Organized assets folder/files and modified all tests to point to prop…

…er asset (#519) * Organized all assets and modified all tests that use each asset to find the proper directory * Update test_validation.py * fixed black errors * Update test_tables.py * fixed some failing tests * Update test_base_service.py
CDCgov · May 8, 2023 · cb21800 · cb21800
1 parent 3bdb40f
commit cb21800
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diff --git a/containers/message-parser/tests/test_parse_message_endpoint.py b/containers/message-parser/tests/test_parse_message_endpoint.py
@@ -11,6 +11,7 @@
     Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "general"
     / "patient_bundle.json"
 )
 

diff --git a/containers/tabulation/tests/test_tabulation.py b/containers/tabulation/tests/test_tabulation.py
@@ -13,6 +13,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "tabulation"
     / "valid_schema.json"
 )
 

diff --git a/containers/tabulation/tests/test_utils.py b/containers/tabulation/tests/test_utils.py
@@ -77,6 +77,7 @@ def test_check_schema_validity_valid_schema():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "tabulation"
         / "valid_schema.json"
     )
     valid_schema = json.load(open(valid_schema_path))

diff --git a/containers/validation/tests/test_utils.py b/containers/validation/tests/test_utils.py
@@ -43,6 +43,7 @@ def test_validate_config_bad():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "validation"
         / "sample_ecr_config_bad.yaml",
         "r",
     ) as file:
@@ -56,6 +57,7 @@ def test_validate_config_good():
         pathlib.Path(__file__).parent.parent.parent.parent
         / "tests"
         / "assets"
+        / "validation"
         / "sample_ecr_config.yaml",
         "r",
     ) as file:

diff --git a/containers/validation/tests/test_validation.py b/containers/validation/tests/test_validation.py
@@ -17,6 +17,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_good.xml"
 ).read()
 
@@ -25,6 +26,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_bad.xml"
 ).read()
 
@@ -33,6 +35,7 @@
     pathlib.Path(__file__).parent.parent.parent.parent
     / "tests"
     / "assets"
+    / "validation"
     / "ecr_sample_input_good_with_RR.xml"
 ).read()
 

diff --git a/tests/assets/cp1252-sample.txt → tests/assets/cloud/cp1252-sample.txt b/tests/assets/cp1252-sample.txt → tests/assets/cloud/cp1252-sample.txt
diff --git a/tests/assets/test_description.md → tests/assets/containers/test_description.md b/tests/assets/test_description.md → tests/assets/containers/test_description.md
diff --git a/tests/assets/ccda_sample.xml → ...ssets/fhir-converter/ccda/ccda_sample.xml b/tests/assets/ccda_sample.xml → ...ssets/fhir-converter/ccda/ccda_sample.xml
diff --git a/tests/assets/ccda_sample_unknowntype.xml → ...onverter/ccda/ccda_sample_unknowntype.xml b/tests/assets/ccda_sample_unknowntype.xml → ...onverter/ccda/ccda_sample_unknowntype.xml
diff --git a/tests/assets/example_eicr_with_rr_data.xml → ...nverter/ecr/example_eicr_with_rr_data.xml b/tests/assets/example_eicr_with_rr_data.xml → ...nverter/ecr/example_eicr_with_rr_data.xml
@@ -2650,7 +2650,7 @@
         <entry>
             <act classCode="ACT" moodCode="EVN">
                 <templateId extension="2017-04-01" root="2.16.840.1.113883.10.20.15.2.3.29"/>
-                <id root="39d966b9-8a3a-4024-93d8-138e97d5898a"/>
+                <id root="8675309a-7754-r2d2-c3p0-973d9f777777"/>
                 <code code="RRVS19" codeSystem="2.16.840.1.114222.4.5.274" codeSystemName="PHIN VS (CDC Local Coding System)" displayName="eICR processed"/>
             </act>
         </entry>

diff --git a/...ple_eicr_with_rr_data_fhir_converter.json → ...ple_eicr_with_rr_data_fhir_converter.json b/...ple_eicr_with_rr_data_fhir_converter.json → ...ple_eicr_with_rr_data_fhir_converter.json
diff --git a/...xample_eicr_with_rr_data_with_person.json → ...xample_eicr_with_rr_data_with_person.json b/...xample_eicr_with_rr_data_with_person.json → ...xample_eicr_with_rr_data_with_person.json
diff --git a/tests/assets/fhir-converter/ecr/example_rr.xml b/tests/assets/fhir-converter/ecr/example_rr.xml
diff --git a/tests/assets/hl7_with_msh_3_set.hl7 → ...ir-converter/hl7v2/hl7_with_msh_3_set.hl7 b/tests/assets/hl7_with_msh_3_set.hl7 → ...ir-converter/hl7v2/hl7_with_msh_3_set.hl7
diff --git a/tests/assets/sample_hl7.hl7 → ...ssets/fhir-converter/hl7v2/sample_hl7.hl7 b/tests/assets/sample_hl7.hl7 → ...ssets/fhir-converter/hl7v2/sample_hl7.hl7
diff --git a/tests/assets/FHIR_server_extracted_data.json → ...s/general/FHIR_server_extracted_data.json b/tests/assets/FHIR_server_extracted_data.json → ...s/general/FHIR_server_extracted_data.json
diff --git a/.../assets/FHIR_server_observation_data.json → ...general/FHIR_server_observation_data.json b/.../assets/FHIR_server_observation_data.json → ...general/FHIR_server_observation_data.json
diff --git a/...IR_server_query_response_200_example.json → ...IR_server_query_response_200_example.json b/...IR_server_query_response_200_example.json → ...IR_server_query_response_200_example.json
diff --git a/tests/assets/patient_bundle.json → tests/assets/general/patient_bundle.json b/tests/assets/patient_bundle.json → tests/assets/general/patient_bundle.json
diff --git a/tests/assets/patient_bundle_census.json → ...assets/general/patient_bundle_census.json b/tests/assets/patient_bundle_census.json → ...assets/general/patient_bundle_census.json
diff --git a/...sets/patient_bundle_census_extension.json → ...eral/patient_bundle_census_extension.json b/...sets/patient_bundle_census_extension.json → ...eral/patient_bundle_census_extension.json
diff --git a/tests/assets/censusResponseFullAddress.json → ...geospatial/censusResponseFullAddress.json b/tests/assets/censusResponseFullAddress.json → ...geospatial/censusResponseFullAddress.json
diff --git a/...sets/FileSingleMessageInvalidSegments.hl7 → ...tion/FileSingleMessageInvalidSegments.hl7 b/...sets/FileSingleMessageInvalidSegments.hl7 → ...tion/FileSingleMessageInvalidSegments.hl7
diff --git a/tests/assets/FileSingleMessageLongDate.hl7 → ...rmonization/FileSingleMessageLongDate.hl7 b/tests/assets/FileSingleMessageLongDate.hl7 → ...rmonization/FileSingleMessageLongDate.hl7
diff --git a/tests/assets/FileSingleMessageLongTZ.hl7 → ...harmonization/FileSingleMessageLongTZ.hl7 b/tests/assets/FileSingleMessageLongTZ.hl7 → ...harmonization/FileSingleMessageLongTZ.hl7
diff --git a/tests/assets/FileSingleMessageSimple.hl7 → ...harmonization/FileSingleMessageSimple.hl7 b/tests/assets/FileSingleMessageSimple.hl7 → ...harmonization/FileSingleMessageSimple.hl7
diff --git a/tests/assets/dibbs_basic_algorithm.json → ...assets/linkage/dibbs_basic_algorithm.json b/tests/assets/dibbs_basic_algorithm.json → ...assets/linkage/dibbs_basic_algorithm.json
diff --git a/tests/assets/dibbs_enhanced_algorithm.json → ...ets/linkage/dibbs_enhanced_algorithm.json b/tests/assets/dibbs_enhanced_algorithm.json → ...ets/linkage/dibbs_enhanced_algorithm.json
diff --git a/...sets/patient_bundle_to_link_with_mpi.json → ...kage/patient_bundle_to_link_with_mpi.json b/...sets/patient_bundle_to_link_with_mpi.json → ...kage/patient_bundle_to_link_with_mpi.json
diff --git a/tests/assets/patient_lol.csv → tests/assets/linkage/patient_lol.csv b/tests/assets/patient_lol.csv → tests/assets/linkage/patient_lol.csv
diff --git a/...ssets/patient_with_linking_id_bundle.json → ...nkage/patient_with_linking_id_bundle.json b/...ssets/patient_with_linking_id_bundle.json → ...nkage/patient_with_linking_id_bundle.json
diff --git a/...s/synthetic_patient_mpi_seed_data.parquet → ...e/synthetic_patient_mpi_seed_data.parquet b/...s/synthetic_patient_mpi_seed_data.parquet → ...e/synthetic_patient_mpi_seed_data.parquet
diff --git a/tests/assets/invalid_json.json → tests/assets/tabulation/invalid_json.json b/tests/assets/invalid_json.json → tests/assets/tabulation/invalid_json.json
diff --git a/tests/assets/invalid_schema.yaml → tests/assets/tabulation/invalid_schema.yaml b/tests/assets/invalid_schema.yaml → tests/assets/tabulation/invalid_schema.yaml
diff --git a/...ets/invalid_schema_no_invalid_values.yaml → ...ion/invalid_schema_no_invalid_values.yaml b/...ets/invalid_schema_no_invalid_values.yaml → ...ion/invalid_schema_no_invalid_values.yaml
diff --git a/.../assets/observation_reference_schema.yaml → ...ulation/observation_reference_schema.yaml b/.../assets/observation_reference_schema.yaml → ...ulation/observation_reference_schema.yaml
diff --git a/tests/assets/tabulation/sample_hl7.hl7 b/tests/assets/tabulation/sample_hl7.hl7
@@ -0,0 +1,4 @@
+MSH|^~\&|GHH LAB|ELAB-3|GHH OE|BLDG4|200202150930||ORU^R01|CNTRL-3456|P|2.4
+PID|||555-44-4444||EVERYWOMAN^EVE^E^^^^L|JONES|196203520|F|||153 FERNWOOD DR.^^STATESVILLE^OH^35292||(206)3345232|(206)752-121||||AC555444444||67-A4335^OH^20030520
+OBR|1|845439^GHH OE|1045813^GHH LAB|1554-5^GLUCOSE|||200202150730||||||||555-55-5555^PRIMARY^PATRICIA P^^^^MD^^LEVEL SEVEN HEALTHCARE, INC.|||||||||F||||||444-44-4444^HIPPOCRATES^HOWARD H^^^^MD
+OBX|1|SN|1554-5^GLUCOSE^POST 12H CFST:MCNC:PT:SER/PLAS:QN||^182|mg/dl|70_105|H|||F
diff --git a/tests/assets/tabulated_patients.csv → .../assets/tabulation/tabulated_patients.csv b/tests/assets/tabulated_patients.csv → .../assets/tabulation/tabulated_patients.csv
diff --git a/tests/assets/tabulated_physical_exam.csv → ...ts/tabulation/tabulated_physical_exam.csv b/tests/assets/tabulated_physical_exam.csv → ...ts/tabulation/tabulated_physical_exam.csv
diff --git a/tests/assets/tabulation_schema.yaml → .../assets/tabulation/tabulation_schema.yaml b/tests/assets/tabulation_schema.yaml → .../assets/tabulation/tabulation_schema.yaml
diff --git a/...assets/tabulation_schema_output_data.json → ...lation/tabulation_schema_output_data.json b/...assets/tabulation_schema_output_data.json → ...lation/tabulation_schema_output_data.json
diff --git a/tests/assets/valid_schema.json → tests/assets/tabulation/valid_schema.json b/tests/assets/valid_schema.json → tests/assets/tabulation/valid_schema.json
diff --git a/tests/assets/valid_schema.yaml → tests/assets/tabulation/valid_schema.yaml b/tests/assets/valid_schema.yaml → tests/assets/tabulation/valid_schema.yaml
diff --git a/tests/assets/ecr_sample_input_bad.xml → ...ssets/validation/ecr_sample_input_bad.xml b/tests/assets/ecr_sample_input_bad.xml → ...ssets/validation/ecr_sample_input_bad.xml
diff --git a/tests/assets/ecr_sample_input_error.xml → ...ets/validation/ecr_sample_input_error.xml b/tests/assets/ecr_sample_input_error.xml → ...ets/validation/ecr_sample_input_error.xml
diff --git a/tests/assets/ecr_sample_input_good.xml → ...sets/validation/ecr_sample_input_good.xml b/tests/assets/ecr_sample_input_good.xml → ...sets/validation/ecr_sample_input_good.xml
diff --git a/.../assets/ecr_sample_input_good_with_RR.xml → ...idation/ecr_sample_input_good_with_RR.xml b/.../assets/ecr_sample_input_good_with_RR.xml → ...idation/ecr_sample_input_good_with_RR.xml
diff --git a/tests/assets/sample_ecr_config.yaml → .../assets/validation/sample_ecr_config.yaml b/tests/assets/sample_ecr_config.yaml → .../assets/validation/sample_ecr_config.yaml
diff --git a/tests/assets/sample_ecr_config_bad.yaml → ...ets/validation/sample_ecr_config_bad.yaml b/tests/assets/sample_ecr_config_bad.yaml → ...ets/validation/sample_ecr_config_bad.yaml
diff --git a/...ts/sample_ecr_config_custom_messages.yaml → ...on/sample_ecr_config_custom_messages.yaml b/...ts/sample_ecr_config_custom_messages.yaml → ...on/sample_ecr_config_custom_messages.yaml
diff --git a/tests/assets/sample_ecr_config_with_rr.yaml → ...validation/sample_ecr_config_with_rr.yaml b/tests/assets/sample_ecr_config_with_rr.yaml → ...validation/sample_ecr_config_with_rr.yaml
diff --git a/tests/cloud/test_cloud.py b/tests/cloud/test_cloud.py
@@ -359,7 +359,8 @@ def test_azure_download_object_cp1252(mock_get_client):
     object_path = "output/path/some-bundle-type/some-filename-1.fhir"
 
     with open(
-        pathlib.Path(__file__).parent.parent / "assets" / "cp1252-sample.txt", "rb"
+        pathlib.Path(__file__).parent.parent / "assets" / "cloud" / "cp1252-sample.txt",
+        "rb",
     ) as cp1252file:
         object_content = cp1252file.read()
 

diff --git a/tests/containers/test_base_service.py b/tests/containers/test_base_service.py
@@ -11,10 +11,8 @@
 
 def test_base_service():
     service = BaseService(
-        service_name="test_service",
-        description_path=Path(__file__).parent.parent
-        / "assets"
-        / "test_description.md",
+        "test_service",
+        Path(__file__).parent.parent / "assets" / "containers" / "test_description.md",
     )
     assert service.app.title == "test_service"
     assert service.app.version == default_app_version
@@ -33,6 +31,7 @@ def test_base_service_alternate_license():
         service_name="test_service",
         description_path=Path(__file__).parent.parent
         / "assets"
+        / "containers"
         / "test_description.md",
         license_info=alternate_app_license,
     )

diff --git a/tests/fhir/geospatial/test_fhir_census_client.py b/tests/fhir/geospatial/test_fhir_census_client.py
@@ -27,6 +27,7 @@ def test_geocode_resource_census():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle_census.json"
         )
     )
@@ -92,6 +93,7 @@ def test_geocode_resource_census():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle_census_extension.json"
         )
     )
@@ -163,6 +165,7 @@ def test_geocode_bundle_census():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle_census.json"
         )
     )

diff --git a/tests/fhir/geospatial/test_fhir_core.py b/tests/fhir/geospatial/test_fhir_core.py
@@ -9,6 +9,7 @@ def test_store_lat_long():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )

diff --git a/tests/fhir/geospatial/test_fhir_smarty_client.py b/tests/fhir/geospatial/test_fhir_smarty_client.py
@@ -29,6 +29,7 @@ def test_geocode_resource():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -86,6 +87,7 @@ def test_geocode_bundle():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )

diff --git a/tests/fhir/harmonization/test_fhir_harmonization.py b/tests/fhir/harmonization/test_fhir_harmonization.py
@@ -18,6 +18,7 @@ def test_double_metaphone_bundle():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "FHIR_server_extracted_data.json"
         )
     )
@@ -56,6 +57,7 @@ def test_double_metaphone_patient():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -140,6 +142,7 @@ def test_standardize_names():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -178,6 +181,7 @@ def test_standardize_phones():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -228,6 +232,7 @@ def test_standardize_dob():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )

diff --git a/tests/fhir/harmonization/test_standardization_helpers.py b/tests/fhir/harmonization/test_standardization_helpers.py
@@ -15,6 +15,7 @@ def test_standardize_names_in_resource():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -30,6 +31,7 @@ def test_standardize_phones_in_resource():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -44,6 +46,7 @@ def test_extract_countries_from_resource():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )
@@ -66,6 +69,7 @@ def test_standardize_dob_in_resource():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "general"
             / "patient_bundle.json"
         )
     )

diff --git a/tests/fhir/linkage/test_fhir_link.py b/tests/fhir/linkage/test_fhir_link.py
@@ -33,6 +33,7 @@ def test_add_patient_identifier_by_bundle_overwrite():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "linkage"
             / "patient_with_linking_id_bundle.json"
         )
     )
@@ -63,6 +64,7 @@ def test_patient_identifier_overwrite():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "linkage"
             / "patient_with_linking_id_bundle.json"
         )
     )
@@ -94,6 +96,7 @@ def test_add_patient_identifier_by_bundle():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "linkage"
             / "patient_with_linking_id_bundle.json"
         )
     )
@@ -126,6 +129,7 @@ def test_add_patient_identifier():
         open(
             pathlib.Path(__file__).parent.parent.parent
             / "assets"
+            / "linkage"
             / "patient_with_linking_id_bundle.json"
         )
     )