dsifford/academic-bloggers-toolkit

WordPress plugin providing an all-in-one solution for effective academic blogging.

academic-bloggers-toolkit's Issues

Finish test coverage for all remaining files

Font size of reference list

To my eyes, it looks preferable to have font size of the references as being smaller size than the article. Here is a mock article for you to judge for yourself:
http://www.earthmedresearch.org/wordpress-resources-at-siteground/
You can see I have three reference lists at the end.

The first of these three lists is what it looks like if you add the following < span> tags inside every < li>< /li> tag:

< ol >
< li >< span style="font-size: 8pt;"> LIST ITEM GOES HERE < / span></ li>
< li >< span style="font-size: 8pt;"> LIST ITEM GOES HERE < / span></ li>
< /ol >

The second list is what it looks like if you add the following < span> tag only once, inside the < ol>< /ol> tags. I think this looks the best:

< ol>
< span style="font-size: 8pt;">
< li>LIST ITEM GOES HERE</ li>
< li>LIST ITEM GOES HERE < /li>
< /span>
< /ol>

The third list is the default appearance.

I prefer the second of these three styling examples. Though it is true I could manually add the tags to every reference list I write without much effort, to do so I have to switch from the WYSIWYG editor to the text editor. And it just makes me really nervous doing that, because I know sometimes when you then switch back to the WYSIWYG editor, your article may have been altered in ways you didn't want by some automatic filtering or something. Hence I want to avoid any need to go to the text editor entirely.

I previously tried solving this issue with a plugin called TinyMCE, which adds an option to edit font size while still in he WYSIWYG editor, but I did not like it as it made my headings in my WYSIWYG editor turn white (and therefore invisible) for no apparent reason.

Not sure if you can think of any easy way to make this font size change happen. Don't think too hard about this one as it is not crucial. I imagine this has nothing to do with CSS and hence could not be solved with CSS override.

Refactor JS into Typescript + minify resources

Relax the permission checks so that 'subscribers' can also use.

Currently, the plugin checks to see if current_user_can edit-posts or edit-pages, which is fine, but prevents contributors or subscribers from being able to use the plugin.

Relax these permissions.

Preview text disappears!

Hey Derek,

Great work on this so far! I'm quite excited to use it.

After activating the plugin I noticed that the 'preview text' under the titles of the blog posts on my homepage disappeared. Deactivating the plugin resolved the issue so I'm confident that it's related.

Specifically what I'm referring to can be seen if you go to http://boringem.org - under a post title (e.g. "#TipsForNewDocs | Using spaced repetition to study") the text description (e.g. "The Canadian Royal College licensing exam in emergency medicine has a certain mystique. While the pass rate for Canadian graduates is spectacular [1], exam survivors speak of the test in hushed whispers that have an air of PTSD. Having recently survived the exam myself, I have some understanding of where these whispers come from. Prior to my exam year I had planned to write a blog post to reassure the residents following me that it was not that bad… Except that it was. Or at least it would have...") disappears!

I'm not sure if this is just an issue with this theme (it's from Elegant Themes) or will affect people more broadly. Regardless, there will be a theme change for my blog in the future so if it's an isolated issue it won't be bothering me for long.

Thanks!

-Brent

Z-index issue

I've had this problem with a couple other plugins as well. I have floating social media icons which can appear on top of the tooltip, obstructing it. This is fixed by changing the z-index to something big in the CSS, like:

z-index: 10000100;

So this is no longer a problem for me, but you might want to hardcode this for sake of others.

Feature request

I'll start by saying great job on the plugin, it is great!
I've been looking for a citation plugin to include on a prototype I need to present in two months and after a long search I stumbled upon yours. Unfortunately I still cannot use it though, one of the reasons being that it only uses PMIDs. So if I may, the following features would make it in my opinion the best reference plugin out there (and the only one for that matter):

1. First just some small details from the little I tested:
   a) Maybe add an option to put a title for the bibliography section.
   b) If I delete the Smart Bibliography part from the post, the Generate button is disabled unless I save the post, then I can add it again.
   c) If I add a formatted reference before generating Smart Bibliography, that reference is not included in the bibliography. Maybe add an option to automatically generate smart bib if its the first time I'm inserting a reference.
2. And now the features that would make it the best plugin ever:
   a. As I said, only PMID. Could you add DOI too, and retrieval through multiple sources, CrossRef, DataCite, etc. (Check the KCite plugin). IT-related papers for instance are not in PubMed.
   b. Import from file, e.g. most notably bibTex, others if you like. So as an author, I can just e.g. export the references from my literature management software, and upload them onto the article through your plugin. There is a bibTex parser for php here you can use, but there are others too I think.
   c. Export reference option for each single one, and one file containing all. So, just to be clear, a reader sees the bibliography at the end of the post, and can download a bibTex file for each reference available, and also a single file that contains all the references.
   These killer features would make it possible for anyone to easily use citations on a blog, since they can either find it through DOI etc. or most academics have a lit.management sw already, so they can just export them. It would really become a proper reference management plugin for WP.
3. Some additional features when you get the time:
   a) Option to select citation styles through using CSL, or at least some more styles available.
   b) Filtering options for the bibliography (check papercite, teachpress)
   c) this would get complicated, but maybe sometime in the future, a reference manager from the dashboard, to keep a list of reusable references and stuff (check teachpress). Maybe by using the Links feature from WordPress, check here and here

I mentioned the other plugins just to give you an idea of what I mean, or how you can implement the features, I hope you don't take it as a negative feedback thing, it is quite the opposite. Your plugin is the best looking and promising so far from what I've found, and it pains me to not be able to use it. But if you could at least add the bibtex importing for authors, and bibtex exporting for readers, within two months, then I will certainly add it to my prototype, and recommend it further.
Let me know what you think, or if I can help. Great job either way!

Editor toolbar disappears when ABT active

Hey, just wanted to let you know that I just tried the plugin, and noticed that the editor buttons toolbar disappears when ABT is activated, in visual mode. Not in text mode though.
I tried in in IE and Chrome, and in two different WP setups. Am I missing something or is it a bug?

Nice touch on the jsfiddle in the settings, it's a good idea.

Issue with Advanced Custom Fields

If i click add reference, i have two pop ups, one on top of the other, with no error in the console. It won't let me add a reference, the button just clicks, but doesn't close the pop up or add the reference to the page.

I have tracked the issue down to an issue with the plugin advanced custom fields. https://wordpress.org/plugins/advanced-custom-fields/

I thought it might be an issue with my theme, so i have tried a new blank WordPress install (4.5.1) running twentyfifteen. With the only plugins being ACF and the toolkit (which works great without ACF active!), but the error still occurs.

I'm not too sure whats causing the issue though.

Add import references by file URL

Hi again,
So as discussed, it would be nice to provide an option to enter the URL of a reference file (RIS in this case) and directly import the references from there without uploading the file locally.

Object.remove() and Object.assign() issue with IE browsers

Look into using webpack HTML loader to create the static view files automatically.

Switch from sass to postcss

IE tooltips

I now have access to a computer with IE, and tooltips do not display.

Create URL for DOI in imported RIS

Just noticed that if I import a RIS with a DOI number, but no separate URL field, the doi just appears as text. I know it is not a bug, but it would be better and much more practical if the doi is automatically linked to the resolver, especially as I said, when the imported RIS has no URL but just a DOI number.

Just an additional question: Since from what I saw, you just generate the formatting and place it in the post, how do you recognize the list again if the post is opened in edit mode again? do you parse the text again to show the list on the widget, or something else? just curious.

Highlight and drag reference -- bold text stays

Error when no authors selected on website insertion

related to string.prototype.substr()

Indentation issue

Hi Derek,

I finally updated the plugin, and now it totally doesn't work. =) But one thing at a time! The first major issue is that any new post I write is indented:
http://www.earthmedresearch.org/testing-citations-indentations/
If I deactivate the plugin and reload this page, the indentation will no longer be there. Any ideas?

Thanks,
David

Anchor links for citations interfering with anchor links not created by the plugin

Need to better scrutinize the selectors.

Spacing between numbers and text in reflist

Reference List shows endless spinner when Visual Editor is disabled

The Reference List shows an endless spinner when loading the Edit Post page with the "Text" tab selected. It only loads if you click on the Visual editor.

I usually have the visual editor disabled by default since I prefer to be in control of the HTML - the visual editor can sometimes cause formatting problems.

Therefore it would be nice if it worked as it does with the visual editor, but inserts the "span" HTML wherever you have your cursor in the Text editor.

Add general url reference functionality

I want to link to a lot of articles, but want them to also appear as inline citations like the PMID inline citations your plugin produces. I think it looks sloppy to have a mixture of normal text links and numerical superscript citations. I want everything to be numerical supercripts - both links to articles, and links to PMID references. I notice that you can already manually add references to the ordered list, and then cite those references with your numerical inline citation option. So that half of the picture is already done. The other half of the picture that needs implementation is adding a dialogue box to add a url to the references ordered list.

I don't know the best practices for references a url, but things that would be desired are as folllows. And note that most of these could conceivable be parsed automatically from the target url.

• the title of the site (or maybe the domain name?)
• the title of the article (note that this may not always apply. There are other things on the web to link to besides articles, but articles will generally be the case.)
• the date (also does not always apply. And some articles intentionally remove the date too because they want the article to seem timeless.

It seems conceivable to me that the only input the user would need to give is the url.

And like my previous thread, tooltips for such url references should also be clickable and take you to a new url. And of course all clickable tooltip links should be target=blank.

Peer review content not allowing line breaks

Reference List on Pages

I just noticed that the Reference List is not appearing when editing Pages, and it's not on the screen options. Is it just me? If not, can you enable it for pages at least.

BTW, great job on everything until now. It's a great plugin.

Pagination of Long Bibliographies

Not sure how much effort this would involve. Or even how important it would be if there are year breakdowns ... One of the things I like about the biblio plugin on drupal is it does paginate and let you sort by year ... Here's my current publish on a test site in your tool ..

http://datascience.goggins.com/7-2/

BTW, love this plugin MUCH more than ZOTPAD ... I like how its built to be movable and not dependent on wordpress. Really good, durable software engineering decisions. :)

Add download option to front end reference list

As discussed again, a download option for each reference to a reference container file (RIS as you said) for front end users if they want to reuse the reference. Maybe also an additional option to download all references in one file. Good luck!

Add optional collapse reference list & peer review boxes

An idea just came to my mind. It's not essential, and may not be possible anyway, but it would be cool. Make the ordered list of references expandable and collapsible. An example of this is Mercola.com:
http://articles.mercola.com/sites/articles/archive/2010/08/10/making-sense-of-your-cholesterol-numbers.aspx
Default position would be collapsed. This would make it easier to scroll down past the article to reach the comments section, without having to scroll past 100 references first.

I'll test out your new 2.4.0 changes shorty, then give you my feedback.

z-index question

I have manually coded in a z-index for .abt_tooltip. I am wondering if I also need to do it for the following:

.abt_arrow_up
.abt_arrow_down
.abt_tooltip_touch_close

In other words, I want to make sure all parts of the tooltip stick together. Have I got this list right, or did I miss any other elements I need to add the same z-index to?

Duplicate references

I really don't care about this, but just giving you a heads up. The plugin allows for repeating the same references multiple times. Of course, anyone manually writing a paper in real life can always make that mistake, so I don't consider an automated check on that to be a necessary feature. Just letting you know though.

Fully localize the options page and all menus

Desktop tooltips can be choppy -- make hover padding larger

Fix typo on options page

FYI, you need to change the dashboard CSS documentation to say "#abt-smart-bib" rather than ".abt-smart-bib", which is what it presently says. The first selector works. The latter selector does not.

"Autogenerate" Reference List feature

This may be opening a can of worms, in which case just forget it. But to me, here is the ideal way workflow should happen:

1. I start writing the text of an article
2. I insert an inline citation, not by inputting a number (as is currently the case with the plugin), but by inputting a PMID or a URL. No number is manually inputted.
3. I keep writing my article like this and keep inputting citations.
4. I finish my article.
5. I click publish
6. I view the article and am happy to see that the article has "autogenerated" numbers for my inline citations as 1, 2, 3, etc, according to the order in which they appear in the article. I also am happy to see that the article also "autogenerated" a reference list at the bottom of the article, and has numbered it accordingly.

Okay, that's the ideal, and would be less work for the user. A few things to consider:

1.There would be no more such thing as a user needing to create an ordered list at the end of their article, as is presently the case.
Though this is a time saver, this might just be too different from the plugin you have now for you to want to mess with. I don't know. Though maybe what the plugin can do is have the user enter a shortcode [ ] at the end of the article, which will then be the cue to parse the info from the inline-citations, and print an ordered list once published.

2. A reference might be cited inline more than once.
Oh, I guess this is where time-savings for the user might disappear. It might be easier to cite the same reference "3" several times in the article (as would presently be done with the plugin) than it would be to cite the same "PMID: 123456" several times in an article. Though maybe not. From my standpoint, citing a PMID or URL multiple times in an article is relatively rare.

Another issue here is that when "autogenerating" the references list at the bottom, it would need to make sure not to include a repeatedly-cited reference more than once. For a given list item, the logical checks would be:

If(it's a PMID), then check if that PMID already appears earlier in the list. If so, skip placing it in the references list since it is already there. B

If(it's a general URL), then check if that url already appears earlier in the list. If so, skip placing it in the references list since it is already there.

Similarly, the "autogeneration" of inline citation numbers also would need to check if a reference has already been cited, in which case a new unique citation number should not be assigned. But rather, a number already assigned just needs to be repeated.

3. User may wish to add references, but not cite them in the article
I personally don't think I'd ever need this. But others might. This overall feature suggestion I am giving in this post would so far only create a reference list for items that were cited in the article. Suppose I wanted to include a reference, but not cite it anywhere inline. This might require something like as follows:

• First, have an input box where user inputs a list of "uncited" PMIDS and/or URLs
• Then also make the shortcode I mentioned earlier do a check and see if that box has any contents. If it does, it parses that info and also prints those references.

Fix mobile touch tooltip position

Thumb covers the tooltip if tooltip is below the inline citation.

CSS conflict with mobile tooltip close button

Look into using Pug (jade) for HTML within the php

#abt-smart-bib:before bug

Awesome updates Derek. I will test it out more thoroughly probably tomorrow. One bug on my site is that if I try to add the before text, it does not appear:
http://www.earthmedresearch.org/community-guidelines/
The word "References" is something I wrote manually, so ignore that.

When I click Update on the override CSS box, it keeps adding more slashes "" to the code. The more you click update, the more slashes appear, like this:

abt-smart-bib:before {

content: \'Bibliography\';
margin-left: -20px;
font-weight: 900;
line-height: 50px;
}

TinyMCE button appears twice on pages.

Make tooltip links clickable

Hi. First of all, thank you for this plugin. It is the only citations plugin that I could get to work at all on my site. I am rather dumbfounded that citations plugins are virtually non-existent. I would have thought it is a basic requirement that thousands of sites would be using. I guess not...I also appreciate the convenient CSS override which has allowed be to easily style the citations into superscripts.

Anyway, I am going to start a few threads with my suggestions, I hope you can possibly make them happen.

Suggestion 1: Make tool tips clickable. For an example, look at a wikipedia article. The tooltips allow you to click a link that sends you to an external url. I would dearly like this. It is just more user friendly. Otherwise you have to scroll down to to the references, click the link there, then scroll back up to the article to continue reading where you left off. So once more, what I am suggesting is that the PMID link in the tooltip be functional.

Rlelated Question: Are the anchor links (inline citations) intended to scroll down to the references when you click on them? They don't do anything on my site. This is actually fine for me, and is the way I would want it to stay, if the tooltips were clickable. Then there wouldn't be any need to want to scroll down to the references with a click. Though since the word "anchor" does imply clicking it should do something, I am just curious about whether or not I have a bug in this regard. This is just a question, rather than a suggestion for a change.

More threads coming...

Tooltip in different browsers

I haven't installed your 2.4.0 update yet, but this issue probably still applies. No tooltip shows when I use Firefox or IE. I tested this with some online browser comparison tools, so this does not seem to be an issue with my local machine as far as I can tell. I tested the following URL:
http://www.earthmedresearch.org/wordpress-resources-at-siteground/
Works fine in Chrome, which is what I use, so I did not notice the issue until now. I didn't test any other browsers besides these three.

Cannot insert citations when set locales to Thai

I tried to add a citation when set locales to Thai and got the error in the console.

Failed to load resource: the server responded with a status of 404 (Not Found)
https://raw.githubusercontent.com/citation-style-language/locales/8c976408d3cb287d0cecb29f97752ec3a28db9e5/locales-th.xml

But adding a citation in English was fine.

Outgoing links and SEO

Just wondering if having virtually all my links ultimately ending up in a tooltip would have any adverse effects on SEO? Maybe search engines don't see those links?

Actually, now it occurs to me the actual links are in the references list as well, so I suppose there should be no issue. Unless collapsing a reference list somehow hid those links in the references from search engines.

Feedback on 2.4.1

Okay, so I have tested the plugin and here is all my feedback:

1. FYI, your active installs of the plugin went from like 50 down to 30. Probably because the update messed up posts already published with citations in them. For me, what it did is it made all the tooltips blank. I could fix this by editing the article, enabling smart biblio mode, and then moving my references list (which was presently above the smart biblio line) to be below the line. Though due to funny list auto-formatting things, that is actually more difficult than it sounds. You basically have to cut/paste one item at a time for the list auto-formatting to not mess things up. Though perhaps it could have been easier had I done it in text mode rather than WYSIWYG mode. In any case, I wouldn't feel bad about it, as the development of the plugin is totally worth it.
2. FYI, sent you a small thank you $$.
3. The general URL entry works fine as far as I can tell. Thanks a lot. Ideally, it would be automatically able to parse all the other info just after entering the URL, but it's okay as is.
4. The smart biblio feature also seems to work fine as far as I can tell. This is totally workable. Though the ideal way to do this would actually not generate the references list at all, until you actually clicked Publish (or clicked a "Regenerate References List" button). This way, you could reorder sentences that have inline references in your post all you want, and when you publish, the inline citation numbers will always be in ascending order. This is what I described in my original thread about this, but I understand if this is just way too complicated. For this to work, there wouldn't actually be any such thing as "inline citations". Actually there would only be "inline references". The citation number is something assigned on the fly once you click Publish (or a button called "Regenerate References List"). Anyway, just making sure you understand the concept. Even if this appears doable, it does have some caveats. If you ever decide to work on this, let me know and I can help you brainstorm on this. I have some ideas....You see, I can give you an example of why this feature would be cool. Say I write an article with citations 1 to 100. Then I suddenly realize I want to add a new reference to the very first sentence of the article. It has citation number 101. Now my article looks sloppy for having citations 101, 1, 2, 3...100. And if I were to try to fix this by putting that new reference as number 1 on the ordered list, then all the other references on the list get bumped up by one index, which then makes all the inline citations off by one. So there is no easy way to make sure inline citation numbers are always in ideal order at present. Also there is no easy way to delete a reference from the reference list without getting citations off by one.
5. Keep in mind such a development as described in number 5 might affect how one would implement a collapsible reference. Though maybe not.
6. FYI, you need to change the dashboard CSS documentation to say "#abt-smart-bib" rather than ".abt-smart-bib", which is what it presently says. The first selector works. The latter selector does not.
7. The CSS arrow styling selectors you have written do not do anything for me:
   .abt_arrow_up { border-color: transparent transparent magenta; } .abt_arrow_down { border-color: magenta transparent transparent; }
8. I don't know what .abt_tooltip_touch_close is. Do I need to know? Is that like an X button to close a tooltip or something? If so, I don't see it.
9. FYI, tooltips now work in Mozilla. I tested IE through the following website:
   https://www.browserstack.com/start
   The "Live" tab lets you test live browsers live. The tooltips do not seem to appear on IE still.
10. Indentation issue, I already mentioned. Just repeating it for my own mental organization.
11. I'm having a new issue with favicons not showing up on new posts I make. I don't think it has anything to do with ABT plugin, but just wanted to mention it to make sure. I still have the problem when I deactivate ABT, so it's probably unrelated.
12. Inserting multiple comma-separated PMIDs at once is buggy. There are 4 cases:
    a) When I am not in smart-biblio mode, and I add 2 PMIDs, it seems to work.
    b) When I am not in smart-biblio mode and I add 3 PMIDs, it just makes the loading-wheel spin forever
    c) when I am in smart-biblio mode, and I add 2 PMIDs, sometimes it works, and sometimes it does nothing at all.
    d) when I am in smart-biblio mode and I add 3 PMIDs, it adds 1 inline citation number (should add three) and does not add nothing to the references list.
13. I think I may have already mentioned this to you. If so, sorry for duplication. I test mobile devices by using online tools. On mobile it appears that the horizontal location of the tooltip arrow does not stay with the citation number.

Holy guacamole. I hope all this feedback is considered helpful information rather than a pain in the ***!

David

Add RIS (refman) import

See #24

cc: @someonehere15

Improve error handling of pubmed api calls

Headings by Year for "APA CV"

I think for websites most academics want to be able to have headings by year.

Also, "APA CV" is kind of a guess. One that worked, but just a guess. So, having a way to sort by year or alphabetically is generally useful regardless of the citation style, I think.

Add attachments to the references

So, again: one nice additional feature would be to add an attachment link to references, e.g. by using the WordPress Media Library, or just entering a url to a file (and show a download icon to differentiate from the download reference link), in case e.g. someone wants to include a paper as a PDF with the reference. You can e.g. check out the papercite plugin that does it, just as a reference.

mobile rendering possible bug

Again, I am using an emulator, so this could be a false observation, but look at this:
http://mobiletest.me/iphone_5_emulator/?u=http://www.earthmedresearch.org/community-guidelines/
Hover over the first tooltip (i.e. [1,2]). Note that the long URLs do not wrap properly. Those two references are of type "Website". I don't see this problem with other types of references, which don't have long urls in them.

Add help text for how to add a title to the reference list with css

Citations need "white-space: no-wrap"