[Ala-portal] issues with the Collectory module.
Tim Robertson [GBIF]
trobertson at gbif.org
Mon Apr 28 10:34:18 CEST 2014
Thanks for testing that Daniel
For background information: This issue came following the GBIF API deploy last week which tightened up security. Previously people could discover download status without actually authenticating - while this posed no real risk, it was an oversight in the API security, and we addressed that. You will also note, that downloads are now much “wider” as GBIF support the full width of Darwin Core in the index now.
Thanks,
Tim
On 28 Apr 2014, at 08:49, Daniel Lins <daniel.lins at gmail.com> wrote:
> Hi Santiago,
>
> I tried to add some GBIF resources from Brazil in my database, using the same functionality "Add all GBIF resources for a country" and works for me (resources with 0 records were not created and the download process was killed).
> After I tried to add one dataset of Spain (like your test case), and the system didn't raise any error message. However, the download never ends (In my GBIF profile page these download process was successfully finished).
>
> Your Downloads
> FILTER Dataset SANT-Algae
> STATUS Ready for download (0 B 28.626 records - 1 datasets)
> CREATED 28/04/2014
>
> Check the username and password and make sure if the folder "/data/collectory/upload" has write permission, because the downloaded files are saved in this folder by default.
>
> Hope that this helps.
>
> Cheers.
>
>
> 2014-04-25 3:46 GMT-03:00 sama <sama at gbif.es>:
> -----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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> _______________________________________________
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>
>
>
> --
> Daniel Lins da Silva
> (Cel) 11 6144-4050
> daniel.lins at gmail.com
> _______________________________________________
> Ala-portal mailing list
> Ala-portal at lists.gbif.org
> http://lists.gbif.org/mailman/listinfo/ala-portal
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