DOI problem

[Péter Király]

Dear Community,

I have a problem with setting up the system to use with DOI server. I
followed carefully the documentation and set everything what was suggested,
but in the log
(/usr/local/glassfish4/glassfish/domains/domain1/logs/server.log) I found
error messages saying that the DOI username has not been set:

[2018-05-23T12:10:23.541+0200] [glassfish 4.1] [SEVERE] []
[edu.harvard.iq.dataverse.DOIDataCiteRegisterService] [tid: _ThreadID=57
_ThreadName=jk-connector(5)] [timeMillis: 1527070223541] [levelValue: 1000]
[[
Error creating DOI at DataCite: Fail to init Client]]

[2018-05-23T12:10:23.541+0200] [glassfish 4.1] [SEVERE] []
[edu.harvard.iq.dataverse.DOIDataCiteRegisterService] [tid: _ThreadID=57
_ThreadName=jk-connector(5)] [timeMillis: 1527070223541] [levelValue: 1000]
[[
Exception
java.lang.RuntimeException: Fail to init Client
at
edu.harvard.iq.dataverse.DataCiteRESTfullClient.<init>(DataCiteRESTfullClient.java:63)
...
Caused by: java.lang.IllegalArgumentException: Username may not be null
at org.apache.http.util.Args.notNull(Args.java:54)
at
org.apache.http.auth.UsernamePasswordCredentials.<init>(UsernamePasswordCredentials.java:78)
at
edu.harvard.iq.dataverse.DataCiteRESTfullClient.<init>(DataCiteRESTfullClient.java:55)
... 162 more

My settings:

> curl http://localhost:8080/api/admin/settings/:Authority -w "\n"
{"status":"OK","data":{"message":"10.25360"}}
> curl http://localhost:8080/api/admin/settings/:DoiProvider -w "\n"
{"status":"OK","data":{"message":"DataCite"}}
> curl http://localhost:8080/api/admin/settings/:DoiSeparator -w "\n"
{"status":"OK","data":{"message":"/"}}
> curl http://localhost:8080/api/admin/settings/:Protocol -w "\n"
{"status":"OK","data":{"message":"doi"}}

> asadmin list-jvm-options | grep -i doi
-Ddoi.username=[my username]
-Ddoi.password=[my password]
-Ddoi.baseurlstring=https://mds.datacite.org

What should I set, and how can I check my settings - other that what I
listed?

Any hints are welcome!
Péter

--
Péter Király
software developer
GWDG, Göttingen - Europeana - eXtensible Catalog - The Code4Lib Journal
http://linkedin.com/in/peterkiraly

[Philip Durbin]

I just tried visiting https://mds.datacite.org in my browser and got "504 Gateway Time-out".

Over at http://status.datacite.org I'm seeing "Major Outage" for "Metadata Store (MDS) API".

I'll attach some screenshots.

Phil

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http://www.iq.harvard.edu/people/philip-durbin

[Leonhard Maylein]

Yes, the last days we observed several outages of DataCite API
(also with our other services/repositories).

Leonhard Maylein




Zitat von Philip Durbin <philip...@harvard.edu>:

>> email to dataverse-commu...@googlegroups.com.
>> To post to this group, send email to dataverse...@googlegroups.com.

>> To view this discussion on the web visit https://groups.google.com/d/
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>> qg2zgGNQNzZ241ifuVDm0HKANGWEiQ%40mail.gmail.com.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
>
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> Philip Durbin
> Software Developer for http://dataverse.org
> http://www.iq.harvard.edu/people/philip-durbin
>

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[Péter Király]

Dear Philip and Leonhard,

thanks for you reply.

I tried it again several times, when the Datacite site was up and running
(checked in browser and with ping). I still have issue, and from the log my
impression is that the system properties are not picked up.

The error message:

[2018-05-25T17:53:43.167+0200] [glassfish 4.1] [SEVERE] []
[edu.harvard.iq.dataverse.DataCiteRESTfullClient] [tid: _ThreadID=56
_ThreadName=jk-connector(4)] [timeMillis: 1527263623167] [levelValue: 1000]
[[
Fail to init Client

java.lang.IllegalArgumentException: Username may not be null
at org.apache.http.util.Args.notNull(Args.java:54)
at

org.apache.http.auth.UsernamePasswordCredentials.<init>(UsernamePasswordCredentials.java:78)
at
edu.harvard.iq.dataverse.DataCiteRESTfullClient.<init>(DataCiteRESTfullClient.java:55)

at
edu.harvard.iq.dataverse.DOIDataCiteRegisterService.openClient(DOIDataCiteRegisterService.java:40)
at
edu.harvard.iq.dataverse.DOIDataCiteRegisterService.createIdentifier(DOIDataCiteRegisterService.java:90)
...

line 40 of DOIDataCiteRegisterService.java:
return new DataCiteRESTfullClient(System.getProperty("doi.baseurlstring"),
System.getProperty("doi.username"), System.getProperty("doi.password"));

Now it seems that the only way I can check the whether the property is set
up is via asadmin tool (asadmin list-jvm-options | grep -i doi). It reports
correct settings.
Is there a way within Dataverse (in the GUI or an API call) or in Glassfish
to check whether what I set with asadmin is really landing in
System.getProperty(...)?

Best,
Péter
Leonhard Maylein <May...@ub.uni-heidelberg.de> ezt írta (időpont: 2018.
máj. 23., Sze, 21:07):

https://groups.google.com/d/msgid/dataverse-community/20180523190722.Horde.BdDCtLxBIJdpMHhY8kT5hna%40heidi.ub.uni-heidelberg.de

.
> For more options, visit https://groups.google.com/d/optout.



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[Péter Király]

Another related question: is there a way to export a dataset's data in
Datacite compilant format?
In the UI the "Cite Dataset" link provide EndNote XML, RIS and BibTeX, but
not Datacite format.
Péter Király <kiru...@gmail.com> ezt írta (időpont: 2018. máj. 25., P,
18:03):

[Philip Durbin]

Here's where "doi.username" is looked up but I don't see any debugging
lines: https://github.com/IQSS/dataverse/blob/v4.8.6/src/main/java/edu/harvard/iq/dataverse/DOIDataCiteRegisterService.java#L40

Unfortunately, this means that you can't simply increase logging as
mentioned at http://guides.dataverse.org/en/4.8.6/admin/troubleshooting.html#glassfish

You could manually add a debugging line or two but you'd have to
recompile a war file. If you go to this trouble, please make a pull
request! If this sounds like a crazy amount of work, please open a
GitHub issue saying that you need these debug lines for
troubleshooting.

I hope you have already tried restarting Glassfish. When editing
domain.xml by hand, you have to restart Glassfish for it to pick up
the change.

Phil

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[Philip Durbin]

There's a pull request in the works to add DataCite XML as a
exportable format for dataset metadata:
https://github.com/IQSS/dataverse/pull/4664

It wouldn't appear under "Cite Dataset" though. It would appear under
"Metadata" and then "Export Metadata" like the other formats
documented at http://guides.dataverse.org/en/4.8.6/admin/metadataexport.html

I'll include a screenshot of the current list of four formats.

Phil

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[Péter Király]

Thanks for the tip!

I did not edit the domain.xml, I use only the asadmin tool. Should I edit
it instead/above using asadmin?

Péter
Philip Durbin <philip...@harvard.edu> ezt írta (időpont: 2018. máj.
25., P, 18:31):

https://groups.google.com/d/msgid/dataverse-community/CABbxx8FkDsRmJp9VNubw0cwmYEZQszsNw14dPTK9RpVK_AePsw%40mail.gmail.com

[Philip Durbin]

I prefer using asadmin because I don't have to restart Glassfish, but
it's up to you. I documented both ways at
http://guides.dataverse.org/en/4.8.6/installation/config.html#jvm-options

> To view this discussion on the web visit https://groups.google.com/d/msgid/dataverse-community/CABFhGt%3DRQo27imCBOsPJWruRNYYf9QxNzZBx-TEpfq92g6%2BipA%40mail.gmail.com.

[Péter Király]

Hi,

it turned out, that it happened because of my fault: I set up the prefix
received from mds.test.datacite.org instead of mds.datacite.org (in both
test and production server there is a test and non-test prefix, and I
thought that the non-test prefix in the test environment is a production
prefix, which generate proper, broadcastable DOIs. Now I know that it was a
false assumption, only the non test prefix of the non test enviroment works
properly).
Now I changed it, and for new datasets it picks up the proper prefix.

The question: is there a way to change the ID of an old dataset? There is
one important dataset for which it is expected to be available in the DOI
databases. One way is to recreate the dataset, but I am wondering whether
is there a programmable way?

Best,

Péter

Philip Durbin <philip...@harvard.edu> ezt írta (időpont: 2018. máj.

25., P, 18:47):

https://groups.google.com/d/msgid/dataverse-community/CABbxx8GjXMf3WoWO17e%2B-q--O7ss3GiT72UsoYzF55wdP9sgqw%40mail.gmail.com

[Philip Durbin]

I'm glad to hear that the original problem has been resolved!

Please forgive me if I'm not following, but are you saying that you have dataset that you've published under a test DOI prefix and now you want to change its prefix to another? As you said, one way to to recreate the dataset and you might find this newly rewritten "Update Metadata For a Dataset" section of the API Guide helpful: https://github.com/IQSS/dataverse/blob/1e01f8fd4fe3b9d68c69ba4bc78e23075fc05958/doc/sphinx-guides/source/api/native-api.rst#update-metadata-for-a-dataset

Alternatively, you could hack on the prefix in the database, but we generally don't recommend hacking on the database. From the database perspective the prefix is stored in a column called "authority" and in the latest code it's stored in the "dvobject" table ( http://phoenix.dataverse.org/schemaspy/latest/tables/dvobject.html ) but in your version it's probably in the "dataset" table. You can find a story of hacking on DOIs in the database at https://groups.google.com/d/msg/dataverse-community/j1D8Fy9FJbc/ZiR3jsuCCQAJ

I hope this helps.

Phil

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> >> > Péter Király
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Journal
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> Philip Durbin
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Péter Király
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http://linkedin.com/in/peterkiraly

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