diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/README.md b/statvar_imports/who/tuberculosis_estimated_incidence_rate/README.md new file mode 100644 index 0000000000..04942332cb --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/README.md @@ -0,0 +1,76 @@ +# WHO Tuberculosis Estimated Incidence Rate Import + +## Overview +This dataset contains national-level statistics for the Estimated Tuberculosis Incidence Rate (per 100,000 population). +Specifically, it provides incidence rates for two categories: +- Overall TB incidence +- HIV-positive TB incidence + +The generated statistical variables capture the incidence rate for these conditions. +Examples of the statvars generated: +- `dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person` +- `dcid:Count_MedicalConditionIncident_ConditionTuberculosisAndHIV_AsAFractionOf_Count_Person` + +**type of place:** Country, Region (M49 codes), WHO Regions, Overseas Territory, Special Administrative Regions +**years:** 2000 to 2024 +**place_resolution:** Resolved to DCIDs (e.g., dcid:country/FRA, dcid:country/IND) + +## Data Source +**Source URL:** +https://data.who.int/indicators/i/EB68992/2674B39 + +**Provenance Description:** +The data comes from the World Health Organization (WHO) master database and the public API. It tracks the estimated TB incidence rate globally (Indicator ID: `EB689922674B39`). + +## Refresh Type +Automatic Refresh + +For refresh of the data, the import includes a Python script (`tb_data_download.py`) to automatically fetch the data from the WHO API, join it with ISO3 geographic identifiers, and save the formatted CSV. + +## Data Publish Frequency +Release Frequency = Annual + +## How To Download Input Data +To download the data, run the provided script: +```bash +python3 tb_data_download.py +``` +This will fetch the latest full dataset, process the ISO3 codes, and save it locally as `input_files/Estimated_incidence_rate_per_100_000_population.csv` making it available for stat var processing. + +## Processing Instructions +To process the WHO Tuberculosis Incidence Rate data and generate statistical variables, use the following command from the import directory: + +**For Data Run** +```bash +python3 ../../../tools/statvar_importer/stat_var_processor.py \ + --input_data=input_files/* \ + --pv_map=tuberculosis_estimated_incidence_rate_pvmap.csv \ + --output_path=tuberculosis_estimated_incidence_rate_output \ + --config_file=tuberculosis_estimated_incidence_rate_metadata.csv +``` + +This generates the following output files: +- tuberculosis_estimated_incidence_rate_output.csv +- tuberculosis_estimated_incidence_rate_output_stat_vars_schema.mcf +- tuberculosis_estimated_incidence_rate_output_stat_vars.mcf +- tuberculosis_estimated_incidence_rate_output.tmcf + +**For Data Quality Checks and validation** +Validation of the data is done using the lint flag in the DataCommons import tool. + +```bash +java -jar datacommons-import-tool-0.1-jar-with-dependencies.jar lint tuberculosis_estimated_incidence_rate_output_stat_vars_schema.mcf tuberculosis_estimated_incidence_rate_output.csv tuberculosis_estimated_incidence_rate_output.tmcf tuberculosis_estimated_incidence_rate_output_stat_vars.mcf +``` + +This generates the following output files: +- report.json +- summary_report.csv +- summary_report.html + +The report files can be analyzed to check for errors and warnings. Further, linting is performed on the generated output files using the DataCommons import tool. + +## Testing +Testing is performed using the provided `test_data` directory: +- Input: `test_data/tuberculosis_estimated_incidence_rate_input.csv` +- Output (expected): `test_data/tuberculosis_estimated_incidence_rate_output.csv` +- MCF (expected): `test_data/tuberculosis_estimated_incidence_rate_output.tmcf` diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/manifest.json b/statvar_imports/who/tuberculosis_estimated_incidence_rate/manifest.json new file mode 100644 index 0000000000..b253f1a1a5 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/manifest.json @@ -0,0 +1,22 @@ +{ + "import_specifications": [ + { + "import_name": "WHO_TuberculosisEstimatedIncidenceRate", + "curator_emails": ["support@datacommons.org"], + "provenance_url": "https://data.who.int/indicators/i/EB68992/2674B39", + "provenance_description": "Estimated number of new episodes of TB cases arising in a given year per 100 000 population.", + "scripts": ["tb_data_download.py", + "../../tools/statvar_importer/stat_var_processor.py --input_data=gs://unresolved_mcf/who/TB_Estimated_Incidence_Rate/input_files/* --pv_map=gs://unresolved_mcf/who/TB_Estimated_Incidence_Rate/tuberculosis_estimated_incidence_rate_pvmap.csv --config_file=gs://unresolved_mcf/who/TB_Estimated_Incidence_Rate/tuberculosis_estimated_incidence_rate_metadata.csv --output_path=gs://unresolved_mcf/who/TB_Estimated_Incidence_Rate/tuberculosis_estimated_incidence_rate_output --existing_statvar_mcf=gs://unresolved_mcf/scripts/statvar/stat_vars.mcf" +], + "import_inputs": [ + { + "template_mcf": "tuberculosis_estimated_incidence_rate_output.tmcf", + "cleaned_csv": "tuberculosis_estimated_incidence_rate_output.csv" + } + ], + "source_files": ["input_files/*.csv"], + "cron_schedule": "15 22 15 12 *" + } + ] + } + diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/tb_data_download.py b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tb_data_download.py new file mode 100644 index 0000000000..27c836ab10 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tb_data_download.py @@ -0,0 +1,68 @@ +import os +import requests +import io +import pandas as pd + +def download_who_data(): + # 1. Get the Clean Data from the API using the new Indicator ID + api_url = "https://xmart-api-public.who.int/DATA_/RELAY_TB_DATA" + params = { + "$filter": "IND_ID eq 'EB689922674B39'", + "$format": "csv" + } + + print("1. Fetching clean percentage data from WHO API...") + # Timeout set to 5s for connection, 300s for data transfer + api_response = requests.get(api_url, params=params, timeout=(5, 300)) + + if api_response.status_code != 200: + print(f"Failed to fetch API data. HTTP {api_response.status_code}") + return + + # 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" + + # Fetch data first to ensure timeout is applied correctly + master_response = requests.get(master_url, timeout=(5, 300)) + master_response.raise_for_status() + + # Load from the response text to avoid a second unprotected download call + geo_columns = ['country', 'iso3'] + 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...") + # The API uses uppercase 'COUNTRY', the master uses lowercase 'country' + merged_df = pd.merge(api_df, master_df, left_on='COUNTRY', right_on='country', how='left') + + # 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', 'DISAGGR_1', 'VALUE' + ] + merged_df = merged_df[final_columns] + + # 4. Save to CSV in a new folder + output_dir = "input_files" + filename = os.path.join(output_dir, "Estimated_incidence_rate_per_100_000_population.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__": + try: + download_who_data() + except requests.exceptions.Timeout: + print("Error: The request timed out. The server may be slow or offline.") + except Exception as e: + print(f"An unexpected error occurred: {e}") + diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_input.csv b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_input.csv new file mode 100644 index 0000000000..88e13f1ba4 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_input.csv @@ -0,0 +1,100 @@ +IND_ID,INDICATOR_NAME,YEAR,COUNTRY,iso3,DISAGGR_1,VALUE +EB689922674B39,Estimated TB incidence rate per 100 000 population,2003,France,FRA,TB incidence,12 +EB689922674B39,Estimated TB incidence rate per 100 000 population,2004,France,FRA,TB incidence,10 +EB689922674B39,Estimated TB incidence rate per 100 000 population,2005,France,FRA,TB incidence,9.8 +EB689922674B39,Estimated TB incidence rate per 100 000 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b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_output.csv new file mode 100644 index 0000000000..b15b39fe62 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_output.csv @@ -0,0 +1,100 @@ +observationDate,value,observationAbout,variableMeasured +2003,12,country/FRA,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2004,10,country/FRA,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2005,9.8,country/FRA,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2006,9.7,country/FRA,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2007,11,country/FRA,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person 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+2023,142,country/GMB,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2024,138,country/GMB,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2000,229,country/GEO,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person +2001,222,country/GEO,dcid:Count_MedicalConditionIncident_ConditionTuberculosis_AsAFractionOf_Count_Person diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_output.tmcf b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_output.tmcf new file mode 100644 index 0000000000..494f5fd3cd --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/test_data/tuberculosis_estimated_incidence_rate_output.tmcf @@ -0,0 +1,8 @@ +Node: E:tuberculosis_estimated_incidence_rate_output->E0 +observationDate: C:tuberculosis_estimated_incidence_rate_output->observationDate +value: C:tuberculosis_estimated_incidence_rate_output->value +observationAbout: C:tuberculosis_estimated_incidence_rate_output->observationAbout +variableMeasured: C:tuberculosis_estimated_incidence_rate_output->variableMeasured +measurementMethod: WorldHealthOrganizationEstimates +typeOf: dcs:StatVarObservation +scalingFactor: 100000 diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_metadata.csv b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_metadata.csv new file mode 100644 index 0000000000..a432351995 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_metadata.csv @@ -0,0 +1,2 @@ +parameter,value +output_columns,"observationDate,value,observationAbout,variableMeasured" \ No newline at end of file diff --git a/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_pvmap.csv b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_pvmap.csv new file mode 100644 index 0000000000..e642456d03 --- /dev/null +++ b/statvar_imports/who/tuberculosis_estimated_incidence_rate/tuberculosis_estimated_incidence_rate_pvmap.csv @@ -0,0 +1,6 @@ +key,p1,v1,p2,v2,p3,v3,p4,v4,p5,v5,p6,v6 +TB incidence,populationType,MedicalConditionIncident,measuredProperty,count,medicalCondition,Tuberculosis,measurementMethod,WorldHealthOrganizationEstimates,scalingFactor,100000,measurementDenominator,Count_Person +HIV-positive TB incidence,populationType,MedicalConditionIncident,measuredProperty,count,medicalCondition,TuberculosisAndHIV,measurementMethod,WorldHealthOrganizationEstimates,scalingFactor,100000,measurementDenominator,Count_Person +YEAR,observationDate,{Number},,,,,,,,,, +iso3,observationAbout,country/{Data},,,,,,,,,, +VALUE,value,{Number},,,,,,,,,,