epm_import_xml: Import PubMed Records from Local Files.

In dami82/easyPubMed: Search and Retrieve Scientific Publication Records from PubMed

Import PubMed Records from Local Files.

Description

Read one or more text files including XML-decorated raw PubMed records and rebuild an 'easyPubMed' object. The function expects all files to be generated from the same query using 'easyPubMed>3.0' and the 'epm_fetch()' function setting 'write_to_file' to 'TRUE'. This function can import a fraction or all of the files resulting from a single query. Files resulting from non-compatible fetch jobs will be dropped.

Usage

epm_import_xml(x)

Arguments

x	Character vector, the paths to text files including XML-decorated raw PubMed records saved using 'easyPubMed>3.0'.

Value

an 'easyPubMed' object including raw XML PubMed records.

Author(s)

Damiano Fantini, [e-mail]

References

https://www.data-pulse.com/dev_site/easypubmed/

Examples

# Note: a time limit can be set in order to kill the operation when/if 
# the NCBI/Entrez server becomes unresponsive.
setTimeLimit(elapsed = 4.9)
try({
  x <- epm_query(query_string = 'Damiano Fantini[AU] AND "2018"[PDAT]')
  x <- epm_fetch(x = x, format = 'xml', write_to_file = TRUE, 
                 outfile_prefix = 'test', store_contents = FALSE)
  y <- epm_import_xml('test_batch_01.txt')
  tryCatch({unlink('test_batch_01.txt')}, error = function(e) { NULL }) 
  print(paste0('       Raw Record Num (fetched): ', 
               getEPMMeta(x)$raw_record_num))
  print(paste0('Raw Record Num (read & rebuilt): ', 
               getEPMMeta(y)$raw_record_num))
}, silent = TRUE)
setTimeLimit(elapsed = Inf)

 

dami82/easyPubMed documentation built on Jan. 4, 2024, 6:21 a.m.