covid-data

Covid-data

COVID-19 Data

Read all the .csv data files from Johns Hopkins Corona Virus Tracking Data into InfluxDB 2

Usage

The environment file .env is read, if present, for any variables listed below.

The following ENV variables are checked:

INFLUX_TOKEN
INFLUX_BUCKET
INFLUX_ORG
INFLUX_MEASURE
INFLUX_URL
DATA_DIR
MAPS_TOKEN

If present, they are used. They over-ride any command-line flags given at runtime.

Usage:

    -d --dir:         Path to where the .csv data files live.
    -u --url:         URL of your InfluxDB server, including port.
    -b --bucket:      Bucket name -- default: $INFLUX_BUCKET
    -g --org:         Organization name -- default: $INFLUX_ORG
    -m --measurement: Measurement name -- default: $INFLUX_MEASURE
    -t --token:       InfluxDB Token -- default: $INFLUX_TOKEN
    -a --apitoken:    Google Maps API Token -- default: $MAPS_TOKEN
    -o --out          Output line-protocol to stdout
    -f --file         file to output line-protocol to (must use -o as well)
    -s --split        split line-protocol files up by dates default directory: ./data

$ go build covid.go

$ ./covid dir path/to/data -b bucket_name -g org_name measurement measure_name -url http://your.server.com:9999 -token yourToken

$ ./covid -dir path/to/data -s=data

Notice that if you're sending it to files, you don't need the InfluxDB credentials, etc. This last command will create the following:

├── data
│   ├── 01-22-2020.lp
│   ├── 01-23-2020.lp

...

with one output line-protocol file for each input csv file.

Notice that you can use flags with or without the - or a -- if you choose.

Output

Scanning Data Directory:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports
Processing File:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports/01-22-2020.csv
Processing File:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports/01-23-2020.csv
Processing File:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports/01-24-2020.csv
Processing File:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports/01-25-2020.csv
Processing File:  ../../COVID-19/csse_covid_19_data/csse_covid_19_daily_reports/01-26-2020.csv
...

Data is read from those files and written directly to your InfluxDB instance.

If you are using the -o without an output file (output to stdoud) all program output is redirected to stderr. If this is not what you want, supply an output file via the -file flag.

Batch Processing

By default (now) data is sent to InfluxDB in batches of 500 points/write. You can change this by changing the value of BatchSize. A BatchSize of 0 will write each result as it is read.

Saved Configuration

The last processing time is saved into a file called .last. On subsequent runs, only datafiles added after this time will be read and processed into InfluxDB. The time is saved as a Unix timestamp.

Geopsatial Data

Starting sometime in February the dataset started including geospatial data (lat/lng) with all the data. This is now also written to the InfluxDB instance.

In addition, since InfluxDB now also supports using s2 GeoHashes, the s2 GeoHash is also written to the database at the same time as a tag called s2_cell_id. If there is no lat/lng data available, lat/lng is written as 0.00 and 0.00 respectively, and an empty-string is entered as the s2 GeoHash tag.

If you've provided a Google Maps API token, the Country and Province data from the record is used to reverse-encode the location and add a rough lat/lng before the s2_cell_id is calculated. The new data format includes