How to get all of the records in COVID-19 Data Lake linelistrecords - r

Question

I'd like to use the https://api.c3.ai/covid/api/1/linelistrecord/fetch API but only get 2000 records back. I know that there are more than 2000 records -- how do I get them?
Here's my code in R:
library(tidyverse)
library(httr)
library(jsonlite)
resp <- POST(
"https://api.c3.ai/covid/api/1/linelistrecord/fetch",
body = list(
spec = {}
) %>% toJSON(auto_unbox = TRUE),
accept("application/json")
)
length(content(resp)$objs)
I get 2000 records.

Answer 1

The spec you are passing in has the following optional fields, among others:
limit // maximum number of objects to return
offset // offset to use for paged reads
The default value of limit is 2000.
The fetch result that is returned has a boolean field, along with the array of objects, called hasMore, which indicates whether there are more records in the underlying data store.
You can write a loop that ends once hasMore is false. Start with an offset of 0, and limit n (say , n=2000), and then iteratively increase offset by n.
library(tidyverse)
library(httr)
library(jsonlite)
limit <- 2000
offset <- 0
hasMore <- TRUE
all_objs <- c()
while(hasMore) {
resp <- POST(
"https://api.c3.ai/covid/api/1/linelistrecord/fetch",
body = list(
spec = list(
limit = limit,
offset = offset,
filter = "contains(location, 'California')" # just as an example, to cut down on the dataset
)
) %>% toJSON(auto_unbox = TRUE),
accept("application/json")
)
hasMore <- content(resp)$hasMore
offset <- offset + limit
all_objs <- c(all_objs, content(resp)$objs)
}
length(all_objs)

Answer 2

You could also do something similar in Python too. Here is a code snippet for doing the same in Python
import requests
headers = {'Accept': 'application/json'}
import io
import pandas as pd
def read_data(url, payload, headers = headers):
df_list = []
has_more = True
offset = 0
payload['spec']['offset'] = offset
while has_more:
response = requests.post('https://api.c3.ai/covid/api/1/linelistrecord/fetch', json=payload, headers = headers)
df = pd.DataFrame.from_dict(response.json()['objs'])
has_more = response.json()['hasMore']
payload['spec']['offset'] += df.shape[0]
df_list.append(df)
df = pd.concat(df_list)
return df
url = 'https://api.c3.ai/covid/api/1/linelistrecord/fetch'
payload = {
"spec":{
"filter": "exists(hospitalAdmissionDate)",
"include": "caseConfirmationDate, outcomeDate, hospitalAdmissionDate, age"
}
}
df = read_data(url, payload)