Does "Get PDF" from Internet use my EZProxy?

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livin1965
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Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

Is this option intended to use my ezproxy settings or just access only "open access" content or other items in the public domain?
Jon
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

It does not use your EZProxy. That is used when you're in Bookends Browser, not direct HTTP access.

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livin1965
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

If some of my references can no longer find the PDF previously associated with them, is there a way to use my EZProxy to find those PDFs online or is the only option to reimport them using the bookends browser?
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

I'm not sure what you mean -- Bookends Browser is the way to find them online (and will use EZProxy).

I don't know about your institution of course, but many (most) also use IP authentication, so if you're using Bookends on the institution's network (e.g. on campus) or via a VPN client you don't need EZProxy, and direct Internet searches will work with sites behind paywalls.

You should contact your IT support about this.

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livin1965
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

Jon, thanks. I'm thinking of a process that worked in Papers3 where a pdf might get "lost" for some reason and I could select a command that searched for the pdf online called "Match". It worked within the record and a mini-browser appeared where the PDF would normally appear. This would then login to any institution which was accessible through my EZProxy and go right to the PDF. I would click on the PDF link as one would normally in a web browser and then Papers3 would automatically download that PDF as the new PDF attachment for the record. It was quite seamless and very helpful when a paper was lost or disconnected somehow. Perhaps Bookends doesn't "lose" PDF attachments as Papers3 occasionally did. However, since my migration over to Bookends there are a number of records that do not have PDFs attached to them which did prior to the migration. So, something happened and the connection was lost. I understand any migration comes with issues as it's impossible to negotiate all the trivialities of another program when importing and Bookends did a remarkable job of minimizing the pain. I'm just trying to find out if there is a way to directly find the missing PDFs through the references records themselves via EZProxy and it sounds like there is not a way to do this and it must be found through the Bookends Browser search? When I do "search internet" the PDFs are not found within a record, but if I put the same title of the article that is listed in the record in the search window of the Bookends Browser it often finds it and imports it as a new record. Just a more time consuming process.
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

If the reference has a unique identifier (e.g. DOI or PMID) the Refs -> Get PDF from Internet works in many (not all) cases (not all because Bookends has to scrape the HTML results, and each publisher is different, and the often change their HTML).

Assuming that these references have URLs in Bookends, have you tried using the Bookends Browser in the lower display pane? It will take you to the references's URL, which may be the PDF already, or where you can navigate to the PDF. You can then immediately download it and attach it to the selected reference by clicking the paper clip icon. And it will use EZProxy. It sounds similar in nature to the Papers feature you describe.

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DrJJWMac
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by DrJJWMac »

> I'm just trying to find out if there is a way to directly find the missing PDFs ...

My AppleScript to create a stand-alone library will generate a report on the number of bibliography entrees that have MISSING attachments. I am in the process of updating the script to generate a CSV report file with a fuller documentation of the library status. This report may help you mitigate some of the "one step at a time" tedium (see at the end below).

> I would click on the PDF link as one would normally in a web browser and then Papers3 would automatically download that PDF as the new PDF attachment for the record. It was quite seamless ... Bookends Browser it often finds it and imports it as a new record. Just a more time consuming process.

It would be a boon to Bookends when it would be able to mimic the approach from Papers. What Jon describes using the Bookends browser goes somewhat in the right direction. Unfortunately, the PAPER CLIP ICON step does not REPLACE a missing attachment. It just adds the found attachment as another one.

> Perhaps Bookends doesn't "lose" PDF attachments as Papers3 occasionally did.

Unfortunately, in my experience, on occasion, Bookends does tend to loose track of an attachment (it goes "missing"). My ongoing frustration is that the processes that one needs to undertake to a) find which bibliography items have missing attachments and b) reattach the missing attachment are far more cumbersome than what I've had to do in any other of the apps that I've used (as you note, Papers is significantly more efficient in the second step by comparison).
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

Bookends does not "lose" attachments, it never "had" them to begin with. If the attachment name in the database is correct and it is in an attachment folder (default or ad hoc) with the same name, Bookends will find it. If you find this isn't the case report it and provide the screen shots showing that these conditions have been met and Bookends still says the file can't be found.

To the OP and anyone else reading this, you can easily find orphaned attachments using either a right-click or the Global Change menu, and then deal with them.

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DrJJWMac
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by DrJJWMac »

> Bookends does not "lose" attachments, it never "had" them to begin with.

In the process of processing a library through certain actions such as those that move or copy files to other folders, I have routinely discovered that attachments that once were with a bibliography item went missing. This error is not easy to reproduce.

We are not disagreeing that Bookends cannot loose an attachment that it never had. We are disagreeing that one can do certain things such as process attachments in the library attachment folder and/or move bibliography items from one library to another and/or ... and NEVER have an attachment go missing. My experience tells me that Bookends is still not fully bullet-proof in what it does and does not allow itself to do to manage its attachments, despite all that you may wish otherwise to believe.

> you can easily find orphaned attachments

But you cannot **EASILY** view a list of bibliography items that have MISSING attachments, nor can you **EASILY** just replace a MISSING attachment with a replacement.

We are not disagreeing on the things that can be done in Bookends (finding orphaned attachments). We are disagreeing on what is NOT AT ALL EASY in Bookends (finding and replacing MISSING attachments).
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livin1965
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

Jon wrote: Wed Jul 14, 2021 3:20 pm If the reference has a unique identifier (e.g. DOI or PMID) the Refs -> Get PDF from Internet works in many (not all) cases (not all because Bookends has to scrape the HTML results, and each publisher is different, and the often change their HTML).

Assuming that these references have URLs in Bookends, have you tried using the Bookends Browser in the lower display pane? It will take you to the references's URL, which may be the PDF already, or where you can navigate to the PDF. You can then immediately download it and attach it to the selected reference by clicking the paper clip icon. And it will use EZProxy. It sounds similar in nature to the Papers feature you describe.

Jon
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Jon, thanks. I wasn't aware of the browser option in the lower pane. That does work for references that have URLs. Papers3 used multiple search options and found virtually every PDF which became detached from reference, whether it had a URL or not. I believe it searched title and other fields. But, if it was accessible through my EZProxy (which Papers3 also accessed when using its universal search feature) Paper3 would find it and reconnect it. Would be great if Bookends could enhance the features of the lower pane browser to optimize the number of disconnected files that can be more readily found using that feature.
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

DrJJWMac wrote: Thu Jul 15, 2021 12:27 pm > Bookends does not "lose" attachments, it never "had" them to begin with.
We are not disagreeing that Bookends cannot loose an attachment that it never had. We are disagreeing that one can do certain things such as process attachments in the library attachment folder and/or move bibliography items from one library to another and/or ... and NEVER have an attachment go missing. My experience tells me that Bookends is still not fully bullet-proof in what it does and does not allow itself to do to manage its attachments, despite all that you may wish otherwise to believe.
By "never had them" I mean the attachment isn't stored in the database. Just the name. And that is never lost.

You're manipulating attachments outside of Bookends (e.g. via AS) so you're evading protections Bookends has in place.

I'm still waiting for concrete information from you, such as reproducible steps to orphan an attachment, or evidence that you've met the criteria I outlined above and the attachment is still not found. Until you do I can't do anything about whatever it is you think is Bookends' fault.
> you can easily find orphaned attachments
But you cannot **EASILY** view a list of bibliography items that have MISSING attachments, nor can you **EASILY** just replace a MISSING attachment with a replacement.
You lost me. Missing attachments ARE orphaned attachments. So yes, it's easy to have Bookends find and display them. If you don't know how to do this, ask. As for replacing them, there are a variety of ways to do that, which may or may not meet one's criterion of "easy". FWIW there are improvements in this regard in the next update.

And please stop SHOUTING.

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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

Jon, thanks. I wasn't aware of the browser option in the lower pane. That does work for references that have URLs. Papers3 used multiple search options and found virtually every PDF which became detached from reference, whether it had a URL or not. I believe it searched title and other fields. But, if it was accessible through my EZProxy (which Papers3 also accessed when using its universal search feature) Paper3 would find it and reconnect it. Would be great if Bookends could enhance the features of the lower pane browser to optimize the number of disconnected files that can be more readily found using that feature.
I've just spent some time with Papers 3, and AFAICT they use the URL to locate a missing PDF as well. For example, when I deliberately delete an attached PDF in the Finder and they try to open the PDF by double clicking on the reference, Papers 3 takes me to the PDF on the web site (PubMed). If I edit the reference to remove the URL that links to the PDF, a double click takes me to the HTML page on PubMed, not the PDF. If I remove other key information from the reference, the double click takes me to a Google search and a list of possible hits.

I'm not nearly as conversant with Papers 3 as you are, so perhaps you know more about this than I've discovered. But in my tests it seems Papers 3 relies on a URL or a Google search.

If you want to explore this further, please contact tech support directly and send screen snap (and a PDF I can attach in Papers 3 here) so I can see if there's more to this then I saw.

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livin1965
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

Jon wrote: Thu Jul 15, 2021 1:20 pm
Jon, thanks. I wasn't aware of the browser option in the lower pane. That does work for references that have URLs. Papers3 used multiple search options and found virtually every PDF which became detached from reference, whether it had a URL or not. I believe it searched title and other fields. But, if it was accessible through my EZProxy (which Papers3 also accessed when using its universal search feature) Paper3 would find it and reconnect it. Would be great if Bookends could enhance the features of the lower pane browser to optimize the number of disconnected files that can be more readily found using that feature.
I've just spent some time with Papers 3, and AFAICT they use the URL to locate a missing PDF as well. For example, when I deliberately delete an attached PDF in the Finder and they try to open the PDF by double clicking on the reference, Papers 3 takes me to the PDF on the web site (PubMed). If I edit the reference to remove the URL that links to the PDF, a double click takes me to the HTML page on PubMed, not the PDF. If I remove other key information from the reference, the double click takes me to a Google search and a list of possible hits.

I'm not nearly as conversant with Papers 3 as you are, so perhaps you know more about this than I've discovered. But in my tests it seems Papers 3 relies on a URL or a Google search.

If you want to explore this further, please contact tech support directly and send screen snap (and a PDF I can attach in Papers 3 here) so I can see if there's more to this then I saw.

Jon
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Jon, When I would select a reference in Papers3 where the attachment had been disconnected, it would automatically take me to my university page to sign in through the ezproxy and then from there directly to the page with the paper. I would then have to click on the PDF link at the publisher site and it would automatically then re-connect the PDF as an attachment. So, the lower pane browser was using the EZProxy settings in that way. As the other poster on this thread indicated, it was quite efficient. I can no longer use Papers3 as it's not working on Big Sur 11.4 on my MacBook Pro, the final straw in my transition to Bookends. So, I don't have any way to demonstrate or work with that app at this point.
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by Jon »

As I said, AFAICT Papers 3 seems to be using the URL, just like Bookends. It wasn't performing magic, it needed some information to get to the PDF (just like Bookends) -- without it Papers just offers a Google search. The Bookends Browser display pane will do the same thing as you describe, take you to the URL where you can find the PDF (whether it takes a few clicks or not depends on the URL) and import the PDF with the paper clip icon. In the next update the orphaned PDF will be removed when the new one is attached. Until then, after attaching the new PDF you can remove the old one (e.g. with the Attachment Inspector or showing the attachment in the PDF pane and selecting Detach).

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livin1965
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Re: Does "Get PDF" from Internet use my EZProxy?

Post by livin1965 »

Jon, thanks. Learning more about how the browser within the lower pane works is definitely a very helpful step.
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