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[EP-tech] Admin Screen JavaScript Problem

Hi James,

I generally discourage people from using the DEB or Yum repositories for 
EPrints, as managing upgrades is difficult, as there will almost always 
be some change, even for a new minor version that does not work out of 
the box and would be difficult to script within the DEB/RPM installer.? 
Especially due to how much an EPrints repository can be customised.

The main reason I continue to produce new DEBs and RPMs is that this 
allows for a generic and quite prescriptive method for someone with 
minimal EPrints knowledge to install a new EPrints repository that 
should work pretty much out of the box.? However, the intention is that 
people would just want this so they can try out EPrints before deciding 
if they wanted to create their own production EPrints repository.? 
(However, I can appreciate how using a OS package repository make seem 
like the more official/robust way to install an application).? 
Installing from source (tarball or Git) can be more difficult, although 
with the dependencies listed on the wiki pages [1] [2] but it comes with 
significant advantages when it comes to upgrading.

My general advice for installing EPrints, if you are reasonably 
experienced, is to install from GitHub.? This allows you to install a 
specific version using a tag.? It also then allow you to see any core 
code files you might have modified before trying to upgrade. Although, I 
would advise against doing a "git fetch -> git checkout NEW_TAG" on a 
live repository without backing up and having allocated a decent length 
at-risk period, (e.g. 2 hours or more if your repository is quite 
bespoke), where users either cannot access or are advised against trying 
to use your EPrints repository.? An important part of the upgrade is to 
check for any new dependencies or changes (e.g. [3]) that may mean your 
upgraded repository does not work straight out of the box.

I wrote some instructions for upgrading between 3.4.x versions [4] but 
only got as far as writing the schedule for upgrading using a source 
tarball, which I think could still be improved.? I will try to find time 
to write the schedules for the other two.? However, I suspect the one 
for the upgrading a Linux package will be either don't do this or if you 
do follow a similar approach to using Git to checkout a new released 
version tag.

Regards

David Newman

[1] https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FInstalling_EPrints_on_Debian%2FUbuntu&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JPkm%2BcH3e5TVQaxNoAErl9sNHb5Yvis5HBtzmRTfJM8%3D&reserved=0
[2] https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FInstalling_EPrints_on_RHEL%2FFedora%2FCentOS&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TQdYvltmArntDZdsO4lNQH%2B6CIcTeg%2FgGxWqdaxszc4%3D&reserved=0
[3] https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FEPrints_3.4.4&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=D4Gpz5Uli1xZdEzXzFUAfi1qaVFa9MP3ZYXiWgyTsLM%3D&reserved=0
[4] https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FUpgrading_between_EPrints_3.4_versions&data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xmmnHUTNebtVg0HnEyOcG%2B9CWbDPZrM15Bn8gy0iMB4%3D&reserved=0


On 14/11/2022 9:21 am, James Kerwin wrote:
> *CAUTION:* This e-mail originated outside the University of Southampton.
> Morning David, and the rest of the list I forgot to remove from my 
> reply on Friday,
>
> Once you helped me understand that I'd actually done an upgrade 
> everything became much easier and was generally a positive experience.
>
> In my initial panic I reverted to eprints default templates and 
> JavaScript. Disabled all custom plugins etc to take it right back to 
> default. Adding the new fields to the database fixed a lot of 
> problems. Manually copying over some JavaScript and images (plus.png, 
> warning, loading bar images etc) to my local archive fixed everything 
> else. Then I sequentially re-enabled plugins, local?JavaScript and 
> templates/citations etc then everything was fine.
>
> I'll not be in a rush to do this again, but not the disaster I thought 
> it was on Friday.
>
> Thanks,
> James
>
> On Fri, Nov 11, 2022 at 2:59 PM David R Newman <drn at ecs.soton.ac.uk> 
> wrote:
>
>     Hi James,
>
>     Yes you were correct with you amendment to the
>     flavours/pub_lib/inc.? Based on the added fields this sounds like
>     a 3.4.3 to 3.4.4 upgrade.? Therefore, check for information at:
>
>     https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FEPrints_3.4.4&amp;data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=D4Gpz5Uli1xZdEzXzFUAfi1qaVFa9MP3ZYXiWgyTsLM%3D&amp;reserved=0
>     <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.eprints.org%2Fw%2FEPrints_3.4.4&amp;data=05%7C01%7Ceprints-tech%40ecs.soton.ac.uk%7Cc7fa84da55d84167840e08dac627c0c5%7C4a5378f929f44d3ebe89669d03ada9d8%7C0%7C0%7C638040171319611700%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=D4Gpz5Uli1xZdEzXzFUAfi1qaVFa9MP3ZYXiWgyTsLM%3D&amp;reserved=0>
>
>     However, the fix I suggested is the only know new dependency on a
>     3.4.3 -> 3.4.4 upgrade.? However, if you do find any others let me
>     know and I will update this wiki page.
>
>     The issue you look to be reporting now seems to be a permissions
>     one.? I guess there is a chance that the OS package upgrade has
>     changed the permissions on some directories which? prevents files
>     from being copied. This is not something I have noted before but
>     it is worth checking the
>     /usr/share/eprints/archives/liverpool_rdm/html/en/style/images/
>     directory and its ancestor directories.? Alternatively, it could
>     be an SELinux file contexts issue.? However, that seems unlikely,
>     as if you knowingly had SELinux enabled, you would probably know
>     that on any upgrade you need to check the audit log of any
>     thinking SELinux may be now blocking.? The EPrints OS packages do
>     not contain their own SELinux policies.? Mainly due to how much
>     EPrints can be customised, (e.g. Bazaar plugins, ingredients and
>     bespoke code for the archive).? This would be near impossible to
>     write an SELinux policy that would cover all bases, whilst also
>     not be being overly lax.
>
>     Regards
>
>     David Newman
>
>     On 11/11/2022 14:32, James Kerwin wrote:
>
>>     *CAUTION:* This e-mail originated outside the University of
>>     Southampton.
>>     To spare the wider list of my woes I'll send this to you.
>>
>>     I've added:
>>
>>     ingredients/prototypejs
>>
>>     to inc.
>>
>>     Though I still appear to be having problems. I'll keep at it
>>     today to see where I get.
>>
>>     Thanks,
>>     James
>>
>>     On Fri, Nov 11, 2022 at 2:23 PM James Kerwin
>>     <jkerwin2101 at gmail.com> wrote:
>>
>>         Hi David,
>>
>>         Thank you so much for your response.
>>
>>         The files were weird. In my logs I had:
>>
>>         Can't copy
>>         /usr/share/eprints/lib/static/style/images/bar_24px.png to
>>         /usr/share/eprints/archives/liverpool_rdm/html/en/style/images/bar_24px.png:
>>         Permission denied
>>
>>         I went through and copied each one and they vanished from my
>>         error list in Chrome inspector. Not the end of my problems.
>>
>>         Doing the dry run of UPDATE yielded:
>>         Dry run: Fixed subject__rindex.field collation
>>         Dry run: Fixed eprint__rindex.field collation
>>         Dry run: Added additional_recipients to dataset saved_search
>>         Dry run: Fixed saved_search__rindex.field collation
>>         Dry run: Added upload_url to dataset document
>>         Dry run: Fixed document__rindex.field collation
>>         Dry run: Fixed user__rindex.field collation
>>         Dry run: Fixed request__rindex.field collation
>>         Dry run: 0 datasets added
>>         Dry run: 2 fields added
>>         Dry run: 0 counters were added
>>
>>         So it's adding two new fields when I run it properly?
>>         upload_url in Document and additional_recipients to saved_search?
>>
>>         Now on to inc. I currently have:
>>
>>         flavours/pub_lib
>>         ingredients/bazaar
>>         #ingredients/jquery
>>         #site_lib
>>
>>         At risk of sounding incredibly stupid, what do I need to do
>>         to add prototype here? I have seen a prototype.js file
>>         somewhere today. Do I need to point it to that?
>>
>>         Thanks,
>>         James
>>
>>
>>         On Fri, Nov 11, 2022 at 1:15 PM David R Newman
>>         <drn at ecs.soton.ac.uk> wrote:
>>
>>             Hi James,
>>
>>             /"appeared to be some eprints updates//amongst them.//"/
>>
>>             Do you mean you have EPrints installed as an OS (RPM or
>>             Deb) package?? If so there may be a number of issues if
>>             EPrints source code has been updated.? The first thing I
>>             would do is check to see if there are any updates
>>             required to the database:
>>
>>             bin/epadmin update_dry_run REPOID
>>
>>             If these looks sane then run "epadmin update REPOID" to
>>             actually do the update.
>>
>>             If you are getting Internal server error messages you can
>>             usually see them in the webserver error log files. As I
>>             assume you have HTTPS enabled this will likely be in the
>>             ssl_error_log or a similarly named file. (Check what you
>>             have set in your archive's ssl/securevhost.conf file).
>>
>>             It may be that you need to tinker with the ingredients
>>             included fro EPrints.? One requirement of upgrading an
>>             existing EPrints 3.4 repository to 3.4.4 is to add the
>>             prototypejs ingredient to flavours/pub_lib/inc.? This the
>>             first step in trying to make EPrints JavaScript API
>>             agnostic and ultimately replace EPrints underlying
>>             JavaScript library (Prototype) either with a more
>>             commonly used JS library or just to use native JS.
>>
>>             I am not sure what would be causing PNG images to give
>>             internal server errors that does seem very odd.?
>>             Hopefully the error messages in the webserver log files
>>             will explain.
>>
>>             Regards
>>
>>             David Newman
>>
>>             On 11/11/2022 12:55, James Kerwin via Eprints-tech wrote:
>>>             *CAUTION:* This e-mail originated outside the University
>>>             of Southampton.
>>>             Hi All,
>>>
>>>             I've just applied some Ubuntu updates and to my horror
>>>             noticed there appeared to be some eprints updates
>>>             amongst them.
>>>
>>>             Now the page where I login to edit an eprint or upload
>>>             files etc. is messed up. All of the tabs (Preview,
>>>             Details, Actions, Messages, History and Issues) show all
>>>             of their content under each tab. Eg. under details I see
>>>             the preview, details, actions and so on. Same if I click
>>>             on another tab.
>>>
>>>             It is also not allowing me to upload files. I can go
>>>             through the motions of adding a file, but when I click
>>>             "upload" the page appears to refresh and do nothing.
>>>
>>>             My guess is that this has introduced some JavaScript
>>>             problems. Irritatingly?I think I've fixed this same
>>>             problem previously.
>>>
>>>             Can anybody offer some advice on where to look? If I
>>>             "inspect" the page in Crome?I can see that we can't
>>>             access minus.png, plus.png, warning.png etc giving a
>>>             "500 (internal server error)".
>>>
>>>             Thanks,
>>>             James
>>>
>>>             *** Options:http://mailman.ecs.soton.ac.uk/mailman/listinfo/eprints-tech
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>>
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