Lens Troubles

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Juan Pablo Pazmin Sevillano

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Apr 24, 2014, 12:51:45 PM4/24/14
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Dear all, 

I have downloaded the Lens prj from https://github.com/elifesciences/lens. also have the lens
converter https://github.com/elifesciences/lens-converter. as far as I understand this lens converter takes an
XML and transforms it into something, an NLM format file, that Lens
can understand and process -load it in the LENS interface. I am having
problems with this transformation. starting with, how to load the file
to be transformed? can anyone point me to examples as to how to use
the lens converter? So far I am lost with this, have no idea where to
start.

Thanks in advance

Ivan Grubisic

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Apr 24, 2014, 12:54:13 PM4/24/14
to Juan Pablo Pazmin Sevillano, elife...@googlegroups.com
The lens-converter needs to take a NLM formatted XML file. The simplest way is to get the Lens server running locally, open Chrome and then drag and drop the XML file into it. If you have an XML file that is in another format, that would take some thinking about how to convert it into NLM. 

Are you still working with scientific literature or another content type?

Thanks,
Ivan


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Michael Aufreiter

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Apr 24, 2014, 5:23:24 PM4/24/14
to Ivan Grubisic, Juan Pablo Pazmin Sevillano, elife...@googlegroups.com
You can just download the official 1.0.0 release here…


then you can adapt the index.html to point to your own NLM-XML.

Please note that you need to access the page through a static webserver… e.g. on osx you can do:

python -m SimpleHTTPServer

then point your browser to http://localhost:8000

Good luck, Michael

Michael Aufreiter

Lachlan Coin

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Feb 10, 2015, 8:06:19 PM2/10/15
to elife...@googlegroups.com, juanpa...@gmail.com
Hi,

I have started playing with lens and have found it difficult to get a correctly formatted xml file.  I use meTypeSet to convert a word document to a nlm xml file . meTypeSet runs fine and generates the xml file, but I can't get lens to load it.

I was wondering if there was a lens error log during the conversion process which might help me figure out what is wrong with the xml file I generated (nothing is displayed on the console).


Thanks!

Ivan Grubisic

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Feb 11, 2015, 9:22:05 PM2/11/15
to Lachlan Coin, elife...@googlegroups.com, juanpa...@gmail.com

Hey Lachlan,

In my experience the best thing was to do a 1:1 comparison of the XML files with respect to attributes, hierarchy, etc. If you build custom conversions for every type then you could also have print statements come into the console. If you have an example someone might be able to have a look and help you out.

Thanks,
Ivan

Lachlan Coin

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Feb 12, 2015, 12:25:27 AM2/12/15
to Ivan Grubisic, elife...@googlegroups.com, juanpa...@gmail.com
Thanks Ivan, yeah have basically done that now  I used a jats xml verifier and style checker to check the xml was valid (with a few changes it was) and even then it didn't render, but I was able to figure out which tags I needed to add to get it to render by comparison to your examples.

Thanks for the quick reply

Lachlan
--
Group leader, Institute for Molecular Bioscience, University of Queensland
Senior Lecturer, Imperial College

Ivan Grubisic

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Feb 12, 2015, 12:00:15 PM2/12/15
to Lachlan Coin, elife...@googlegroups.com, juanpa...@gmail.com

Glad to hear it. If your adaption of lens is for public consumption it would be great to see how you are using it.

Thanks,
Ivan

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