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Re: [EP-tech] indexing full text document pdf with tag get empty word in eprint__rindex table

Hi Mario,

I was looking at this a bit further and although I am more confident that the fix I suggested should work an allows you to apply it at an archive level rather than needing to change core code.  It will exclude the characters that could not be recognised from being indexed and potentially other characters that could be indexed.  What I observed was that the problematic strings in the document I reviewed all seemed to be mathematical alphanumeric symbols in specific font-styles (i.e. 0x1df400 to 0x1df7ff [1]).  These can all be mapped to characters that can be indexed.  So I have spent some time writing these mappings for the GitHub issue I created [2].  You could try downloading the latest version of perl_lib/EPrints/Index/Tokenkizer.pm [3] and replace your existing one in your core codebase.  I don't think these changes or any changes since 3.4.3 should be incompatible with 3.4.3.  However, as I said in my earlier email, you will need to make sure you restart your indexer and also click on the "Reindex Item" under the Actions tab for affected eprint records.  As re-indexing from the command line does not regenerate indexcodes files.

It is likely that there will be other characters that are in the extended (4-byte) Unicode planes (i.e. outside the Basic Multilingual Plane (BMP)), which could be used in publications and lead to an issue.  I think the long term solution would be to move EPrints to using utf8mb4 for its database character set rather than using the 3-byte utf8 character set.  Changes required to make new EPrints repositories use utf8mb4 would be relatively straightforward the major task would be facilitating existing repositories converting to utf8mb4.  This has already been logged as a task (issue) for EPrints 3.5 [3].  As it was realised quite early on that changing to utf8mb4 was not something that should be tackled as part of a minor version release.

Regards

David Newman

[1] https://en.wikibooks.org/wiki/Unicode/Character_reference/1D000-1DFFF
[2] https://github.com/eprints/eprints3.4/issues/320
[3] https://github.com/eprints/eprints3.4/blob/master/perl_lib/EPrints/Index/Tokenizer.pm
[3] https://github.com/eprints/eprints3.4/issues/140

On 06/04/2023 12:30 pm, David R Newman via Eprints-tech wrote:
Hi Mario,

I think I may have a solution to your problem.  What you need to do is edit you archive's cfg/cfg.d/indexing.pl and add the following block of code:

        if( $word =~ m/[^\x20-\xEF]/ )
        {
            $ok=0;
        }

If you put this after the block of code like this:

        if( $word =~ m/^[A-Z][A-Z0-9]+$/ )
        {
            $ok=1;
        }

If you do not have a cfg/cfg.d/indexing.pl in your archive copy the one in lib/cfg.d/ to your archive and then edit this copy.  Once you have finished editing make sure you restart the indexer and probably best to reload the webserver as well.  Oddly, if you try to  run "epadmin reindex" for this eprint from the command line it won't work, as it will reuse the existing indexcodes.txt file that has the offending strings.  However, if you click in the "Reindex Item" under the "Actions" tab of the eprint item it should regenerate the indexcodes.txt file.  I am going to look into whether this can be added as a feature to epadmin.  At present epadmin has the option "erase_fulltext_index" but this will cause all your indexcodes.txt files to be regenerated and all eprint items to be reindexed.

The aim of this code is to avoid strings like '𝑒𝑥𝑝' attempting to be indexed.  As these will fail due to MySQL ignoring certain characters and then trying to insert empty string into the eprint__rindex table, when there is already an entry for empty string, probably due to a previous string that had non-standard characters being saved as an empty string.  The way that the SQL queries are written to insert multiple entries at once into the eprint__rindex table means that if one entry fails then the remaining entries never get attempted. 

With this block of code it should not allow any strings into the indexcodes.txt that would break the inserts into the eprint__rindex table.  However, I am not yet confident this is the best regular _expression_ to use, as it may disqualify perfectly legitimate strings.  However, it looks like all printable ASCII characters are allowed as well as various non-English characters that may be used both Latin alphabet languages (French, German, Spanish, Italian, etc.) and non-Latin alphabet Languages (Chinese, Japanese, Korean and Cyrillic-based).  I am not sure if ultimately some of the non-Latin characters strings will get indexed but they will be added to the indexcodes.txt files, which is all that the block of code should directly affect.

Regards

David Newman

On 05/04/2023 11:16 pm, David R Newman wrote:
Hi Mario,

I managed to find you document with a bit of detective work.  I found the query causing the duplicate error line was:

INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES ('75','documents','𝑒𝑥𝑝')

The '𝑒𝑥𝑝' is special characters that do not get recognised by MySQL and therefore MySQL treats this as an empty string, which it cannot insert as there is already an empty string.  The first insert of any empty string was this:

INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES ('75','documents','')

It looks like virtually every document tries to insert an eprint__rindex record for empty string.  So there are two problems to look at:

1. Why does EPrints bother trying to index an empty string?
2. Why can't MySQL interpret special characters and treat them as missing?

I suspect the latter is down to character encoding.  If that is the case EPrints could try to check whether the special characters will not be writeable to the database.  However, I am not sure how easy it would be to do this and whether it would add significant effort to the indexing process.  The first thing to do would be to make sure that any SQL commands that lead to an error to not stop any further indexing of terms.  I think that fix should be a lot more straightforward.  I have created a general GitHub issue for investigating this:

https://github.com/eprints/eprints3.4/issues/320

Regards

David Newman

On 05/04/2023 9:26 pm, David R Newman via Eprints-tech wrote:
Hi Mario,

I have never seen empty words indexed but I have seen the Duplicate entry error message you reported.  If you would be happy to share the PDF for your eprint 75 with me (drn@ecs.soton.ac.uk), that would be really useful as that would give a reliable test case.  I will only upload it to my EPrints development repository, which is not publicly accessible.

My suspicion is that the word may not initially be empty but contains a character that cannot be stored in the database, so when the eprint__rindex record is inserted the word becomes empty.  Words to be indexed from a PDF are extracted by the Unix tool pdftotext.  You could try running pdftotext against your PDF and see if the output gives you any clues to why an empty word is being indexed.  Index codes may contain words that are not indexed for a number of reasons.  They may be stop words, the word may be too short (I know in some case two character words are not index) or as I said before they have special characters that causes and issue when trying to add to the eprint__rindex database table.  However, you may be right that something fails and then prevents all further indexing of that document.

One thing you can do is temporarily run a MySQL query log for all queries (Adding config to /etc/my.cnf.d temporarily and restarting MySQL) and then try running epadmin reindex.  There will be quite a lot of output but it may tell you something useful.

Regards

David Newman

On 05/04/2023 8:45 pm, Beaudoin, Mario via Eprints-tech wrote:
CAUTION: This e-mail originated outside the University of Southampton.

Hello,

 

We use eprints 3.4.3 and  14 repositories with a lot of pdf on each and we have an indexing bug with tagged PDF.

All the eprint__rindex tables with theses PDF got an empty “word”.  They index only some documents word not all.

The sql command give to me all the bugged PDF

select * from eprint__rindex where word='';

 

The reindex of these eprint makes an error

./epadmin reindex eprints_fra1 --verbose eprint 75;

DBD::mysql::st execute failed: Duplicate entry 'documents--75' for key 'PRIMARY' at /opt/eprints3/bin/../perl_lib/EPrints/Database.pm line 1289.

 

I try to modify the file indexing.pl but they already include bypass empty word.

 

I check the indexcodes.txt for this document and it is complete with a lot of words not include in the database eprint__rindex

 

I download another PDF document for these eprints not tagged reindex the document with no error.

 

I think that epadmin reindex  got some empty word and stop to index soon as it got another empty word because it indexes some words but not all. The double –verbose of the function gives that.

 

[eprints_fra1] Database execute debug: SELECT `eprintid`,`pos`,`projects` FROM `eprint_projects` WHERE `eprintid` IN (75)

Database execute debug: SELECT `eprintid`,`pos`,`skill_areas` FROM `eprint_skill_areas` WHERE `eprintid` IN (75)

[eprints_fra1] Database execute debug: SELECT `eprintid`,`pos`,`skill_areas` FROM `eprint_skill_areas` WHERE `eprintid` IN (75)

Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)

[eprints_fra1] Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)

DBD::mysql::st execute failed: Duplicate entry 'documents--75' for key 'PRIMARY' at /opt/eprints3/bin/../perl_lib/EPrints/Database.pm line 1289.

Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)

[eprints_fra1] Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)

Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)

[eprints_fra1] Database execute debug: INSERT INTO `eprint__index_grep` (`eprintid`,`fieldname`,`grepstring`) VALUES (?,?,?)

Database execute debug: INSERT INTO `eprint__rindex` (`eprintid`,`field`,`word`) VALUES (?,?,?)

 

I notice that if we take the bugged .pdf to .PS and convert to .pdf it work fine but it’s not a solution for us

 

Thank you for your help

 

Mario


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