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breast cancer download throwing an subscript out of bounds error #14

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deathinvenice opened this issue Mar 23, 2017 · 1 comment
Open

breast cancer download throwing an subscript out of bounds error #14

deathinvenice opened this issue Mar 23, 2017 · 1 comment

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@deathinvenice
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deathinvenice commented Mar 23, 2017 •
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Hello,

An issue came up. When I use this query the function breaks and returns a subscript out of bounds error.

breast_list <- clinicaltrials_download(query=c('cond=breast cancer', 'intr=drug','locn=USA'),
count = NULL, include_results = TRUE,
include_textblocks=TRUE)

Is it related to volume? It is 5K+ trials Im trying to retrieve.
titaniumtroop added a commit to titaniumtroop/rclinicaltrials that referenced this issue Sep 19, 2017
@titaniumtroop
Fix issue sachsmc#12, sachsmc#14
250dc69 
Fix for Issue sachsmc#12:
gather_results expected complete values for baseline/measure_list in
XML file, which isn’t necessarily there. Trapped missing value.

Fixed Issue sachsmc#14: In clinicaltrials_download, number of downloaded files
can be shorter than the list of NCT numbers submitted in a tframe
(e.g., where bad NCT IDs are introduced from an external source). The
expected number of files was a list the same length as the submitted
NCT IDs in tframe. Omitted missing values.
@titaniumtroop titaniumtroop mentioned this issue Sep 19, 2017
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@titaniumtroop
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The line throwing this error is line 56 in gather_results.R:

measures <- parsed[["//baseline/measure_list"]]

An NCT ID throwing this error is NCT01602016. There are no baseline measures because the study was terminated early. So, the attempt to use an array reference with the parsed dataframe fails with the subscript out of bounds error, as that subscript doesn't exist. I'm submitting a pull request #17 to trap this error.

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@titaniumtroop @deathinvenice