[Ala-portal] issues with the Collectory module.
David.Martin at csiro.au
David.Martin at csiro.au
Mon Apr 28 07:56:50 CEST 2014
Hi Santiago,
The Collectory has two ways of getting data from GBIF (listed at the bottom of here http://ala-demo.gbif.org/collectory/manage):
1. Add all GBIF resource for a country
2. Upload GBIF file
1 - this attempts to download data from GBIF for you using the web services.
2 - this allows you to upload a file yourself into the collectory that you have previously downloaded yourself through GBIF portal [2].
These tools are mutually exclusive but the result should be the same - a data resource(s) is created and an archive of data is attached to the resource.
We did have some problems last week with (1) which were caused by necessary changes to the GBIF API that we hadn't kept up with.
These are now fixed in the latest build [1].
I hope this helps,
Dave Martin
ALA
[1] http://maven.ala.org.au/repository/au/org/ala/collectory/1.0/collectory-1.0.war
[2] I took the liberty of testing this on your install and the resultant data resource is here: http://193.146.75.144:8080/collectory/dataResource/show/dr2
________________________________________
From: sama [sama at gbif.es]
Sent: 25 April 2014 16:46
To: Martin, Dave (CES, Black Mountain); ala-portal at lists.gbif.org
Subject: Re: [Ala-portal] issues with the Collectory module.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Dear David,
I tried to add one dataset through the option, all GBIF resource for a
country, with your credentials and I also tried with my credentials:
http://193.146.75.144:8080/collectory/manage/gbifLoadCountry
But the Portal always shows me the next message:
- -----
Failed. Please check your authentication credentials are valid.
- -----
Could you check it?
Thank you.
- ------------------------------------------------------------
Santiago Martínez de la Riva Vivanco
GBIF.ES, Unidad de Coordinación
Real Jardín Botánico CSIC
Plaza de Murillo, 2
28014 Madrid, Spain
Tel: +34 91 4293917 x 273 - sama at gbif.es - www.gbif.es -
https://twitter.com/smr_sama
El 24/04/2014 12:29, David.Martin at csiro.au escribió:
> I should have added, you'll need to remove the existing collectory.war and the expanded war from /var/lib/tomcat7/webapps and copy this war file into /var/lib/tomcat7/webapps renaming it to collectory.war.
>
> Dave
> ________________________________________
> From: sama [sama at gbif.es]
> Sent: 24 April 2014 20:26
> To: Martin, Dave (CES, Black Mountain); ala-portal at lists.gbif.org
> Subject: Re: [Ala-portal] issues with the Collectory module.
>
> Thanks so much for your quick reply.
>
> I´m going to test it.
>
> Kind regards.
> Santi.
>
> ------------------------------------------------------------
> Santiago Martínez de la Riva Vivanco
> GBIF.ES, Unidad de Coordinación
> Real Jardín Botánico CSIC
> Plaza de Murillo, 2
> 28014 Madrid, Spain
> Tel: +34 91 4293917 x 273 - sama at gbif.es - www.gbif.es -
> https://twitter.com/smr_sama
>
>
> El 24/04/2014 12:24, David.Martin at csiro.au escribió:
>> Thanks for posting Santiago.
>
>> There is a new build of the collectory that should fix the problems you mentioned with the manual GBIF file upload and editing the data resource:
>
>> http://maven.ala.org.au/repository/au/org/ala/collectory/1.0/collectory-1.0.war
>
>> This is now deployed on the demo server (http://ala-demo.gbif.org).
>
>> Hope this helps.
>
>> Dave Martin
>> ALA
>
>> ________________________________________
>> From: ala-portal-bounces at lists.gbif.org [ala-portal-bounces at lists.gbif.org] on behalf of sama [sama at gbif.es]
>> Sent: 24 April 2014 17:03
>> To: ala-portal at lists.gbif.org
>> Subject: Re: [Ala-portal] issues with the Collectory module.
>
>> My name is Santiago Martínez de la Riva. I'm member of node of Gbif
>> Spain. We have installed the data portal of ALA and we have a problem
>> with the collectory module.
>
>> We can't create new collections or institutions. When we try to add
>> collections or institutions, the Portal shows the next message:
>
>> http://193.146.75.144:8080/collectory/dataResource/uploadGBIFFile
>
>
>> Could be an error caused by problems with permissions in the directory
>> /data/collectory/upload? Because It seems that the server doesn't create
>> the temporal file.
>
>> --------------------------------------
>> An unexpected error has occurred.
>
>> If this is the first time this page has appeared, try the refresh button
>> in your browser.
>
>> If this fails, try to return to the home page and start again.
>
>> If this page is still displayed, please report the incident to ALA
>> support. Click here to email ALA support.
>
>> The following is useful information that helps us discover what has
>> happened. Please copy it into emails requesting support.
>
>> You might also like to expand the more detailed information by clicking
>> on 'Show stack trace' and copying that text to us as well.
>
>> Thanks for your patience.
>> Error 500: Executing action [uploadGBIFFile] of controller
>> [au.org.ala.collectory.DataResourceController] caused exception: Runtime
>> error executing action
>> Servlet: grails
>> URI: /collectory/grails/dataResource/uploadGBIFFile.dispatch
>> Exception Message: /data/collectory/upload/tmp/1398257201760 (No such
>> file or directory)
>> Caused by: /data/collectory/upload/tmp/1398257201760 (No such file or
>> directory)
>> Class: ProviderGroupController
>> At Line: [522]
>> Code Snippet:
>> Show stack trace
>> Stack Trace
>
>> java.io.FileNotFoundException: /data/collectory/upload/tmp/1398257201760
>> (No such file or directory)
>
>> at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
>
>> at java.io.FileOutputStream.<init>(FileOutputStream.java:171)
>
>> at
>> org.apache.commons.fileupload.disk.DiskFileItem.write(DiskFileItem.java:449)
>
>> at
>> au.org.ala.collectory.GbifService.createGBIFResourceFromMultipart(GbifService.groovy:211)
>
>> at
>> au.org.ala.collectory.ProviderGroupController$_closure22.doCall(ProviderGroupController.groovy:522)
>
>> at
>> grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:195)
>
>> -----------------------------
>
>
>> We have realized too that in the demo portal of ala shows another error
>> which is related to updated process of one resource. When we try to
>> modify the information of one resource.
>> For example, for this resource:
>
>> http://ala-ono.it.csiro.au/collectory/dataResource/show/dr172
>
>> If we try to modify some field: the name, the url.., and we try to
>> update the resource, the portal shows the next error message:
>
>
>> -------------------
>
>> An unexpected error has occurred.
>
>> If this is the first time this page has appeared, try the refresh button
>> in your browser.
>
>> If this fails, try to return to the home page and start again.
>
>> If this page is still displayed, please report the incident to ALA
>> support. Click here to email ALA support.
>
>> The following is useful information that helps us discover what has
>> happened. Please copy it into emails requesting support.
>
>> You might also like to expand the more detailed information by clicking
>> on 'Show stack trace' and copying that text to us as well.
>
>> Thanks for your patience.
>> Error 500: Executing action [updateBase] of controller
>> [au.org.ala.collectory.DataResourceController] caused exception: Runtime
>> error executing action
>> Servlet: grails
>> URI: /collectory/grails/dataResource/updateBase.dispatch
>> Exception Message: No signature of method: static
>> au.org.ala.collectory.BaseCommand.get() is applicable for argument
>> types: (java.lang.String) values: [173] Possible solutions:
>> getAt(java.lang.String), getId(), grep(), grep(java.lang.Object),
>> wait(), any()
>> Caused by: No signature of method: static
>> au.org.ala.collectory.BaseCommand.get() is applicable for argument
>> types: (java.lang.String) values: [173] Possible solutions:
>> getAt(java.lang.String), getId(), grep(), grep(java.lang.Object),
>> wait(), any()
>> Class: Unknown
>> At Line: [-1]
>> Code Snippet:
>> Show stack trace
>> Stack Trace
>
>> groovy.lang.MissingMethodException: No signature of method: static
>> au.org.ala.collectory.BaseCommand.get() is applicable for argument
>> types: (java.lang.String) values: [173]
>> Possible solutions: getAt(java.lang.String), getId(), grep(),
>> grep(java.lang.Object), wait(), any()
>
>> at
>> grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:195)
>
>> at
>> grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)
>
>> at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
>
>> at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
>
>> at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
>
>> -------
>
>
>> Kind regards.
>> Santi.
>> ------------------------------------------------------------
>> Santiago Martínez de la Riva Vivanco
>> GBIF.ES, Unidad de Coordinación
>> Real Jardín Botánico CSIC
>> Plaza de Murillo, 2
>> 28014 Madrid, Spain
>> Tel: +34 91 4293917 x 273 - sama at gbif.es - www.gbif.es -
>> https://twitter.com/smr_sama
>
>
>> _______________________________________________
>> Ala-portal mailing list
>> Ala-portal at lists.gbif.org
>> http://lists.gbif.org/mailman/listinfo/ala-portal
>> .
>
> .
>
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