fix: round to 5 decimal places by default (#185)

* fix: round to 5 decimal places by default * fix flake8 line too long
miracum · Aug 8, 2024 · 46eeca2 · 46eeca2
1 parent 5230a65
commit 46eeca2
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Showing 4 changed files with 68 additions and 30 deletions.
diff --git a/ahd2fhir/mappers/ahd_to_medication_statement.py b/ahd2fhir/mappers/ahd_to_medication_statement.py
@@ -189,14 +189,16 @@ def get_medication_dosage_from_annotation(annotation) -> Dosage:
 
     dosage.text = drug["coveredText"]
 
-    dose_and_rate = DosageDoseAndRate.construct()
-    quantity = Quantity.construct()
+    quantity_value = drug["strength"]["value"]
+    quantity_value = round(quantity_value, 5)
 
-    quantity.value = drug["strength"]["value"]
+    quantity = Quantity.construct()
+    quantity.value = quantity_value
     quantity.unit = drug["strength"]["unit"]
     quantity.code = drug["strength"]["unit"]
     quantity.system = "http://unitsofmeasure.org"
 
+    dose_and_rate = DosageDoseAndRate.construct()
     dose_and_rate.doseQuantity = quantity
     dosage.doseAndRate = [dose_and_rate]
 

diff --git a/requirements-dev.in b/requirements-dev.in
@@ -6,5 +6,4 @@ flake8==7.0.0
 pycodestyle==2.11.1
 pre-commit==3.7.1
 flake8-bugbear==24.4.26
-pip-tools==7.4.1
 isort==5.13.2
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -85,10 +85,6 @@ black==24.4.2 \
     --hash=sha256:eaea3008c281f1038edb473c1aa8ed8143a5535ff18f978a318f10302b254063 \
     --hash=sha256:ef703f83fc32e131e9bcc0a5094cfe85599e7109f896fe8bc96cc402f3eb4b6e
     # via -r requirements-dev.in
-build==1.2.1 \
-    --hash=sha256:526263f4870c26f26c433545579475377b2b7588b6f1eac76a001e873ae3e19d \
-    --hash=sha256:75e10f767a433d9a86e50d83f418e83efc18ede923ee5ff7df93b6cb0306c5d4
-    # via pip-tools
 certifi==2024.7.4 \
     --hash=sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b \
     --hash=sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90
@@ -197,7 +193,6 @@ click==8.1.7 \
     --hash=sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de
     # via
     #   black
-    #   pip-tools
     #   typer
     #   uvicorn
 coverage[toml]==7.6.0 \
@@ -623,17 +618,12 @@ packaging==24.1 \
     # via
     #   aiokafka
     #   black
-    #   build
     #   deprecation
     #   pytest
 pathspec==0.12.1 \
     --hash=sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08 \
     --hash=sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712
     # via black
-pip-tools==7.4.1 \
-    --hash=sha256:4c690e5fbae2f21e87843e89c26191f0d9454f362d8acdbd695716493ec8b3a9 \
-    --hash=sha256:864826f5073864450e24dbeeb85ce3920cdfb09848a3d69ebf537b521f14bcc9
-    # via -r requirements-dev.in
 platformdirs==4.2.2 \
     --hash=sha256:2d7a1657e36a80ea911db832a8a6ece5ee53d8de21edd5cc5879af6530b1bfee \
     --hash=sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3
@@ -772,12 +762,6 @@ pygments==2.18.0 \
     --hash=sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199 \
     --hash=sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a
     # via rich
-pyproject-hooks==1.1.0 \
-    --hash=sha256:4b37730834edbd6bd37f26ece6b44802fb1c1ee2ece0e54ddff8bfc06db86965 \
-    --hash=sha256:7ceeefe9aec63a1064c18d939bdc3adf2d8aa1988a510afec15151578b232aa2
-    # via
-    #   build
-    #   pip-tools
 pytest==8.2.1 \
     --hash=sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd \
     --hash=sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1
@@ -1208,13 +1192,3 @@ websockets==12.0 \
     --hash=sha256:fc4e7fa5414512b481a2483775a8e8be7803a35b30ca805afa4998a84f9fd9e8 \
     --hash=sha256:ffefa1374cd508d633646d51a8e9277763a9b78ae71324183693959cf94635a7
     # via uvicorn
-wheel==0.43.0 \
-    --hash=sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85 \
-    --hash=sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81
-    # via pip-tools
-
-# WARNING: The following packages were not pinned, but pip requires them to be
-# pinned when the requirements file includes hashes and the requirement is not
-# satisfied by a package already installed. Consider using the --allow-unsafe flag.
-# pip
-# setuptools
diff --git a/tests/test_ahd_to_medication_statement.py b/tests/test_ahd_to_medication_statement.py
@@ -1,5 +1,6 @@
 import datetime
 import json
+from decimal import Decimal
 
 from fhir.resources.R4B.attachment import Attachment
 from fhir.resources.R4B.documentreference import (
@@ -12,6 +13,7 @@
 
 from ahd2fhir.mappers.ahd_to_medication_statement import (
     get_fhir_medication_statement,
+    get_medication_dosage_from_annotation,
     get_medication_interval_from_annotation,
 )
 from ahd2fhir.utils.resource_handler import AHD_TYPE_MEDICATION
@@ -71,3 +73,64 @@ def test_fhir_medication_v6():
     assert statement_v6.status is not None
     assert statement_v6.medicationReference is None
     assert statement_v6.medicationCodeableConcept is not None
+
+
+def test_get_medication_dosage_from_annotation_should_round_quantity_value():
+    annotation = {
+        "type": "de.averbis.types.health.Medication",
+        "coveredText": "Therapie mit Piperacillin 4x4g i.v. sowie 4x500mg",
+        "id": 82560,
+        "administrations": ["i.v."],
+        "drugs": [
+            {
+                "begin": 3055,
+                "end": 3099,
+                "type": "de.averbis.types.health.Drug",
+                "coveredText": "antibiotische Therapie mit Piperacillin 4x4g",
+                "id": 82561,
+                "ingredient": {
+                    "begin": 3055,
+                    "end": 3077,
+                    "type": "de.averbis.types.health.Ingredient",
+                    "coveredText": "antibiotische Therapie",
+                    "id": 82562,
+                    "matchedTerm": "antibiotische Therapie",
+                    "dictCanon": "Antibakterielle Mittel",
+                    "conceptID": "255631004",
+                    "source": "SNOMED-DrugClasses-DE_2023-11",
+                    "uniqueID": "SNOMED-DrugClasses-DE_2023-11:255631004",
+                },
+                "strength": {
+                    "begin": 3097,
+                    "end": 3099,
+                    "type": "de.averbis.types.health.Strength",
+                    "coveredText": "4g",
+                    "id": 82563,
+                    "unit": "g",
+                    "normalizedUnit": "kg",
+                    "normalizedValue": 0.004,
+                    "value": 1.111111111111,
+                    "dimension": "[M]",
+                },
+            }
+        ],
+        "atcCodes": [
+            {
+                "begin": 3055,
+                "end": 3099,
+                "type": "de.averbis.types.health.ATCCode",
+                "coveredText": "antibiotische Therapie mit Piperacillin 4x4g",
+                "id": 82574,
+                "dictCanon": "ANTIBIOTIKA ZUR SYSTEMISCHEN ANWENDUNG",
+                "conceptID": "J01",
+                "source": "ATCA_2024",
+            }
+        ],
+    }
+
+    dosage = get_medication_dosage_from_annotation(annotation)
+
+    assert len(dosage.doseAndRate) == 1
+    assert dosage.doseAndRate[0].doseQuantity.system == "http://unitsofmeasure.org"
+    assert dosage.doseAndRate[0].doseQuantity.unit == "g"
+    assert dosage.doseAndRate[0].doseQuantity.value == Decimal("1.11111")