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r-geoflow / geoflow

Tools to Orchestrate Geospatial (Meta)Data Management Workflows and Manage FAIR Services
https://github.com/r-geoflow/geoflow/wiki
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no native format for coverages #279

Closed juliepierson closed 1 year ago

juliepierson commented 2 years ago

Hi, When creating a coverage from a geotiff image with geoflow, WMS is ok but WCS cannot be accessed. When I add <nativeFormat>GeoTIFF</nativeFormat> in coverage with the geoserver rest API, WCS works ok. Thanks !

eblondel commented 1 year ago

@juliepierson on this specific issue, I'd need to spend some time with you, if you can show me lively the issue with a run of workflow.

juliepierson commented 1 year ago

Just tested now to access a WCS via QGIS, here's geoserver logs : 2022-10-13 13:04:55,190 ERROR [geoserver.ows] - java.io.IOException at org.geoserver.wcs.response.Wcs10DescribeCoverageResponse.write(Wcs10DescribeCoverageResponse.java:36) at org.geoserver.ows.Dispatcher.response(Dispatcher.java:1029) at org.geoserver.ows.Dispatcher.handleRequestInternal(Dispatcher.java:269) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:177) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:52) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:1040) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:943) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:1006) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:898) at javax.servlet.http.HttpServlet.service(HttpServlet.java:634) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:883) at javax.servlet.http.HttpServlet.service(HttpServlet.java:741) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.ThreadLocalsCleanupFilter.doFilter(ThreadLocalsCleanupFilter.java:26) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(SpringDelegatingFilter.java:69) at org.geoserver.wms.animate.AnimatorFilter.doFilter(AnimatorFilter.java:70) at org.geoserver.filters.SpringDelegatingFilter$Chain.doFilter(SpringDelegatingFilter.java:66) at org.geoserver.filters.SpringDelegatingFilter.doFilter(SpringDelegatingFilter.java:41) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.platform.AdvancedDispatchFilter.doFilter(AdvancedDispatchFilter.java:37) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:70) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:127) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:91) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:74) at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:70) at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:119) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:74) at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.geoserver.security.filter.GeoServerAnonymousAuthenticationFilter.doFilter(GeoServerAnonymousAuthenticationFilter.java:51) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:70) at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:74) at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91) at org.geoserver.security.filter.GeoServerBasicAuthenticationFilter.doFilter(GeoServerBasicAuthenticationFilter.java:81) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.geoserver.security.filter.GeoServerPreAuthenticationFilter.doFilter(GeoServerPreAuthenticationFilter.java:71) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:70) at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105) at org.geoserver.security.filter.GeoServerSecurityContextPersistenceFilter$1.doFilter(GeoServerSecurityContextPersistenceFilter.java:52) at org.geoserver.security.filter.GeoServerCompositeFilter$NestedFilterChain.doFilter(GeoServerCompositeFilter.java:74) at org.geoserver.security.filter.GeoServerCompositeFilter.doFilter(GeoServerCompositeFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334) at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215) at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178) at org.geoserver.security.GeoServerSecurityFilterChainProxy.doFilter(GeoServerSecurityFilterChainProxy.java:142) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.LoggingFilter.doFilter(LoggingFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.XFrameOptionsFilter.doFilter(XFrameOptionsFilter.java:77) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.GZIPFilter.doFilter(GZIPFilter.java:47) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.SessionDebugFilter.doFilter(SessionDebugFilter.java:46) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.geoserver.filters.FlushSafeFilter.doFilter(FlushSafeFilter.java:42) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.filters.CorsFilter.handleNonCORS(CorsFilter.java:352) at org.apache.catalina.filters.CorsFilter.doFilter(CorsFilter.java:171) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92) at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:688) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343) at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:375) at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65) at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1639) at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.base/java.lang.Thread.run(Unknown Source) Caused by: javax.xml.transform.TransformerException: Translator error at org.geotools.xml.transform.TransformerBase.transform(TransformerBase.java:122) at org.geotools.xml.transform.TransformerBase.transform(TransformerBase.java:100) at org.geoserver.wcs.response.Wcs10DescribeCoverageResponse.write(Wcs10DescribeCoverageResponse.java:34) ... 104 more Caused by: java.lang.RuntimeException: Unexpected error occurred during describe coverage xml encoding at org.geoserver.wcs.response.Wcs10DescribeCoverageTransformer$WCS100DescribeCoverageTranslator.encode(Wcs10DescribeCoverageTransformer.java:194) at org.geotools.xml.transform.TransformerBase$XMLReaderSupport.parse(TransformerBase.java:990) at org.apache.xalan.transformer.TransformerIdentityImpl.transform(TransformerIdentityImpl.java:485) at org.geotools.xml.transform.TransformerBase$Task.run(TransformerBase.java:283) at org.geotools.xml.transform.TransformerBase.transform(TransformerBase.java:118) ... 106 more Caused by: java.lang.RuntimeException: Error while committing XML elements; specific element was: End(wcs:supportedFormats) at org.geotools.xml.transform.TransformerBase$TranslatorSupport.commit(TransformerBase.java:697) at org.geoserver.wcs.response.Wcs10DescribeCoverageTransformer$WCS100DescribeCoverageTranslator.encode(Wcs10DescribeCoverageTransformer.java:189) ... 110 more Caused by: java.lang.NullPointerException (sorry for the long text !)

juliepierson commented 1 year ago

Le lien vers le XML : view-source:https://portail.indigeo.fr/geoserver/rest/workspaces/TEST/coveragestores/test_sougeal_2017-07-07/coverages/test_sougeal_2017-07-07.xml

juliepierson commented 1 year ago

J'ai testé en ajoutant <nativeFormat>GeoTIFF</nativeFormat> (sur une autre couche) et ça ne résout pas le problème... J'ai dû me tromper en faisant mes tests la 1ère fois ?

eblondel commented 1 year ago

L'erreur renvoyée par QGIS suppose que c'est la version 1.0.0 du WCS qui est appelée... Si on regarde la description coverage en 2.0.1 cela passe bien (https://portail.indigeo.fr/geoserver/ows?service=WCS&version=2.0.1&request=DescribeCoverage&CoverageId=TEST__test_sougeal_2017-07-07), en revanche cela ne passe pas pour la 1.0.0 https://portail.indigeo.fr/geoserver/ows?service=WCS&version=1.0.0&coverage=TEST:test_sougeal_2017-07-07&request=DescribeCoverage Ce dernier lien devrait renvoyer un XML et ce n'est pas le cas... Est-ce que le module QGIS WCS fonctionne pour tes autres couches geotiff?

eblondel commented 1 year ago

This supposes 2 issues:

If I use the ows4R WCS client, It works well:

require(ows4R)
require(terra)
WCS = ows4R::WCSClient$new(url = "https://portail.indigeo.fr/geoserver/ows", serviceVersion = "2.0.1", logger = "DEBUG")
rr = WCS$getCoverage("TEST:test_sougeal_2017-07-07")
plot(rr)
juliepierson commented 1 year ago

Hi, thanks for your input !

WCS seems to work ok for the geotiff layers I created with geoserver API, I only have this problem for layers created with geoflow.

From the QGIS doc : QGIS has a native WCS provider and supports both version 1.0 and 1.1 (which are significantly different), but currently it prefers 1.0, because 1.1 has many issues (i.e., each server implements it in a different way with various particularities).

eblondel commented 1 year ago

Can we have a call to go through your geoflow?

Le mar. 18 oct. 2022 à 16:36, Julie Pierson @.***> a écrit :

Hi, thanks for your input !

WCS seems to work ok for the geotiff layers I created with geoserver API, I only have this problem for layers created with geoflow.

From the QGIS doc https://docs.qgis.org/3.22/en/docs/user_manual/working_with_ogc/ogc_client_support.html#wcs-client: QGIS has a native WCS provider and supports both version 1.0 and 1.1 (which are significantly different), but currently it prefers 1.0, because 1.1 has many issues (i.e., each server implements it in a different way with various particularities).

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eblondel commented 1 year ago

I suppose that you solved this issue. In case not, feel free to reopen