search

rfhb / ctrdata

Aggregate and analyse information on clinical trials from public registers
https://rfhb.github.io/ctrdata/
Other
43 stars 6 forks source link

Error message printed with ctrLoadQueryIntoDb() #21

Closed rfhb closed 3 years ago

rfhb commented 3 years ago

This issue is opened to collect and document issues with content from registers that has errors and where package ctrdata cannot mitigate the errors. Commands and output are in the next sections. 

db <- nodbi::src_sqlite(dbname = "db.sqlite", collection = "errorTrials")
ctrdata::ctrLoadQueryIntoDb(queryterm = "2020-000876-40", register = "EUCTR", verbose = TRUE, con = db)

The messages to the user from the above command are ending with, 

Error: lexical error: invalid char in json text.
                           { "_id": "{"e521_timepoints_of_evaluation_o
                     (right here) ------^

The published trial record included in section "E.5.2 Secondary end point(s)" the following content, which since opening the issue has been corrected in the register:

- Toxicity
- Compliance to treatment
EudraCT Number: 2020-000876-40
Sponsor Protocol Number: IJB-REGINA-2020
ClinicalTrials.gov Number: NCT04503694
[...]

The field contains in the register specific identifiers that are not expected in a field and which are used by ctrdata for splitting downloaded information on a series of trials. This error in content in the register is not readily fixable by ctrdata.

rfhb commented 3 years ago

Closing the issue, does not need to be kept open.