Adding fields to Dublin Core

lwieck · January 21, 2020, 7:10pm

Hello!

I’m in the process of testing an import from DSpace to Omeka S via the DSpace connector. DSpace uses additional Dublin Core fields that aren’t in Omeka’s DC vocabulary, as well as a different format…e.g Omeka S (dc:spatial) and DSpace (dc.coverage.spatial). Right now, what happens is that the spatial coverage metadata from DSpace duplicates when coming into Omeka, populating the coverage and the spatial coverage fields.

Is there a way to change the Omeka S Dublin Core vocabulary to match the nested format of DSpace, or am I better to change the fields in DSpace to remove the nesting?

lwieck · January 22, 2020, 4:31am

The problem might also lie somewhere within Dspace having a Dublin Core vocab and a DCMI vocab…?

jflatnes · January 22, 2020, 7:58pm

I think this is actually just a function of how the DSpace Connector module works: when it sees those DSpace-style “dc.coverage.spatial” terms, it maps them to both “coverage” and “spatial.”

The module needs to be changed to change this behavior. I assume what you’d want is for elements to be mapped only to their most specific match (i.e.: dc.coverage.spatial mapping only to dcterms:spatial and not also to coverage).

lwieck · January 24, 2020, 5:40pm

Yes. That seems to be the issue.

I’ve also tried importing into dspace with the dc.coverage.spatial and with dcterms:spatial, and the items with dcterms don’t seem to be bringing the metadata into omeka.

Also, yes, I’d think that it should only go to the most specific field (spatial, not coverage and spatial)

jflatnes · January 24, 2020, 6:03pm

I’ve made a change to the DspaceConnector code that accomplishes “deduplicating” the metadata in the way we were talking about, mapping each value only once, to the most specific available property on the Omeka S side.

Can you share the URL to your DSpace repository? The “dcterms” issue is also a problem on the connector side, I think: it only knows how to handle “dc” elements… examples of usage of dcterms-namespaced metadata on the DSpace side of things would be helpful for us improving that support. Mostly (only?) we’ve had repositories using the older-style “nested” elements to test against.

lwieck · January 24, 2020, 8:04pm

Awesome! Do I need to reinstall the DSpace connector to get it to work?

I’ll go back to the nested style before we do our big import, if that will work.

Is there anyway that I can add customized fields and have it work with the import (for example, we have three subject fields - one of subjects-people, subjects-topics of coverage, subjects-institutions)?

jflatnes · January 26, 2020, 6:53pm

The change to the connector is currently on a branch.

If you’re looking to try it out, probably the simplest option is to just take the file src/Job/Import.php from your copy of the DspaceConnector and replace it with this one.

lwieck · January 27, 2020, 7:33pm

The updated connector file has fixed that issue. The only problem that remains is that Dspace auto adds these two fields when you import to Dspace:

dc.date.accessioned	2020-01-24T17:34:52Z
dc.date.available	2020-01-24T17:34:52Z

Dc.date.accessioned is appearing under “Date” when imported into Omeka.

jflatnes · January 28, 2020, 9:47pm

Yeah, I think the tricky part on our end is that for some use cases, people do probably want that DSpace-generated data (plus people could have “real” metadata in those same fields).

The only workable option I can think of is some kind of setting to choose fields to ignore in the connector.

lwieck · February 6, 2020, 5:17pm

Yes, the select-to-ignore fields would work perfectly (and/or an override for matching metadata fields?)

jflatnes · February 6, 2020, 5:42pm

By an override you mean like a manual crosswalk kind of thing? Certainly that would address the issue, but it’s a pretty major undertaking in terms of UI and functionality that’s not currently there.

The “ignore” option is much simpler, though: I’ve done a quick implementation of that as well. It and the previous “no duplicates” change are on the dedupe-dc branch. The ignore feature touches more than one file, so if you wanted to try it out you’d have to download or check out that branch rather than just a new copy of one file.

lwieck · February 6, 2020, 6:54pm

Yes, re: manual crosswalk, but the ignore will do the trick in this case I think. Will download and check it out!

lwieck · February 6, 2020, 9:00pm

My first pass with the updated item resulted in an error. Here’s an excerpt from the error log info below:

under the ignore field, I entered:
dc.date.accessioned

Errors:
{
“o:media”: [
{
“file”: [
“Error validating “/rest/bitstreams/9af2c701-d0b9-47f8-bf93-7ab5684cdde4/retrieve”. Cannot store files with the media type “text/troff”.”,
“Error validating “/rest/bitstreams/9af2c701-d0b9-47f8-bf93-7ab5684cdde4/retrieve”. Cannot store files with the resolved extension “t”.”
]
}
]
}
Stack trace:
#0 /var/www/html/omeka-s/application/src/Api/Adapter/AbstractEntityAdapter.php(276): Omeka\Api\Adapter\AbstractEntityAdapter->hydrateEntity(Object(Omeka\Api\Request), Object(Omeka\Entity\Item), Object(Omeka\Stdlib\ErrorStore))
#1 /var/www/html/omeka-s/application/src/Api/Manager.php(224): Omeka\Api\Adapter\AbstractEntityAdapter->create(Object(Omeka\Api\Request))
#2 /var/www/html/omeka-s/application/src/Api/Manager.php(78): Omeka\Api\Manager->execute(Object(Omeka\Api\Request))
#3 /var/www/html/omeka-s/application/src/Api/Adapter/AbstractEntityAdapter.php(321): Omeka\Api\Manager->create(‘items’, Array, Array, Array)
#4 /var/www/html/omeka-s/application/src/Api/Manager.php(227): Omeka\Api\Adapter\AbstractEntityAdapter->batchCreate(Object(Omeka\Api\Request))
#5 /var/www/html/omeka-s/application/src/Api/Manager.php(97): Omeka\Api\Manager->execute(Object(Omeka\Api\Request))
#6 /var/www/html/omeka-s/modules/DspaceConnector/src/Job/Import.php(313): Omeka\Api\Manager->batchCreate(‘items’, Array, Array, Array)
#7 /var/www/html/omeka-s/modules/DspaceConnector/src/Job/Import.php(97): DspaceConnector\Job\Import->createItems(Array)
#8 /var/www/html/omeka-s/modules/DspaceConnector/src/Job/Import.php(54): DspaceConnector\Job\Import->importCollection(’/rest/collectio…’)
#9 /var/www/html/omeka-s/application/src/Job/DispatchStrategy/Synchronous.php(34): DspaceConnector\Job\Import->perform()
#10 /var/www/html/omeka-s/application/src/Job/Dispatcher.php(105): Omeka\Job\DispatchStrategy\Synchronous->send(Object(Omeka\Entity\Job))
#11 /var/www/html/omeka-s/application/data/scripts/perform-job.php(43): Omeka\Job\Dispatcher->send(Object(Omeka\Entity\Job), Object(Omeka\Job\DispatchStrategy\Synchronous))
#12 {main}
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2020-02-06T20:44:19+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:21+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:23+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:25+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:27+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:29+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:30+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:32+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:34+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:36+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:37+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:39+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:40+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:41+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:44+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:47+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:48+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:50+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:51+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:54+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:55+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:57+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:44:59+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:01+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:02+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:04+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:06+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:08+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:10+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:12+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:14+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:16+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:19+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:21+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:48+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:49+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:51+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:52+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:54+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:55+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:56+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:57+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:58+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:45:59+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:00+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:01+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:02+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:04+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:05+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:06+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:08+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:09+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:10+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:11+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:13+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:14+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:15+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:16+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:17+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:19+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:20+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:21+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:23+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:24+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:26+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:27+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:29+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:31+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:32+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:34+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:35+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:37+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:39+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:41+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:43+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:44+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:46+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:48+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:49+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:51+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:53+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:54+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:55+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:57+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
2020-02-06T20:46:58+00:00 ERR (3): Command “command -v ‘pdftotext’” failed with status code 1.
Fatal error: Allowed memory size of 134217728 bytes exhausted (tried to allocate 2487712 bytes)
in /var/www/html/omeka-s/vendor/lsolesen/pel/src/PelJpeg.php on line 286

jflatnes · February 6, 2020, 9:08pm

This looks like an error that should be unrelated: you ran out of memory. Though obviously that’s a problem on its own, it shouldn’t have anything to do with the “ignore” feature. Increasing the memory_limit setting for PHP on your server is one option that may help here.

Also there’s a bunch of errors coming from the ExtractText module, I think, complaining about the missing “pdftotext” command.

As for why it’s happening now and didn’t before: it could simply be that you’re doing a larger import than before, or that you made other changes (like installing other modules, possibly) that are making the import use more memory. It may also be something we need to fix in the Connector, but I’d have to do some more investigation to say much one way or the other about that.

lwieck · February 7, 2020, 12:34am

I don’t have the pdftotext enabled…22%20PM|690x171

lwieck · February 10, 2020, 2:35pm

@jflatnes - I do have the extract text module installed, and the filegetcontents item is enabled. I don’t have the additional pieces to run the pdftotext installed (and don’t need it running, since filegetcontents is doing the trick). Is there a way to stop it from erroring out on every item b/c of the pdftotext?

jflatnes · February 10, 2020, 6:01pm

I think those messages are basically just “noise”: the module is trying to autodetect the path to that utility several times. It’s the memory “fatal” error that’s the main issue. You could of course disable Extract Text to see if it’s what’s causing the import as a whole to fail.

lwieck · February 10, 2020, 6:27pm

Okay - thanks! So, if the import is back to functioning, just disregard the pdf errors? Thanks!

jflatnes · February 10, 2020, 6:41pm

Yes, if it is working, you should be fine to ignore those error messages.