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Zotero: An open-source tool to help collect, organize, cite, and share research

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Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#121

Post by jknz »

sixdimensional wrote: post #118
jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

I love the passive nature of your workflow. I’ve always thought that, as soon as I had consumed (read, viewed, heard) some content (text, audio, video) it would be nice to have a “shadow copy” of it stored in a personal, private knowledgebase, with a simple keyword or more complex semantic search on top. Basically, a personal search engine with a passively gathered corpus of my experienced content - maybe even filter…

It is not limited to academic PDFs, although I mostly use the script to find those. When typing academic keywords (author names, scientific jargon, etc), the personal PDF that also lie in ~/Downloads/ are filtered out.

I recently used the command with some combination of airport/city/airline and the only match was the boarding pass I was looking for. It could probably be used for receipts from hotel or whatnot, as soon as pdftotext can retrieve the text. It should find tax returns and related PDFs by querying "IRS + SSN".

A current issue that I would like to fix is the preview window that does not always highlight the query in full if a single match was found before the full query was typed. It is linked to how fzf handles previewing. I do not have plans for any big enhancements.

edit: I created a public repo to replace the gist. Feel free to post your thoughts or suggestions in the issues!

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#122

Post by blattimwind »

bovine3dom wrote: post #85
blattimwind wrote: post #80

Earlier quoted context omitted.

> you can store `~/.local/share/okular/docdata/` in version control What kind of annotations are that? I think GP refers to document annotations, which are stored in the PDF file itself.

Annotations meaning notes, highlights, etc. If they are stored in the file itself, that's news to me. Last time I used it, Okular didn't modify the actual PDF and considered that a feature.

You have to explicitly save the file after making the annotations. I've been doing this for years with Okular, indeed, Okular having out-of-file annotations is news to me :)

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#124

Post by nanna »

jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

A downside would be that you can't search all the pdfs of a particular author? For me that's crucial.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#125

Post by detaro »

nanna wrote: post #124
jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

A downside would be that you can't search all the pdfs of a particular author? For me that's crucial.

I don't think full names of non-authors are very commonly mentioned on the first page of papers, so just including the name in the query should be a useful approximation?

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#126

Post by atrus »

jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

What are you using for passively downloading all those pdfs?

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#127

Post by hyperpape »

detaro wrote: post #125
nanna wrote: post #124

Earlier quoted context omitted.

A downside would be that you can't search all the pdfs of a particular author? For me that's crucial.

I don't think full names of non-authors are very commonly mentioned on the first page of papers, so just including the name in the query should be a useful approximation?

This heavily depends on the field/journal style.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#128

Post by bovine3dom »

blattimwind wrote: post #122
bovine3dom wrote: post #85

Earlier quoted context omitted.

Annotations meaning notes, highlights, etc. If they are stored in the file itself, that's news to me. Last time I used it, Okular didn't modify the actual PDF and considered that a feature.

You have to explicitly save the file after making the annotations. I've been doing this for years with Okular, indeed, Okular having out-of-file annotations is news to me :)

Oh, wow. That will make collaboration so much easier. I resorted to Adobe Reader on multiple occasions in the past...

Thanks!

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#129

Post by jknz »

atrus wrote: post #126
jknz wrote: post #101

I use a little script [1] and a passive approach to quickly find a PDF I am looking for among a few thousands of academic PDF. The workflow (illustrated in the GIF [2]): - as I read new PDFs in the browser, the PDFs are passively downloaded typically in a Downloads/ folder. - This results in thousands in papers lying in Downloads/ or elsewhere. - The command p from the script [1] let me instantaneously fuzzy-search o…

What are you using for passively downloading all those pdfs?

Firefox or any other browser that downloads the PDFs that you browse. When searching/browsing PDFs, my firefox is set up to download the file into ~/Downloads/.

Re: Zotero: An open-source tool to help collect, organize, cite, and share research

#130

Post by hyeonwho4 »

dstillman wrote: post #83
zwaps wrote: post #63

Earlier quoted context omitted.

yeah so I just reinstalled Zotero and imported my Mendeley library. It does that, and it can actually look up metadata from pdfs. But: It can NOT update already existing entries from such a lookup. You have to delete the pdf and re-import. Why? No reason. It's this sort of really bad usability decision that makes Zotero just not very good imo.

It's not a usability decision — it's just one feature that hasn't yet been implemented [1]. Updating metadata is more complicated than creating a new item, because you have to deal with the existing metadata somehow. (Mendeley just overwrites the existing item, often with incorrect data, which we don't consider acceptable.) Disclosure: Zotero developer [1] https://github.com/zotero/zotero/issues/1515

I really love the "duplicate finder" and its ability to pick and choose metadata to keep. Perhaps just create a duplicate item and deal with merge conflicts later?
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