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[EP-tech] Antwort: Re: Antwort: Re: perl module update introduced some trouble with entities

Subject: [EP-tech] Antwort: Re: Antwort: Re: perl module update introduced some trouble with entities
From: drn at ecs.soton.ac.uk (David R Newman)
Date: Tue, 1 Dec 2020 17:21:08 +0000
In-reply-to: <5bbc265f-380f-20ab-b8f1-017315937acf@soton.ac.uk>
References: <20180830161544.0B998135D797@localhost> <84842409.399790.1605633809226@mail.vodafone.de> <880575761.176288.1606824032406@mail.vodafone.de> <880575761.176288.1606824032406@mail.vodafone.de> <EMEW3|d1ddd336236de133ca0033c05ce15024wB0C1p14eprints-tech-bounces|ecs.soton.ac.uk|880575761.176288.1606824032406@mail.vodafone.de> <948755b7-8823-8107-bc5c-8dd82a384a4d@ecs.soton.ac.uk> <EMEW3|23ce7e0c6cad94cb5dc6b1063adbdc5dwB0DLG03drn|ecs.soton.ac.uk|948755b7-8823-8107-bc5c-8dd82a384a4d@ecs.soton.ac.uk> <OF9927B075.76D5BD1D-ONC1258631.004A5761-C1258631.004AA3E1@lotus.uzh.ch> <c6c10e6d-f0d1-b7f8-3cd6-77cfb63768cb@ecs.soton.ac.uk> <OF8026049F.8CAB393B-ONC1258631.004F190F-C1258631.004F4CA6@lotus.uzh.ch> <e0bba1ea-30f9-4b41-d327-d44906234ab1@ecs.soton.ac.uk> <EMEW3|64bc7f3151898ec58662b8bcc449fc8awB0EpM03drn|ecs.soton.ac.uk|e0bba1ea-30f9-4b41-d327-d44906234ab1@ecs.soton.ac.uk> <5bbc265f-380f-20ab-b8f1-017315937acf@soton.ac.uk> <9515c7c2-8f76-7708-9e75-a16ad2226bb5@ecs.soton.ac.uk>

Hi all,

I think what was catching me out is that "epadmin test" will pick up 
genuine issues with entities that are not defined but I was not using 
the correct incantations with xmllint when I was using this to test 
individual XML files.? The special incantation you need is:

xmllint --path /opt/eprints3/lib/ --loaddtd 
/opt/eprints3/flavours/pub_lib/lang/en/templates/default.xml --noout

If this produces no output them your XML is valid based on the DTDs it 
specifies to load. E.g. the following line in an XML file:

<!DOCTYPE html SYSTEM "entities.dtd">

So for future reference if you see an error like the one Thomas 
originally described ( 
/usr/share/eprints/site_lib/lang/en/phrases/modified.xml: Entity: line 
226: parser error : Entity 'auml' not defined ), then:

1. Check XML file references "entities.dtd" in a <!DOCTYPE after the 
<?xml line.

2. Check that EPRINTS_PATH/lib/entities.dtd is present.

3. Check that the entity that the error message says is not defined is 
present in EPRINTS_PATH/lib/entities.dtd. If not, this entity may have 
been typo-ed.

4. Check that xmllint validates the file that error mesage complains 
about using the --path, --loaddtd and --noout switches (e.g. the line 
below should produce no output if valid):

 ??? xmllint --path /usr/share/eprints/lib/ --loaddtd 
/opt/eprints3/flavours/pub_lib/lang/en/templates/default.xml 
/usr/share/eprints/site_lib/lang/en/phrases/modified.xml --noout

5. If (4) shows the XML file to be valid. Check which version of LibXML 
you have installed and if it is 2.0201+ then apply the appropriate patch 
from:

EPrints 3.3 - https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints%2Fissues%2F511&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=J66DlDwElebvMqlSwin%2FHRIxS7Wq1WeIru%2FSkT8rctw%3D&amp;reserved=0

EPrints 3.4 - https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints3.4%2Fissues%2F41&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=iKZTfky7LhMRgefYcgcswihZF%2FAbgsEn8joBM%2BifTqM%3D&amp;reserved=0

If anyone is still having XML validation issues after this, we will have 
a new problem on our hands but hopefully that won't come to pass.

Regards

David Newman

On 01/12/2020 15:07, Christopher Gutteridge wrote:
>
> This was a bit of a fiddle to make it possible to do things like 
> &pound; &eacute; etc.? to make people's lives a little easier when 
> writing the templates which are XHTML.
>
> The obvious other approach would be to preprocess them with something 
> like this
>
> s/&([a-z]+);/expandentitiy($1)/ge
>
> but that would break with the wisdom that you should never parse XML 
> with a regular expression.
>
>
> On 01/12/2020 14:37, David R Newman via Eprints-tech wrote:
>>
>> Hi all,
>>
>> I have been blind.? EPrints (at least latest 3.4) already has an 
>> entities.dtd in lib/ and is already used in most of the standard XML 
>> template, phrase, etc. files.? I think the problem is that it does 
>> not link in properly in most if not all cases.? So I will investigate 
>> how that can be done better to avoid encountering undefined entities 
>> errors.
>>
>> Regards
>>
>> David Newman
>>
>> On 01/12/2020 14:26, martin.braendle at uzh.ch wrote:
>>> *CAUTION:* This e-mail originated outside the University of 
>>> Southampton.
>>>
>>> The entities file we have here has the following preamble
>>>
>>> <!-- Portions (C) International Organization for Standardization 1986
>>> ? ? ?Permission to copy in any form is granted for use with
>>> ? ? ?conforming SGML systems and applications as defined in
>>> ? ? ?ISO 8879, provided this notice is included in all copies.
>>> -->
>>>
>>> and contains more than 500 lines.
>>>
>>> It stems most probably from here: 
>>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.w3.org%2FTR%2FREC-html40-971218%2Fsgml%2Fentities.html&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=iu9eTMSmbCBkDIDwy8lptFDR828z3A4ykpTc0d19daw%3D&amp;reserved=0 
>>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.w3.org%2FTR%2FREC-html40-971218%2Fsgml%2Fentities.html&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=iu9eTMSmbCBkDIDwy8lptFDR828z3A4ykpTc0d19daw%3D&amp;reserved=0>
>>>
>>> Kind regards,
>>>
>>> Martin
>>>
>>> --
>>> Dr. Martin Br?ndle
>>> Zentrale Informatik
>>> Universit?t Z?rich
>>> Stampfenbachstr. 73
>>> CH-8006 Z?rich
>>>
>>> Inactive hide details for "David R Newman" ---01/12/2020 
>>> 15:19:06---Hi all, EPrints 3.4 has has the patch applied for issues 
>>> wi"David R Newman" ---01/12/2020 15:19:06---Hi all, EPrints 3.4 has 
>>> has the patch applied for issues with newer versions of
>>>
>>> Von: "David R Newman" <drn at ecs.soton.ac.uk>
>>> An: eprints-tech at ecs.soton.ac.uk
>>> Kopie: th.lauke at arcor.de, martin.braendle at uzh.ch
>>> Datum: 01/12/2020 15:19
>>> Betreff: Re: Antwort: Re: [EP-tech] perl module update introduced 
>>> some trouble with entities
>>>
>>> ------------------------------------------------------------------------
>>>
>>>
>>>
>>> Hi all,
>>>
>>> EPrints 3.4 has has the patch applied for issues with newer versions 
>>> of LibXML and EPrints 3.4.2 onwards should have this particular 
>>> issue resolved. ?Regarding special characters, I will look into 
>>> producing (or hopefully finding) an entities.dtd for all the special 
>>> characters that EPrints repositories may want use and then update 
>>> standard template and phrase files to use this. ?In fact it is 
>>> probably even worth doing this for citation and workflow files as 
>>> well. ?I have created an issue for EPrints 3.4 to address this:
>>>
>>> _https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints3.4%2Fissues%2F112_&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=H%2FMWdWok6CibcXpjPZkMB4t4XHcMuULop51jDsNEA7g%3D&amp;reserved=0 
>>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feprints%2Feprints3.4%2Fissues%2F112&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703639912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=qXBze6oepInLS3ehJTUqk9kD29jlWUS1HXzcXsySuX8%3D&amp;reserved=0> 
>>>
>>>
>>> Regards
>>>
>>> David Newman
>>>
>>> On 01/12/2020 13:35, _martin.braendle at uzh.ch_ 
>>> <mailto:martin.braendle at uzh.ch>?wrote:
>>>
>>>     *CAUTION:*?This e-mail originated outside the University of
>>>     Southampton.
>>>
>>>     Hi Thomas,
>>>
>>>     there should be ?an entities.dtd file in [eprints_root]/lib/,
>>>     maybe this is missing or entries are missing in it?
>>>
>>>     Also a phrase file should mention that in the
>>>
>>>     <!DOCTYPE phrases SYSTEM "entities.dtd">
>>>
>>>     definition right at the beginning after the XML declaration.
>>>
>>>     Kind regards,
>>>
>>>     Martin
>>>
>>>     --
>>>     Dr. Martin Br?ndle
>>>     Zentrale Informatik
>>>     Universit?t Z?rich
>>>     Stampfenbachstr. 73
>>>     CH-8006 Z?rich
>>>
>>>
>>>     Inactive hide details for "David R Newman via Eprints-tech"
>>>     ---01/12/2020 14:24:14---Hi Thomas, Named HTML entities are not
>>>     sup"David R Newman via Eprints-tech" ---01/12/2020 14:24:14---Hi
>>>     Thomas, Named HTML entities are not supported in XML you need to
>>>     use the decimal
>>>
>>>     Von: "David R Newman via Eprints-tech"
>>>     _<eprints-tech at ecs.soton.ac.uk>_
>>>     <mailto:eprints-tech at ecs.soton.ac.uk>
>>>     An: _<eprints-tech at ecs.soton.ac.uk>_
>>>     <mailto:eprints-tech at ecs.soton.ac.uk>, _<th.lauke at arcor.de>_
>>>     <mailto:th.lauke at arcor.de>
>>>     Datum: 01/12/2020 14:24
>>>     Betreff: Re: [EP-tech] perl module update introduced some
>>>     trouble with entities
>>>     Gesendet von: _<eprints-tech-bounces at ecs.soton.ac.uk>_
>>>     <mailto:eprints-tech-bounces at ecs.soton.ac.uk>
>>>
>>>     ------------------------------------------------------------------------
>>>
>>>
>>>
>>>     Hi Thomas,
>>>
>>>     Named HTML entities are not supported in XML you need to use the
>>>     decimal code XML entity for &auml; which is &#228;
>>>
>>>     This is the same as needing to replace things like &amp; and
>>>     &copy; with their equivalent decimal code XML entities.
>>>
>>>     Regards
>>>
>>>     David Newman
>>>
>>>     On 01/12/2020 12:00, th.lauke--- via Eprints-tech wrote:
>>>
>>>
>>>     CAUTION: This e-mail originated outside the University of
>>>     Southampton.
>>>
>>>     Hi all,
>>>
>>>     any hint where to start digging for reason(s) after following error:
>>>     Failed to parse XML file:
>>>     /usr/share/eprints/site_lib/lang/en/phrases/modified.xml:
>>>     Entity: line 226: parser error : Entity 'auml' not defined
>>>
>>>     This error occurs after updating some perl modules ... :(
>>>
>>>     Is the 'bad' module already known?
>>>     What is more effective: Fixing the module (version) or the
>>>     phrase file?
>>>
>>>     Thanks for any idea in advance
>>>     Thomas
>>>
>>>     *** Options:
>>>     _http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech_
>>>     <http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech>
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>>>     <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.eprints.org%2F&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703649868%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=vKTiKjQemQzdGEpr7mp0ANoad2tDUoJNBgQLisU6okw%3D&amp;reserved=0>
>>>
>>>     	
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>>>
>>>     *** Options:
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>>>     *** Archive: _https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eprints.org%2Ftech.php%2F_&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703649868%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=aU2TwKKNpsPDprWiEycl0QFCp5JDgHMz419yItTYbIo%3D&amp;reserved=0
>>>     <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.eprints.org%2Ftech.php%2F&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703649868%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=97Q6PxoacGfFw9PwHuWpj4DnRvcVRXo%2FPemNMcDanPg%3D&amp;reserved=0>
>>>     *** EPrints community wiki: _https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.eprints.org%2F_&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703649868%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=q5jvyoAf8E1JkL4c32ngp5Sj%2F%2BqKTQdZQnnSoOKjscY%3D&amp;reserved=0
>>>     <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.eprints.org%2F&amp;data=04%7C01%7C%7C759fb7c1aaa14d9bbfef08d8961d7e77%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C637424400703649868%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=vKTiKjQemQzdGEpr7mp0ANoad2tDUoJNBgQLisU6okw%3D&amp;reserved=0>
>>>
>>> 	
>>>
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>>>
>>>
>>>
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> -- 
> Christopher Gutteridge<totl at soton.ac.uk>  
> You should read our team blog athttp://blog.soton.ac.uk/webteam/


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References:
- [EP-tech] misconfigured or failed upgrade to 3.4.1?
  - From: th.lauke at arcor.de (th.lauke at arcor.de)
- [EP-tech] perl module update introduced some trouble with entities
  - From: th.lauke at arcor.de (th.lauke at arcor.de)
- [EP-tech] perl module update introduced some trouble with entities
  - From: drn at ecs.soton.ac.uk (David R Newman)
- [EP-tech] Antwort: Re: perl module update introduced some trouble with entities
  - From: martin.braendle at uzh.ch (martin.braendle at uzh.ch)
- [EP-tech] Antwort: Re: Antwort: Re: perl module update introduced some trouble with entities
  - From: martin.braendle at uzh.ch (martin.braendle at uzh.ch)
- [EP-tech] Antwort: Re: Antwort: Re: perl module update introduced some trouble with entities
  - From: drn at ecs.soton.ac.uk (David R Newman)
- [EP-tech] Antwort: Re: Antwort: Re: perl module update introduced some trouble with entities
  - From: totl at soton.ac.uk (Christopher Gutteridge)

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