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Corrupt PDFs from EuropePMC #166

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petermr opened this issue Sep 24, 2017 · 7 comments
Open

Corrupt PDFs from EuropePMC #166

petermr opened this issue Sep 24, 2017 · 7 comments

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@petermr
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petermr commented Sep 24, 2017

I am running getpapers and every PDF download is corrupt.

localhost:workspace pm286$ node --version
v6.2.1
localhost:workspace pm286$ getpapers --version
0.4.12
localhost:workspace pm286$ getpapers -p -x -q "systematic review" -k 200 -o systematic

none of the PDFs read into AdobeReader or PDFDebugger (PDFBox). The structure of the document appears to be correct (it identifies pages, but they are visually blank and have virtually no content).

I have uninstalled and then reinstalled getpapers .

Running on MACOsx 10.9.5
@petermr
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petermr commented Sep 24, 2017

Have repeated with arXiv : --api arxiv -p. This gives PDFs of uniformly 2KB. This is clearly wrong but I don't know what the correct answer is.

@larsgw
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larsgw commented Sep 24, 2017

Confirmed on node 8.5.0 using Okular as PDF reader. However, it seems to work fine for me with getpapers 0.4.14.

@larsgw
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larsgw commented Sep 24, 2017 •
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The second thing gives a 403 message concerning the user agent, confirmed on 0.4.14 as well.

Edit: Confirmed with ModHeader that User-Agent is the problem. See https://arxiv.org/denied.html, https://arxiv.org/help/robots. Using User-Agent: getpapers/TDM worked once, but after changing the header to that in config.js, it broke too (some sort of blacklist, I guess). The error page, however, changed too, changing

Sadly, your client "getpapers/(TDM Crawler contact@contentmine.org)" violates the automated access guidelines posted at arxiv.org, and is consequently excluded.

into


Sadly, you do not currently appear to have permission to access
https://arxiv.org/pdf/0710.0054v1.pdf

so I might have only blacklisted myself.

@larsgw larsgw mentioned this issue Oct 18, 2017
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@silviaegt
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silviaegt commented Mar 5, 2021 •
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I had a similar issue with PDFs from a arxiv search (I'm running the process with getpapers 0.4.17 on a Windows 10.0.19041 machine)
I used the following query:

getpapers --api "arxiv" --query "abs:wikidata" --pdf --outdir wikidataarticles --limit 10

When I opened the downloaded pdf file in Notepad++ I got this:

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head><title>403 Forbidden</title></head>
<body>
<h1>Access Denied</h1>

 <p>Sadly, your client "<b>getpapers/(TDM Crawler contact@contentmine.org)</b>" violates
 the automated access guidelines posted at arxiv.org,
 and is consequently excluded.</p>

Hope this information works to solve the issue :)

@petermr
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petermr commented Mar 5, 2021

arxiv don't like crawlers . I think it was OK 5 years ago. It banned the crawler through its email. I am not sure how they would want it to be mined - they have a raw file download dump, I think.
The files aren't corrupt - they are replaced by HTML

We (@ayushgarg) are writing pygetpapers and will need to think about this. If there is enough demand we will go back to arxiv and work out an. agreed solution.

@silviaegt
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Thanks for the quick reply @petermr!
It may or may not have something to do with what they say here in the "Play nice" section of this text i.e. on how harvesting should be done using the dedicated site (export.arxiv.org) and how one should use the 1 second sleep per burst?

@petermr
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petermr commented Mar 5, 2021 via email

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@petermr @silviaegt @larsgw