Re: [dspace-tech] Issues with REST find-by-metadata-field in DSpace 5

[Ilja Sidoroff]

Hi,

I tried to do something similar (all items with something in the field X), but 
it seems that find-by-metadata-field does not support wildcards, only exact 
matches. Helix84 suggested SOLR for me, There's also a new REST api for reports 
in 6.0 (Terry Brady suggested that to me). You can probably find the threads 
with my name & those mentioned.

For the other question, are there differences in the item access permissions 
and/or if any of the items are in the workflow or in the collections. I think 
the SQL queries will give you all the items, but I think there is some 
filtering done with the REST - didn't look very deeply into that, though.

Ilja


From: dspace-tech@googlegroups.com  on behalf of 
Alan Orth 
Sent: Thursday, November 10, 2016 1:38:34 PM
To: DSpace Technical Support
Subject: [dspace-tech] Issues with REST find-by-metadata-field in DSpace 5

Hi,

We're trying to build an application that uses metadata from DSpace's REST API 
and I'm having some issues. We're testing on DSpace 5.5 with PostgreSQL.

First, it seems there is no way to use a wildcard value with the 
find-by-metadata-field endpoint—I want all items where a field 
`cg.subject.ilri` exists. Second, for another query, I'm not sure that the API 
is returning the correct results. Taking into account the text_lang of the 
metadata, the following database queries and REST API results don't add up. 
Here are the database results for null, blank, and en_US text_lang values:

dspace=# select count(text_value) from metadatavalue where resource_type_id=2 
and metadata_field_id=203 and text_value='SEEDS' and text_lang is null;
 count
---
15
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 
and metadata_field_id=203 and text_value='SEEDS' and text_lang='';
 count
---
 4
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 
and metadata_field_id=203 and text_value='SEEDS' and text_lang='en_US';
 count
---
66

Then the API results, in the order of null, blank, and en_US language:

$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X 
POST "http://localhost:8080/rest/items/find-by-metadata-field; -d '{"key": 
"cg.subject.ilri","value": "SEEDS"}' | jq length
55
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X 
POST "http://localhost:8080/rest/items/find-by-metadata-field; -d '{"key": 
"cg.subject.ilri","value": "SEEDS", "language":""}' | jq length
34
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X 
POST "http://localhost:8080/rest/items/find-by-metadata-field; -d '{"key": 
"cg.subject.ilri","value": "SEEDS", "language":"en_US"}' | jq length

The results don't even remotely match, and there are actually more results from 
the API than from the database (85 vs 89).

Does anyone know what's up with either of these issues? Thanks,
--

Alan Orth
alan.o...@gmail.com
https://englishbulgaria.net
https://alaninkenya.org
https://mjanja.ch

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[dspace-tech] DSpace current master: ERROR: prepared statement "S_29" does not exist

[Ilja Sidoroff]

I've been testing the latest git master (upcoming DS 6), and since pulling the 
latest changes on Tuesday, I've encountered errors like:

ERROR: prepared statement "S_29" does not exist
(a paste for the full stack trace: http://pastebin.com/2mLKNNHD)

(where "S_29" varies). The errors seem to happen when I use workflow 
functionality and try to submit something, or directly try to submit something 
to a collection. When the error state is on, I cannot start new submissions, 
upload bitstreams from the workflow, or upload bitstreams from 
administration->edit item - and possibly more. I don't know exactly what are 
the conditions for reproducing this nor I know how to recover from the state. I 
managed recovery once by restarting postgres, but in general it doesn't seem to 
help.

I first encountered this on Tuesday and asked help on irc. Helix84 did some 
googling and one reason this might happen, is some sort of concurrency problem, 
where the original PSTMT gets deleted/flushed out and is not available when 
resumed (unfortunately I don't have the reference or the irc log).

My environment is: Ubuntu 16.04, Java 1.8, Jetty 9, PostgreSQL 9.5. I'll 
continue examining the issue to determine if it is just something in my own 
environment or a genuine bug.

br,

Ilja Sidoroff
University of Eastern Finland

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[dspace-tech] Moving a collection to a different community

[Ilja Sidoroff]

Is there a "canonical" way of moving collections to different community? There 
is some old advice on this, which involves direct modifications to the 
database, and a recent one here: 
https://gist.github.com/alanorth/392c4660e8b022d99dfa

Is this still the way to do this?

br,

Ilja Sidoroff
University of Eastern Finland

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Re: [dspace-tech] REST Interface Sample App on Rails

[Ilja Sidoroff]

The /rest/login api changed a bit in version 6, but now the docs are updated: 
https://wiki.duraspace.org/display/DSDOC6x/REST+API

br,

Ilja Sidoroff
University of Eastern Finland

From: dspace-tech@googlegroups.com <dspace-tech@googlegroups.com> on behalf of 
Bruno Nocera Zanette <brunonzane...@gmail.com>
Sent: Tuesday, September 6, 2016 8:12:45 PM
To: DSpace Technical Support
Subject: [dspace-tech] REST Interface Sample App on Rails

Hey all!!

I've been writting, on my spare time, a REST interface sample app on Ruby on 
Rails and it finally got to a point where i can show it to you. It is fully 
based on "dspace-rest-client" ruby gem:

The link to the app is:
https://drcgem-sample-interface.herokuapp.com/

The code can be found here:
https://gitlab.c3sl.ufpr.br/bnzanette/DspaceRestSample
(P.s.: I plan to move it to github, but for now this is the only source. It's 
completely safe and hosted by a research group on the University where i 
study.).

I decided to keep it as simple as possible so that other people can use it as 
basis for other apps. Like a "live documentation".

There are somethings that i still have to do to make it more usable, like 
adding links to add collections/items/bitstreams on a community/collection/item 
page, so that you don't need to always choose a parent object when creating a 
new object. I also need to add a footer and an "about page" to add "powered 
by..." infos and stuff like that.

However, for some reason, Dspace's REST login isn't working on 
demo.dspace.org<http://demo.dspace.org>, so the app crashes everytime the 
buttons to save/edit are clicked. On my tests on a 5.x version everything works 
fine.

Feel free to do whatever you want with it!! Hope you like it and find some 
utility for it.
Cheers!!
--
Bruno Nocera Zanette
+55 41 9992-2508

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Re: [dspace-tech] Querying items by metadata item via SOLR and REST

[Ilja Sidoroff]

Thanks! That script would indeed do what I'd need, but I'm bit concerned about 
the scalability, since it will have to do one request per item - and if I have 
thousands of items, that might get a bit heavy? Or would it? I really don't 
know don't know how long for instance 10.000 item/id/metadata requests would 
take.

Ilja


From: Monika Mevenkamp <mome...@gmail.com>
Sent: Thursday, September 1, 2016 6:30:33 PM
To: Ilja Sidoroff
Cc: DSpace Tech
Subject: Re: [dspace-tech] Querying items by metadata item via SOLR and REST

Hi Ilja

I have a script that given a metadata field, e.g. pu.workflow.state, produces a 
tab separated list so:

field   id  handle  value
pu.workflow.state   969 9/fk4w099v32approved
pu.workflow.state   903 nullemailed
pu.workflow.state   753 nullemailed
pu.workflow.state   752 nullemailed
pu.workflow.state   902 nullorphaned


The script is written in jruby and based on my dspace-jruby gem, see Script 
here<https://github.com/akinom/dspace-cli/blob/master/metadata/list_values.rb>.
The gem as well as the script are available from github:   jrdspace 
gem<https://github.com/akinom/dspace-jruby>.  and 
cli-dspace<https://github.com/akinom/dspace-cli> , which has a bunch of other 
scripts.

The script is quite small, its ‘action’ is in the doit method

def doit(metadata_field)
  puts ['field', 'id', 'handle', 'value'].join("\t")
  dsos = DSpace.findByMetadataValue(metadata_field, nil, DConstants::ITEM)
  dsos.each  do  |dso|
vals = dso.getMetadataByMetadataString(metadata_field).collect { |v| 
v.value }
puts [metadata_field, dso.getID, dso.getHandle.nil? ? "null" : 
dso.getHandle, vals  ].join("\t")
  end
end

if you want to try this out , there are instructions on GitHUb. If you want to 
work in Java, look at the implementation of the DSpace.findByMetadataValue  
method. It has the SQL statement. see 
HERE<https://github.com/akinom/dspace-jruby/blob/master/lib/dspace/dspace.rb#L150-L171>

Monika

—
Monika Mevenkamp
Digital Repository Infrastructure Developer
Princeton University
Phone: 609-258-4161
Skype: mo-meven



On Sep 1, 2016, at 6:43 AM, Ilja Sidoroff 
<ilja.sidor...@uef.fi<mailto:ilja.sidor...@uef.fi>> wrote:

Hello,

I am using DSpace 5.5.

Am I correct, that SOLR queries return only items that are in
*collections* and not in the *workflow*? At least my search attemps
indicate that?

In the REST API, however, it seems that GET /items returns only
results that are in the collections. However, with POST
/items/find-by-metadata-field I can get all items in the DSpace, both
those in the collections and those in the workflow?

What I need, is a list of *all items* (both in the workflow and the
collections) that have certain metadata field set and *the value of
that field*. I don't see other way of doing that, except by direct SQL
query to the database. I have one for 5.x, but I'm not happy with it
since, I need to update it for 6.x etc. Is there any other way of
doing this?

Also, it seems that

dspace import -d -m mapfile ...

does not delete items currently in the workflow? Is this intentional or a bug?

regards,

Ilja Sidoroff
University of Eastern Finland

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[dspace-tech] LICENSE-bundle in BTE imported items

[Ilja Sidoroff]

Is it so, that LICENSE-bundle is not created for items imported via 
BTE-import (CSV)? Also, is there any way of adding files to other than the 
default bitstream in the UPLOAD step in the submission phase? The only way 
of adding license files to BTE-imported items seems to be after they are 
ingested, via "Edit Item"?

Also, I'm not seeing that the configuration option 
"webui.licence_bundle.show" has any effect in XMLUI. Has anyone any insight 
how that option should actually to work? I'm using DSpace 5.4 with XMLUI 
(Mirage).

Ilja Sidoroff
Information Specialist
University of Eastern Finland, Library

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[dspace-tech] Re: LICENSE-bundle in BTE imported items

[Ilja Sidoroff]

Regarding the latter question, it seems that the configuration property is 
used only in
dspace-xmlui/src/main/java/org/dspace/app/xmlui/objectmanager/ItemAdapter.
java

(in XMLUI, there are couple of references in JSPUI).

According to the comments in that file, 

This is an adapter which translates a DSpace item into a METS document 
 
 * following the DSpace METS profile, err well mostly.

Does this mean that in XMLUI, the property gets used only in METS export, 
or is the METS format used also in other places?

Ilja

torstai 17. maaliskuuta 2016 12.43.20 UTC+2 Ilja Sidoroff kirjoitti:
>
> Is it so, that LICENSE-bundle is not created for items imported via 
> BTE-import (CSV)? Also, is there any way of adding files to other than the 
> default bitstream in the UPLOAD step in the submission phase? The only way 
> of adding license files to BTE-imported items seems to be after they are 
> ingested, via "Edit Item"?
>
> Also, I'm not seeing that the configuration option 
> "webui.licence_bundle.show" has any effect in XMLUI. Has anyone any insight 
> how that option should actually to work? I'm using DSpace 5.4 with XMLUI 
> (Mirage).
>
> Ilja Sidoroff
> Information Specialist
> University of Eastern Finland, Library
>

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Re: [dspace-tech] jQuery 1.6.2

[Ilja Sidoroff]

Oops, I accidentally deleted my reply when trying to remove a spurious 
empty message. Anyway, I made a pull request for non Mirage2 themes in 
XMLUI (see issue) [1].

Ilja

[1] https://jira.duraspace.org/browse/DS-3099

lauantai 12. maaliskuuta 2016 0.43.25 UTC+2 Hardy Pottinger kirjoitti:
>
> Hi, Ilja, alas we manage our JS dependencies a bit differently than our 
> Java dependencies. [1] In the case of Mirage2, Bower is used to fetch 
> jQuery, and the version is specified with a tilde, which according to NPM 
> translates to "close enough to."[2][3]
>
> I have made a Jira ticket for upgrading our jQuery version with the UIs we 
> have right now [4]. As Tim said previously, we welcome a pull request to 
> address this.
>
> --Hardy
>
> [1] https://github.com/DSpace/DSpace/search?q=jquery
> [2] 
> http://stackoverflow.com/questions/19541494/bower-dependency-tilde-in-node
> [3] https://github.com/npm/node-semver
> [4] https://jira.duraspace.org/browse/DS-3099
>
> --
> *From:* dspac...@googlegroups.com  [dspac...@googlegroups.com 
> ] on behalf of Tim Donohue [tdon...@duraspace.org 
> ]
> *Sent:* Thursday, March 10, 2016 1:59 PM
> *To:* dspac...@googlegroups.com 
> *Subject:* Re: [dspace-tech] jQuery 1.6.2
>
> Hi Ilja,
>
> Yes, we'd encourage a Pull Request if you are willing. Thanks for making 
> us aware of this.
>
> - Tim
>
> On 3/8/2016 6:55 AM, Ilja Sidoroff wrote:
>
> At routine system scan by our IT department noticed, that mirage theme 
> uses jQuery version 1.6.2, which is vulnerable to a XSS attack [1]. I don't 
> know if this actually exploitable in DSpace, but anyway it seems that this 
> is fixable by simple bumping the version to 1.6.4. Is it worth of making a 
> pull request to fix this?
>
> Ilja Sidoroff
> Information Specialist
> University of Eastern Finland, Library
>
> [1] CVE-2011-4969 
> https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2011-4969
> -- 
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>
> -- 
> Tim Donohue
> Technical Lead for DSpace & DSpaceDirect
> DuraSpace.org | DSpace.org | DSpaceDirect.org
>
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Re: [dspace-tech] jQuery 1.6.2

[Ilja Sidoroff]

Thanks for the pointers - the issue I found was in Mirage 1, where the 
jQuery version was hardcoded in the source code. I'll try to look into 
making a pull request later today or tomorrow.

Ilja

lauantai 12. maaliskuuta 2016 0.43.25 UTC+2 Hardy Pottinger kirjoitti:
>
> Hi, Ilja, alas we manage our JS dependencies a bit differently than our 
> Java dependencies. [1] In the case of Mirage2, Bower is used to fetch 
> jQuery, and the version is specified with a tilde, which according to NPM 
> translates to "close enough to."[2][3]
>
> I have made a Jira ticket for upgrading our jQuery version with the UIs we 
> have right now [4]. As Tim said previously, we welcome a pull request to 
> address this.
>
> --Hardy
>
> [1] https://github.com/DSpace/DSpace/search?q=jquery
> [2] 
> http://stackoverflow.com/questions/19541494/bower-dependency-tilde-in-node
> [3] https://github.com/npm/node-semver
> [4] https://jira.duraspace.org/browse/DS-3099
>
> --
> *From:* dspac...@googlegroups.com  [dspac...@googlegroups.com 
> ] on behalf of Tim Donohue [tdon...@duraspace.org 
> ]
> *Sent:* Thursday, March 10, 2016 1:59 PM
> *To:* dspac...@googlegroups.com 
> *Subject:* Re: [dspace-tech] jQuery 1.6.2
>
> Hi Ilja,
>
> Yes, we'd encourage a Pull Request if you are willing. Thanks for making 
> us aware of this.
>
> - Tim
>
> On 3/8/2016 6:55 AM, Ilja Sidoroff wrote:
>
> At routine system scan by our IT department noticed, that mirage theme 
> uses jQuery version 1.6.2, which is vulnerable to a XSS attack [1]. I don't 
> know if this actually exploitable in DSpace, but anyway it seems that this 
> is fixable by simple bumping the version to 1.6.4. Is it worth of making a 
> pull request to fix this?
>
> Ilja Sidoroff
> Information Specialist
> University of Eastern Finland, Library
>
> [1] CVE-2011-4969 
> https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2011-4969
> -- 
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>
>
> -- 
> Tim Donohue
> Technical Lead for DSpace & DSpaceDirect
> DuraSpace.org | DSpace.org | DSpaceDirect.org
>
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[dspace-tech] Re: jQuery 1.6.2

[Ilja Sidoroff]

tiistai 8. maaliskuuta 2016 14.55.23 UTC+2 Ilja Sidoroff kirjoitti:
>
> At routine system scan by our IT department noticed, that mirage theme 
> uses jQuery version 1.6.2, which is vulnerable to a XSS attack [1]. I don't 
> know if this actually exploitable in DSpace, but anyway it seems that this 
> is fixable by simple bumping the version to 1.6.4. Is it worth of making a 
> pull request to fix this?
>
> Ilja Sidoroff
> Information Specialist
> University of Eastern Finland, Library
>
> [1] CVE-2011-4969 
> https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2011-4969
>

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[dspace-tech] jQuery 1.6.2

[Ilja Sidoroff]

At routine system scan by our IT department noticed, that mirage theme uses 
jQuery version 1.6.2, which is vulnerable to a XSS attack [1]. I don't know 
if this actually exploitable in DSpace, but anyway it seems that this is 
fixable by simple bumping the version to 1.6.4. Is it worth of making a 
pull request to fix this?

Ilja Sidoroff
Information Specialist
University of Eastern Finland, Library

[1] CVE-2011-4969 
https://cve.mitre.org/cgi-bin/cvename.cgi?name=CVE-2011-4969

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[dspace-tech] Re: Possible bug in DSpace 5.4 with batch metadata import, workflow edit metadata and file upload

[Ilja Sidoroff]

It seems that Sherpa/Romeo isn't the thing to blame (expect for perhaps 
showing up in the wrong page). There doesn't seem to be a possibility to 
upload new files when reviewing and editing items in the workflow phase. It 
seems that the code for initial submission and reviewing are almost, but 
not quite the same. Has anyone got any pointers, where I this happens in 
the source code, so I could take a look?

I will probably be filing a bug on this, after I pinpoint the cause, as I 
don't think this is the intended behaviour.

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[dspace-tech] Re: Possible bug in DSpace 5.4 with batch metadata import, workflow edit metadata and file upload

[Ilja Sidoroff]

I changed dspace.cfg not to require uploads

webui.submit.upload.required = false

And I didn't get stuck on the "Upload" page anymore. However, Sherpa/Romeo 
information still gets printed in the wrong page. Also, upload page doesn't 
display any possibilities to actually upload any files, so it still seems 
to be broken.


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