[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
globaldothealth · Jun 24, 2024 · 782986b · 782986b
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -22,4 +22,4 @@ sphinx:
 python:
    install:
      - method: pip
-       path: .[docs]
+       path: .[docs]
diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ for the [ISARIC](https://isaric.org) 3.0 project and data pipelines. Portions of
 the code are specific to the ISARIC project, such as ISARIC specific FHIR
 extensions.
 
-The FHIRflat FHIR resources are derived from the 
+The FHIRflat FHIR resources are derived from the
 [fhir.resources](https://github.com/nazrulworld/fhir.resources) package.
 
 For more information, howtos and tutorials, see the
@@ -35,8 +35,8 @@ https://github.com/globaldothealth/fhirflat/main.tar.gz
 ## Development
 
 To test and develop fhirflat, from a cloned version of fhirflat use an editable install
-including the development dependencies(`pip install -e ".[dev]"`). This will allow you 
+including the development dependencies(`pip install -e ".[dev]"`). This will allow you
 to test the packages, and installs formatting and linting tools, and
 [pre-commit](https://pre-commit.com).
 
-Setup pre-commit hooks (`pre-commit install`) which will do linting checks before commit.
+Setup pre-commit hooks (`pre-commit install`) which will do linting checks before commit.
diff --git a/docs/conf.py b/docs/conf.py
@@ -37,12 +37,12 @@
 
 html_theme = "better"
 html_static_path = ["_static"]
-html_theme_path=[better.better_theme_path]
+html_theme_path = [better.better_theme_path]
 html_short_title = "Home"
 
 html_theme_options = {
     "rightsidebar": True,
     "sidebarwidth": "25rem",
     "cssfiles": ["_static/style.css"],
     "showheader": False,
-}
+}
diff --git a/docs/howto/conversion-data.md b/docs/howto/conversion-data.md
@@ -11,14 +11,14 @@ fhirflat transform data-file google-sheet-id date-format timezone-name
 
 Here *data-file* data file that fhirflat will transform, and *google-sheet-id* is the unique
 ID of the google sheet containing the mapping information (found in the url; the format
-if usually https://docs.google.com/spreadsheets/d/{spreadsheet_id}/edit#gid={sheet_id}, 
+if usually https://docs.google.com/spreadsheets/d/{spreadsheet_id}/edit#gid={sheet_id},
 you want the spreadsheet_id. The sheet has to be public, i.e. share settings must be set
 to 'Anyone with the link' for this to work). *date-format* is the format dates follow in
 the raw data, e.g. a "2020-04-20" date has a date format of "%Y-%m-%d", and *timezone*
-is the time zone the data was recorded in, e.g. "America/New_York". A full list of 
+is the time zone the data was recorded in, e.g. "America/New_York". A full list of
 timezones can be found [here](https://nodatime.org/timezones).
 
-Further information on the structure of the mapping file can be found 
+Further information on the structure of the mapping file can be found
 [in the specification](../spec/mapping.md)
 
 ## Library

diff --git a/docs/howto/conversion-fhir.md b/docs/howto/conversion-fhir.md
@@ -38,7 +38,7 @@ from fhirflat import Patient
 Patient.fhir_file_to_flat("patient_export.ndjson")
 ```
 creates a "patient_export.parquet" FHIRflat file.
-This first initialises a `Patient` data class for each row to make use of the Pydantic 
+This first initialises a `Patient` data class for each row to make use of the Pydantic
 data validation, then creates a FHIRflat file.
 
 ## From FHIRflat
@@ -47,4 +47,4 @@ FHIR resources can also be created directly from FHIRflat files
 Patient.from_flat("patient_flat.parquet")
 ```
 which returns either a single Patient resource, or a list of Patient resources if
-the Parquet file contains multiple rows of data.
+the Parquet file contains multiple rows of data.
diff --git a/docs/index.md b/docs/index.md
@@ -100,4 +100,4 @@ maxdepth: 1
 fhirflat
 resources_base
 resources
-```
+```
diff --git a/docs/resources.rst b/docs/resources.rst
@@ -1,2 +1,2 @@
 .. automodule:: fhirflat.resources
-    :members:
+    :members:
diff --git a/docs/resources_base.rst b/docs/resources_base.rst
@@ -2,4 +2,4 @@ FHIRFlat Base Class
 ===================
 
 .. autoclass:: fhirflat.resources.base.FHIRFlatBase
-    :members:
+    :members:
diff --git a/docs/spec/fhirflat.md b/docs/spec/fhirflat.md
@@ -51,7 +51,7 @@ normalising a FHIR structure, noted below.
         "display": "Donald Duck"
     }
     ```
-    becomes 
+    becomes
     | subject.reference |
     |-------------------|
     |"Patient/f001"     |
@@ -154,7 +154,7 @@ normalising a FHIR structure, noted below.
         },
     ]
     ```
-    becomes 
+    becomes
     | encounter.diagnosis_dense            |
     |--------------------------------------|
-    |"[{"condition": [{"reference"...}]}]" |
+    |"[{"condition": [{"reference"...}]}]" |
diff --git a/docs/spec/isaric-fhir-extensions.rst b/docs/spec/isaric-fhir-extensions.rst
@@ -1,3 +1,3 @@
 .. automodule:: fhirflat.resources.extensions
     :members:
-    :exclude-members: elements_sequence
+    :exclude-members: elements_sequence
diff --git a/docs/spec/mapping.md b/docs/spec/mapping.md
@@ -114,4 +114,4 @@ Conditional assignments are made using the **`if not`** statement. A value of
 FHIR resource entries can be lists, such as a set of codes. This is handled in
 the mapping specification by allowing multiple matches for a (`raw_variable`,
 `raw_response`) tuple. The corresponding resource assignments (such as
-`coding.code`) are then collected into lists.
+`coding.code`) are then collected into lists.
diff --git a/fhirflat/__init__.py b/fhirflat/__init__.py
@@ -18,4 +18,4 @@
 )
 from .ingest import convert_data_to_flat
 
-__all__ = ["convert_data_to_flat"]
+__all__ = ["convert_data_to_flat"]
diff --git a/fhirflat/fhir2flat.py b/fhirflat/fhir2flat.py
@@ -213,7 +213,6 @@ def flattenExtensions(df: pd.DataFrame, extension: str) -> pd.DataFrame:
     """
 
     def expand_and_redefine(df, extension):
-
         def redefine(
             row: pd.Series | pd.DataFrame, extension: str
         ) -> pd.Series | pd.DataFrame:

diff --git a/fhirflat/resources/extension_validators.py b/fhirflat/resources/extension_validators.py
@@ -96,9 +96,9 @@ def fhir_model_validator(
         self, model_name: str, v: Union[StrBytes, dict, Path, FHIRAbstractModel]
     ):
         """ """
-        model_class: Type[BaseModel] | Type[FHIRAbstractModel] = (
-            self.get_fhir_model_class(model_name)
-        )
+        model_class: Type[BaseModel] | Type[
+            FHIRAbstractModel
+        ] = self.get_fhir_model_class(model_name)
 
         if isinstance(v, (str, bytes)):
             try:

diff --git a/tests/data/patient.ndjson b/tests/data/patient.ndjson
@@ -1,3 +1,3 @@
 {"resourceType":"Patient","id":"ewnMwMK-UNvVvM.bakFSlkw3","identifier":[{"use":"usual","type":{"text":"EPIC"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.5.737384.0","value":"E9254"},{"use":"usual","type":{"text":"EXTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"Z11363"},{"use":"usual","type":{"text":"FHIR"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-dstu2-fhir-id","value":"TYO3ktvhYAUhbae7JuBwDdpyIbUZc8kZG.bMW2ZwVnwgB"},{"use":"usual","type":{"text":"FHIR STU3"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-fhir-id","value":"ewnMwMK-UNvVvM.bakFSlkw3"},{"use":"usual","type":{"text":"PAS"},"system":"urn:oid:2.16.840.1.113883.2.1.3.12.1.1","value":"2005294"},{"use":"usual","type":{"text":"INTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"    Z11363"}],"active":true,"name":[{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"official","text":"Test ADVANCEPREPTWO","family":"ADVANCEPREPTWO","given":["Test"],"_family":{"extension":[{"valueString":"Advancepreptwo","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}},{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"usual","text":"Test ADVANCEPREPTWO","family":"ADVANCEPREPTWO","given":["Test"],"_family":{"extension":[{"valueString":"Advancepreptwo","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}}],"gender":"female","birthDate":"2006-10-07","deceasedBoolean":false,"maritalStatus":{"text":"Single"}}
 {"resourceType":"Patient","id":"exU8JSL0p8npSw5g1QYAyOw3","identifier":[{"use":"usual","type":{"text":"EPIC"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.5.737384.0","value":"E9340"},{"use":"usual","type":{"text":"EXTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"Z11449"},{"use":"usual","type":{"text":"FHIR"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-dstu2-fhir-id","value":"TwzgMHMPt5OhnHkFA2H2DudL3FU8qcRZkZyn0F3extkAB"},{"use":"usual","type":{"text":"FHIR STU3"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-fhir-id","value":"exU8JSL0p8npSw5g1QYAyOw3"},{"use":"usual","type":{"text":"PAS"},"system":"urn:oid:2.16.840.1.113883.2.1.3.12.1.1","value":"2005380"},{"use":"usual","type":{"text":"INTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"    Z11449"}],"active":true,"name":[{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"official","text":"BcnScTenAugTwentyOne UPGRADETEST","family":"UPGRADETEST","given":["BcnScTenAugTwentyOne"],"_family":{"extension":[{"valueString":"UpgradeTest","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}},{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"usual","text":"BcnScTenAugTwentyOne UPGRADETEST","family":"UPGRADETEST","given":["BcnScTenAugTwentyOne"],"_family":{"extension":[{"valueString":"UpgradeTest","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}}],"gender":"female","birthDate":"2019-09-21","deceasedBoolean":false,"maritalStatus":{"text":"Single"}}
-{"resourceType":"Patient","id":"ezER-U3fAMP-WvI-Fc8V9wQ3","identifier":[{"use":"usual","type":{"text":"EPIC"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.5.737384.0","value":"E9411"},{"use":"usual","type":{"text":"EXTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"Z11522"},{"use":"usual","type":{"text":"FHIR"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-dstu2-fhir-id","value":"T2oDrcOUw0w.1ZUdthu24c7V95lTOTEOUPRqBqGn99KEB"},{"use":"usual","type":{"text":"FHIR STU3"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-fhir-id","value":"ezER-U3fAMP-WvI-Fc8V9wQ3"},{"use":"usual","type":{"text":"PAS"},"system":"urn:oid:2.16.840.1.113883.2.1.3.12.1.1","value":"2005452"},{"use":"usual","type":{"text":"INTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"    Z11522"}],"active":true,"name":[{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"official","text":"Fred TEST","family":"TEST","given":["Fred"],"_family":{"extension":[{"valueString":"Test","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}},{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"usual","text":"Fred TEST","family":"TEST","given":["Fred"],"_family":{"extension":[{"valueString":"Test","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}}],"telecom":[{"system":"phone","value":"07594 832748","use":"mobile"},{"system":"email","value":"fred@email.com"}],"gender":"male","birthDate":"1967-01-19","deceasedBoolean":false,"address":[{"use":"old","line":["123 Anywhere"],"city":"Bristol","postalCode":"BS1 6JY","country":"ENG"},{"use":"home","line":["123 Anywhere"],"city":"Bristol","postalCode":"BS1 6JY","country":"ENG","period":{"start":"2022-01-19"}}],"maritalStatus":{"text":"Single"},"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en","display":"English"}],"text":"English"},"preferred":true}]}
+{"resourceType":"Patient","id":"ezER-U3fAMP-WvI-Fc8V9wQ3","identifier":[{"use":"usual","type":{"text":"EPIC"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.5.737384.0","value":"E9411"},{"use":"usual","type":{"text":"EXTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"Z11522"},{"use":"usual","type":{"text":"FHIR"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-dstu2-fhir-id","value":"T2oDrcOUw0w.1ZUdthu24c7V95lTOTEOUPRqBqGn99KEB"},{"use":"usual","type":{"text":"FHIR STU3"},"system":"http://open.epic.com/FHIR/StructureDefinition/patient-fhir-id","value":"ezER-U3fAMP-WvI-Fc8V9wQ3"},{"use":"usual","type":{"text":"PAS"},"system":"urn:oid:2.16.840.1.113883.2.1.3.12.1.1","value":"2005452"},{"use":"usual","type":{"text":"INTERNAL"},"system":"urn:oid:1.2.840.114350.1.13.520.3.7.2.698084","value":"    Z11522"}],"active":true,"name":[{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"official","text":"Fred TEST","family":"TEST","given":["Fred"],"_family":{"extension":[{"valueString":"Test","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}},{"extension":[{"valueCode":"NL4","url":"http://hl7.org/fhir/StructureDefinition/humanname-assembly-order"}],"use":"usual","text":"Fred TEST","family":"TEST","given":["Fred"],"_family":{"extension":[{"valueString":"Test","url":"http://hl7.org/fhir/StructureDefinition/humanname-own-name"}]}}],"telecom":[{"system":"phone","value":"07594 832748","use":"mobile"},{"system":"email","value":"fred@email.com"}],"gender":"male","birthDate":"1967-01-19","deceasedBoolean":false,"address":[{"use":"old","line":["123 Anywhere"],"city":"Bristol","postalCode":"BS1 6JY","country":"ENG"},{"use":"home","line":["123 Anywhere"],"city":"Bristol","postalCode":"BS1 6JY","country":"ENG","period":{"start":"2022-01-19"}}],"maritalStatus":{"text":"Single"},"communication":[{"language":{"coding":[{"system":"urn:ietf:bcp:47","code":"en","display":"English"}],"text":"English"},"preferred":true}]}
diff --git a/tests/dummy_data/combined_dummy_data.csv b/tests/dummy_data/combined_dummy_data.csv
@@ -2,4 +2,4 @@
 1,10,2020-05-01,0,,,,,,,cough,,,7,2020-01-01,36.2,120,30,70,120,5,,75,1,1,1,150
 2,11,,1,2021-04-01,18:00,fish,1,,2,,,2021-04-10,1,2021-02-02,37,100,40,80,130,6,10,85,0,2,1,200
 3,12,,1,2021-05-10,17:30,,1,,1,flu,,2021-05-15,4,2022-03-03,35.5,70,50,90,140,7,,95,0,3,1,
-4,13,,1,2022-06-15,21:00,dolphin,0,Malaria,,,,2022-06-20,2,,,,,,,,,,,,,
+4,13,,1,2022-06-15,21:00,dolphin,0,Malaria,,,,2022-06-20,2,,,,,,,,,,,,,
diff --git a/tests/dummy_data/encounter_dummy_data_multi_patient.csv b/tests/dummy_data/encounter_dummy_data_multi_patient.csv
@@ -2,4 +2,4 @@
 1,10,2020-05-01,0,,,,,,,cough,,,7
 2,11,,1,2021-04-01,18:00,fish,1,,2,,,2021-04-10,1
 3,12,,1,2021-05-10,17:30,,1,,1,flu,,2021-05-15,4
-4,13,,1,2022-06-15,21:00,dolphin,0,Malaria,,,,2022-06-20,2
+4,13,,1,2022-06-15,21:00,dolphin,0,Malaria,,,,2022-06-20,2
diff --git a/tests/dummy_data/encounter_dummy_data_single.csv b/tests/dummy_data/encounter_dummy_data_single.csv
@@ -1,2 +1,2 @@
 subjid,visitid,dates_enrolment,dates_adm,dates_admdate,dates_admtime,non_encounter_field,outco_denguediag,outco_denguediag_main,outco_denguediag_class,outco_not_dengue,outco_secondiag_oth,outco_date,outco_outcome
-2,11,2021-04-02,1,2021-04-01,18:00,fish,1,,2,,,2021-04-10,1
+2,11,2021-04-02,1,2021-04-01,18:00,fish,1,,2,,,2021-04-10,1
diff --git a/tests/dummy_data/observation_dummy_mapping.csv b/tests/dummy_data/observation_dummy_mapping.csv
@@ -17,4 +17,4 @@ vital_avpu,"1, Alert",,http://terminology.hl7.org/CodeSystem/observation-categor
 ,"3, Pain",,http://terminology.hl7.org/CodeSystem/observation-category,vital-signs,Vital Signs,<daily_date>,https://snomed.info/sct,1.10444E+15,Alert Confusion Voice Pain Unresponsive scale score (observable entity),Patient/+<subjid>,Encounter/+<visitid>,,,,,https://snomed.info/sct,450847001,Responds to pain (finding),,
 ,"4, Unresponsive",,http://terminology.hl7.org/CodeSystem/observation-category,vital-signs,Vital Signs,<daily_date>,https://snomed.info/sct,1.10444E+15,Alert Confusion Voice Pain Unresponsive scale score (observable entity),Patient/+<subjid>,Encounter/+<visitid>,,,,,https://snomed.info/sct,422768004,Unresponsive (finding),,
 vital_gcs,,,http://terminology.hl7.org/CodeSystem/observation-category,vital-signs,Vital Signs,<daily_date>,https://snomed.info/sct,9269-2,Glasgow coma score total,Patient/+<subjid>,Encounter/+<visitid>,,,,,,,,,<FIELD>
-vital_urineflow,,,http://terminology.hl7.org/CodeSystem/observation-category,vital-signs,Vital Signs,<daily_date>,https://loinc.org,9192-6,Urine output 24 hour,Patient/+<subjid>,Encounter/+<visitid>,<FIELD>,https://snomed.info/sct,258861009,Millilitre/24 hours (qualifier value),,,,,
+vital_urineflow,,,http://terminology.hl7.org/CodeSystem/observation-category,vital-signs,Vital Signs,<daily_date>,https://loinc.org,9192-6,Urine output 24 hour,Patient/+<subjid>,Encounter/+<visitid>,<FIELD>,https://snomed.info/sct,258861009,Millilitre/24 hours (qualifier value),,,,,
diff --git a/tests/dummy_data/vital_signs_dummy_data.csv b/tests/dummy_data/vital_signs_dummy_data.csv
@@ -1,4 +1,4 @@
 subjid,visitid,daily_date,vital_highesttem_c,vital_hr,vital_rr,vital_systolicbp,vital_diastolicbp,vital_spo2,vital_fio2spo2_02110,vital_fio2spo2_pcnt,vital_capillaryr,vital_avpu,vital_gcs,vital_urineflow
 1,10,2020-01-01,36.2,120,30,70,120,5,,75,1,1,1,150
 2,11,2021-02-02,37,100,40,80,130,6,10,85,0,2,1,200
-3,12,2022-03-03,35.5,70,50,90,140,7,,95,0,3,1,
+3,12,2022-03-03,35.5,70,50,90,140,7,,95,0,3,1,