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robertandremitchellrobertandremitchell
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Adding text-to-code coverage (#411)
## Description Updating `models` and `services`: https://app.codecov.io/gh/CDCgov/dibbs-text-to-code/tree/main/packages%2Ftext-to-code%2Fsrc%2Ftext_to_code Should then be at 100% coverage: https://app.codecov.io/gh/CDCgov/dibbs-text-to-code/tree/rob%2F410-code-coverage-increasing-coverage-on-text_to_code/packages%2Ftext-to-code%2Fsrc%2Ftext_to_code ## Related Issues Closes #410 ## Additional Notes [Add any additional context or notes that reviewers should know about.] <--------------------- REMOVE THE LINES BELOW BEFORE MERGING ---------------------> ## Checklist Please review and complete the following checklist before submitting your pull request: - [ ] I have ensured that the pull request is of a manageable size, allowing it to be reviewed within a single session. - [ ] I have reviewed my changes to ensure they are clear, concise, and well-documented. - [ ] I have updated the documentation, if applicable. - [ ] I have added or updated test cases to cover my changes, if applicable. - [ ] I have minimized the number of reviewers to include only those essential for the review. ## Checklist for Reviewers Please review and complete the following checklist during the review process: - [ ] The code follows best practices and conventions. - [ ] The changes implement the desired functionality or fix the reported issue. - [ ] The tests cover the new changes and pass successfully. - [ ] Any potential edge cases or error scenarios have been considered.
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‎packages/augmentation-lambda/src/augmentation_lambda/lambda_function.py‎

Lines changed: 1 addition & 1 deletion
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@@ -5,10 +5,10 @@
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from aws_lambda_typing import context as lambda_context
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from aws_lambda_typing import events as lambda_events
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from botocore.client import BaseClient
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import lambda_handler
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from augmentation.models import TTCAugmenterConfig
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from botocore.client import BaseClient
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from augmentation.models.application import TTCAugmenterOutput
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from augmentation.services.eicr_augmenter import EICRAugmenter
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from shared_models import TTCAugmenterInput

‎packages/text-to-code/tests/unit/models/test_labs.py‎

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@@ -21,6 +21,19 @@ def test_base_lab_element_requires_xpaths(self):
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schematron_errors=[],
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)
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def test_base_lab_element_accepts_valid_xpaths(self):
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"""Tests returning xpaths when valid xpaths are provided."""
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xpaths = [next(iter(LabXPaths))]
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lab_field = BaseLabField(
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data_field="Lab Test Name Resulted",
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min_word_count=2,
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xpaths=xpaths,
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schematron_errors=[],
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)
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assert lab_field.xpaths == xpaths
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def test_lab_test_name_resulted_defaults(self):
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"""Tests default values for LabTestNameResulted schema."""
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lab_test = LabTestNameResulted(

‎packages/text-to-code/tests/unit/test_eicr_processor.py‎

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@@ -18,6 +18,8 @@
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"/ClinicalDocument/component/structuredBody/component/section/entry/component/observation"
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)
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NO_MATCH_FOUND_ERROR_MESSAGE = "No ID element found in eICR XML."
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class TestEmptyEicrProcessor:
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def test_init(self):
@@ -52,6 +54,40 @@ def test_get_text_candidates_logs_when_xpath_lookup_fails(self):
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},
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)
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def test_resolve_reference_returns_none_for_empty_reference_value(self):
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processor = EicrProcessor("<ClinicalDocument />")
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assert processor.resolve_reference(None) is None
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assert processor.resolve_reference("") is None
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assert processor.resolve_reference(" ") is None
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def test_resolve_reference_returns_none_when_reference_is_missing(self):
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processor = EicrProcessor(
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"<ClinicalDocument><section><text>ID exists</text></section></ClinicalDocument>"
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)
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assert processor.resolve_reference("#missing-id") is None
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def test_extract_text_candidates_from_element_includes_child_tail_text(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<section>
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<text>
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<target>first<inner>second</inner>third</target>
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</text>
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</section>
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</ClinicalDocument>
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"""
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)
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element = processor._xml_root.find(".//target")
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assert element is not None
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result = processor._extract_text_candidates_from_element(element)
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assert result == ["first second third third"]
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class TestBadEicr:
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def test_bad_eicr(self):
@@ -100,6 +136,139 @@ def test_metadata(self, eicr_metadata: Metadata):
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eicr_vendor="Test eCR Vendor Name",
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)
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def test_metadata_raises_when_id_is_missing(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<author>
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<assignedAuthor>
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<assignedAuthoringDevice>
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<softwareName>Test eCR Vendor Name</softwareName>
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</assignedAuthoringDevice>
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</assignedAuthor>
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</author>
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</ClinicalDocument>
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"""
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)
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with pytest.raises(ValueError, match=NO_MATCH_FOUND_ERROR_MESSAGE):
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_ = processor.eicr_metadata
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def test_metadata_raises_when_id_has_null_flavor(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<id nullFlavor="UNK" />
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<author>
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<assignedAuthor>
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<assignedAuthoringDevice>
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<softwareName>Test eCR Vendor Name</softwareName>
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</assignedAuthoringDevice>
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</assignedAuthor>
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</author>
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</ClinicalDocument>
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"""
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)
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with pytest.raises(ValueError, match=NO_MATCH_FOUND_ERROR_MESSAGE):
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_ = processor.eicr_metadata
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def test_metadata_parses_false_displayable(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<id
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root="test-root"
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extension="test-extension"
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assigningAuthorityName="test-authority"
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displayable="false"
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/>
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<author>
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<assignedAuthor>
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<assignedAuthoringDevice>
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<softwareName>Test eCR Vendor Name</softwareName>
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</assignedAuthoringDevice>
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</assignedAuthor>
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</author>
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</ClinicalDocument>
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"""
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)
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assert processor.eicr_metadata == Metadata(
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eicr_id=CdaInstanceIdentifier(
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root="test-root",
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extension="test-extension",
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assigning_authority_name="test-authority",
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displayable=False,
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null_flavor=None,
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),
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eicr_vendor="Test eCR Vendor Name",
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)
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def test_metadata_parses_unknown_displayable_as_none(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<id
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root="test-root"
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extension="test-extension"
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assigningAuthorityName="test-authority"
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displayable="not-a-bool"
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/>
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<author>
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<assignedAuthor>
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<assignedAuthoringDevice>
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<softwareName>Test eCR Vendor Name</softwareName>
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</assignedAuthoringDevice>
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</assignedAuthor>
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</author>
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</ClinicalDocument>
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"""
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)
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assert processor.eicr_metadata == Metadata(
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eicr_id=CdaInstanceIdentifier(
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root="test-root",
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extension="test-extension",
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assigning_authority_name="test-authority",
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displayable=None,
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null_flavor=None,
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),
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eicr_vendor="Test eCR Vendor Name",
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)
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def test_metadata_parses_true_displayable(self):
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processor = EicrProcessor(
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"""
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<ClinicalDocument>
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<id
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root="test-root"
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extension="test-extension"
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assigningAuthorityName="test-authority"
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displayable="true"
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/>
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<author>
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<assignedAuthor>
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<assignedAuthoringDevice>
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<softwareName>Test eCR Vendor Name</softwareName>
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</assignedAuthoringDevice>
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</assignedAuthor>
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</author>
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</ClinicalDocument>
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"""
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)
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assert processor.eicr_metadata == Metadata(
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eicr_id=CdaInstanceIdentifier(
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root="test-root",
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extension="test-extension",
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assigning_authority_name="test-authority",
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displayable=True,
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null_flavor=None,
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),
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eicr_vendor="Test eCR Vendor Name",
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)
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103272

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class TestReferences:
105274
@pytest.fixture(scope="class")

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