What is the purpose of the file fulltext_html_urls.txt

[anusharanganathan]

What is the purpose of the file fulltext_html_urls.txt available as a part of the output?

Purpose: Search open access papers in eupmc for the query dinosaurs and download fulltext XMLs, supplementary files and fulltext PDFs if available

Query used

$ getpapers -q 'dinosaurs' -x -s -p -o dinosaursOutput2 >> dinosaursOutput2.log

This generated a fulltext_html_urls.txt file with 22 urls

Not all pmids listed in fulltext_html_urls.txt had a corresponding fulltext.xml or fulltext.html file downloaded. Of the 22 urls with pmcids listed in the file, the breakdown of what I found was as follows:

• 20 of the pmcids had an empty dir
• 2 of the pmcids had a dir with a fulltext.xml file but an empty fulltext.html file
• For each of the pmcids in the fulltext_html_urls.txt file, the output produced a message similar to the following one
  warn: Article with pmcid "PMC3381548" had no fulltext PDF url

[blahah]

the fulltext HTML file is just a list of the fulltext HTML urls that were available. I'm moving it to an --html option so that users can request the HTML to be downloaded, and there will no longer be a fulltex_html_urls.txt file

[blahah]

done in 0.4.1