diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/README.md b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/README.md new file mode 100644 index 0000000000..0f9e03c667 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/README.md @@ -0,0 +1,48 @@ +# WHO Tuberculosis Dataset: Bacteriologically Confirmed Pulmonary TB + +## Overview +This dataset provides the number of people diagnosed with a new episode of pulmonary TB whose disease was bacteriologically confirmed, sourced directly from the World Health Organization (WHO). + +## Data Source + +**Source URL:** +https://data.who.int/indicators/i/1891124/5D51DB1 + +The data comes from the official WHO reporting database and includes comprehensive, country-level health metrics detailing annual Tuberculosis notifications and case classifications. + +## How To Download Input Data +To download the data, you'll need to run the provided download script `download_tb_data.py`. This script automatically queries the WHO API for the indicator, merges it with the WHO geographical master list to append standard `iso3` country codes, and saves the cleaned `TB_Bacteriologically_Confirmed_input.csv` file inside an "source_files" folder. + +type of place: Country. + +statvars: Health / Tuberculosis. + +years: Historical to present. + +## Processing Instructions +To process the WHO Tuberculosis data and generate statistical variables, use the following commands from your root `data` directory: + +**Download input file** +```bash +python3 statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/download_tb_data.py +``` +**For Test Data Run** +```bash +python3 tools/statvar_importer/stat_var_processor.py \ + --input_data=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_input.csv \ + --pv_map=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv \ + --output_path=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output \ + --config_file=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv \ + --existing_statvar_mcf=gs://unresolved_mcf/scripts/statvar/stat_vars.mcf +``` + +**For Main data run** +```bash +python3 tools/statvar_importer/stat_var_processor.py \ + --input_data=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/source_files/TB_Bacteriologically_Confirmed_input.csv \ + --pv_map=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv \ + --output_path=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/TB_Bacteriologically_Confirmed_output \ + --config_file=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv\ + --existing_statvar_mcf=gs://unresolved_mcf/scripts/statvar/stat_vars.mcf +``` + diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/download_tb_data.py b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/download_tb_data.py new file mode 100644 index 0000000000..c8d45a3369 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/download_tb_data.py @@ -0,0 +1,72 @@ +import os +import requests +import io +import pandas as pd + +def download_who_tb_data_with_iso3(): + # 1. Get the Clean Data from the API + api_url = "https://xmart-api-public.who.int/DATA_/RELAY_TB_DATA" + params = { + "$filter": "IND_ID eq '18911245D51DB1'", + "$select": "IND_ID,INDICATOR_NAME,YEAR,COUNTRY,VALUE", + "$format": "csv" + } + + print("1. Fetching clean indicator data from WHO API...") + # FIX: Added 60-second timeout + api_response = requests.get(api_url, params=params, timeout=60) + + # FIX: Replaced manual status check with raise_for_status() + api_response.raise_for_status() + + # Load the clean API data into a pandas table + api_df = pd.read_csv(io.StringIO(api_response.text)) + + # 2. Get ONLY the iso3 code from the master database + print("2. Fetching country iso3 codes from WHO master database...") + master_url = "https://extranet.who.int/tme/generateCSV.asp?ds=notifications" + geo_columns = ['country', 'iso3'] + + # FIX: Use requests to fetch the CSV so we can enforce a timeout + master_response = requests.get(master_url, timeout=60) + master_response.raise_for_status() + + # Load the text from the requests response into pandas + master_df = pd.read_csv(io.StringIO(master_response.text), usecols=geo_columns).drop_duplicates() + + # 3. Merge the two datasets together based on the country name + print("3. Merging data and formatting...") + merged_df = pd.merge(api_df, master_df, left_on='COUNTRY', right_on='country', how='left') + + # FIX: Validate that the left join did not result in missing iso3 codes + missing_iso3_df = merged_df[merged_df['iso3'].isna()] + if not missing_iso3_df.empty: + unmapped_countries = missing_iso3_df['COUNTRY'].unique() + error_msg = ( + f"Merge validation failed! {len(unmapped_countries)} country names " + f"did not match the master database and are missing iso3 codes:\n" + f"{', '.join(unmapped_countries)}" + ) + raise ValueError(error_msg) + + # Drop the duplicate lowercase 'country' column used for joining + merged_df = merged_df.drop(columns=['country']) + + # Reorder columns so the iso3 code sits right next to the Country name + final_columns = [ + 'IND_ID', 'INDICATOR_NAME', 'YEAR', 'COUNTRY', 'iso3', 'VALUE' + ] + merged_df = merged_df[final_columns] + + # 4. Save to CSV + output_dir = "statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/source_files" + filename = os.path.join(output_dir, "TB_Bacteriologically_Confirmed_input.csv") + + os.makedirs(output_dir, exist_ok=True) + + # Save without the pandas index column + merged_df.to_csv(filename, index=False) + print(f"Success! Data saved locally as '{filename}'") + +if __name__ == "__main__": + download_who_tb_data_with_iso3() \ No newline at end of file diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/manifest.json b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/manifest.json new file mode 100644 index 0000000000..b55c7aa582 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/manifest.json @@ -0,0 +1,27 @@ +{ + "import_specifications": [ + { + "import_name": "WHO_TuberculosisBacteriologicallyConfirmed", + "curator_emails": [ + "support@datacommons.org" + ], + "provenance_url": "https://data.who.int/indicators/i/1891124/5D51DB1", + "provenance_description": "Number of people diagnosed with a new episode of pulmonary TB whose disease was bacteriologically confirmed", + "scripts": [ + "download_tb_data.py", + "../../tools/statvar_importer/stat_var_processor.py --input_data=source_files/*.csv --pv_map=pulmonary_tb_bctpb_pvmap.csv --config_file=pulmonary_tb_bctpb_metadata.csv --output_path=TB_Bacteriologically_Confirmed_output" + ], + "source_files": [ + "source_files/*.csv" + ], + "import_inputs": [ + { + "template_mcf": "TB_Bacteriologically_Confirmed_output.tmcf", + "cleaned_csv": "TB_Bacteriologically_Confirmed_output.csv", + "stat_var_mcf": "TB_Bacteriologically_Confirmed_output_stat_vars.mcf" + } + ], + "cron_schedule": "0 0 1 1,4,7,10 *" + } + ] +} diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv new file mode 100644 index 0000000000..7cfcb3782f --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv @@ -0,0 +1,14 @@ +config,value +provenance_url,https://data.who.int/indicators/i/1891124/5D51DB1 +output_columns,"observationDate,observationAbout,value,variableMeasured" +places_within,country/ALL +#place_types,"AdministrativeArea,AdministrativeArea1,AdministrativeArea2,State" +#debug,1 +#input_rows,100 +#word_delimiter,'' +#skip_rows,1 +header_rows,1 +mapped_columns,5 +dc_api_root,https://api.datacommons.org + + diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv new file mode 100644 index 0000000000..ea0131a166 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv @@ -0,0 +1,9 @@ +key,p1,v1,p2,v2,p3,v3,p4,v4,p5,v5 +,,,,,,,,,, +VALUE,measuredProperty,count,populationType,MedicalConditionIncident,statType,measuredValue,value,{Number},,, +pulmonary TB,medicalCondition,PulmonaryTuberculosis,,,,,,,, +new episode,medicalStatus,NewCase,,,,,,,, +bacteriologically confirmed,medicalTestingMethod,BacteriologicalTest + +iso3,observationAbout,country/{Data},,,,,,,, +YEAR,observationDate,{Number},,,,,,,, \ No newline at end of file diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_input.csv b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_input.csv new file mode 100644 index 0000000000..08ed6a06c5 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_input.csv @@ -0,0 +1,100 @@ +IND_ID,INDICATOR_NAME,YEAR,COUNTRY,iso3,VALUE +18911245D51DB1,Number of people diagnosed with a new episode of pulmonary TB whose disease was bacteriologically confirmed,2002,American Samoa,ASM,1 +18911245D51DB1,Number of people diagnosed with a new episode of pulmonary TB whose disease was bacteriologically confirmed,2003,American Samoa,ASM,2 +18911245D51DB1,Number of people 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new episode of pulmonary TB whose disease was bacteriologically confirmed,2006,Antigua and Barbuda,ATG,4 +18911245D51DB1,Number of people diagnosed with a new episode of pulmonary TB whose disease was bacteriologically confirmed,2007,Antigua and Barbuda,ATG,3 diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.csv b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.csv new file mode 100644 index 0000000000..77335af2c9 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.csv @@ -0,0 +1,100 @@ +observationDate,observationAbout,value,variableMeasured +2002,country/ASM,1,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2003,country/ASM,2,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2004,country/ASM,2,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2005,country/ASM,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2006,country/ASM,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2007,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2008,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2009,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2010,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2011,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2013,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2014,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2015,country/ASM,4,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2016,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2017,country/ASM,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2018,country/ASM,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2019,country/ASM,1,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2020,country/ASM,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest 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+2023,country/AIA,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2024,country/AIA,0,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2000,country/ATG,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2001,country/ATG,1,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2002,country/ATG,2,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2003,country/ATG,1,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2005,country/ATG,6,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2006,country/ATG,4,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +2007,country/ATG,3,dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.tmcf b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.tmcf new file mode 100644 index 0000000000..f4b040a4cd --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output.tmcf @@ -0,0 +1,6 @@ +Node: E:TB_Bacteriologically_Confirmed_output->E0 +observationDate: C:TB_Bacteriologically_Confirmed_output->observationDate +observationAbout: C:TB_Bacteriologically_Confirmed_output->observationAbout +value: C:TB_Bacteriologically_Confirmed_output->value +variableMeasured: C:TB_Bacteriologically_Confirmed_output->variableMeasured +typeOf: dcs:StatVarObservation diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars.mcf b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars.mcf new file mode 100644 index 0000000000..34f86e06e7 --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars.mcf @@ -0,0 +1,11 @@ +# Auto generated using command: "tools/statvar_importer/stat_var_processor.py --input_data=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_input.csv --pv_map=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_pvmap.csv --output_path=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output --config_file=statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/pulmonary_tb_bctpb_metadata.csv --existing_statvar_mcf=gs://unresolved_mcf/scripts/statvar/stat_vars.mcf" on 2026-04-15 09:22:18.833724 + +Node: dcid:Count_MedicalConditionIncident_ConditionPulmonaryTuberculosis_NewCase_BacteriologicalTest +typeOf: dcid:StatisticalVariable +populationType: dcid:MedicalConditionIncident +measuredProperty: dcid:count +statType: dcid:measuredValue +medicalCondition: dcid:PulmonaryTuberculosis +medicalStatus: dcid:NewCase +medicalTestingMethod: dcid:BacteriologicalTest + diff --git a/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars_schema.mcf b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars_schema.mcf new file mode 100644 index 0000000000..e4b64e729d --- /dev/null +++ b/statvar_imports/PulmonaryTuberculosis_Bacteriologically_Confirmed/testdata/TB_Bacteriologically_Confirmed_output_stat_vars_schema.mcf @@ -0,0 +1,20 @@ +Node: dcid:NewCase +typeOf: dcid:MedicalEventEnum +name: "New Case" +isProvisional: dcs:True + +Node: dcid:PulmonaryTuberculosis +typeOf: dcid:Disease +name: "Pulmonary Tuberculosis" +isProvisional: dcs:True + +Node: dcid:medicalTestingMethod +typeOf: dcs:Property +name: "medicalTestingMethod" +domainIncludes: dcid:MedicalConditionIncident + +Node: dcid:BacteriologicalTest +typeOf: dcid:MedicalTestingMethodEnum +name: "Bacteriological Test" +isProvisional: dcs:True +