Divadoxml: local path inside WMS and OPeNDAP URLs about divand.jl

[Alexander-Barth]

Can you try using relative file names?
Have you seen this explanation?
https://github.com/gher-ulg/DIVAnd.jl/blob/master/src/SDNMetadata.jl#L702

How can we make it clearer?

[meliezer]

I'll propose later how to change this text, but must I have the Julia file in the folder right above the files mentioned in 'files'? I wanted to avoid copy&paste and having many Julia files, but possibly one file for creating the xml files for all sea regions. Il giorno gio 22 nov 2018 alle ore 13:04 Alexander Barth < [email protected]> ha scritto:

…

Can you try using relative file names? Have you seen this explanation? https://github.com/gher-ulg/DIVAnd.jl/blob/master/src/SDNMetadata.jl#L702 How can we make it clearer? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJrAFyj2MHnNbLx34FlhpMcAIuk-AqYuks5uxpLagaJpZM4YvFO9> .

[Alexander-Barth]

The idea is to the have a similar directory tree locally than on the remote server so that the pathname match.
Can you try to do the following?

• in your work-directory /home/menashe/netcdf/ (for example), can you create the following sub-directories
  • Baltic Sea/Autumn (September-November) - 6-years running averages
  • Baltic Sea/Summer (June-August) - 6-years running averages
  • Baltic Sea/Spring (March-May) - 6-years running averages
  • Baltic Sea/Winter (December-February) - 6-years running averages
• move the files Water_body_silicate.4Danl.nc in the corresponding directory
• Note the tools rsync allows you to easily mirror a directory structure from a remote server:

rsync -avzu [email protected]:"/production/apache/data/emodnet-domains/Baltic\ Sea" /home/menashe/netcdf/

• In julia, change to directory "Baltic Sea" in your work directory:

cd("/home/menashe/netcdf/Baltic Sea")
files = ["Winter (December-February) - 6-years running averages/Water_body_silicate.4Danl.nc","Spring (March-May) - 6-years running averages/Water_body_silicate.4Danl.nc","Summer (June-August) - 6-years running averages/Water_body_silicate.4Danl.nc","Autumn (September-November) - 6-years running averages/Water_body_silicate.4Danl.nc"]
@show files
DIVAnd.divadoxml(files,"Water_body_silicate","EMODNET-chemistry","export.zip","test.xml";
    ignore_errors = true,
    additionalvars = Dict("abstract" => "Here goes the abstract"),
    WMSlayername = ["winter","spring","summer","autumn"]
)

Double-check that the file names are relative files (i.e. not starting with /home ...)

The issue with the multi-season XML files is that we must tell divadoxml also the part about Autumn (September-November) - 6-years running averages to construct correct URLs.

[meliezer]

Sounds great! Thank you for the detailed guidance! Later I'll propose a clearer text. Il giorno ven 23 nov 2018, 16:00 Alexander Barth <[email protected]> ha scritto:

…

The idea is to the have a similar directory tree locally than on the remote server so that the pathname match. Can you try to do the following? - in your work-directory /home/menashe/netcdf/ (for example), can you create the following sub-directories - Baltic Sea/Autumn (September-November) - 6-years running averages - Baltic Sea/Summer (June-August) - 6-years running averages - Baltic Sea/Spring (March-May) - 6-years running averages - Baltic Sea/Winter (December-February) - 6-years running averages - move the files Water_body_silicate.4Danl.nc in the corresponding directory - Note the tools rsync allows you to easily mirror a directory structure from a remote server: rsync -avzu ***@***.***:"/production/apache/data/emodnet-domains/Baltic\ Sea" /home/menashe/netcdf/ - In julia, change to directory "Baltic Sea" in your work directory: cd("/home/menashe/netcdf/Baltic Sea")using Glob # can be installed with import Pkg; Pkg.add("Glob") files = ***@***.*** files DIVAnd.divadoxml(files,"Water_body_silicate","EMODNET-chemistry","export.zip","test.xml"; ignore_errors = true, additionalvars = Dict("abstract" => "Here goes the abstract"), WMSlayername = ["winter","spring","summer","autumn"] ) Double-check that the file names are relative files (i.e. not starting with /home ...) The issue with the multi-season XML files is that we must tell divadoxml also the part about Autumn (September-November) - 6-years running averages to construct correct URLs. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#27 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJrAFxDeuS4fdNX4no2zuXofIkYg8Eeiks5uyA15gaJpZM4YvFO9> .

[Alexander-Barth]

To override the NetCDF_URL use the following:

 DIVAnd.divadoxml(files,"Water_body_silicate","EMODNET-chemistry","export.zip","test2.xml";
           ignore_errors = true,
           additionalvars = Dict("abstract" => "Here goes the abstract", "NetCDF_URL" => "http://hostname/path/to/the/zip/file"),
           WMSlayername = ["winter","spring","summer","autumn"]
       )

By the way, do not use the function glob that I mentioned earlier because the order of the season is then alphabetical and not chronological.

The resulting XML file has:

• 1 NetCDF link
• 4 OpenDAP links (1 per season)
• 8 WMS links (4 seasons and for the maps "observations" and "masked analysis")

This is committed to the master 4f4ba08 . CI checks are running https://travis-ci.org/gher-ulg/DIVAnd.jl/builds/460271579.
Attached is the produced XML file.
test2.xml.txt

[meliezer]

Thank you!