JATS Parser v2.0: JATS XML to HTML and PDF conversion

jats
#44

JATS Parser plugin version 2.0.1 is released. It’s a compatibility release for OJS 3.1.2: https://github.com/Vitaliy-1/JATSParserPlugin/releases/tag/2.0.1

#45

Hi @GabeLon

I’ve fixed this problem for a new release. But it’s only for OJS 3.1.2.

#46

Hi, but the pdf conversion in not yet working. It shows a HTTP ERROR 500. On health science theme and 3.1.2 OJS

Error log:

> [24-Mar-2019 06:38:41 UTC] PHP Warning:  Declaration of SubmissionKeywordEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL) should be compatible with ControlledVocabEntryDAO::getByControlledVocabId($controlledVocabId, $rangeInfo = NULL, $filter = NULL) in /home/u796555399/public_html/journals/jcrs/lib/pkp/classes/submission/SubmissionKeywordEntryDAO.inc.php on line 20
> [24-Mar-2019 06:38:41 UTC] PHP Warning:  require_once(/home/u796555399/public_html/journals/jcrs/plugins/generic/jatsParser/JATSParser/src/JATSParser/PDF/../../../vendor/tecnickcom/tcpdf/tcpdf.php): failed to open stream: No such file or directory in /home/u796555399/public_html/journals/jcrs/plugins/generic/jatsParser/JATSParser/src/JATSParser/PDF/TCPDFDocument.php on line 5
> [24-Mar-2019 06:38:41 UTC] PHP Fatal error:  require_once(): Failed opening required '/home/u796555399/public_html/journals/jcrs/plugins/generic/jatsParser/JATSParser/src/JATSParser/PDF/../../../vendor/tecnickcom/tcpdf/tcpdf.php' (include_path='.:/home/u796555399/public_html/journals/jcrs/classes:/home/u796555399/public_html/journals/jcrs/pages:/home/u796555399/public_html/journals/jcrs/lib/pkp:/home/u796555399/public_html/journals/jcrs/lib/pkp/classes:/home/u796555399/public_html/journals/jcrs/lib/pkp/pages:/home/u796555399/public_html/journals/jcrs/lib/pkp/lib/adodb:.:/opt/alt/php71/usr/share/pear') in /home/u796555399/public_html/journals/jcrs/plugins/generic/jatsParser/JATSParser/src/JATSParser/PDF/TCPDFDocument.php on line 5
1 Like
#48

Hi @Vitaliy,
I installed the parser but then I do not open the plugin window anymore, use OJS 3.1.1.4. I always see the wheel that turns loading.

53

How can fix?

Thanks
Best!

Tiziano

#49

Hi @Tiziano,

What release are you using? Keep in mind that the latest release (or master branch) is compatible only with OJS 3.1.2.

#50

Hi @Vitaliy,
i downloaded this version:

44

and my OJS version is 3.1.1.4.

#51

Hmm, can you review the error log for errors or fatal errors?

#52

Hi @varshilmehta,

Sorry for the delay. This problem was simply related to packing the release. Can you test this new one? https://github.com/Vitaliy-1/JATSParserPlugin/releases/tag/2.0.1.1

1 Like
#53

Hi @Vitaliy, works great en 3.1.2!
Awesome work.
Many thanks!!

1 Like
#55

It works now. Thanks a ton.

#58

Hi @Vitaliy, now my JATS Parser works with my XML, at the beginning it didn’t read images and tables, but if I move them from the bottom of the XML file to the middle of the code, where they are mentioned, they are displayed.

I would report two things: the first is that the link <xref ref-type="fig" rid="fig001">Figure 1</xref> does not work and I can not understand why, the second is that when I click on the PDF to convert it, I return this error:

TCPDF ERROR: [Image] Unable to get the size of the image: https://audiologyresearch.org/index.php/audio/article/download/214/252/2042

is there any way to correct these errors?
Thanks!

Bye
Tiziano

#59

Hi @Tiziano,

Not sure why the link isn’t working. Looks correct to me. Regarding the image, it’s possible that 1) TCPDF library doesn’t support the image’s format for some reason or is failing to find/upload it. Can you send me this XML and images?

#60

Hi @Vitaliy,
thanks for your help, now i send you XML and images.

Bye!
Tiziano

#61

Hi @Tiziano,

Yes, I can confirm that links for figures and tables don’t work and I’ll make a fix for that.

Regarding conversion to PDF, all works fine on my OJS instance with your example. In my opinion, the error means from TCPDF means that there is a problem with accessing that image, for some reason; or the PHP library that helps to perform this action (detemine the image size) is missing. The latter is unlikely because TCPDF relies only on standard libraries and the former is unlikely because the path is correct and is accessible. So I have no idea.
Actually, check this answer on StackOverflow: https://stackoverflow.com/a/28007106/6711224

#62

Hi @Vitaliy,
I update you on the PDF problem, I installed the latest version of OldGreg template with the JATSParser and PDF Parsing, great thing this for us! It works, but I’ll tell you that, the link <xref ref-type="fig" rid="fig001">Figure 1</xref> does not work, and now process the PDF correctly and view the table, but not the figures and as in the display of HTML do not work links. I hope I’ve made myself clear. :smile:

Best regards
Bye
Tiziano