Error trying to save locally a metadata fetched with getRecordById

[ptaconet]

I am trying to get a metadata sheet from the Geoplateforme and then to save it locally. However, I get "Error: attempt to apply non-function" when executing the last line of the code below :

`
library(ows4R)
library(geometa)

CSW <- CSWClient$new("https://data.geopf.fr/csw", "2.0.2", logger = "INFO")
md <- CSW$getRecordById("IGNF_OCS-GE", outputSchema = "http://www.isotc211.org/2005/gmd")

md$save("xml_metadata/geopf/IGNF_OCS-GE.xml")

`

I tried it on several R plateforms.

Am I missing something ?

Thanks for the help !

[ptaconet]

Note that when trying with another catalogue, it works... eg, the following code does work :

CSW2 <- CSWClient$new("https://sdi.eea.europa.eu/catalogue/srv/eng/csw", "2.0.2", logger = "INFO")

md <- CSW2$getRecordById("4635cd57-65d9-47b4-b18e-98a781ef27bb", outputSchema = "http://www.isotc211.org/2005/gmd")
md$save("xml_metadata/copernicus/4635cd57-65d9-47b4-b18e-98a781ef27bb.xml")`

`

[eblondel]

It is a Geonetwork: https://data.geopf.fr/geonetwork/srv/fre/csw?service=CSW&request=GetCapabilities&version=2.0.2

Try using the following url to instantiate your CSW client: https://data.geopf.fr/geonetwork/srv/fre/csw

It should work

[ptaconet]

Thanks for your answer.
However, still having the problem with that new URL..

[eblondel]

CSW <- CSWClient$new("https://data.geopf.fr/csw", "2.0.2", logger = "DEBUG")
md <- CSW$getRecordById("IGNF_OCS-GE", outputSchema = "http://www.isotc211.org/2005/gmd")

works for me
The object md is not NULL, and is an ISOMetadata from geometa package.
If such record object you can then use the $save method.

[ptaconet]

Yes, works for me too up to that point.
But then md$encode() or md$save("IGNF_OCS-GE.xml") does not work (getting "Error: attempt to apply non-function").

Do you get the same error ?

Strange thing is that it works well with other catalogues (eg #145 (comment))

[eblondel]

Which version of ows4R and geometa are you using? Le lun. 30 juin 2025, 08:06, Paul Taconet ***@***.***> a écrit :

…

*ptaconet* left a comment (eblondel/ows4R#145) <#145 (comment)> Yes, works for me too up to that point. But then md$encode() or md$save("IGNF_OCS-GE.xml") does not work (getting "Error: attempt to apply non-function"). Do you get the same error ? Strange thing is that it works well with other catalogues (eg #145 (comment) <#145 (comment)>) — Reply to this email directly, view it on GitHub <#145 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKDK3FJ7IUNJKEYOENAPET3GDHURAVCNFSM6AAAAACAINML7OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTAMJXHEYTENZYGQ> . You are receiving this because you were assigned.Message ID: ***@***.***>

[ptaconet]

ows4R : v0.5
geometa : v0.9.1

Also note that I get the same errors on the imarine d4science RStudio server with ows4R v0.3-5 and geometa v0.7-1

[eblondel]

Forget about this remote server, it's quite outdated from what I see in term of package version.

Use your setting, If you set the logger = "DEBUG", can you copy paste what you get in your R Console (including red messages including the payload sent to CSW server, and any information you see there).
What do you get in the output md, a NULL object?

[ptaconet]

> CSW <- CSWClient$new("https://data.geopf.fr/geonetwork/srv/fre/csw", "2.0.2", logger = "DEBUG")
[ows4R][INFO] OWSGetCapabilities - Fetching https://data.geopf.fr/geonetwork/srv/fre/csw?service=CSW&version=2.0.2&request=GetCapabilities 
-> GET /geonetwork/srv/fre/csw?service=CSW&version=2.0.2&request=GetCapabilities HTTP/2
-> Host: data.geopf.fr
-> user-agent: libcurl/7.81.0 r-curl/6.2.2 httr/1.4.7
-> accept-encoding: deflate, gzip, br, zstd
-> cookie: JSESSIONID=node013k9dfit61l5o1tmflja2acd3x152246.node0; XSRF-TOKEN=7a17699a-a44e-447c-b765-921d01b91311
-> accept: application/json, text/xml, application/xml, */*
-> 
<- HTTP/2 200 
<- date: Mon, 30 Jun 2025 11:46:20 GMT
<- set-cookie: XSRF-TOKEN=608bd5e2-f35c-466e-abd7-fbee6b6c53ad; Path=/geonetwork
<- set-cookie: JSESSIONID=node01ng061mtw7hdx61igg4tho847151395.node0; Path=/geonetwork; HttpOnly
<- content-type: application/xml; charset=UTF-8
<- www-authenticate: Key realm="kong"
<- expires: Thu, 01 Jan 1970 00:00:00 GMT
<- x-frame-options: SAMEORIGIN
<- content-security-policy: frame-ancestors 'self'
<- pragma: no-cache
<- cache-control: no-cache
<- content-encoding: gzip
<- strict-transport-security: max-age=31536000; includeSubDomains
<- access-control-allow-origin: *
<- access-control-allow-credentials: true
<- access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS
<- access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization,Content-Disposition,Content-Length,X-Community
<- access-control-max-age: 1728000
<- x-iplb-request-id: 9364AC4B:F330_91EFC1E7:01BB_6862790C_E2179325:1487
<- x-iplb-instance: 61218
<- 
> md <- CSW$getRecordById("IGNF_COSIA", outputSchema = "http://www.isotc211.org/2005/gmd")
[ows4R][INFO] CSWClient - Fetching record 'IGNF_COSIA' ... 
-> POST /geonetwork/srv/fre/csw HTTP/2
-> Host: data.geopf.fr
-> user-agent: libcurl/7.81.0 r-curl/6.2.2 httr/1.4.7
-> accept-encoding: deflate, gzip, br, zstd
-> cookie: JSESSIONID=node01ng061mtw7hdx61igg4tho847151395.node0; XSRF-TOKEN=608bd5e2-f35c-466e-abd7-fbee6b6c53ad
-> accept: application/xml
-> content-type: text/xml
-> content-length: 385
-> 
>> <csw:GetRecordById xmlns:csw="http://www.opengis.net/cat/csw/2.0.2" xmlns:ows="http://www.opengis.net/ows/1.1" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" service="CSW" version="2.0.2" outputSchema="http://www.isotc211.org/2005/gmd">
>>   <csw:Id>IGNF_COSIA</csw:Id>
>>   <csw:ElementSetName>full</csw:ElementSetName>
>> </csw:GetRecordById>

<- HTTP/2 200 
<- date: Mon, 30 Jun 2025 11:46:24 GMT
<- set-cookie: XSRF-TOKEN=967c90aa-8ffe-413a-94eb-93cc20b2a079; Path=/geonetwork
<- set-cookie: JSESSIONID=node0736tan4a9kt23ygkye2l3njd152256.node0; Path=/geonetwork; HttpOnly
<- content-type: application/xml; charset=UTF-8
<- www-authenticate: Key realm="kong"
<- expires: Thu, 01 Jan 1970 00:00:00 GMT
<- x-frame-options: SAMEORIGIN
<- content-security-policy: frame-ancestors 'self'
<- pragma: no-cache
<- cache-control: no-cache
<- content-encoding: gzip
<- strict-transport-security: max-age=31536000; includeSubDomains
<- access-control-allow-origin: *
<- access-control-allow-credentials: true
<- access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS
<- access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization,Content-Disposition,Content-Length,X-Community
<- access-control-max-age: 1728000
<- x-iplb-request-id: 9364AC4B:F330_91EFC1E7:01BB_6862790C_E217CE0F:1487
<- x-iplb-instance: 61218
<- 
> md$encode()
Erreur : tentative d'appliquer un objet qui n'est pas une fonction

md is not null, I actually get an ISOMetadata object that looks like fine.

> class( md)
[1] "ISOMetadata"       "ISOAbstractObject" "geometaLogger"     "R6"      

[eblondel]

So weird.... What if you you look at names(md) what do you get?

[ptaconet]

names(md)
[1] ".enclos_env" "applicationSchemaInformation" "portrayalCatalogueInfo" "metadataMaintenance" "resourceLineage"
[6] "dataQualityInfo" "distributionInfo" "contentInfo" "identificationInfo" "metadataExtensionInfo"
[11] "referenceSystemInfo" "spatialRepresentationInfo" "locale" "metadataLinkage" "dataSetURI"
[16] "otherLocale" "alternativeMetadataReference" "metadataProfile" "metadataStandard" "metadataStandardVersion"
[21] "metadataStandardName" "dateInfo" "dateStamp" "contact" "metadataScope"
[26] "hierarchyLevelName" "hierarchyLevel" "parentMetadata" "parentIdentifier" "characterSet"
[31] "defaultLocale" "language" "metadataIdentifier" "fileIdentifier" "anyElement"
[36] "isNull" "value_as_field" "value" "parentAttrs" "printAttrs"
[41] "attrs" "defaults" "namespace" "element" "wrap"
[46] "clone" "delContentInfo" "addContentInfo" "setMetadataMaintenance" "delResourceLineage"
[51] "addResourceLineage" "delDataQualityInfo" "setDataQualityInfo" "addDataQualityInfo" "setDistributionInfo"
[56] "delIdentificationInfo" "setIdentificationInfo" "addIdentificationInfo" "delMetadataExtensionInfo" "addMetadataExtensionInfo"
[61] "delReferenceSystemInfo" "setReferenceSystemInfo" "addReferenceSystemInfo" "delSpatialRepresentationInfo" "setSpatialRepresentationInfo"
[66] "addSpatialRepresentationInfo" "delLocale" "addLocale" "delMetadataLinkage" "addMetadataLinkage"
[71] "setDataSetURI" "delAlternativeMetadataReference" "addAlternativeMetadataReference" "delMetadataProfile" "addMetadataProfile"
[76] "delMetadataStandard" "addMetadataStandard" "setMetadataStandardVersion" "setMetadataStandardName" "delDate"
[81] "addDate" "setDateStamp" "delContact" "addContact" "delMetadataScope"
[86] "addMetadataScope" "delHierarchyLevelName" "addHierarchyLevelName" "delHierarchyLevel" "addHierarchyLevel"
[91] "setParentMetadata" "setParentIdentifier" "setCharacterSet" "setDefaultLocale" "setLanguage"
[96] "setMetadataIdentifier" "setFileIdentifier" "initialize" "createLocalisedProperty" "isFieldInheritedFrom"
[101] "isDocument" "setValue" "setCodeSpace" "setCodeListValue" "setCodeList"
[106] "setHref" "setId" "addFieldAttrs" "setAttr" "delListElement"
[111] "addListElement" "contains" "setIsNull" "wrapBaseElement" "getClass"
[116] "getClassName" "getNamespaceDefinition" "save" "validate" "encode"
[121] "decode" "print" "stopIfMetadataStandardIsNot" "checkMetadataStandardCompliance" "ERROR"
[126] "WARN" "INFO"

[eblondel]

so you have all the methods here...
it's really weird. if you try to do md$encode() can you let me know if you get some stacktrace?

[eblondel]

@ptaconet can you try after updating both ows4R/geometa packages (from CRAN).

[ptaconet]

Hi

Still not working after updating ows4r and geometa from CRAN.. :S
A colleague of mine has also tried, by installing the packages 'from scratch' from CRAN but gets the same error.

[eblondel]

Ok thanks, i've isolated the issue (that relates to geometa). I will let you know asap, when I have a fix ready.

[eblondel]

Dear @ptaconet I've investigated the issue. For some unknown reasons the record you fetch with ows4R (wiht a POST request operated on the CSW) doesn't match the what we get through a GET request. https://data.geopf.fr/csw?SERVICE=CSW&REQUEST=GetRecordById&VERSION=2.0.2&Id=IGNF_OCS-GE&outputSchema=http://www.isotc211.org/2005/gmd
I suspect there is an issue with this catalogue

However, it could also be due to some internal conversion as I suspect the original metadata is provided in ISO 19115-3 and not ISO 19139. See equivalent GET request in ISO 19115-3: https://data.geopf.fr/csw?SERVICE=CSW&REQUEST=GetRecordById&VERSION=2.0.2&Id=IGNF_OCS-GE&outputSchema=http://standards.iso.org/iso/19115/-3/mdb/2.0
Luckily, the ISO 19115-3 has been added recently to geometa and ows4R.

In the get record request, try to change the outputschema and set it to http://standards.iso.org/iso/19115/-3/mdb/2.0, and let me know if it works.

CSW <- CSWClient$new("https://data.geopf.fr/csw", "2.0.2", logger = "DEBUG")
md <- CSW$getRecordById("IGNF_OCS-GE", outputSchema = "http://standards.iso.org/iso/19115/-3/mdb/2.0")
md$save("test.xml")

[ptaconet]

Hi @eblondel , thanks a lot ! working like a charm with that solution :)