso21090-nullFlavor` extension on the element or a v3
+NullFlavor coding of `dataAbsentReason` (whose binding is extensible). v3 NullFlavor has no Asked and Refused;
+data-absent-reason does.
+
+| ISO 21090 | Written as | Class |
+|---|---|---|
+| UNK | data-absent-reason `unknown` | preserved |
+| ASKU | data-absent-reason `asked-unknown` | preserved |
+| NAV | data-absent-reason `temp-unknown` | preserved |
+| NASK | data-absent-reason `not-asked` | preserved |
+| ASKR | data-absent-reason `asked-declined` | preserved |
+| MSK | data-absent-reason `masked` | preserved |
+| NA | data-absent-reason `not-applicable` | preserved |
+| NINF | data-absent-reason `negative-infinity` | preserved |
+| PINF | data-absent-reason `positive-infinity` | preserved |
+| NI, INV, DER, OTH, UNC, QS, TRC | v3 NullFlavor, the same code | preserved |
+
+A mapping file cannot change this table.
+
+## What FHIR cannot hold here
+
+- **The record's provenance and audit.** FHIR's Provenance and AuditEvent require a recorded instant with a time
+  zone, and the FAIR Data Demo records' times carry none; the PROV and audit values are reported as not representable,
+  with that reason.
+- **Times without a time zone.** FHIR's dateTime requires a time zone with a time; an observation's date and time is
+  written as its date.
+- Validity windows and recording times (act, vtb, vte, tr), and the definitions each component is bound to beyond the
+  codes written.
+
+## Tests
+
+```
+pip install -e ".[dev]"
+python -m pytest
+```
+
+Every sample record is mapped and each resource validated against the FHIR R4 JSON schema; Bundles are byte-stable;
+lookups, Exceptional Values and refused mappings are exercised.

sdc_gdr2fhir-4.0.0/README.md

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+# sdc-gdr2fhir
+
+Governed Data Records as HL7 FHIR R4 Bundles. A target mapper for
+[sdc-mapper](https://github.com/SemanticDataCharter/sdc-mapper): the core validates the record, resolves every value
+against its model and reports each one; this package says which FHIR resource and element each value goes in and
+writes the Bundle. Outbound only. Apache 2.0.
+
+**Status:** 4.0.0 in development. Models so far, from the FAIR Data Demo:
+
+| Model | ct_id | Resources | Rules |
+|---|---|---|---|
+| NHANES Participant | `xy8upneajsb8vdcmnve01g6g` | Patient, Observation, QuestionnaireResponse | 112 |
+| NHANES Medication | `epbdfmvxc3gbh5f66hhb3o2m` | Patient, MedicationStatement, QuestionnaireResponse | 18 |
+
+## Use
+
+```python
+from sdc_mapper import Engine, load_mapping
+from sdc_gdr2fhir import FHIRMapper, mapping_path
+
+result = Engine().map_record(xml, FHIRMapper(), load_mapping(mapping_path("xy8upneajsb8vdcmnve01g6g")))
+result.files["Bundle.json"]     # a FHIR R4 Bundle of type collection
+result.report                   # every value: lookup, declared or not representable; every Exceptional Value
+```
+
+Through sdc-mapper's CLI and MCP server the mapper is the target `fhir`.
+
+## The target
+
+**HL7 FHIR Release 4 (4.0.1)**, JSON. The specification is © HL7 and licensed under Creative Commons "No Rights
+Reserved" (CC0); its terms allow redistribution and implementation-related products, so long as no one claims HL7's
+endorsement and no altered specification is published as FHIR. HL7® and FHIR® are HL7's trademarks. This package
+carries the FHIR R4 JSON schema unmodified (see `NOTICE`) and ships no terminology: LOINC, SNOMED CT, ICD-10-CM and NCI
+Thesaurus codes appear only as the models bind them and the records carry them.
+
+Every Bundle this package writes is valid against the FHIR R4 JSON schema, resource by resource and as a Bundle, or is
+not written. The schema checks structure, types, required members and code patterns; it does not check FHIR's
+invariants or terminology bindings. `tests/` runs the HL7 FHIR validator (`validator_cli.jar`) too, where Java and the
+validator are installed (`FHIR_VALIDATOR_JAR`); it has not been run for this version.
+
+## Where values go
+
+Each record is one Bundle of type `collection`, identified by the record's instance id
+(`https://semanticdatacharter.com/ns/sdc4/instance`). Entry ids and `urn:uuid` fullUrls are derived from the instance
+id, so the same record gives the same bytes.
+
+- **Patient**: the respondent sequence number as an identifier, and the administrative gender.
+- **Observation**: each blood pressure reading (the vital signs blood pressure panel, LOINC 85354-9, with systolic and
+  diastolic as components, body site and status), the heart rate and each laboratory result, with the LOINC code the
+  model binds and UCUM units; smoking status, with the model's LOINC code and the answer's LOINC answer code; each
+  chronic condition indicator, with the SNOMED CT concept the model names as its subject and the Yes or No answer's
+  LOINC answer code. A condition indicator is the answer to "has a doctor ever told you", so it is an Observation of
+  the answer, not a Condition.
+- **MedicationStatement**: the NHANES generic drug code and name, the ICD-10-CM reasons, and the status from "taken in
+  the past month" (Yes is active, No not-taken).
+- **QuestionnaireResponse**: every other survey answer, an item each, linkId the component's identifier and text its
+  label; a Coding where the model binds each of the answer's values to its own code, else the answer as recorded.
+
+**Lookup or declared.** Where the model binds the code FHIR needs (a laboratory result's LOINC code, a condition's
+SNOMED CT subject, an answer's LOINC answer code, an administrative gender, an observation status), the code written
+is the model's own and the value is a **lookup**; `tools/build_mapping.py` copies those bindings from the model into
+the mapping file, and the mapper checks at run time that the code it writes is one the model binds. Which resource and
+element a value goes in is **declared**, one mapping file per model.
+
+For the 200 sample records of each model:
+
+| Model | lookup | declared | not representable |
+|---|---|---|---|
+| NHANES Participant | 9,093 (65.8% of the data values) | 4,733 | 5,400 (provenance and audit) |
+| NHANES Medication | 0 | 1,591 (100% of the data values) | 5,400 (provenance and audit) |
+
+The medication model binds its ICD-10-CM and drug code components to their code systems, not each value to a code,
+so its codes are written as the record holds them: declared.
+
+## Exceptional Values: every one preserved
+
+FHIR is the target that can say what an Exceptional Value says. Where the data-absent-reason code system
+(`http://terminology.hl7.org/CodeSystem/data-absent-reason`) has the concept, an Observation's (or component's) value
+is replaced by `dataAbsentReason`, and any other element carries the data-absent-reason extension. The null flavors
+data-absent-reason has no concept for are written exactly from v3 NullFlavor
+(`http://terminology.hl7.org/CodeSystem/v3-NullFlavor`), as the `iso21090-nullFlavor` extension on the element or a v3
+NullFlavor coding of `dataAbsentReason` (whose binding is extensible). v3 NullFlavor has no Asked and Refused;
+data-absent-reason does.
+
+| ISO 21090 | Written as | Class |
+|---|---|---|
+| UNK | data-absent-reason `unknown` | preserved |
+| ASKU | data-absent-reason `asked-unknown` | preserved |
+| NAV | data-absent-reason `temp-unknown` | preserved |
+| NASK | data-absent-reason `not-asked` | preserved |
+| ASKR | data-absent-reason `asked-declined` | preserved |
+| MSK | data-absent-reason `masked` | preserved |
+| NA | data-absent-reason `not-applicable` | preserved |
+| NINF | data-absent-reason `negative-infinity` | preserved |
+| PINF | data-absent-reason `positive-infinity` | preserved |
+| NI, INV, DER, OTH, UNC, QS, TRC | v3 NullFlavor, the same code | preserved |
+
+A mapping file cannot change this table.
+
+## What FHIR cannot hold here
+
+- **The record's provenance and audit.** FHIR's Provenance and AuditEvent require a recorded instant with a time
+  zone, and the FAIR Data Demo records' times carry none; the PROV and audit values are reported as not representable,
+  with that reason.
+- **Times without a time zone.** FHIR's dateTime requires a time zone with a time; an observation's date and time is
+  written as its date.
+- Validity windows and recording times (act, vtb, vte, tr), and the definitions each component is bound to beyond the
+  codes written.
+
+## Tests
+
+```
+pip install -e ".[dev]"
+python -m pytest
+```
+
+Every sample record is mapped and each resource validated against the FHIR R4 JSON schema; Bundles are byte-stable;
+lookups, Exceptional Values and refused mappings are exercised.

sdc_gdr2fhir-4.0.0/pyproject.toml

@@ -0,0 +1,40 @@
+[build-system]
+requires = ["setuptools>=77"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "sdc-gdr2fhir"
+version = "4.0.0"
+description = "Governed Data Records as HL7 FHIR R4 Bundles, through sdc-mapper: one mapping file per model, every value reported, Exceptional Values preserved."
+readme = "README.md"
+requires-python = ">=3.12"
+license = "Apache-2.0"
+license-files = ["LICENSE", "NOTICE"]
+authors = [{ name = "Axius SDC, Inc." }]
+keywords = ["sdc", "semantic data charter", "governed data record", "fhir", "hl7", "r4", "mapping", "null flavor"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+dependencies = [
+    "sdc-mapper>=4.2,<5",     # placements, '=name' joins, declared cluster order (4.2.0)
+    "jsonschema>=4.20",       # the FHIR R4 JSON schema (draft-06)
+]
+
+[project.optional-dependencies]
+dev = ["pytest>=8.0", "pyyaml>=6.0", "lxml>=5.0"]
+
+[project.entry-points."sdc_mapper.targets"]
+fhir = "sdc_gdr2fhir:FHIRMapper"
+
+[project.urls]
+Repository = "https://github.com/SemanticDataCharter/sdc-gdr2fhir"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+sdc_gdr2fhir = ["mappings/*.yaml", "schemas/*.json"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+markers = ["validator: needs Java and the HL7 FHIR validator jar"]

sdc_gdr2fhir-4.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

sdc_gdr2fhir-4.0.0/src/sdc_gdr2fhir/__init__.py

@@ -0,0 +1,26 @@
+"""sdc-gdr2fhir: Governed Data Records as HL7 FHIR R4 Bundles, through sdc-mapper.
+
+    from sdc_mapper import Engine, load_mapping
+    from sdc_gdr2fhir import FHIRMapper, mapping_path
+    result = Engine().map_record(xml, FHIRMapper(), load_mapping(mapping_path("xy8upneajsb8vdcmnve01g6g")))
+
+One mapping file per model, in `mappings/`. Registered with sdc-mapper as the target `fhir`.
+"""
+from pathlib import Path
+
+__version__ = "4.0.0"
+
+MAPPINGS = Path(__file__).with_name("mappings")
+
+
+def mapping_path(ct_id: str) -> Path:
+    """The mapping file this package publishes for a model, by the model's identifier."""
+    found = sorted(MAPPINGS.glob(f"*-{ct_id}.yaml"))
+    if not found:
+        raise FileNotFoundError(f"sdc-gdr2fhir has no mapping for model {ct_id}")
+    return found[-1]
+
+
+from .mapper import FHIRMapper  # noqa: E402
+
+__all__ = ["FHIRMapper", "mapping_path", "MAPPINGS", "__version__"]

sdc_gdr2fhir-4.0.0/src/sdc_gdr2fhir/codes.py

@@ -0,0 +1,70 @@
+"""Codes as FHIR writes them: an IRI the model binds a value to, as a (system, code) pair FHIR's Coding takes.
+
+A model binds an enumerated value to its definition (`rdfs:isDefinedBy`) and a component to concepts (`skos:exactMatch`,
+`dcterms:subject`). Where such an IRI names one concept of a code system FHIR knows, the pair below is that concept as a
+FHIR Coding; an IRI that names a whole system, or a page that defines a variable rather than one answer, gives none.
+"""
+from __future__ import annotations
+
+import re
+
+LOINC = "http://loinc.org"
+SNOMED = "http://snomed.info/sct"
+NCIT = "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"
+UCUM = "http://unitsofmeasure.org"
+
+_PATTERNS = [
+    (re.compile(r"^https?://loinc\.org/((?:LA|LP|LG)?[0-9]+-[0-9])/?$"), LOINC),
+    (re.compile(r"^https?://snomed\.info/id/([0-9]+)$"), SNOMED),
+    (re.compile(r"^https?://purl\.obolibrary\.org/obo/NCIT_(C[0-9]+)$"), NCIT),
+]
+_FRAGMENT = re.compile(r"^(https?://(?:hl7\.org/fhir|terminology\.hl7\.org/CodeSystem)/[A-Za-z0-9./-]+)#([^#\s]+)$")
+
+
+def coding(iri: str | None) -> tuple[str, str] | None:
+    """The (system, code) an IRI names, or None."""
+    if not iri:
+        return None
+    for pattern, system in _PATTERNS:
+        m = pattern.match(iri)
+        if m:
+            return system, m.group(1)
+    m = _FRAGMENT.match(iri)
+    if m:
+        return m.group(1), m.group(2)
+    return None
+
+
+def bound_codes(value) -> set[str]:
+    """Every code the model binds a resolved value to: its enumeration value's definition, and the component's
+    exact matches and subjects. A target code that is one of these comes from the model: a lookup."""
+    iris = []
+    if value.code and value.code.defined_by:
+        iris.append(value.code.defined_by)
+    for predicate, targets in (value.links or {}).items():
+        if predicate.endswith(("#exactMatch", "/subject")):
+            iris.extend(targets)
+    return {c[1] for c in map(coding, iris) if c}
+
+
+#: The Default library's unit symbols that are not already UCUM codes.
+UCUM_CODES = {"mmHg": "mm[Hg]"}
+
+#: ISO 21090 null flavors as FHIR R4 writes them. Where the data-absent-reason code system has the same concept, it is
+#: written (as Observation.dataAbsentReason, or the data-absent-reason extension on any other element); every other
+#: code is written exactly, from v3 NullFlavor, with the iso21090-nullFlavor extension (or as a v3 NullFlavor coding of
+#: dataAbsentReason, whose binding is extensible). v3 NullFlavor has no Asked and Refused; data-absent-reason does.
+DATA_ABSENT_REASON = "http://terminology.hl7.org/CodeSystem/data-absent-reason"
+V3_NULL_FLAVOR = "http://terminology.hl7.org/CodeSystem/v3-NullFlavor"
+DAR_EXTENSION = "http://hl7.org/fhir/StructureDefinition/data-absent-reason"
+NULL_FLAVOR_EXTENSION = "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor"
+DAR = {"UNK": "unknown", "ASKU": "asked-unknown", "NAV": "temp-unknown", "NASK": "not-asked", "ASKR": "asked-declined",
+       "MSK": "masked", "NA": "not-applicable", "NINF": "negative-infinity", "PINF": "positive-infinity"}
+V3_ONLY = ("NI", "INV", "DER", "OTH", "UNC", "QS", "TRC")
+
+
+def absent(code: str) -> tuple[str, str, str]:
+    """(code system, code, extension url) FHIR writes for an ISO 21090 code."""
+    if code in DAR:
+        return DATA_ABSENT_REASON, DAR[code], DAR_EXTENSION
+    return V3_NULL_FLAVOR, code, NULL_FLAVOR_EXTENSION