aimedicalcoding 0.3.1__tar.gz → 0.3.3__tar.gz

{aimedicalcoding-0.3.1/aimedicalcoding.egg-info → aimedicalcoding-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.1
+Version: 0.3.3
 Summary: Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / ICD-10-CM / CVX) in CCDA and FHIR documents, with recovery evidence
 Author: Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan
 License: MIT

{aimedicalcoding-0.3.1 → aimedicalcoding-0.3.3}/README.md

@@ -56,11 +56,20 @@ Run tests:
 ```bash
 pytest
 ```
-Build distributables (version comes from the git tag):
-```bash
-python -m build
+
+### Publish to PyPI
+
+See **`PUBLISHING.md`** for the full release guide (version bump in `setup.py`,
+clean build, `twine check`, upload, verify, troubleshooting). Short version:
+
+```powershell
+# bump version in setup.py first — PyPI rejects re-uploads of the same version
+Remove-Item -Recurse -Force dist; python -m build
+python -m twine check dist/*
+python -m twine upload dist/*      # credentials from ~/.pypirc
 ```
-Publish privately to AWS CodeArtifact (the repo is on CodeCommit):
+
+Alternative: private publish to AWS CodeArtifact (the repo is on CodeCommit):
 ```bash
 aws codeartifact login --tool twine --domain <domain> --repository <repo>
 twine upload --repository codeartifact dist/*

{aimedicalcoding-0.3.1 → aimedicalcoding-0.3.3}/aimedicalcoding/serialize.py

@@ -121,13 +121,18 @@ def _dedupe(items) -> list:
     return out
 
 
-# SNOMED search-term enrichment: sections whose gaps also get the CODE-slot
-# labels appended (Problems 11450-4, Allergies 48765-2, Social History 29762-2),
-# matched by section LOINC or by the contexts those sections route to
-# (FHIR resources often carry no meta.tag/section code).
-_SNOMED_LABEL_SECTIONS = {"11450-4", "48765-2", "29762-2"}
-_SNOMED_LABEL_CONTEXTS = {"problem", "allergy_substance", "allergy_reaction",
-                          "social_history"}
+# SNOMED search-term enrichment (Problems 11450-4, Allergies 48765-2, Social
+# History 29762-2), matched by section LOINC or by the contexts those sections
+# route to (FHIR resources often carry no meta.tag/section code). Which slot's
+# labels get appended differs by section:
+#   - Social History  -> CODE tag labels (the question, e.g. "Gender identity" —
+#     the value label is often a placeholder like "Not on file")
+#   - Problems / Allergies -> VALUE tag labels (the concept; the code tag is a
+#     generic marker like ASSERTION / "Problem" — appending it is noise)
+_SNOMED_CODE_LABEL_SECTIONS = {"29762-2"}
+_SNOMED_CODE_LABEL_CONTEXTS = {"social_history"}
+_SNOMED_VALUE_LABEL_SECTIONS = {"11450-4", "48765-2"}
+_SNOMED_VALUE_LABEL_CONTEXTS = {"problem", "allergy_substance", "allergy_reaction"}
 
 
 def _recovery(record: NormalizedRecord, slot: str, system: str) -> dict:
@@ -141,13 +146,18 @@ def _recovery(record: NormalizedRecord, slot: str, system: str) -> dict:
         terms = [stmt.display_name, stmt.original_text]
     # add any normalized term the handler produced
     terms += [ev.get("analyte_normalized"), ev.get("term_normalized"), ev.get("ingredient")]
-    # SNOMED only, Problems/Allergies/Social History only: append the CODE
-    # tag's displayName/originalText (never the value's) as trailing context —
-    # e.g. the question label when the value label is a placeholder.
-    if system == System.SNOMEDCT.value and (
-            stmt.section_code in _SNOMED_LABEL_SECTIONS
-            or stmt.context in _SNOMED_LABEL_CONTEXTS):
-        terms += [stmt.display_name, stmt.original_text]
+    # SNOMED only, Problems/Allergies/Social History only: append trailing
+    # label context from the section-appropriate slot (see constants above).
+    if system == System.SNOMEDCT.value:
+        if (stmt.section_code in _SNOMED_CODE_LABEL_SECTIONS
+                or stmt.context in _SNOMED_CODE_LABEL_CONTEXTS):
+            terms += [stmt.display_name, stmt.original_text]
+        elif (stmt.section_code in _SNOMED_VALUE_LABEL_SECTIONS
+                or stmt.context in _SNOMED_VALUE_LABEL_CONTEXTS):
+            if stmt.value:
+                terms += [stmt.value.coded_value.display
+                          if stmt.value.coded_value else None,
+                          stmt.value.original_text]
 
     rec = {
         "search_terms": _dedupe(terms),

{aimedicalcoding-0.3.1 → aimedicalcoding-0.3.3/aimedicalcoding.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.1
+Version: 0.3.3
 Summary: Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / ICD-10-CM / CVX) in CCDA and FHIR documents, with recovery evidence
 Author: Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan
 License: MIT

{aimedicalcoding-0.3.1 → aimedicalcoding-0.3.3}/docs/GAP_SCHEMA.md

@@ -89,10 +89,12 @@ Each record separates four concerns:
 - `target.slot = "code"` (LOINC) → search `observation.code.display_text` / `.original_text`.
 - `target.slot = "value"` (SNOMED value-slot) → search `observation.value.display_text` / `.original_text`.
 `recovery.search_terms` already gives you the right ones, deduped.
-For **SNOMED-CT** targets in **Problems (11450-4), Allergies (48765-2) and
-Social History (29762-2)**, the CODE tag's `display_text`/`original_text`
-are additionally appended at the end (never the value's) — search context
-for when the value label is a placeholder like "Not on file".
+For **SNOMED-CT** targets, extra label context is appended at the end,
+section-specific: **Social History (29762-2)** appends the CODE tag's
+`display_text`/`original_text` (the question — useful when the value label
+is a placeholder like "Not on file"); **Problems (11450-4)** and
+**Allergies (48765-2)** append the VALUE tag's labels (the concept — the
+code tag there is a generic marker like ASSERTION/"Problem").
 
 ---
 

{aimedicalcoding-0.3.1 → aimedicalcoding-0.3.3}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name="aimedicalcoding",
-    version="0.3.1",
+    version="0.3.3",
     author="Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan",
     description=(
         "Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / "