OJS3: Problems with eLife Lens Article Viewer plugin

Good day!

Lens Article Viewer is really great plugin.
I already spent several days for investigation JATS XML modification for Lens Viewer.
There are several problems with this plugin use, one of them I saw on OJS3 demo. And it was successfully solved.
The problem is that labels “content”, “figures”, “references”, “info” in the middle of the page are not displaying. But they work.
So I am wondering how to fix it.

Additional info:

Problem appears when using OJS3 bootstrap themes.
When choosing default OJS3 theme problem disappears.

Problem solved by adding other than default color settings in css file.

As XML Lens viewer provides good option for publishing JATS XML directly through transformation to HTML I would like to learn more about it.

After some modification with my low skills in programming I made this plugin work for our journal. It`s needed to point out that Lens viewer plugin is not ready as out of the box solution for OJS3.

But I see that even after javascript file adaptation it is not ideal in terms of indexing by google. For example on page header can be seen not article title, but title of journal with its volume and issue.

As a result in google search results link to xml full text looks like this:

Vol 1 No 1 (2016) | my Journal title

Is there a person (probably staff member) that could help me with modifications of Lens viewer plugin to enter correct article metadata? JATS XML is highly structural language and it is to bad to lost it all on the front end. For many journals published JATS XML is only source of article metadata in HTML front-end. I have tried to work with PLoS ONE Ambra and there, as I can see, published article contains all needed metadata from parsed jats xml file. They use XML transformation process through Java app. Think the same can be done with javascript.

Hi @Vitaliy,

Try editing plugins/generic/lensGalley/templates/articleGalley.tpl and changing…

{include file="frontend/components/header.tpl" pageTitleTranslated=$issue->getIssueSeries()|escape}

…to…

{include file="frontend/components/header.tpl" pageTitleTranslated=$article->getLocalizedTitle()|escape}

Please let me know if that behaves as you’d expect with respect to titles, and I can commit the change to our code repository.

Regards,
Alec Smecher
Public Knowledge Project Team

Greetings,

Yep. After applying changes I see in header article title. Its on language that pointed in the preamble.

Hi @Vitaliy,

Thanks for confirming! This change will be included in the next release.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher and @Vitaliy
My installation is OJS 3.0.2. My XML file is not rendering in lensGalley. I have validated my xml file at PMC xml validator which shows no error.
In the inspect element console I am getting .js errors

Can anyone tell the solution?

Hi @hannanhazari,

You might consider upgrading to the latest release of Lens Reader – but note the discussion at https://github.com/asmecher/lensGalley/issues/9 about limitations with respect to the mobile interface. Note that we don’t develop or support lens reader directly – the eLife team does that – though we do maintain the OJS integration.

Regards,
Alec Smecher
Public Knowledge Project Team

Are you maybe using my fork: https://github.com/ajnyga/lensGalley/?

I am testing with translating the UI there, so I think that you are missing a locale for you language selection?

I should had put the translation test to a different branch.

Hi @ajnyga
I have tried your forked version of lensGalley also. Few things are better in it like

  1. Type of article is displayed
  2. Title of the article and author names are center aligned
  3. In ‘info’ tab: ‘Acknowledgments’ and ‘Copyright & License’ are bold and font size increased

but there are few issues

  1. ‘back button’ added is not properly rendered.It shows
    ##translate.back##

The main features in that fork are that it supports OJS artwork files attached to the XML-file (images), supports footnotes and uses the latest development branch of lens. I have also stripped most of the eLife filters that are not needed.

What is your language selection when you open lens? At the moment the back button is only translated in English and Finnish. I was testing how to translate lens using the OJS locale files.

Hi @asmecher
I am using the latest version of lens viewer bundled in https://github.com/asmecher/lensGalley. I have found four peculiar problems:

Firstly, XML is rendered and displayed in Chrome browser. In Mozilla Firefox: after initial loading square, the screen becomes blank white. In Microsoft Edge browser: The loading square is ‘loading’ forever.

Second, display of history and publication dates are ‘one’ day less than the dates present in the xml file. See the xml data and rendered lens display below

<pub-date iso-8601-date="2016-12-31" pub-type="epub">
<day>31</day>
<month>12</month>
<year>2016</year>
</pub-date>
<pub-date iso-8601-date="2016-12-31" pub-type="ppub">
<day>31</day>
<month>12</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection">
<month>1-3</month>
<year iso-8601-date="2017">2017</year>
</pub-date>
<volume>1</volume>
<issue>1</issue>
<fpage>1</fpage>
<lpage>2</lpage>
<history>
<date iso-8601-date="2016-12-29" date-type="received">
<day>29</day>
<month>12</month>
<year>2016</year>
</date>
<date iso-8601-date="2016-12-31" date-type="accepted">
<day>31</day>
<month>12</month>
<year>2016</year>
</date>
</history>

Third, in reference citations (Bibliography), if a cited literature contains only single page and is tagged with and is left empty, it is not reflected unless you put the first page number again in tag

Four, in reference citations (Bibliography), if xml contains PMID contained in
<pub-id pub-id-type="pmid">23802825</pub-id>
it is not displayed

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Hi @hannanhazari,

Those sound like issues with the Lens Reader, not specifically its integration with OJS – you might be better off inquiring with the eLife Lens development team. See https://github.com/elifesciences/lens/ for details.

Regards,
Alec Smecher
Public Knowledge Project Team

Hi @asmecher @ajnyga,

I’ve been scrambling to get Lens-viewable XML articles ready for the launch of a journal issue this week and was stunned to see that footnotes aren’t rendered with the Lens Galley plug-in we’re using. (We’re hosted by PKP and are running OJS 3.1.2.)

Do I understand correctly that @ajnyga’s fork of the plugin does support footnotes? Is there any reason why we wouldn’t be able to switch to this version of the plug-in (if it’s stable enough)?

Thanks,
-bh

Hi,

My fork did support footnotes, I basically built an own lens using their instructions to get that fixed. However, we have a very low request for JATS at the moment so I have not been maintaining it actively. Also I think the plugin has many other problems, the biggest being it is not responsive and you can not use it with mobile devices.

Have you tested @Vitaliy’s JATS parses plugin?

I briefly experimented with @Vitaliy 's plugin, but I don’t think I quite got the hang of it. I’ll give it a second, more thorough trial now that I better appreciate the limitations of the Lens plugin!

I’m curious that you haven’t been seeing much request for JATS. From what I had seen over the last couple of years, I thought that adopting a JATS-centric production workflow would help our journal keep up with publishing trends. Is your sense that it’s actually becoming less popular among journals?

Hi, by “we” I mean the installation I am personally maintaining. It includes 80 journals from very small publishers. For them the problem with JATS is the cost and the lack of knowhow. I believe and hope it will become more popular and do plan to support it in the future in our installation as well. However, the presentation part of JATS is the easy one, creating JATS is more difficult and I think the current toolset is not quite ready for non-tech editors to be able to produce it. But that will probably change eventually.

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Hi @horne.b and @ajnyga,

Regarding producing JATS, DOCX to JATS XML converter plugin is almost ready for testing: https://github.com/Vitaliy-1/docxConverter I will compose beta-release soon. From crucial elements, it cannot transform references and figures yet but they can be added with, e.g., Texture plugin. So, development of JATS XML centered workflow is moving forward :slight_smile:

Hi @horne.b, @ajnyga and @Vitaliy

It’s true the Elife Lens which is the core of the lensGalley plugin has some lacks. I have worked in the generation of some JATS XML for a Journal here in Mexico for 3 years a long, and in this time I could identify some of these lacks. for example:

  1. The footnotes are not displayed as cross references just as the citations and bibliographic references are.
  2. In the tab References, the bibliographic references of kind book, sometimes the authors only add the publisher but no the location, these values are marked in the JATS XML using the publisher-name and publisher-loc tags, if in the xml only there is one, Lens does not display them in the resulting HTML. It’s the same for the tags fpage and lpage.
  3. Following with the reference of book kind, the source is repeated, as this reference has not article-title tag, then Lens use the value of the tag source as title, causing the effect in the below image:

Well to finish, when I started in this of the JATS/XML I found meTypeset, a tool developed by Martin Paul Eve, I used this tool for 2 years for generate my JATS XML files; however approximately one year ago I started to use Scielo Markup, a plugin for Microsoft Word useful to mark your Word documents and convert them in a beautiful JATS/XML. I let you the web page of Scielo Markup here, is in spanish :slight_smile:

Well I hope this information would be very useful for someone more,

Best Regards.

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