Upgrade StorageZotero 7 highlighting and annotation overview unexpected results and wishlist
Hi I am using Zotero 7, and am loving it - am having a few issues with annotation and highlighting. Detailed comments as follows -
1. Annotation order in left sidebar when highlighting a pdf - images get put at the top even if the image is below other highlight/notes - I would have expected the marked up order of the pdf to be preserved. Notes are also misordered if highlighting only one or two words in a line of source document text, and on some web pages the highlight gets applied to the entire first paragraph as opposed to the text that was selected.
2. Annotation notes collapse and expand options are expected to preserve screen real estate - as a suggestion, pdfexchange editor has some excellent functionality at the top of the left sidebar for collapsing and expanding comments
3. Notes (in the left sidebar from highlights) which have a note of more than a few lines of added text tend to display as unreadable in the left sidebar
4. Want to be able to display highlights/annotations in the righthand pane of the main library window when a file is selected (without opening a tab for the actual document) in the same format as the left hand pane for the individual document file, and ideally have a column in the main library pane to indicated the presence/number of notes/comments (leave blank if there are none).
5. Export to pdf does not work with a password protected file - would like it to export a file with annotations that is also password protected - there is a 12 step workaround but it would be great to save the time and have it happen automatically -
(Manual process - a) Close file in tab b) find in main pane c) open in system folder d) open pdf in pdfexchange editor e) remove security in properties f) zotero - file - export pdf g) go to system folder h) reapply password i) reopen in tab j) go to exported pdf in system folder k) open pdf in pdfexchange editor l) reapply security password in properties)
6. New text box annotations (T) in pdf files that are exported with the file | export pdf menu item do not show up in either the browser pdf reader or in external readers
7. In the left hand sidebar pane of a tab for an opened document, you see the highlighted text at the top of each annotation. This is great. But after using the file | export pdf menu item, the resulting pdf that is generated does not display the highlighted text as the subject in the comment that appears in the pdf reader. I would like at least an option to do so, set within the export dialog.
8. Highlighting annotations - this article -
https://www.octantacademics.com/stormport/color-coded-highlighting-system
discusses the idea of highlighting annotations. (*Note: In general, we encourage students to place more emphasis on highlighting their personal annotations than the actual text itself. This is because student annotations not only make summaries and important information easily accessible in the margins, but they also provide personal insights that can prove helpful later during test prep or essay writing.*)
This point could do with some discussion, but where for example I highlight some text on a webpage and then add some text in the comment in the lefthand sidebar, I would like to be able to highlight some of the text I add, so that the lefthand sidebar note can itself display highlighted text (which may be in different colors to the original webpage highlight).
The post important priorities for me are items 6 and 7, then 1, 3, and 4
If all these things were done, Zotero would go from wonderful to amazing ! Many thanks
@moderator if you would like me to break up this post into multiple items, please let me know - happy to oblige
1. Annotation order in left sidebar when highlighting a pdf - images get put at the top even if the image is below other highlight/notes - I would have expected the marked up order of the pdf to be preserved. Notes are also misordered if highlighting only one or two words in a line of source document text, and on some web pages the highlight gets applied to the entire first paragraph as opposed to the text that was selected.
2. Annotation notes collapse and expand options are expected to preserve screen real estate - as a suggestion, pdfexchange editor has some excellent functionality at the top of the left sidebar for collapsing and expanding comments
3. Notes (in the left sidebar from highlights) which have a note of more than a few lines of added text tend to display as unreadable in the left sidebar
4. Want to be able to display highlights/annotations in the righthand pane of the main library window when a file is selected (without opening a tab for the actual document) in the same format as the left hand pane for the individual document file, and ideally have a column in the main library pane to indicated the presence/number of notes/comments (leave blank if there are none).
5. Export to pdf does not work with a password protected file - would like it to export a file with annotations that is also password protected - there is a 12 step workaround but it would be great to save the time and have it happen automatically -
(Manual process - a) Close file in tab b) find in main pane c) open in system folder d) open pdf in pdfexchange editor e) remove security in properties f) zotero - file - export pdf g) go to system folder h) reapply password i) reopen in tab j) go to exported pdf in system folder k) open pdf in pdfexchange editor l) reapply security password in properties)
6. New text box annotations (T) in pdf files that are exported with the file | export pdf menu item do not show up in either the browser pdf reader or in external readers
7. In the left hand sidebar pane of a tab for an opened document, you see the highlighted text at the top of each annotation. This is great. But after using the file | export pdf menu item, the resulting pdf that is generated does not display the highlighted text as the subject in the comment that appears in the pdf reader. I would like at least an option to do so, set within the export dialog.
8. Highlighting annotations - this article -
https://www.octantacademics.com/stormport/color-coded-highlighting-system
discusses the idea of highlighting annotations. (*Note: In general, we encourage students to place more emphasis on highlighting their personal annotations than the actual text itself. This is because student annotations not only make summaries and important information easily accessible in the margins, but they also provide personal insights that can prove helpful later during test prep or essay writing.*)
This point could do with some discussion, but where for example I highlight some text on a webpage and then add some text in the comment in the lefthand sidebar, I would like to be able to highlight some of the text I add, so that the lefthand sidebar note can itself display highlighted text (which may be in different colors to the original webpage highlight).
The post important priorities for me are items 6 and 7, then 1, 3, and 4
If all these things were done, Zotero would go from wonderful to amazing ! Many thanks
@moderator if you would like me to break up this post into multiple items, please let me know - happy to oblige
2.
3. Could you provide a screenshot because it's unclear what's the issue.
4. Something like this is planned.
5. Could you clarify the scenarios in which you'd need to annotate a password-protected PDF file?
6. This is not implemented in the beta yet, but it will be.
7. Do you have an example of other PDF doing this?
8. Some formatting options like bold or italic are supported in annotation comments, but supporting highlights in comments is a bit too much at the moment. Again, do you have an example of other PDF viewers doing something similar?
a) preserving comment order as per your comment about Zotero sidebar order
b) making the annotation and highlighting system as functional and friction free as possible
c) aiming for parity in functionality between highlighting and annotation of pdf documents and stored webpages
d) having Zotero's internal pdf reader provide at least as good functionality as other pdf readers for the purpose of annotation/highlighting
e) enabling interoperability as far as possible with other pdf readers for collaboration purposes
The Zotero version I am using is 7.0.0-beta.47+f012a348a (64-bit). I did my testing between 10.4.2023 and 10.24.2023 but did not take a note of the beta version I was using at the earlier of these dates, which is when I noticed the first 3 items. (I am using Acrobat Reader continuous release version 2023.006.20360 and PDF-XChange Editor version 10.1.1 build 381.)
1. My original post issue #1 had 3 sub-issues - I have also noticed a 4th sub-issue see (d) below
a) images get put at the top even if the image is below other highlight/notes
I am unable to duplicate this reported issue. I do not know if the beta version was updated after I originally noticed the problem.
b) Notes are misordered if highlighting only one or two words in a line of source pdf document text. [Issue 1 example 1.jpg and Issue 1 link 1 - pdf] - (I suspect this issue is dependent on the exact example selected)
c) on some web pages the highlight gets applied to the entire first paragraph as opposed to the text that was selected - [Issue 1 example 2.jpg and Issue 1 link 2 - webpage]
d) on some web pages the highlighting does not appear - [Issue 1 example 2a.jpg and Issue 2 link 2a - webpage]
2. Here are 2 screenshots showing expansion/collapse of a highlight/annotation in PDF-XChange editor (this function does not exist - as far as I know - in Acrobat Reader). [Issue 2 example 2a.jpg and Issue 2 example 2aa.jpg - Issue 2 link 1 - pdf]
3. I am currently unable to duplicate this issue. It was a type of vertical squashing of the lower text rows in the added comment in the left hand side bar.
4. Excellent news ! Any idea on timescales ?
5. The scenario in which this happened was when someone sent me a password protected pdf for my comments. The easiest way of providing my comments back to them was to mark up and annotate the document, export it, renaming the exported document to indicate that it had comments inserted, and send it back to them, with the same password.
6. Great ! Given you are fixing this, although the resizing of the box to reduce the text font size is very innovative, it might be worth testing alternatives such as clicking to add the box, typing the text, setting the font size, and then the box would resize automatically, that resizing being "tweakable" though the adjustment points on the box.
7. Here is a screenshot example of a document I highlighted and annotated in PDF-XChange, and read in Acrobat Reader. In both PDF-XChange and Acrobat Reader, you can use the comment subject field to put the highlighted text, so - at least in PDF-XChange - it appears approximately like a standard left hand sidebar comment on a pdf in Zotero. (Even a whole paragraph of text fitted when I tried it.) [Issue 7 example 1.jpg in PDF-XChange, and Issue 7 example 2.jpg in Acrobat Reader, Issue 7 example pdf.pdf sample file]
It would be nice to be able, as a preset option, to put the highlighted original text into this subject field, but I have no idea whether this fits with the usage of that field as intended by the current PDF standard (https://pdfa.org/sponsored-standards/).
8. "Again do you have an example of other pdf viewers doing something similar". There is no pdf viewer out there I know of that does this. As I mentioned, this is a feature that could do with some discussion. It would be very easy simply to file this suggestion in the "too difficult" category, nevertheless, it seems that there is some value in the comment from the referenced source. My suggestion was mainly for visuals, as a color highlight is easier to see at a glance than emboldened or underlined text. The two readers I use do not have this facility - and I wish they did.
The main implementation issue would seem to be compatibility with existing readers, and if this is implemented, there would probably need to be some kind of translation routine when exporting a pdf so that the comment text can be converted and read. (I know of no current mechanism in any other reader to do this.) As I am writing this, it strikes me that the main priority is to provide a color visual for the benefit of the annotator rather than for collaboration purposes, but of the color options that come to mind,
- text color
- underline color
- highlight color
the second most readable option in my view (behind highlight color) would be the underline color - tests can be done with sample documents to see what happens when this type of pdf is read by another reader. It might be a whole lot easier to modify this suggestion to provide instead a facility to change the annotation underline color (and set a default underline color). The underline facility in comments text is present in Acrobat Reader's sidebar and hopefully that does not represent a problem to implement. PDF-XChange does allow for underlined comment text, but seems to display it only in the callout from the highlighted body text. Adding color to the underlining in comments text looks spectacular - see Issue 8 example 1.jpg which I mocked up with a graphics program.
Perhaps the main pdf standard makers will jump up and down at the mere suggestion of bending the standard, but I think it is undeniable that the feature could be of use to some people. As are comment tags. Perhaps this discussion should be hived off and put into a separate thread (as it may have implications for the pdf standard itself), so it can be kicked around a bit ?
N.B. Acrobat Reader converts all highlight colors (which display correctly in the main document body within reader), into a comment in the right hand sidebar with a blue stripe at the left of the comment. In PDF-XChange, the comment colors are displayed correctly in the sidebar.)
9. Where the file type in the Zotero main pane is a web page, I would still like the ability to annotate it and then export it as an annotated pdf, and to receive responses from others, and integrate them somehow into the library. (issue added)
10. (Issue added) There is a wrinkle in text management when there is a hyphen at the end of a line of highlighted text. Some hyphens should be removed when the highlighted text breaks a line and the word appears in mid-line of the text in the top of the highlighted text in the sidebar, but sometimes this happens when a pair of words are intended to be hyphenated - Zotero still removes the hyphen. [Please see screenshot Issue 7 example 1.jpg left sidebar evidenceinformed should read evidence-informed.]
All of these issues are small individually, but if addressed as a group could make a substantial difference. These suggestions are not exhaustive, and there may be other annotation/highlighting aspects that I have missed. All the examples and links have been provided to you by PM and should be in your inbox - thanks very much for the comments. As a newcomer here I hope this is OK for forum protocol !
2. Highlight/underline text collapse/expansion was recently fixed, but I'm not yet sure if this is already in the beta. Normally it should expand the text once you click on it.
10. This is quite difficult to fix, but'll try to do that in future.
For issues related to web page annotations, please share your screenshots with @AbeJellinek, who has a better understanding of this.
>> to receive responses from others, and integrate them somehow into the library. << this last part of Issue 9 also relates to pdf documents
Please consider issue 8 request to now be modified to something that is probably easier -
a) Add the facility in the left hand pane added text to be able to underline text as well (currently Bold, Italic, Superscript and Subscript). This is compatible with at least PFD-XChange and Acrobat Reader.
b) Add the facility to change the underline color and set a default underline color (or leave the default as the last selected underline color) to be tested with various readers for compatibility
What is your opinion on Issue 7 ? This would seem to be compatible with the current design of the left hand sidebar in Zotero 7 beta ? Some solution like this v important for collaboration .....
And what is your view on Issue 5 ? - for most of us I think the % of password protected documents we receive and comment on is probably very small
Link now provided to @AbeJellinek
I have just gone through a pdf to with 100 highlighted comments painstakingly pasting the highlighted text into the subject field for each comment - would very much appreciate a quick view on this issue 7, so if it will not be done somekind person might write a pdf script to achieve the same result in an exported pdf ..... ! Many thanks
Issue 1 has now been duplicated - the source pdf was produced with Microsoft Word and then pdf-ized - the comment text was scrunched up as before - it is fixed by closing and reopening the document tab or the whole Zotero program and reopening. (FWIW)
7) Sorry, but currently we can't help with putting highlighted text into comment field.
3) Yes, done ! see Issue 3 example 1.jpg and Issue 3 example 2.jpg To reproduce get a web page with a lot of text, paste into Word, print using Microsoft Print to pdf driver, add to library, open the document, select and highlight some text, add lots of text in a comment, and you get Issue 3 example 1 - then close the tab and reopen, and you get Issue 3 example 2
7) highlighted text was originally Issue 8 in the original post - the issue 7 I was asking about in my post above is
" 7. Here is a screenshot example of a document I highlighted and annotated in PDF-XChange, and read in Acrobat Reader. In both PDF-XChange and Acrobat Reader, you can use the comment subject field to put the highlighted text, so - at least in PDF-XChange - it appears approximately like a standard left hand sidebar comment on a pdf in Zotero. (Even a whole paragraph of text fitted when I tried it.) [Issue 7 example 1.jpg in PDF-XChange, and Issue 7 example 2.jpg in Acrobat Reader, Issue 7 example pdf.pdf sample file]
It would be nice to be able, as a preset option, to put the highlighted original text into this subject field, but I have no idea whether this fits with the usage of that field as intended by the current PDF standard (https://pdfa.org/sponsored-standards/). "
(Whether this is done is perhaps a question of how highlights and their annotations can be exported together.)
Issue 8 - the original post request to be able to highlight text within the comments text added to a highlight, is not on the cards now, I see from your post above. However, I modified this feature request 8 (see https://forums.zotero.org/discussion/comment/448342/#Comment_448342) to become - to be able to underline text within the comments text added to a highlight, and to change that underline color. (Currently, this type of text can already be modified with Bold, Italic, Superscript and Subscript options, and underline is already an option within Acrobat Reader). This would be brilliant, and works very well visually - see Issue 8 example 1 (this should apply equally to Webpages and PDF annotation - workability for PDFs subject to export/import compatibility with other pdf readers
@dstillman the issue thewalrus.ca (the firefox element at least) is the same as Issue 1(d) in my post https://forums.zotero.org/discussion/comment/447510/#Comment_447510 - I don't know if you have seen this thread yet, but there are a few areas where some policy input arising from this thread could be very useful, and a few other webpage related issues are here which might capture your interest (I have sent you a private link to the file examples and links) ..... btw the more I use this 7 beta the more I like it ...... thanks to you and the dev team! This is getting tantalisingly close to being a work of genius !
Issue 1 (e) For pdf pages with 2 columns of text, highlight order gets changed where there is one highlight say halfway down on the lefthand column, and another highlight that spans the bottom of the lefthand column and the top of the righthand column, the second highlight appears in the sidebar above the first.
Issue 1 (f) Where there is a highlight that spans the bottom of the righthand column and the top of the lefthand column, in a document where there is a footer, the footer gets selected as well and that highlight tends to appear higher than it should in the sidebar. Removing any headers and footers from being selected/highlighted with any main body text might fix that ?
I have had no feedback on the webpage issues - that seems to have stalled for now ? I am continuing to provide examples here so everything is noted. I am keen to get these issues resolved so that the plugin writers can sort out the integration with other programs. Good luck !