Re: [Ala-portal] Collectory issue

4 Sep 2014


      Thanks Santiago.
This is a bug with the order in which the charts are loaded. 
Will send an update to the list with a fix soon.
Cheers
Dave
________________________________________
From: Santiago Martinez de la Riva [sama@gbif.es]
Sent: 03 September 2014 23:32
To: Martin, Dave (NRCA, Black Mountain); ala-portal@lists.gbif.org
Subject: RE: Collectory issue
Hi Dave,
I think that the problem is that show.gsp uses the variables from Config.groovy and not the variables from collectory-config.properties:
biocacheServicesUrl = "${grailsApplication.config.biocacheServicesUrl}";
          biocacheWebappUrl = "${grailsApplication.config.biocacheUiURL}";
And the values of these variables are:
/******************************************************************************\
 *  EXTERNAL SERVERS
******************************************************************************/
if (!bie.baseURL) {
     bie.baseURL = "http://bie.ala.org.au/"
}
if (!bie.searchPath) {
    bie.searchPath = "/search"
}
if (!biocacheUiURL) {
    biocacheUiURL = "http://biocache.ala.org.au"
}
if(!biocacheServicesUrl){
    biocacheServicesUrl = "http://biocache.ala.org.au/ws"
}
I changed this values but again the json calls point to biocache.ala.org.aul!!
I don't understand it :(
Thanks.
---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama@gbif.es
28014 Madrid, Spain                                 www.gbif.es
________________________________________
De: David.Martin@csiro.au [David.Martin@csiro.au]
Enviado el: miércoles, 03 de septiembre de 2014 13:05
Para: Santiago Martinez de la Riva; ala-portal@lists.gbif.org
Asunto: RE: Collectory issue
Correction:
biocacheUiURL=http://datos.gbif.es/generic-hub
Cheers
Dave
________________________________________
From: ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of David.Martin@csiro.au [David.Martin@csiro.au]
Sent: 03 September 2014 20:55
To: sama@gbif.es; ala-portal@lists.gbif.org
Subject: [ExternalEmail] Re: [Ala-portal] Collectory issue
Thanks Santiago.
Use the codes that the provider wrote in the occurrence.txt. The listAllProviderMaps.png screenshot you sent earlier in the thread looked good to me.
Yes those biocache.ala.org.au... URLs are wrong. Which suggest we're missing some configuration. Check your /data/collectory/config/collectory-config.properties (template is here [1]) for the property biocacheServicesUrl which should look something like:
# Biocache integration
biocacheUiURL=http://datos.gbif.es/
biocacheServicesUrl=http://datos.gbif.es/biocache-service/
Cheers
Dave
[1] https://github.com/AtlasOfLivingAustralia/ala-install/blob/master/ansible/ro...
________________________________________
From: Santiago Martinez de la Riva [sama@gbif.es]
Sent: 03 September 2014 20:33
To: Martin, Dave (NRCA, Black Mountain); ala-portal@lists.gbif.org
Subject: RE: Collectory issue
Thanks Dave,
But I have not been able to resolve my problem. :/
I have some question. When you have to create the code of the institution/collection, Do i have to use the internal codes (in1, co3) that the collectory module  assigns when I create that Institution/collection or I have to use the codes that the provider wrote in the occurrence.txt? I've checked it with both cases, and I don't get to create these relations.
Can you see my particular case? http://datos.gbif.es/collectory/public/show/in1. Maybe you see something weird in the javascript calls, why does this page need to call to biocache of ala service?
Javascript: http://biocache.ala.org.au/ws/occurrences/search.json?facets=type_status&... [attached image]
I mean, this service would be:  http://datos.gbif.es/ws....is it Right??
Could you explain me how works this part??
I did the re-process and re-index of this dataset dr40, but the problem didn't resolve :(
In other hand, I solved the problem with the density imagen, how you told me, but It's a Australian mapa.
Thanks,
SaMa.
---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama@gbif.es
28014 Madrid, Spain                                 www.gbif.es
________________________________________
De: David.Martin@csiro.au [David.Martin@csiro.au]
Enviado el: miércoles, 03 de septiembre de 2014 10:44
Para: Santiago Martinez de la Riva; ala-portal@lists.gbif.org
Asunto: RE: Collectory issue
Thanks Santi. Its looking really nice :)
If there are any changes to provider codes etc, then you'll need to run:
biocache process -dr dr174
and after that
biocache index -dr dr174
for the changes to take affect. "biocache ingest -dr dr174" runs the load, sample, process and index. Its the process step that links up the information in the collectory to the records in cassandra. Then to pick up the changes in SOLR we need to run the indexing again.
The map URL [1]  looks like its is throwing an error because its missing write access to the directory "/data/output/heatmap". This might be a bug with the ansible scripts - we'll have to check. This directory can be changed with the following property in /data/biocache/config/biocache-config.properties.
# Base directory for heatmap images
heatmap.output.dir=/data/output/heatmap
The problems with logger.ala.org.au are something we'll have to look into. We haven't included the logger application with the ala-demo ansible playbook (something we've overlooked), so we'll need to include it or disable references to it by default in the collectory.
Cheers,
Dave
[1]  http://datos.gbif.es/biocache-service/density/map?q=collection_uid:co3
________________________________________
From: ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of Santiago Martinez de la Riva [sama@gbif.es]
Sent: 03 September 2014 17:43
To: ala-portal@lists.gbif.org
Subject: Re: [Ala-portal] Collectory issue
Sorry, I forgot that the last step,
6) Re-index the dataset.
Cheers.
---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama@gbif.es
28014 Madrid, Spain                                 www.gbif.es
________________________________________
De: Santiago Martinez de la Riva
Enviado el: miércoles, 03 de septiembre de 2014 9:17
Para: ala-portal@lists.gbif.org
Asunto: Collectory issue
Hi Nick,
I'm going to try to explain  my current issue. I can't see the information of the records of one particular resource in the page of the related Institution and  Collection. Firstly, I go to explain the steps that I did to get to this situation:
1) I uploaded the data set.
2) I executed the ingest process of the data set.
3) I created the Institution and the collection of this resource.
4) I created the the relationships between this resource, the institution and the collection.
5) Also I created the Providers code, you can see my current Provider Map in the attached image.
It seems that all it's right. But the problem It's that when I access to the public  section of collectory, and I try to see the information to this Institution and this Collection, the app isn't able to show the related records. I think that the calls that are launched in this module are wrong, because it's trying to communicate with the biocache.ala.org.au.
http://datos.gbif.es/collectory/public/show/in1:
Javascript:
-  http://logger.ala.org.au/service/in1/events/1002/counts.json?callback=jQuery...
- http://logger.ala.org.au/service/reasonBreakdown.json?eventId=1002&entit...
And the most important that is related to in1:
-http://biocache.ala.org.au/ws/occurrences/search.json?pageSize=0&q=insti...
-http://biocache.ala.org.au/ws/occurrences/search.json?pageSize=0&q=insti...
http://datos.gbif.es/collectory/public/show/co3:
ERROR:
"NetworkError: 500 Error Interno del Servidor - http://datos.gbif.es/biocache-service/density/map?q=collection_uid:co3"
Javascript:
- http://logger.ala.org.au/service/co3/events/1002/counts.json?callback=jQuery...
- http://biocache.ala.org.au/ws/occurrences/search.json?pageSize=0&q=colle...
- http://biocache.ala.org.au/ws/occurrences/search.json?facets=type_status&...
Thanks so much.
SaMa
---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama@gbif.es
28014 Madrid, Spain                                 www.gbif.es
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Re: [Ala-portal] Collectory issue

David.Martin＠csiro.au