Chell: It's fixed, but (judging by your other thread) you might be having trouble with imported notes before you edit them in Zotero, at which point the problem should go away. Is that the case?
Thanks for your reply. Most of my notes are annotations imported via Zotfile. I went in and made a few changes in one in Zotero, but it didn't seem to make any difference - my report is still full of html code and pretty much illegible...
Is this what you meant? Other suggestions?
Thanks!
e.g. <p><em>Wellbeing (note on p.1)</em></p> <p> </p> <p>"Wellbeing is a lens to understand the distinctive features of artisanal fisheries and helps to understand fishers’ disenchantment with fisheries governance processes" (Trimble and Johnson 2012:1)</p> <p><em>place of artisanal fisheries in academic analysis (note on p.1)</em></p> <p> </p>
I went in and made a few changes in one in Zotero, but it didn't seem to make any difference - my report is still full of html code and pretty much illegible...
I mean for that specific note. If you edit the note in Zotero and then generate a report for just that item, do you see HTML? If so, are you using Zotero 3.0.11?
I am using Zotero 3.0.11. Is there a more recent update?
I selected a single document to test. I have annotated the pdf and extracted annotations via Zotfile.
If I go into the imported annotation note and write some additional stuff up top, it also shows up with html,
e.g. <p> </p> <p>TEST EDIT</p> <p><strong>Extracted annotations...
If I create a new note associated with the same file, it shows up with no html the way I would expect.
e.g. THIS IS A TEST NOTE (no html).
What else can I do to help diagnose/fix? Do you know of a resource that can help me convert my report or source html into regular text in the meantime?
Hmm... it seems that if I generate the same report on my work computer (vs home laptop), the report comes out fine!
What does this mean?
Another problem, I think related to zotfile, is that sections of text extracted from highlighted pdfs are missing spaces. OCR issue?
e.g.
"Wellbeingisalsoavaluableanalyticaltoolwhenthinkingabout governance in artisanal fisheries [9]. Governance is composed of a set of relationships guided by conscious and unconscious norms [12].Inthefisheriescontext,governancehasclearmaterialtargets in such areas as ensuring livelihoods and food security, providing societalrents,andsustainingthecapacityofecosystemstoprovide services.
OK, there are invisible "control characters" in there, which are invalid in XML. ZotFile should probably strip those itself, but we can do it in Zotero as well. I'll have an update shortly.
I installed the above but even so, SOME of sections of my report are still coming out html-y...
<code> <p><strong>Extracted Annotations (Mon, 14 Jan 2013 07:13:45 GMT)</strong><br /><br /></p> <p>"An analysis of livelihood diversification, illustrates that some households are more adaptable to environmental change than others. Unexpectedly, it is not the poorest who are the least able to adapt, but rather fishers who have become locked into an overly specialised fishery." (Coulthard 2008:479)</p> </code>
Is that the code from the HTML source view or the report view? We'd need the former. There's no reason what you have above shouldn't work even in 3.0.11.
code above is from the source (ie from html of note). i added <code> </code>.
in the report it looks the same: <b>Extracted Annotations (Mon, 14 Jan 2013 07:13:45 GMT)</b><br><br><p>"An analysis of livelihood diversification, illustrates that some households are more adaptable to environmental change than others. Unexpectedly, it is not the poorest who are the least able to adapt, but rather fishers who have become locked into an overly specialised fishery." (Coulthard 2008:479)</p>
there are other outputs that are considerably more messy and illegible...
That's not actually the same—the markup is different. The one with the <b> is what you might get straight from ZotFile, and that won't display properly in the report until you edit it in the Zotero note pane. (That's not ideal and we may be able to fix it, but that's how things stand now.) You might need to click off and back onto the note after editing it before generating the new report.
Also, it shouldn't matter for this, but I realized that my previous fix would've only fixed the display of top-level notes with control characters, not child notes with control characters, so you should update to the latest version of the 3.0 dev build. (You may need to clear your browser cache before downloading. The current version is 3.0.12.r11099.) Again, that's not the issue for this example, though.
Ha! p's and b's all look the same to me, apparently :)
Still not sure what you mean when you say I have to edit the notes I import via Zotfile in the Zotero note pane. Can you explain exactly what I need to do?
Does this mean I will need to manually adjust every annotation note I import? Not exactly the functionality promised.
Thanks for your attention and for walking me through this.
Still not sure what you mean when you say I have to edit the notes I import via Zotfile in the Zotero note pane.
I mean exactly that. You have to make some sort of change to the note (even pressing space and then backspace) so that the note is resaved via the note pane. (It might even be enough just to load the note and then click away, though I'm not sure.)
Does this mean I will need to manually adjust every annotation note I import? Not exactly the functionality promised.
You'll have to take that up with the ZotFile dev. Notes saved as XHTML would display fine, but non-XML HTML notes won't until they're resaved through the note pane. I believe he should be able to fix this fairly trivially.
There are some complicated technical reasons for why this happens that we can address eventually [by using an HTML sanitizer outside of TinyMCE], but it's not a priority.
Upgrade Storage
Thanks for your reply.
Most of my notes are annotations imported via Zotfile. I went in and made a few changes in one in Zotero, but it didn't seem to make any difference - my report is still full of html code and pretty much illegible...
Is this what you meant? Other suggestions?
Thanks!
e.g. <p><em>Wellbeing (note on p.1)</em></p> <p> </p> <p>"Wellbeing is a lens to understand the distinctive features of artisanal fisheries and helps to understand fishers’ disenchantment with fisheries governance processes" (Trimble and Johnson 2012:1)</p> <p><em>place of artisanal fisheries in academic analysis (note on p.1)</em></p> <p> </p>
I selected a single document to test. I have annotated the pdf and extracted annotations via Zotfile.
If I go into the imported annotation note and write some additional stuff up top, it also shows up with html,
e.g.
<p> </p>
<p>TEST EDIT</p>
<p><strong>Extracted annotations...
If I create a new note associated with the same file, it shows up with no html the way I would expect.
e.g.
THIS IS A TEST NOTE (no html).
What else can I do to help diagnose/fix? Do you know of a resource that can help me convert my report or source html into regular text in the meantime?
Thanks!
Hmm... it seems that if I generate the same report on my work computer (vs home laptop), the report comes out fine!
What does this mean?
Another problem, I think related to zotfile, is that sections of text extracted from highlighted pdfs are missing spaces. OCR issue?
e.g.
"Wellbeingisalsoavaluableanalyticaltoolwhenthinkingabout governance in artisanal fisheries [9]. Governance is composed of a set of relationships guided by conscious and unconscious norms [12].Inthefisheriescontext,governancehasclearmaterialtargets in such areas as ensuring livelihoods and food security, providing societalrents,andsustainingthecapacityofecosystemstoprovide services.
Who should I ask about this?
complete note html from messy report:
[code removed — D.S.]
Glad all my work was not for naught, and that I will be able to stand by all my recommendations to friends re. Zotero :)
I installed the above but even so, SOME of sections of my report are still coming out html-y...
<code>
<p><strong>Extracted Annotations (Mon, 14 Jan 2013 07:13:45 GMT)</strong><br /><br /></p>
<p>"An analysis of livelihood diversification, illustrates that some households are more adaptable to environmental change than others. Unexpectedly, it is not the poorest who are the least able to adapt, but rather fishers who have become locked into an overly specialised fishery." (Coulthard 2008:479)</p>
</code>
??
Thanks
i added <code> </code>.
in the report it looks the same:
<b>Extracted Annotations (Mon, 14 Jan 2013 07:13:45 GMT)</b><br><br><p>"An analysis of livelihood diversification, illustrates that some households are more adaptable to environmental change than others. Unexpectedly, it is not the poorest who are the least able to adapt, but rather fishers who have become locked into an overly specialised fishery." (Coulthard 2008:479)</p>
there are other outputs that are considerably more messy and illegible...
Also, it shouldn't matter for this, but I realized that my previous fix would've only fixed the display of top-level notes with control characters, not child notes with control characters, so you should update to the latest version of the 3.0 dev build. (You may need to clear your browser cache before downloading. The current version is 3.0.12.r11099.) Again, that's not the issue for this example, though.
Still not sure what you mean when you say I have to edit the notes I import via Zotfile in the Zotero note pane. Can you explain exactly what I need to do?
Does this mean I will need to manually adjust every annotation note I import? Not exactly the functionality promised.
Thanks for your attention and for walking me through this.
There are some complicated technical reasons for why this happens that we can address eventually [by using an HTML sanitizer outside of TinyMCE], but it's not a priority.