[SOLVED] JatsParser PMID issue in reference [OJS 3.1]

anupent · November 20, 2017, 1:43am

Hi @Vitaliy,
I am using JatsParser and JATS xml as galley for HTML view.

When I use both DOI and PMID, both are visible in the reference output, but
when I use only PMID, it is not visible.

In the following picture, there are both IDs in ref1 and both are visible, only PMID in ref2 and is not visible, only doi in ref3 and is visible, again only PMID in ref4 and not visible.

My xml code is as below (one block each for ref1 up to ref4):

<pub-id pub-id-type="doi">10.1097/01.aog.0000298621.98372.62</pub-id>
<pub-id pub-id-type="pmid">18165410</pub-id>


<pub-id pub-id-type="pmid">19947030</pub-id>


<pub-id pub-id-type="doi">10.1136/bcr-2013-203131</pub-id>


<pub-id pub-id-type="pmid">17099802</pub-id>

Am I doing something wrong in xml code?

Regards,
@anupent

varshilmehta · November 20, 2017, 7:06am

Try putting the entire PubMed link (https://www.ncbi.nlm.nih.gov/pubmed/21811022) instead of the id in the word file and see whether it works or not.

Like I have <pub-id pub-id-type="pmid">https://www.ncbi.nlm.nih.gov/pubmed/21811022</pub-id> in my XML.

Vitaliy · November 20, 2017, 7:09am

Hi @anupent,

And with this fix?:

varshilmehta · November 20, 2017, 7:13am

It works for me even without applying the patch as well and I am not sure why, lol. https://jmri.org.in/jmri/article/view/e000095#bib8

anupent · November 20, 2017, 7:24am

This fix alone did not work for me. I do get PMID if there is DOI just before that. But I do not get PMID if it is alone.

Will try with @varshilmehta’s full link advice and report the result.

Regards,

Vitaliy · November 20, 2017, 7:43am

Hmm, interesting…
Can you open an issue on a plugin’s GitHub page?

Vitaliy · November 20, 2017, 7:49am

Also, have found typo:

anupent · November 20, 2017, 7:52am

Thanks @Vitaliy,
Now I do get PMID even if it is alone. (after the typo fix)

@varshilmehta, you can apply fix then use only PMID instead of full link.

Regards.

varshilmehta · November 20, 2017, 8:31am

I had modified this file long back. Dont even have the entire sentence in my file. Hence it was working for me i guess without any fix.

varshilmehta · November 20, 2017, 9:57am

All the RSS/Atoms feeds are now disturbed. https://jmri.org.in/jmri/gateway/plugin/WebFeedGatewayPlugin/atom
Is there any way we can work around with it?

Vitaliy · November 20, 2017, 1:10pm

Don’t know
JATS Parser plugin certainly should not have any interactions with other OJS plugins.

varshilmehta · November 20, 2017, 1:12pm

Its browse plugin and not jatsparser

Vitaliy · November 20, 2017, 1:17pm

Theoretically, they can interact. They are using the same hook:

github.com

Vitaliy-1/browsePlugin/blob/master/BrowsePlugin.inc.php#L44


 * 	the plugin will not be registered.
 */
function register($category, $path) {
    $success = parent::register($category, $path);
    if (!Config::getVar('general', 'installed') || defined('RUNNING_UPGRADE')) return true;
    if ($success && $this->getEnabled()) {

        HookRegistry::register('Templates::Index::journal', array($this, 'browseLatest'), HOOK_SEQUENCE_NORMAL);

        // Add stylesheet and javascript
        HookRegistry::register('TemplateManager::display',array($this, 'displayCallback'));

    }
    return $success;
}

function displayCallback($hookName, $params) {
    $template = $params[1];
    $output =& $params[2];

    if ($template != 'frontend/pages/indexJournal.tpl') return false;

github.com

pkp/ojs/blob/main/plugins/generic/webFeed/WebFeedPlugin.inc.php#L38


 * @return string
 */
public function getDisplayName()
{
    return __('plugins.generic.webfeed.displayName');
}

/**
 * Get the description of this plugin
 *
 * @return string
 */
public function getDescription()
{
    return __('plugins.generic.webfeed.description');
}

/**
 * @copydoc Plugin::register()
 *
 * @param null|mixed $mainContextId

You can play around with hook priorities. Take a look at this thread: Making a plugin for OJS3 - #26 by asmecher

It’s quite easy. Let me know the results.

Vitaliy · November 20, 2017, 1:24pm

But, practically, I don’t see any problems there. Is it not rendered, how it should?