Hi Fanny,
please keep the list in cc so other devs can share their feedback.
On Wed, Nov 2, 2016 at 3:01 PM, MARTIN, FANNY <[email protected]> wrote:
> Hi Daniele,
>
>
>
> My answers to your questions in your email.
>
>
>
> Should I add some settings after uploading my shapefile ? I have edited
> the layer to modify the dimensions and netCDF Output Settings but I still
> get the same error.
>
> How shall the NetCDF Output settings be configured ?
>
If you don't have specific needs (as an instance CF-Compliant name,
Compression, Global attributes to be added...) you shouldn't need to
configure it.
>
> Thanks,
>
> Fanny
>
>
>
>
>
> *From:* [email protected] [mailto:[email protected]] *On
> Behalf Of *Daniele Romagnoli
> *Sent:* Friday, October 28, 2016 3:03 PM
> *To:* MARTIN, FANNY
> *Cc:* [email protected]
> *Subject:* Re: [Geoserver-users] NetCDF-4 Native Libraries installation
>
>
>
> Hi Fanny,
>
> a supported NetCDF layer should be successfully encoded as NetCDF in
> output.
>
>
>
> Additional couple of questions:
>
> - can you run an "ncdump -h" on your sample NetCDF dataset?
>
> My sample NetCDF file comes from CMEMS. I manage to run “ncdump –h” on
> this sample.
>
Can you report the result of that command? :)
>
>
> - once you have configured the NetCDF store for it, which layers did you
> configure? (from a Geoserver point of view, a NetCDF dataset containing
> multiple variables is exposed as a NetCDF store containing multiple
> coverages->layers)
>
> I do not do any configuration for the layers. I upload my netcdf using the
> rest API. The request I send is the following:
>
> curl -u user:pwd -XPUT -H "Content-type:application/zip" --data-binary
> @netcdf.zip https://geoserver/geoserver/rest/workspaces/test/
> coveragestores/testnetcdf/file.netcdf --insecure
>
> It publishes as many layers as variables in the “tetnetcdf” datastore.
>
>
>
> - What request are you sending to get one of the layers encoded back to
> NetCDF? (do you have an url or a posted xml?)
>
> To retrieve one of the encoded layer I use the following xml (retrieved
> from the WCS demo request builder):
>
> <?xml version="1.0" encoding="UTF-8"?><GetCoverage version="1.0.0"
> service="WCS" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
> xmlns="http://www.opengis.net/wcs"; xmlns:ows="http://www.opengis.
> net/ows/1.1" xmlns:gml="http://www.opengis.net/gml"; xmlns:ogc="
> http://www.opengis.net/ogc"; xsi:schemaLocation="http://www.opengis.net/wcs
> http://schemas.opengis.net/wcs/1.0.0/getCoverage.xsd";>
>
> <sourceCoverage>test:analysed_sst</sourceCoverage>
>
> <domainSubset>
>
> <spatialSubset>
>
> <gml:Envelope srsName="EPSG:4326">
>
> <gml:pos>-180.00000610436345 -89.99999847369712</gml:pos>
>
> <gml:pos>180.00000610436345 89.99999847369712</gml:pos>
>
> </gml:Envelope>
>
> <gml:Grid dimension="2">
>
> <gml:limits>
>
> <gml:GridEnvelope>
>
> <gml:low>0 0</gml:low>
>
> <gml:high>7200 3600</gml:high>
>
> </gml:GridEnvelope>
>
> </gml:limits>
>
> <gml:axisName>x</gml:axisName>
>
> <gml:axisName>y</gml:axisName>
>
> </gml:Grid>
>
> </spatialSubset>
>
> </domainSubset>
>
> <output>
>
> <crs>EPSG:4326</crs>
>
> <format>NetCDF</format>
>
> </output>
>
> </GetCoverage>
>
>
>
I would use a WCS 2.0 request instead to access a Multidimensional dataset
(as NetCDF).
Can you try if this simple KVP sample request works for you?
http://HOST:PORT
/geoserver/wcs?request=GetCoverage&service=WCS&version=2.0.1&coverageId=test__analysed_sst&Format=application/x-netcdf&subset=
http://www.opengis.net/def/axis/OGC/0/Long(-180,180)&subset=http://www.opengis.net/def/axis/OGC/0/Lat(-90,90)
> You may find some additional tutorials and samples here:
>
> http://geoserver.geo-solutions.it/edu/en/multidim/netcdf/index.html
>
> http://geoserver.geo-solutions.it/edu/en/multidim/
> accessing_multidim/netcdf_output.html
>
You may take a look to this page to get more info about specifying WCS 2.0
requests against multidimensional datasets.
http://geoserver.geo-solutions.it/edu/en/multidim/accessing_multidim/netcdf_output.html
Please, let me know if it works.
Cheers,
Daniele
>
> Cheers,
>
> Daniele
>
>
>
>
>
>
>
> On Fri, Oct 28, 2016 at 2:44 PM, MARTIN, FANNY <[email protected]>
> wrote:
>
> Dear Daniele,
>
>
>
> Thanks for your answer.
>
>
>
> I do both of the following:
>
> - upload a netcdf file packaged in a zip through the REST API
>
> curl -u user:pwd -XPUT -H "Content-type:application/zip" --data-binary
> @netcdf.zip https://xxxx/geoserver/rest/workspaces/test/
> coveragestores/testnetcdf/file.netcdf
>
> - upload a netcdf file through the Web interface as a NetCDF
> store
>
>
>
> It is then a NetCDF itself that I cannot encode as NetCDF… Are some
> configurations required to handle it ?
>
> Cheers,
>
> Fanny
>
>
>
> *From:* [email protected] [mailto:[email protected]] *On
> Behalf Of *Daniele Romagnoli
> *Sent:* Friday, October 28, 2016 11:27 AM
> *To:* MARTIN, FANNY
> *Cc:* [email protected]
> *Subject:* Re: [Geoserver-users] NetCDF-4 Native Libraries installation
>
>
>
> Dear Fanny,
>
> what format of input coverageStore are you trying to encode as NetCDF?
>
>
>
> NetCDF output is only supported for input coverages being served by a
> coverageStore leveraging on StructuredGridCoverage2DReader.
>
> http://docs.geoserver.org/stable/en/user/extensions/
> netcdf-out/index.html#current-limitations
>
>
>
> StructuredGridCoverage2DReaders expose the underlying dimensions so that
> the GetCoverage of WCS2.0 can setup a stack (a GranuleStack) of
> GridCoverages and assign related input dimension values to each element of
> the stack.
>
> Trivial example:
>
> GridCoverage2D #0 of the stack is related to time=T0 and elevation=Z0,
>
> GridCoverage2D #1 of the stack is related to time=T0 and elevation=Z1,
>
> GridCoverage2D #2 of the stack is related to time=T1 and elevation=Z0,
>
> GridCoverage2D #3 of the stack is related to time=T1 and elevation=Z1)
>
>
>
> This information will then be used by the NetCDF Writer to setup proper
> NetCDF dimensions on output and setup proper multidimensional data array.
>
> So if you have an ImageMosaic on top of a Multidimensional dataset (having
> different times and elevations, as an instance) you can encode it as a
> NetCDF.
>
>
>
> Indeed, at the moment, the only Coverage Reader formats implementing a
> StructuredGridCoverage2DReader are the ImageMosaic and the NetCDF itself.
>
>
>
> To summarize: the "*java.lang.IllegalArgumentException: NetCDF encoding
> only supports granuleStack coverages" *isn't related to a NetCDF4 native
> library issue.
>
> That is a different topic:
>
>
>
> *NetCDF-4 C library not present (jna_path='null', libname='netcdf') *is a
> simple warning reporting that your GeoServer won't be able to encode output
> to NetCDF4-Classic whilst it will be able to encode NetCDF3.
>
> If you want to have NetCDF4-C supported (as an instance to leverage on
> HDF5 compression capabilities), you need to properly install native
> libraries.
>
> http://docs.geoserver.org/2.8.1/user/extensions/netcdf-out/
> nc4.html#linux-install
>
> I know you have already checked these instructions but at the moment I
> have no additional feedbacks on the Native Library building topic.
>
> We never encountered that problem before. (It seems it is unable to find
> the required HDF5 lib so you may want to double check all the dependencies
> are available).
>
>
>
> Cheers,
>
> Daniele
>
>
>
>
>
>
>
>
>
>
>
> On Fri, Oct 28, 2016 at 9:34 AM, MARTIN, FANNY <[email protected]>
> wrote:
>
> Dear all,
>
>
>
> While trying to retrieve a NetCDF4 thanks to WCS request, I get the
> following error:
>
> *java.lang.IllegalArgumentException: NetCDF encoding only supports
> granuleStack coverages*
>
> *NetCDF encoding only supports granuleStack coverages*
>
>
>
> I guess the error is due to the failed installation of the NetCDF-4 Native
> Library. I get the following error when strating Geoserver:
>
> *NetCDF-4 C library not present (jna_path='null', libname='netcdf').*
>
>
>
> And this one at the installation of the NetCDF C Library:
>
> *checking for library containing H5Fflush... configure: error: Can't find
> or link to the hdf5 library. Use --disable-netcdf-4, or see config.log for
> errors.*
>
> *make: *** No rule to make target 'check'. Stop.*
>
>
>
> I try to install the NetCDF Output Format plugin in a Geoserver 2.8.1
> Tomcat installation. For this purpose, I have followed the instruction
> given at http://docs.geoserver.org/2.8.1/user/extensions/netcdf-out/
> nc4.html#nc4. After some searchs on the internet, the problem is mostly
> solved with the use of the CPPFLAGS and LDFLAGS, flags that I already
> use... Any other hints welcome !
>
>
>
> Thanks in advance,
>
> Fanny
>
>
>
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> --
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> ==
>
> GeoServer Professional Services from the experts! Visit
> http://goo.gl/it488V for more information.
> ==
>
> Ing. Daniele Romagnoli
> Senior Software Engineer
>
> GeoSolutions S.A.S.
> Via di Montramito 3/A
> 55054 Massarosa (LU)
> Italy
> phone: +39 0584 962313
> fax: +39 0584 1660272
>
> http://www.geo-solutions.it
> http://twitter.com/geosolutions_it
>
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> --
>
> ==
>
> GeoServer Professional Services from the experts! Visit
> http://goo.gl/it488V for more information.
> ==
>
> Ing. Daniele Romagnoli
> Senior Software Engineer
>
> GeoSolutions S.A.S.
> Via di Montramito 3/A
> 55054 Massarosa (LU)
> Italy
> phone: +39 0584 962313
> fax: +39 0584 1660272
>
> http://www.geo-solutions.it
> http://twitter.com/geosolutions_it
>
> -------------------------------------------------------
>
> *AVVERTENZE AI SENSI DEL D.Lgs. 196/2003*
>
> Le informazioni contenute in questo messaggio di posta elettronica e/o
> nel/i file/s allegato/i sono da considerarsi strettamente riservate. Il
> loro utilizzo è consentito esclusivamente al destinatario del messaggio,
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> stesso, cancellandolo dal Vostro sistema. Conservare il messaggio stesso,
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> utilizzarlo per finalità diverse, costituisce comportamento contrario ai
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>
>
>
> The information in this message and/or attachments, is intended solely for
> the attention and use of the named addressee(s) and may be confidential or
> proprietary in nature or covered by the provisions of privacy act
> (Legislative Decree June, 30 2003, no.196 - Italy's New Data Protection
> Code).Any use not in accord with its purpose, any disclosure, reproduction,
> copying, distribution, or either dissemination, either whole or partial, is
> strictly forbidden except previous formal approval of the named
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>
>
> Ce message et toutes les pièces jointes (ci-après le "message") sont
> établis à l’intention exclusive des destinataires désignés. Il contient des
> informations confidentielles et pouvant être protégé par le secret
> professionnel. Si vous recevez ce message par erreur, merci d'en avertir
> immédiatement l'expéditeur et de détruire le message. Toute utilisation de
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> pourrait être tenu pour responsable des dommages engendrés par la
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> This message and any attachments (the "message") are intended solely for
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--
==
GeoServer Professional Services from the experts! Visit
http://goo.gl/it488V for more information.
==
Ing. Daniele Romagnoli
Senior Software Engineer
GeoSolutions S.A.S.
Via di Montramito 3/A
55054 Massarosa (LU)
Italy
phone: +39 0584 962313
fax: +39 0584 1660272
http://www.geo-solutions.it
http://twitter.com/geosolutions_it
-------------------------------------------------------
*AVVERTENZE AI SENSI DEL D.Lgs. 196/2003*
Le informazioni contenute in questo messaggio di posta elettronica e/o
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loro utilizzo è consentito esclusivamente al destinatario del messaggio,
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The information in this message and/or attachments, is intended solely for
the attention and use of the named addressee(s) and may be confidential or
proprietary in nature or covered by the provisions of privacy act
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Code).Any use not in accord with its purpose, any disclosure, reproduction,
copying, distribution, or either dissemination, either whole or partial, is
strictly forbidden except previous formal approval of the named
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immediately the sender by telephone, fax or e-mail and delete the
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