Reference code separator

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Ricardo Pinho

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Jul 22, 2018, 2:36:32 PM7/22/18
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Hello,

We are using AtoM version 2.4.0-156 on Ubuntu server 16.04.
And would appreciate some help on changing the separator character inside the reference code with "Inherit reference code (information object)" option activated, as documented here:

1. When we change the Admin > Settings >  Global > Reference code separator to "/"
The search result page: "index.php/informationobject/browse?topLod=0" still shows the reference codes with the default "-" separator.
For example it shows:
"PT AMOA APUB-CMOA-004-004.1-017"
Instead of what is display after we click on it:
"PT AMOA APUB/CMOA/004/004.1/017"
Why does this happens?

2. In my country (Portugal) we use the same separator for Country and Repository identifiers, not the space character.
In AtoM the reference code separator is not used for country and repository identifiers. When we change it to "/" the reference code keeps "space" separator for those identifiers and "/" for the rest. For example:
"PT AMOA APUB/CMOA/004/004.1/017"
And we need this result:
"PT/AMOA/APUB/CMOA/004/004.1/017"
Is there any way to achieve this? 

Thank you in advance!
Best regards,
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Ricardo Pinho

Dan Gillean

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Jul 30, 2018, 10:39:44 AM7/30/18
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Hello Ricardo, 

Regarding your first question, it sounds like you may need to repopulate the search index, and clear the various caches. You might also try clearing your browser cache first to see if that helps. Otherwise, repopulate the search index, clear the application cache, and restart PHP-FPM and memcached (which also have their own caches) and this should be resolved. 

One other thing to mention: the slash / is a reserved character in Elasticsearch, so to avoid getting an error every time you include one slash in a reference code search, you might also want to add the slash to the "Escape special characters" setting. See: 
Regarding 2: unfortunately there is no way to do this in AtoM currently without development. We followed the ICA's recommendations when originally implementing this, and currently the reference code separator is only used to compile the individual identifiers. You will need to study the code and make local changes to achieve the result you want. 

Regards, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Ricardo Pinho

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Jul 30, 2018, 12:14:01 PM7/30/18
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Dear Dan, thank you for the answer!

> Regarding 1:  it sounds like you may need to repopulate the search index, and clear the various caches

I've done all this and the problem remains:
sudo service php7.0-fpm restart
sudo service memcached restart
cd /usr/share/nginx/atom
sudo php symfony cc
sudo php symfony search:populate

Is there any other cache we need to clear?
I really think this is a code problem, something on some search result php file. But still haven't found it.


> Regarding 2: unfortunately there is no way to do this in AtoM currently without development.
>  You will need to study the code and make local changes to achieve the result you want. 

I've already did. 
Here is a possible solution for using the settings separator as a unique reference code separator! (I think in FR also use it like us PT)

#Before:

   $identifier = implode(sfConfig::get('app_separator_character', '-'), $identifier);
    if ($includeRepoAndCountry)
    {
      if (isset($repository->identifier))
      {
        $identifier = "$repository->identifier $identifier"; 
      }

      if (isset($repository))
      {
        $countryCode = $repository->getCountryCode();

        if (isset($countryCode))
        {
          $identifier = "$countryCode $identifier"; 
        }
      }
    }
    return $identifier;

# After

// $identifier = implode(sfConfig::get('app_separator_character', '-'), $identifier);
    if ($includeRepoAndCountry)
    {
      if (isset($repository->identifier))
      {
        array_unshift($identifier,$repository->identifier);
      }

      if (isset($repository))
      {
        $countryCode = $repository->getCountryCode();

        if (isset($countryCode))
        {
          array_unshift($identifier,$countryCode);
        }
      }
    }
    $identifier = implode(sfConfig::get('app_separator_character', '-'), $identifier);
    return $identifier;

Other sugestions are welcome!
Best regards,
Ricardo Pinho




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Ricardo Pinho

Dan Gillean

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Jul 30, 2018, 3:55:41 PM7/30/18
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Hi Gregory, 

No, there is no other cache - except the one in your web browser, so remember to check that as well! 

Perhaps you could try manually deleting the search index, and then repopulating it. Note that you will need curl installed for this: 
  • sudo apt-get install curl      # if the curl command isn't currently installed
  • curl -XDELETE 'localhost:9200/atom'
You could then try stopping and restarting the ES service, before running the search:populate command again - you should be able to use the following commands on Ubuntu 16.04: 
  • sudo systemctl stop elasticsearch
  • sudo systemctl enable elasticsearch
  • sudo systemctl start elasticsearch
After restarting, try the search:populate command again: 
  • php symfony search:populate
If it still doesn't work, then yes, it is possible you have found a bug. Let me know and I will try to reproduce it locally. 

Otherwise, thank you so much for sharing the changes that you've made to be able to add the separator to the country and repository code! 

Cheers, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Ricardo Pinho

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Jul 31, 2018, 7:28:19 AM7/31/18
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Hi Dan,

>> Regarding 1:  it sounds like you may need to repopulate the search index, and clear the various caches
> If it still doesn't work, then yes, it is possible you have found a bug. Let me know and I will try to reproduce it locally.

I'm sorry, but I've followed all your instructions and the problem remains.
To reproduce it locally, just go to the settings and change the reference code separator to "/" (or any another diferente than "-")
Then do a description search... or simply: /index.php/informationobject/browse?topLod=0
And you will see that the reference code separator remains: "-"
If click on any description, on that view the reference code separator will use the selected one: "/"

I guess there is something wrong on the "informationobject/browse" code.

> Regarding 2: unfortunately there is no way to do this in AtoM currently without development. 
>  You will need to study the code and make local changes to achieve the result you want. 
> thank you so much for sharing the changes that you've made to be able to add the separator to the country and repository code! 

You are welcome, but I've just followed the "free software way" (AGPL), if you change the code you must share!

I must ask you for help on one possible solution for this problem, probably a call for Breker!

Using a ThemePlugin we are able to override some php files by changing the Theme.

Would it be possible create a ThemePlugin to override this  atom/lib/model/QubitInformationObject.php ?
I think you get the idea: instead of changing the AtoM base code, just change that code for a particular Theme!

Thank you!
Ricardo Pinho


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Dan Gillean

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Jul 31, 2018, 5:10:54 PM7/31/18
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Hi Ricardo, 

Steve is away from the office today, but hopefully he can take a look at your question when he returns. 

In the meantime, regarding 1 - I've now reproduced the issue, and filed the following bug report: 
We are trying to wrap up the 2.4.1 release at the moment, so I'm not sure if we'll be able to address this in the upcoming release, but I've got it on a list for consideration in our next public release. In the meantime, if you manage to fix the issue locally, please consider sending us a pull request!  

Regards, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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sbr...@artefactual.com

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Aug 1, 2018, 8:18:59 PM8/1/18
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Hi Ricardo

It is possible to model files in a plugin although we only use this feature to add new models to AtoM - see qtAccessionPlugin for an example.

It should be possible to include QubitInformationObject.php in a plugin but there are additional steps you will need to take - See this Symfony doc page under the section titled "The Model": http://symfony.com/legacy/doc/jobeet/1_4/en/20?orm=Propel

It should be noted that overriding a core file in AtoM such as the InfoObj model will involve the need for you to merge Artefactual's changes to this file into your custom version before each upgrade.  Changes are made in this file fairly frequently so taking a snapshot and including that in your theme will mean that you will need to make efforts to merge future changes into your custom version of QubitInformationObject to keep it up to date.

Commit history for this file:


Steve
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Ricardo Pinho

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Aug 2, 2018, 4:33:42 AM8/2/18
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Hi Steve,
Thank you for your reply!
Considering your explanation I conclude that it's better to leave the QubitInformationObject out off the ThemePlugin.

Well, apart from this idea, to solve the need of having a separator for Country and Repository identifiers different from "space" in the reference code, I can suggest two ways:
1. Add to the Global Settings a second: "Reference Code separator for Country and Repository identifiers".
2. Add to the Global Settings an option (True/False) "Apply Reference Code separator for all identifiers".
Neither of them seem difficult to implement, but I leave this to AtoM software Architects decision! ;-)
It would be nice to have it on 2.4.1 public release...
In the mean time we will have to hack the QubitInformationObject.php code to respond to our needs.

Cheers,
Ricardo Pinho


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Dan Gillean

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Aug 3, 2018, 2:14:21 PM8/3/18
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Hi Ricardo, 

You've prompted some interesting internal discussion, as this has made us realize that many different jurisdictions will have different use cases and needs, and we'd like to implement a single flexible solution that works for all, rather than add an additional separate setting. 

Our AtoM Director of Technical Services had the following suggestion - and if you wanted to attempt to implement it, we would welcome a pull request. However, it is likely more complex than what you were originally intending, so if you don't have the time or inclination, that's okay too. 

I've tried to outline the proposal in a Wishlist ticket here: 
Let me know if you have questions, or if the description is unclear. 

My hope is that this would replace the current setting, and that we would include a default mask value that matches the current implementation (spaces between country code and repo code, dashes between identifiers, to keep our installation defaults simple. Ideally, a migration script would check the current separator value and use that to update the new default mask value in case upgrading users are using slashes or a different separator - but that also might be more complex. 

I would be very curious for your thoughts on this proposal! And of course anyone else in the AtoM community who is following this thread :)

If we reach consensus and you choose to try to implement this, I'm hoping that studying the way we've implemented the Accessions mask and the Identifier mask settings might help provide some guidance on implementation. I'm sure our devs could provide some suggestions on this thread as well. 

If you do want to try to develop this, don't forget about our Development resources on the wiki for guidance on submitting a PR, how we handle code review, our coding standard, and so forth. 

Otherwise, now that we have a Wishlist ticket, I can try to pitch this to other users if there is interest in the future. 

Regards, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

Ricardo Pinho


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Ricardo Pinho

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Aug 4, 2018, 4:26:17 AM8/4/18
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Hi Dan,

Thank you for taking this issue further and all your time to find a better solution.
I must state that I would prefer to use an unique international standard format for the reference code, like a GUID.
Unfortunately there are still some local different ways that we must cope to, so there must be "some" flexibility on the software.

Your "mask solution" is much better and it's also very clear and easy to understand.
My contribution to improve it further would be if you could consider:
1. Include predefined masks with a clear explanation/description, for the user to select from a list or edit. For example:
%C %R %P-%I - (default) Example:  CA REPO C1-S1-F1-IT1 : Country Repository Parent - Unit of description identifiers.
%C %R %P/%I - Example:  CA REPO C1/S1/F1/IT1 : Country Repository Parent / Unit of description identifiers.
%C-%R/%P-%I - Example: CA-REPO/C1-S1-F1-IT1 : Country - Repository / Parent - Unit of description identifiers.
%C/%R/%P/%I - Example: CA/REPO/C1/S1/F1/IT1 : Country / Repository / Parent / Unit of description identifiers.

2. Remove the "Inherit reference code (information object)" configuration, and replace it with the use of a mask with or without Country and Repository identifiers.You could add to the predefined list some examples:
%P-%I - Example:  C1-S1-F1-IT1 : Parent - Unit of description identifiers.
%P/%I - Example: C1/S1/F1/IT1 : Parent / Unit of description identifiers.

Regarding the invitation to try to develop this. I'm flattered but I'm afraid that I don't have the skills nor the time to achieve that.
It would be great if we could convince the Portuguese entities to sponsor some of those features/improvements.
I strongly believe in: https://publiccode.eu

Cheers,
Ricardo Pinho

Dan Gillean

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Aug 6, 2018, 5:00:46 PM8/6/18
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Hi Ricardo, 

Thank you for these suggestions. I agree that something globally unique like a GUID would be interesting - but a) we must still allow users to follow the ICA recommendations, and other regional standards, and b) a different GUID at every level would mean that the reference code cannot communicat anything meaningful about the structure or arrangement of the holdings, which I think is useful to some institutions. 

In terms of your suggestions for the features: 

I think we would definitely add many examples to the documentation, and it might be possible to add some to a tooltip for the field as well, but I wouldn't want to make the feature overly complex by adding mask values to a separate taxonomy that users must update to add alternatives. 

Removing the "Inherit reference code" setting entirely may be possible, but we need to be cautious about how our changes affect existing users when they upgrade - we don't want to introduce changes that might affect their settings which they don't notice or have to manually correct. That said, if we can read the current state of the setting and update the default mask accordingly as part of a migration task, then anyone with the setting turned off could simply get "%I" as the value (i.e. current identifier only). One of the outstanding issues to this proposal is if we can also read the state of the default separator, and populate the new reference code mask value with the correct value to maintain their current settings when we remove these features. 

I think this should be possible if the migration executes a separate script we include in a release, but I would need input from our developers to find out the possible gotchas and limitations. 

In any case, it's still just a wish list idea! Perhaps we will find a sponsor in the future :)

In the meantime, thank you for your valuable input! 

Regards, 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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John Hewson

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Oct 18, 2018, 2:08:11 PM10/18/18
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Hi Ricardo and Dan,

We ran into Bug #12357 too, having selected / as our ref code separator. It turns out to be a rare case where repopulating the search index is actually the problem rather than the solution.

The ref codes seen in the browse list come from the index, rather than being built on the fly, unlike the ref codes seen in individual descriptions. If we resave an individual description, the ref-code separator seen for that description in the browse list respects the setting (/), but if we repopulate the index it reverts to the default (-). Over time, we end up with a mixture, which looks a bit odd.

The problem arises, or at least is expressed, in

plugins/arElasticSearchPlugin/lib/model/arElasticSearchInformationObjectPdo.class.php

Line 355, in the getReferenceCode function, reads

$refcode .= implode(sfConfig::get('app_separator_character', '-'), $identifiers);

When we resave an individual description, this runs under the app and the app sees the config, so we get the set separator. When we repopulate the index, this runs under the task and the task can't see the config, so we default to '-'.

As a workaround, we could respect the UI setting by replacing the line with something like:

    //$refcode .= implode(sfConfig::get('app_separator_character', '-'), $identifiers);
    $separator_character = QubitPdo::fetchColumn('SELECT value FROM setting_i18n WHERE id IN (SELECT id FROM setting WHERE name = "separator_character")', array());
    if (!$separator_character) {$separator_character = array('-');}
    $refcode .= implode($separator_character[0], $identifiers);

Or, as it's just a workaround, and we're not likely to change the setting, we could hard code it:

    $refcode .= implode('/', $identifiers);

which, pending a more elegant solution, is what we've done.

Ricardo Pinho

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Oct 19, 2018, 12:04:38 PM10/19/18
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Dear John,
Thank you so much for sharing your discover!
I seems a valuate contribution for correcting the bug.
In the mean time, I will try those work around, to avoid confusing different reference codes on screen.
Thank you again!
Cheers,
Ricardo Pinho



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Dan Gillean

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Oct 19, 2018, 12:40:01 PM10/19/18
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Hi John, 

Yes, thank you so much for sharing this. I've added your notes to the issue ticket, here: 
At this point, we've finalized the 2.4.1 release and are just testing the tarballs before we make them available, so a fix for this issue will have to wait. I have checked the qa/2.5.x code base and found the same issue on line 421 of the same file, and have also included this in the issue ticket note.  I've confirmed that we have this bug on an internal list to consider and prioritize for the 2.5 release. 

Really appreciate your sharing your solution as well! 

Regards,

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Ricardo Pinho

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Jan 12, 2019, 8:34:58 AM1/12/19
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Dear Dan, José, Steve or any other AtoM developer,

I'm sorry but I must ask 1 minute of your attention for this Bug #12357  reported here 3 months ago by John Hewson.

I Found that the problem is very simple! on the line 421:
$refcode .= implode(sfConfig::get('app_separator_character', '-'), $identifiers);
"Admin > Settings >  Global > Reference code separator"

Since it can't get the value, it will use the given alternative character "-" for the reference code separator whatever value we have placed in the settings.

I've spend some time (hours) trying to understand why but I haven't been able to fix the problem.

I guess someone that knows the AtoM code better than I, will easily fix this and in a short time.

I appreciate all the attention and help on this.
Thank you in advance!

Best regards,
Ricardo Pinho


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Ricardo Pinho

Dan Gillean

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Jan 14, 2019, 10:52:31 AM1/14/19
to ICA-AtoM Users
Hi Ricardo, 

Thank you for this detective work! I have added your comments to the related ticket (here) to assist our team. This bug is already on our list of issues to review for the 2.5 release, and with all the community-provided feedback and suggestions, I am very hopeful we can prioritize it for inclusion. 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory

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Ricardo Pinho

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Apr 30, 2023, 8:23:31 AM4/30/23
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Dear AtoM users and developers,

Until we wait for a solution regarding the "reference code separator character", that is hardcoded to "space" for the country and repository, we still need to change the AtoM code, each time a new release is published.

The file that needs to be changed is:
(currently lines : L2564 and L2571)

To avoid changing the AtoM main code, I would like to make these changes in a  theme file that could replace the main one, and make it more easily and portable to implement, disseminate and maintain.

But I don't know where to place the replacement file inside the Theme plugin directory structure, so it overrides the main one.
I've tried several alternatives but none of them works, starting by the obvious (example):
arDominionPlugin/lib/model/QubitInformationObject.php

So, I'm asking if anyone knows if this is possible?
And if so, where should I place the changed QubitInformationObject.php file inside the plugin?
So I can override the corresponding AtoM core file when I activate the Theme plugin.

Thank you in advance!
Best regards,
Ricardo Pinho

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Ricardo Pinho

Dan Gillean

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May 1, 2023, 10:42:14 AM5/1/23
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Hi Ricardo, 

As far as I'm aware (and after having talked to one of our developers), I don't think we have ever attempted to override a core model file as part of a custom theme. As such, our team would need to experiment to see what is possible - something we can't unfortunately do as part of our limited time to provide free support via the forum, and which you are in the process of doing anyway. Sorry we can't really be more help!

I would encourage you to keep experimenting and sharing the outcomes, and consider doing some research in the Symfony 1.x documentation to see what you can learn. Best of luck! 

Dan Gillean, MAS, MLIS
AtoM Program Manager
Artefactual Systems, Inc.
604-527-2056
@accesstomemory
he / him


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Ricardo Pinho

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May 2, 2023, 5:45:45 PM5/2/23
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Dear Dan,
Thank you for your reply and honest feedback.
I will try to investigate it further.

Nevertheless if anyone else here has any hint or tip to find a solution, it will be very appreciated.

Thank you again,
Best regards,
Ricardo Pinho


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