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Adding text-to-code coverage #411

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aaf9633
Adding text-to-code coverage
robertandremitchell Apr 1, 2026
c014d33
adding coverage for eirc_processor
robertandremitchell Apr 1, 2026
4b4af14
Add evaluator tests
robertandremitchell Apr 1, 2026
338972f
Add schematron tests
robertandremitchell Apr 1, 2026
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2 changes: 1 addition & 1 deletion packages/augmentation-lambda/src/augmentation_lambda/lambda_function.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,10 @@

from aws_lambda_typing import context as lambda_context
from aws_lambda_typing import events as lambda_events
from botocore.client import BaseClient
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@robertandremitchell robertandremitchell Apr 1, 2026

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I'm not entirely sure why this ruffed now?


import lambda_handler
from augmentation.models import TTCAugmenterConfig
from botocore.client import BaseClient
from augmentation.models.application import TTCAugmenterOutput
from augmentation.services.eicr_augmenter import EICRAugmenter
from shared_models import TTCAugmenterInput
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13 changes: 13 additions & 0 deletions packages/text-to-code/tests/unit/models/test_labs.py
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Expand Up @@ -21,6 +21,19 @@ def test_base_lab_element_requires_xpaths(self):
schematron_errors=[],
)

def test_base_lab_element_accepts_valid_xpaths(self):
"""Tests returning xpaths when valid xpaths are provided."""
xpaths = [next(iter(LabXPaths))]

lab_field = BaseLabField(
data_field="Lab Test Name Resulted",
min_word_count=2,
xpaths=xpaths,
schematron_errors=[],
)

assert lab_field.xpaths == xpaths

def test_lab_test_name_resulted_defaults(self):
"""Tests default values for LabTestNameResulted schema."""
lab_test = LabTestNameResulted(
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169 changes: 169 additions & 0 deletions packages/text-to-code/tests/unit/test_eicr_processor.py
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Expand Up @@ -18,6 +18,8 @@
"/ClinicalDocument/component/structuredBody/component/section/entry/component/observation"
)

NO_MATCH_FOUND_ERROR_MESSAGE = "No ID element found in eICR XML."


class TestEmptyEicrProcessor:
def test_init(self):
Expand Down Expand Up @@ -52,6 +54,40 @@ def test_get_text_candidates_logs_when_xpath_lookup_fails(self):
},
)

def test_resolve_reference_returns_none_for_empty_reference_value(self):
processor = EicrProcessor("<ClinicalDocument />")

assert processor.resolve_reference(None) is None
assert processor.resolve_reference("") is None
assert processor.resolve_reference(" ") is None

def test_resolve_reference_returns_none_when_reference_is_missing(self):
processor = EicrProcessor(
"<ClinicalDocument><section><text>ID exists</text></section></ClinicalDocument>"
)

assert processor.resolve_reference("#missing-id") is None

def test_extract_text_candidates_from_element_includes_child_tail_text(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<section>
<text>
<target>first<inner>second</inner>third</target>
</text>
</section>
</ClinicalDocument>
"""
)

element = processor._xml_root.find(".//target")
assert element is not None

result = processor._extract_text_candidates_from_element(element)

assert result == ["first second third third"]


class TestBadEicr:
def test_bad_eicr(self):
Expand Down Expand Up @@ -100,6 +136,139 @@ def test_metadata(self, eicr_metadata: Metadata):
eicr_vendor="Test eCR Vendor Name",
)

def test_metadata_raises_when_id_is_missing(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<author>
<assignedAuthor>
<assignedAuthoringDevice>
<softwareName>Test eCR Vendor Name</softwareName>
</assignedAuthoringDevice>
</assignedAuthor>
</author>
</ClinicalDocument>
"""
)

with pytest.raises(ValueError, match=NO_MATCH_FOUND_ERROR_MESSAGE):
_ = processor.eicr_metadata

def test_metadata_raises_when_id_has_null_flavor(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<id nullFlavor="UNK" />
<author>
<assignedAuthor>
<assignedAuthoringDevice>
<softwareName>Test eCR Vendor Name</softwareName>
</assignedAuthoringDevice>
</assignedAuthor>
</author>
</ClinicalDocument>
"""
)

with pytest.raises(ValueError, match=NO_MATCH_FOUND_ERROR_MESSAGE):
_ = processor.eicr_metadata

def test_metadata_parses_false_displayable(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<id
root="test-root"
extension="test-extension"
assigningAuthorityName="test-authority"
displayable="false"
/>
<author>
<assignedAuthor>
<assignedAuthoringDevice>
<softwareName>Test eCR Vendor Name</softwareName>
</assignedAuthoringDevice>
</assignedAuthor>
</author>
</ClinicalDocument>
"""
)

assert processor.eicr_metadata == Metadata(
eicr_id=CdaInstanceIdentifier(
root="test-root",
extension="test-extension",
assigning_authority_name="test-authority",
displayable=False,
null_flavor=None,
),
eicr_vendor="Test eCR Vendor Name",
)

def test_metadata_parses_unknown_displayable_as_none(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<id
root="test-root"
extension="test-extension"
assigningAuthorityName="test-authority"
displayable="not-a-bool"
/>
<author>
<assignedAuthor>
<assignedAuthoringDevice>
<softwareName>Test eCR Vendor Name</softwareName>
</assignedAuthoringDevice>
</assignedAuthor>
</author>
</ClinicalDocument>
"""
)

assert processor.eicr_metadata == Metadata(
eicr_id=CdaInstanceIdentifier(
root="test-root",
extension="test-extension",
assigning_authority_name="test-authority",
displayable=None,
null_flavor=None,
),
eicr_vendor="Test eCR Vendor Name",
)

def test_metadata_parses_true_displayable(self):
processor = EicrProcessor(
"""
<ClinicalDocument>
<id
root="test-root"
extension="test-extension"
assigningAuthorityName="test-authority"
displayable="true"
/>
<author>
<assignedAuthor>
<assignedAuthoringDevice>
<softwareName>Test eCR Vendor Name</softwareName>
</assignedAuthoringDevice>
</assignedAuthor>
</author>
</ClinicalDocument>
"""
)

assert processor.eicr_metadata == Metadata(
eicr_id=CdaInstanceIdentifier(
root="test-root",
extension="test-extension",
assigning_authority_name="test-authority",
displayable=True,
null_flavor=None,
),
eicr_vendor="Test eCR Vendor Name",
)


class TestReferences:
@pytest.fixture(scope="class")
Expand Down
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