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utils.py
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utils.py
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import json
from copy import deepcopy
from pyspark.sql import DataFrame
from pyspark.sql.types import *
from pyspark.sql.functions import *
from dbignite.schemas import ENTRY_SCHEMA
# TODO Add Type Hinting
# TODO change to transform
def entries_to_person(entries_df: DataFrame) -> DataFrame:
entry_schema = deepcopy(ENTRY_SCHEMA)
patient_schema = next(
f.dataType for f in entry_schema.fields if f.name == "resource"
)
patient_schema.fields.extend(
[
StructField("name", StringType()),
StructField("gender", StringType()),
StructField("birthDate", DateType()),
StructField("address", StringType()),
StructField(
"extension", ArrayType(StructType([StructField("url", StringType())]))
),
]
)
return (
entries_df.where(col("entry.request.url") == "Patient")
.withColumn("patient", from_json("entry_json", schema=entry_schema)["resource"])
.select(
col("patient.id").alias("person_id"),
col("patient.name").alias("name"),
col("patient.gender").alias("gender_source_value"),
year(col("patient.birthDate")).alias("year_of_birth"),
month(col("patient.birthDate")).alias("month_of_birth"),
dayofmonth(col("patient.birthDate")).alias("day_of_birth"),
col("patient.address").alias("address"),
)
)
def entries_to_condition(entries_df: DataFrame) -> DataFrame:
entry_schema = deepcopy(ENTRY_SCHEMA)
condition_schema = next(
f.dataType for f in entry_schema.fields if f.name == "resource"
)
condition_schema.fields.extend(
[
StructField(
"subject", StructType([StructField("reference", StringType())])
),
StructField(
"encounter", StructType([StructField("reference", StringType())])
),
StructField(
"code",
StructType(
[
StructField(
"coding",
ArrayType(
StructType(
[
StructField("code", StringType()),
StructField("display", StringType()),
]
)
),
),
StructField("text", StringType()),
]
),
),
StructField("onsetDateTime", TimestampType()),
StructField("abatementDateTime", TimestampType()),
]
)
return (
entries_df.where(col("entry.request.url") == "Condition")
.withColumn(
"condition", from_json("entry_json", schema=entry_schema)["resource"]
)
.select(
col("condition.id").alias("condition_occurrence_id"),
regexp_replace(col("condition.subject.reference"), "urn:uuid:", "").alias(
"person_id"
),
regexp_replace(col("condition.encounter.reference"), "urn:uuid:", "").alias(
"visit_occurrence_id"
),
col("condition.onsetDateTime").alias("condition_start_datetime"),
col("condition.abatementDateTime").alias("condition_end_datetime"),
col("condition.code.coding")[0]["display"].alias("condition_status"),
col("condition.code.coding")[0]["code"].alias("condition_code"),
)
)
def entries_to_procedure_occurrence(entries_df: DataFrame) -> DataFrame:
entry_schema = deepcopy(ENTRY_SCHEMA)
procedure_occurrence_schema = next(
f.dataType for f in entry_schema.fields if f.name == "resource"
)
procedure_occurrence_schema.fields.extend(
[
StructField(
"subject", StructType([StructField("reference", StringType())])
),
StructField(
"encounter", StructType([StructField("reference", StringType())])
),
StructField(
"code",
StructType(
[
StructField(
"coding",
ArrayType(
StructType(
[
StructField("code", StringType()),
StructField("display", StringType()),
StructField("system", StringType()),
]
)
),
),
StructField("text", StringType()),
]
),
),
StructField(
"performedPeriod",
StructType(
[
StructField("start", TimestampType()),
StructField("end", TimestampType()),
]
),
),
StructField("category", StringType()),
StructField("performer", StringType()),
StructField(
"location",
StructType(
[
StructField("reference", StringType()),
StructField("display", StringType()),
]
),
),
]
)
return (
entries_df.where(col("entry.request.url") == "Procedure")
.withColumn(
"procedure_occurrence",
from_json("entry_json", schema=entry_schema)["resource"],
)
.select(
col("procedure_occurrence.id").alias("procedure_occurrence_id"),
regexp_replace(
col("procedure_occurrence.subject.reference"), "urn:uuid:", ""
).alias("person_id"),
col("procedure_occurrence.code.coding")[0]["code"].alias("procedure_code"),
col("procedure_occurrence.code.coding")[0]["display"].alias(
"procedure_code_display"
),
col("procedure_occurrence.code.coding")[0]["system"].alias(
"procedure_code_system"
),
col("procedure_occurrence.performedPeriod.start")
.cast("date")
.alias("procedure_start_date"),
col("procedure_occurrence.performedPeriod.end")
.cast("date")
.alias("procedure_end_date"),
col("procedure_occurrence.category").alias("procedure_type"),
col("procedure_occurrence.performer").alias("provider_id"),
regexp_replace(
col("procedure_occurrence.encounter.reference"), "urn:uuid:", ""
).alias("visit_occurrence_id"),
col("procedure_occurrence.location.reference").alias("location_id"),
col("procedure_occurrence.location.display").alias("location_display"),
)
)
def entries_to_encounter(entries_df: DataFrame) -> DataFrame:
entry_schema = deepcopy(ENTRY_SCHEMA)
encounter_schema = next(
f.dataType for f in entry_schema.fields if f.name == "resource"
)
encounter_schema.fields.extend(
[
StructField(
"subject", StructType([StructField("reference", StringType())])
),
StructField(
"period",
StructType(
[
StructField("start", TimestampType()),
StructField("end", TimestampType()),
]
),
),
StructField(
"serviceProvider",
StructType(
[
StructField("reference", StringType()),
StructField("display", StringType()),
]
),
),
StructField(
"type",
ArrayType(
StructType(
[
StructField(
"coding",
ArrayType(
StructType(
[
StructField("code", StringType()),
StructField("display", StringType()),
StructField("system", StringType()),
]
)
),
),
StructField("text", StringType()),
]
)
),
),
StructField(
"participant",
ArrayType(
StructType(
[
StructField(
"type",
ArrayType(
StructType(
[
StructField(
"coding",
ArrayType(
StructType(
[
StructField(
"code", StringType()
),
StructField(
"display", StringType()
),
StructField(
"system", StringType()
),
]
)
),
),
StructField("text", StringType()),
]
)
),
)
]
)
),
),
StructField("status", StringType()),
StructField(
"identifier",
ArrayType(
StructType(
[
StructField("use", StringType()),
StructField("system", StringType()),
StructField("value", StringType()),
]
)
),
),
StructField(
"location",
ArrayType(
StructType(
[
StructField(
"location",
StructType(
[
StructField("reference", StringType()),
StructField("display", StringType()),
]
),
)
]
)
),
),
]
)
return (
entries_df.where(col("entry.request.url") == "Encounter")
.withColumn(
"encounter", from_json("entry_json", schema=entry_schema)["resource"]
)
.select(
col("encounter.id").alias("encounter_id"),
regexp_replace(col("encounter.subject.reference"), "urn:uuid:", "").alias(
"person_id"
),
col("encounter.period.start").alias("encounter_period_start"),
col("encounter.period.end").alias("encounter_period_end"),
col("encounter.serviceProvider.display").alias("serviceProvider"),
col("encounter.type")[0]["coding"][0]["display"].alias("encounter_status"),
col("encounter.type")[0]["coding"][0]["code"].alias("encounter_code"),
col("encounter.type")[0]["text"].alias("encounter_status_text"),
col("encounter.participant"),
col("encounter.status"),
col("encounter.identifier"),
col("encounter.location"),
)
)
def summarize_condition(condition_df: DataFrame) -> DataFrame:
return (
condition_df.orderBy("condition_start_datetime")
.select(col("person_id"), struct("*").alias("condition"))
.groupBy("person_id")
.agg(
collect_list("condition").alias("conditions"),
)
)
def summarize_procedure_occurrence(procedure_occurrence_df: DataFrame) -> DataFrame:
return (
procedure_occurrence_df.orderBy("procedure_start_date")
.select(col("person_id"), struct("*").alias("procedure_occurrence"))
.groupBy("person_id")
.agg(
collect_list("procedure_occurrence").alias("procedure_occurrences"),
)
)
def summarize_encounter(encounter_df: DataFrame) -> DataFrame:
return (
encounter_df.orderBy("encounter_period_start")
.select(col("person_id"), struct("*").alias("encounter"))
.groupBy("person_id")
.agg(
collect_list("encounter").alias("encounters"),
)
)