Code modification

datacommonsorg · Nov 22, 2023 · 57fd2b3 · 57fd2b3
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diff --git a/scripts/us_cdc/heat_related_illness/README.md b/scripts/us_cdc/heat_related_illness/README.md
@@ -7,23 +7,23 @@ The source data is downloaded manually from the EPH [website](https://ephtrackin
 To clean the source data, run:
 
 ```bash
-python clean_data.py --input_path=source_data/ --output_path=<output_path>
+python3 clean_data.py --input_path=source_data/ --output_path=<output_path>
 ```
 
 ## Generating artifacts at a State level:
 The artifacts can be generated from the cleaned data.
 To generate `cleaned.csv`, `output.mcf` run:
 
 ```bash
-python preprocess.py --input_path=<directory path to cleaned data> --config_path=<path to config> --output_path=<directory path to write csv and mcf>
+python3 preprocess.py --input_path=<directory path to cleaned data> --config_path=<path to config> --output_path=<directory path to write csv and mcf>
 ```
 
 ## Aggregating at a Country level
 At a country level, aggregation is performed by summing over the state level `cleaned.csv`.
 To aggregate run:
 
 ```bash
-python aggregate.py --input_path=<path to state level csv> --output_path=<output csv path>
+python3 aggregate.py --input_path=<path to state level csv> --output_path=<output csv path>
 ```
 
 ## Data Caveats:

diff --git a/scripts/us_cdc/heat_related_illness/preprocess_test.py b/scripts/us_cdc/heat_related_illness/preprocess_test.py
@@ -32,7 +32,7 @@ def test_csv(self):
             input_path = os.path.join(_SCRIPT_PATH, 'testdata', 'cleaned_data')
 
             subprocess.call([
-                'python', preprocess_path, f'--input_path={input_path}',
+                'python3', preprocess_path, f'--input_path={input_path}',
                 f'--config_path={config_path}', f'--output_path={tmp_dir}'
             ])
 

diff --git a/scripts/us_cdc/heat_related_illness/source_data/deaths.html b/scripts/us_cdc/heat_related_illness/source_data/deaths.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/edVisits.html b/scripts/us_cdc/heat_related_illness/source_data/edVisits.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/edVisits_age.html b/scripts/us_cdc/heat_related_illness/source_data/edVisits_age.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/edVisits_age_gender.html b/scripts/us_cdc/heat_related_illness/source_data/edVisits_age_gender.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/edVisits_gender.html b/scripts/us_cdc/heat_related_illness/source_data/edVisits_gender.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/hospitalizations.html b/scripts/us_cdc/heat_related_illness/source_data/hospitalizations.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_age.html b/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_age.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_age_gender.html b/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_age_gender.html
diff --git a/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_gender.html b/scripts/us_cdc/heat_related_illness/source_data/hospitalizations_gender.html
diff --git a/scripts/us_cdc/heat_related_illness/testdata/expected.csv b/scripts/us_cdc/heat_related_illness/testdata/expected.csv
@@ -1,4 +1,24 @@
 Year,Geo,StatVar,Quantity
+2000-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,41.0
+2001-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,25.0
+2002-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,43.0
+2003-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,38.0
+2004-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,33.0
+2005-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,62.0
+2006-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,188.0
+2007-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,67.0
+2008-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,42.0
+2009-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,54.0
+2010-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,39.0
+2011-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,26.0
+2012-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,61.0
+2013-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,66.0
+2014-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,47.0
+2015-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,49.0
+2016-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,67.0
+2017-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,98.0
+2018-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,98.0
+2019-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,57.0
 2005-09,geoId/06,Count_MedicalConditionIncident_0To4Years_SummerSeason_Male_ConditionHeatStress_VisitedEmergencyDepartment,55.0
 2005-09,geoId/06,Count_MedicalConditionIncident_0To4Years_SummerSeason_Female_ConditionHeatStress_VisitedEmergencyDepartment,42.0
 2005-09,geoId/06,Count_MedicalConditionIncident_5To14Years_SummerSeason_Male_ConditionHeatStress_VisitedEmergencyDepartment,141.0
@@ -329,23 +349,3 @@ Year,Geo,StatVar,Quantity
 2018-09,geoId/06,Count_MedicalConditionIncident_35To64Years_SummerSeason_Female_ConditionHeatStress_PatientHospitalized,114.0
 2018-09,geoId/06,Count_MedicalConditionIncident_65OrMoreYears_SummerSeason_Male_ConditionHeatStress_PatientHospitalized,285.0
 2018-09,geoId/06,Count_MedicalConditionIncident_65OrMoreYears_SummerSeason_Female_ConditionHeatStress_PatientHospitalized,199.0
-2000-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,41.0
-2001-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,25.0
-2002-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,43.0
-2003-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,38.0
-2004-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,33.0
-2005-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,62.0
-2006-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,188.0
-2007-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,67.0
-2008-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,42.0
-2009-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,54.0
-2010-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,39.0
-2011-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,26.0
-2012-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,61.0
-2013-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,66.0
-2014-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,47.0
-2015-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,49.0
-2016-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,67.0
-2017-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,98.0
-2018-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,98.0
-2019-09,geoId/06,Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased,57.0
diff --git a/scripts/us_cdc/heat_related_illness/testdata/expected_output.mcf b/scripts/us_cdc/heat_related_illness/testdata/expected_output.mcf
@@ -1,3 +1,12 @@
+Node: dcid:Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased
+populationType: dcs:MedicalConditionIncident
+medicalStatus: dcs:PatientDeceased
+medicalCondition: dcs:HeatStress
+climaticSeason: dcs:SummerSeason
+measuredProperty: dcs:count
+statType: dcs:measuredValue
+typeOf: dcs:StatisticalVariable
+
 Node: dcid:Count_MedicalConditionIncident_0To4Years_SummerSeason_Male_ConditionHeatStress_VisitedEmergencyDepartment
 populationType: dcs:MedicalConditionIncident
 medicalStatus: dcs:VisitedEmergencyDepartment
@@ -218,12 +227,3 @@ typeOf: dcs:StatisticalVariable
 age: [65 - Years]
 gender: dcs:Female
 
-Node: dcid:Count_MedicalConditionIncident_SummerSeason_ConditionHeatStress_PatientDeceased
-populationType: dcs:MedicalConditionIncident
-medicalStatus: dcs:PatientDeceased
-medicalCondition: dcs:HeatStress
-climaticSeason: dcs:SummerSeason
-measuredProperty: dcs:count
-statType: dcs:measuredValue
-typeOf: dcs:StatisticalVariable
-