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6_future_date.py
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# version History
# Sept 2022, Stephanie Hong initial version
# May 2023, Yvette Chen, use input filepath, database name and vocabulary dbname parameter
#
# Databricks notebook source
!pip install tableone --quiet
!pip install geopandas --quiet
!pip install venn --quiet
# COMMAND ----------
import sys
if sys.version_info[0] == 3 and sys.version_info[1] < 7:
from packaging import version
else:
from distutils.version import LooseVersion
from io import StringIO
import pandas as pd
import numpy as np
from pyspark.sql import functions as F
from tableone import TableOne
import seaborn as sns
from matplotlib import pyplot as plt
# COMMAND ----------
#Function to convert a number into a human format (adds letters at the end of the number)
def human_format(num):
magnitude = 0
while abs(num) >= 1000:
magnitude += 1
num /= 1000.0
# add more suffixes if you need them
return '%.2f%s' % (num, ['', 'k', 'm', 'b', 't', 'p'][magnitude])
# COMMAND ----------
dbutils.widgets.removeAll()
dbutils.widgets.combobox("databaseName", "crisp_omop",["crisp_jan2022","crisp_sep2021","crisp_apr2021"], "CRISP database name")
dbutils.widgets.combobox("vocabdatabaseName", "omop_vocab_20220602",["omop_vocab_20220602","omop_vocab_20220204"], "OMOP Vocabulary database name")
dbutils.widgets.text("omopconcepts", "omop_concepts", "Concept Sets Database")
# COMMAND ----------
databaseName = dbutils.widgets.get("databaseName")
vocabdatabaseName = dbutils.widgets.get("vocabdatabaseName")
omopconcepts = dbutils.widgets.get("omopconcepts")
# COMMAND ----------
## procedure_occurrence
## count of future date
query="""Select count(*) proc_future_date from """+databaseName+""".procedure_occurrence where procedure_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
proc_future_date = human_format(pandasDF.proc_future_date[0])
proc_future_date
query="""Select count(*) proc_null from """+databaseName+""".procedure_occurrence where procedure_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
proc_null = human_format(pandasDF.proc_null[0])
print([proc_future_date,proc_null])
# COMMAND ----------
## visit_occurrence
## count of future date
query="""Select count(*) visit_future_date from """+databaseName+""".visit_occurrence where visit_start_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
visit_future_date = human_format(pandasDF.visit_future_date[0])
visit_future_date
query="""Select count(*) visit_null from """+databaseName+""".visit_occurrence where visit_start_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
visit_null = human_format(pandasDF.visit_null[0])
print([visit_future_date,visit_null])
# COMMAND ----------
## measurement
## count of future date
query="""Select count(*) measurement_future_date from """+databaseName+""".measurement where measurement_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
measurement_future_date = human_format(pandasDF.measurement_future_date[0])
measurement_future_date
query="""Select count(*) measurement_null from """+databaseName+""".measurement where measurement_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
measurement_null = human_format(pandasDF.measurement_null[0])
print([measurement_future_date,measurement_null])
# COMMAND ----------
displayHTML("""
<!DOCTYPE html>
<html>
<head>
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css">
<!-- Bootstrap Font Icon CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
<style>
.center {
margin-left: 20px;
width: 100%;
}
.value-large {
margin-top: 20px;
color: #4B6AB2;
font-size: 28px;
line-height: 32px;
font-weight: 600;
padding-right: 100px;
}
.title {
color: #8a9ba8;
font-size: 12px;
font-weight: 600;
letter-spacing: 0.5px;
text-transform: uppercase;
padding-right: 70px;
padding-top: 10px;
}
.text {
display: inline-block;
margin-top: 6px;
}
hr {
margin-top: 20px;
margin-left: 10px;
background-color: #D3D3D3;
border: none;
height: 0.5px;
}
.value-small {
color: #4B6AB2;
font-size: 23px;
line-height: 25px;
font-weight: 600;
padding-right: 70px;
}
</style>
<table class='center'>
<tr>
<td>
<div class="value-small">"""+str(proc_future_date )+"""</div>
<div class="title"> Future Date in Procedure Occurrence</div>
</td>
<td>
<div class="value-small"></i> """+str(proc_null)+"""</div>
<div class="title">Null in Procedure Occurrence</div>
</td>
<td>
<div class="value-small">"""+str(visit_future_date)+"""</div>
<div class="title">Future Date in Visit Occurrence</div>
</td>
<td>
<div class="value-small">"""+str(visit_null)+"""</div>
<div class="title">Null in Visit Occurence</div>
</td>
<td>
<div class="value-small">"""+str(measurement_future_date)+"""</div>
<div class="title">Future Date in Measurement</div>
</td>
<td>
<div class="value-small">"""+str(measurement_null)+"""</div>
<div class="title">Null in Measurement</div>
</td>
</tr>
</table>
<hr>
</body>
</html>
""")
# COMMAND ----------
query="""Select count(*) drug_exposure_future_date from """+databaseName+""".drug_exposure where drug_exposure_start_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
drug_exposure_future_date = human_format(pandasDF.drug_exposure_future_date[0])
drug_exposure_future_date
query="""Select count(*) drug_exposure_null from """+databaseName+""".drug_exposure where drug_exposure_start_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
drug_exposure_null = human_format(pandasDF.drug_exposure_null[0])
print([drug_exposure_future_date,drug_exposure_null])
# COMMAND ----------
query="""Select count(*) person_future_date from """+databaseName+""".person where year_of_birth > '2022' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
person_future_date = human_format(pandasDF.person_future_date[0])
person_future_date
query="""Select count(*) person_null from """+databaseName+""".person where year_of_birth is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
person_null = human_format(pandasDF.person_null[0])
print([person_future_date,person_null])
# COMMAND ----------
query="""Select count(*) condition_future_date from """+databaseName+""".condition_occurrence_domain_map where condition_start_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
condition_future_date = human_format(pandasDF.condition_future_date[0])
query="""Select count(*) condition_null from """+databaseName+""".condition_occurrence_domain_map where condition_start_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
condition_null = human_format(pandasDF.condition_null[0])
print([condition_future_date,condition_null])
# COMMAND ----------
query="""Select count(*) cvlab_future_date from """+databaseName+""".cvlab_ext where order_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
cvlab_future_date = human_format(pandasDF.cvlab_future_date[0])
query="""Select count(*) cvlab_null from """+databaseName+""".cvlab_ext where order_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
cvlab_null = human_format(pandasDF.cvlab_null[0])
print([cvlab_future_date,cvlab_null])
# COMMAND ----------
query="""Select count(*) death_future_date from """+databaseName+""".death where death_date > '2022-09-08' """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
death_future_date = human_format(pandasDF.death_future_date[0])
query="""Select count(*) death_null from """+databaseName+""".death where death_date is null """
dataframe = sqlContext.sql(query)
pandasDF = dataframe.toPandas()
death_null = human_format(pandasDF.death_null[0])
print([death_future_date,death_null])
# COMMAND ----------
displayHTML("""
<!DOCTYPE html>
<html>
<head>
<!-- Bootstrap CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css">
<!-- Bootstrap Font Icon CSS -->
<link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/font/bootstrap-icons.css">
<style>
.center {
margin-left: 20px;
width: 100%;
}
.value-large {
margin-top: 20px;
color: #4B6AB2;
font-size: 28px;
line-height: 32px;
font-weight: 600;
padding-right: 100px;
}
.title {
color: #8a9ba8;
font-size: 12px;
font-weight: 600;
letter-spacing: 0.5px;
text-transform: uppercase;
padding-right: 70px;
padding-top: 10px;
}
.text {
display: inline-block;
margin-top: 6px;
}
hr {
margin-top: 20px;
margin-left: 10px;
background-color: #D3D3D3;
border: none;
height: 0.5px;
}
.value-small {
color: #4B6AB2;
font-size: 23px;
line-height: 25px;
font-weight: 600;
padding-right: 70px;
}
</style>
<table class='center'>
<tr>
<td>
<div class="value-small">"""+str(drug_exposure_future_date)+"""</div>
<div class="title"> Future Date in drug Exposure</div>
</td>
<td>
<div class="value-small"></i> """+str(drug_exposure_null)+"""</div>
<div class="title">Null Date in drug Exposure</div>
</td>
<td>
<div class="value-small">"""+str(person_future_date)+"""</div>
<div class="title">Future Brith Year in Person</div>
</td>
<td>
<div class="value-small">"""+str(person_null)+"""</div>
<div class="title">Null Date in Person</div>
</td>
<td>
<div class="value-small">"""+str(condition_future_date)+"""</div>
<div class="title">Future Date in condition occurrence domain map </div>
</td>
<td>
<div class="value-small">"""+str(condition_null)+"""</div>
<div class="title">Null Date in condition occurrence domain map</div>
</td>
<td>
<div class="value-small">"""+str(cvlab_future_date)+"""</div>
<div class="title">Future Date in cvlab_ext </div>
</td>
<td>
<div class="value-small">"""+str(cvlab_null)+"""</div>
<div class="title">Null Date in cvlab_ext</div>
</td>
<td>
<div class="value-small">"""+str(death_future_date)+"""</div>
<div class="title">Future Date in death </div>
</td>
<td>
<div class="value-small">"""+str(death_null)+"""</div>
<div class="title">Null Date in death </div>
</td>
</tr>
</table>
<hr>
</body>
</html>
""")
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.procedure_occurrence
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.procedure_occurrence
# MAGIC WHERE procedure_date > '2022-09-08'
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.procedure_occurrence
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.procedure_occurrence
# MAGIC WHERE procedure_date is null
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.procedure_occurrence
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.measurement
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.measurement
# MAGIC WHERE measurement_date > '2022-09-08'
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.measurement
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.person
# COMMAND ----------
# MAGIC %sql
# MAGIC select * from $databaseName.person where year_of_birth > '2022'
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.person
# MAGIC where year_of_birth > '2022'
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.person
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.cvlab_ext
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.cvlab_ext where order_date > '2022-09-08'
# MAGIC
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.cvlab_ext
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.death
# COMMAND ----------
# MAGIC %sql
# MAGIC DELETE FROM $databaseName.death where death_date is null
# MAGIC
# COMMAND ----------
# MAGIC %sql
# MAGIC select count(*) from $databaseName.death
# COMMAND ----------