Closed rfhb closed 1 year ago
Insert "classic." into search URLs, that is, change e.g.:
Then try the development version with these install steps; it should work with such URLs and with previously stored queries:
install.packages("devtools")
devtools::install_github("rfhb/ctrdata", build_vignettes = TRUE)
library(ctrdata)
q <- "https://classic.clinicaltrials.gov/ct2/results?cond=Neuroblastoma&term=&intr=Investigational+Agent"
dbc <- nodbi::src_sqlite(collection = "my_collection")
ctrLoadQueryIntoDb(q, con = dbc)
# * Found search query from CTGOV: cond=Neuroblastoma&intr=Investigational+Agent
# Checking helper binaries: . . . done
# (1/3) Checking trials in CTGOV:
# Retrieved overview, records of 272 trial(s) are to be downloaded (estimate: 2.2 MB)
# Download status: 1 done; 0 in progress. Total size: 1.85 Mb (100%)... done!
# (2/3) Converting to JSON, 272 records converted
# (3/3) Importing JSON records into database...
# = Imported or updated 272 trial(s)
# No history found in expected format.
# Updated history ("meta-info" in "my_collection")
# $n
# [1] 272
#
# $success
# [1] "NCT00002825" "NCT00003119" "NCT00003191" "NCT00003234" "NCT00003425"
Confirmed. Tested 88 "results?spons=" queries and 23 "cond=xxxx&term=xxx" queries. Everything worked perfectly. Thanks for tackling this so quickly.
Ralf. I got the error below when trying the new package today. I tried tracing the process through the ctrGetQueryUrl function but could not find an issue. I assume you are already on this, but FYI. Thanks, as always, for your work with this package. It is a HUGE help.
ScreenURL <- paste0("https://classic.clinicaltrials.gov/ct2/results?spons=%22",CoStr,"%22") ScreenURL [1] "https://classic.clinicaltrials.gov/ct2/results?spons=%22ACADIA+Pharmaceuticals%22" ResultsTable <- nodbi::src_sqlite(collection="Results")
Status <- try(ctrLoadQueryIntoDb(queryterm=ScreenURL, con=ResultsTable, verbose=FALSE)) Warning: ctrGetQueryUrl(): no clinical trial register search URL found in parameter 'url' or in clipboard. Error : 'queryterm' does not seem to result from ctrQueryHistoryInDb() or ctrGetQueryUrl(): NULL
Thanks! Sorry, but I could not reproduce the error using the ScreenURL
value that is above; here I found 42 records with this value using ctrLoadQueryIntoDb(ScreenURL, only.count = TRUE)
. Do these URLs have the search results you are interested in?
https://classic.clinicaltrials.gov/ct2/results?spons="ACADIA Pharmaceuticals"
https://classic.clinicaltrials.gov/ct2/results?spons=ACADIA+Pharmaceuticals
These work for me. For composing the string for parameter queryterm
, no need to escape characters, it can be kept simple, e.g.
ScreenURL <- paste0('https://classic.clinicaltrials.gov/ct2/results?spons="', CoStr, '"')
Thanks for checking into this, Ralf. l must have messed up a dependency somewhere. I force reinstalled the package from GitHub and completely rebooted my machine. That cleared out everything. All good now. Thanks, again.
Design considerations: create new ctrLoadQueryIntoDb() internal function for CTGOV API, using only JSON, based on experience with implementing this function for CTIS. Aspects for implementation:
Further questions:
Check out the branch ctgov2023api for compatibility with CTGOV REST API 2.0.0-test and CTGOV Classic web interface. Install in R
with
devtools::install_github(repo = "rfhb/ctrdata", ref = "ctgov2023api", build_vignettes = TRUE)
Please report issues here.
Completed with release https://github.com/rfhb/ctrdata/releases/tag/v1.15.0
ClinicalTrials.Gov just made the previous beta website layout now the default layout. Links to the previous website start now with
https://classic.clinicaltrials.gov/
. Search parameters are different.ctrdata
is being updated to handle the situation.