Error when using summary$getCoverage() with `crs = NULL` (the default) #94

annakrystalli · 2022-08-29T09:30:11Z

annakrystalli
Aug 29, 2022

crs = null appears to be the default for the getCoverage() method when using it both from a summary object or a wcs object (although not 100% percent clear from the docs, see #89).

When I explicitly use this default in wcs$getCoverage() it works. However when I use it with summary$getCoverage() it throws an error. All other defaults work however.

This is a problem however when trying to build a wrapper. I need to use the summary$getCoverage() because it's the only way I can also access summary$getCoverageStack() if more than one timepoints are requested. But I also want to allow users to pass additional arguments and set those to the default values in the wrapper. Hence, summary$getCoverage(crs = NULL) needs to work as expected.

library(ows4R)
#> Loading required package: geometa
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Loading IANA mime types...
#> No encoding supplied: defaulting to UTF-8.
#> Loading required package: keyring
coverage <- "Emodnetbio__cal_fin_19582016_L1_err"
wcs <- WCSClient$new(url = "https://geo.vliz.be/geoserver/Emodnetbio/wcs" ,
                     serviceVersion = "2.0.1")
summary <- wcs$getCapabilities()$findCoverageSummaryById(coverage)
cov_bbox <-  summary$getBoundingBox()$BoundingBox$getBBOX()
cov_bbox
#>   xmin   ymin   xmax   ymax 
#> -75.05  34.95  20.05  75.05
bbox <- OWSUtils$toBBOX(0,5,40, 45)

# from wcs crs default
wcs$getCoverage(coverage,
                bbox = bbox,
                time = NULL,
                crs = NULL)
#> Loading required package: sf
#> Linking to GEOS 3.9.1, GDAL 3.4.0, PROJ 8.1.1; sf_use_s2() is TRUE
#> <GMLEnvelope>
#> ....|-- lowerCorner: 40 0 "1958-02-16T00:00:00"
#> ....|-- upperCorner: 45 5 "2016-11-16T00:00:00"
#> class       : SpatRaster 
#> dimensions  : 50, 49, 2  (nrow, ncol, nlyr)
#> resolution  : 0.1, 0.1  (x, y)
#> extent      : 0.05, 4.95, 40.05, 45.05  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : Emodnetbio__cal_fin_19582016_L1_err_2016-11-16T00_00_00.000Z_40,0,45,5.tif 
#> names       : Emodnetbio__cal~00Z_40,0,45,5_1, Emodnetbio__cal~00Z_40,0,45,5_2

# from summary no defaults
summary$getCoverage(coverage,
                bbox = bbox)
#> <GMLEnvelope>
#> ....|-- lowerCorner: 40 0 "1958-02-16T00:00:00"
#> ....|-- upperCorner: 45 5 "2016-11-16T00:00:00"
#> class       : SpatRaster 
#> dimensions  : 50, 49, 2  (nrow, ncol, nlyr)
#> resolution  : 0.1, 0.1  (x, y)
#> extent      : 0.05, 4.95, 40.05, 45.05  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : Emodnetbio__cal_fin_19582016_L1_err_2016-11-16T00_00_00.000Z_40,0,45,5.tif 
#> names       : Emodnetbio__cal~00Z_40,0,45,5_1, Emodnetbio__cal~00Z_40,0,45,5_2

# from summary all defaults
summary$getCoverage(coverage,
                bbox = bbox,
                time = NULL,
                crs = NULL,
                elevation = NULL,
                format = NULL,
                rangesubset = NULL,
                filename = NULL)
#> <GMLEnvelope>
#> ....|-- lowerCorner: 40 0 "1958-02-16T00:00:00"
#> ....|-- upperCorner: 45 5 "2016-11-16T00:00:00"
#> Warning: `/private/var/folders/yb/936h04ss57x2rdmly_tv561m0000gp/
#> T/RtmpsLCdv5/reprex-156b624026c3a-petit-dore/
#> Emodnetbio__cal_fin_19582016_L1_err_2016-11-16T00_00_00.000Z_40,0,45,5.tif' not
#> recognized as a supported file format. (GDAL error 4)
#> Error: [rast] cannot open file: /private/var/folders/yb/936h04ss57x2rdmly_tv561m0000gp/T/RtmpsLCdv5/reprex-156b624026c3a-petit-dore/Emodnetbio__cal_fin_19582016_L1_err_2016-11-16T00_00_00.000Z_40,0,45,5.tif

# from summary all defaults but no crs default
summary$getCoverage(coverage,
                bbox = bbox,
                time = NULL,
                #crs = NULL,
                elevation = NULL,
                format = NULL,
                rangesubset = NULL,
                filename = NULL)
#> <GMLEnvelope>
#> ....|-- lowerCorner: 40 0 "1958-02-16T00:00:00"
#> ....|-- upperCorner: 45 5 "2016-11-16T00:00:00"
#> class       : SpatRaster 
#> dimensions  : 50, 49, 2  (nrow, ncol, nlyr)
#> resolution  : 0.1, 0.1  (x, y)
#> extent      : 0.05, 4.95, 40.05, 45.05  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : Emodnetbio__cal_fin_19582016_L1_err_2016-11-16T00_00_00.000Z_40,0,45,5.tif 
#> names       : Emodnetbio__cal~00Z_40,0,45,5_1, Emodnetbio__cal~00Z_40,0,45,5_2

^{Created on 2022-08-29 by the reprex package (v2.0.1)}

Session info

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Answered by eblondel

Sep 26, 2022

@annakrystalli it's a misuse of summary$getCoverage. The WCSCoverageSummary provides a description of a coverage, including its identifier. When calling getCoverage from the coverage summary, you should not specified the identifier, it's internal part of the coverage summary. In your above tests, remove coverage param and all run fine.

View full answer

annakrystalli · 2022-08-29T09:31:29Z

annakrystalli
Aug 29, 2022
Author

It would also be great if you could address #89 as I need to provide more detail to our users on what arguments are and what type of values are accepted for each.

0 replies

annakrystalli · 2022-09-07T15:56:07Z

annakrystalli
Sep 7, 2022
Author

Same behaviour if bbox is NULL

0 replies

eblondel · 2022-09-26T14:18:21Z

eblondel
Sep 26, 2022
Maintainer

@annakrystalli it's a misuse of summary$getCoverage. The WCSCoverageSummary provides a description of a coverage, including its identifier. When calling getCoverage from the coverage summary, you should not specified the identifier, it's internal part of the coverage summary. In your above tests, remove coverage param and all run fine.

0 replies

annakrystalli · 2022-09-26T14:38:42Z

annakrystalli
Sep 26, 2022
Author

I see! However, from a user perspective, it's strange that the function works if crs is not supplied even though the function is misused while the error returned when it is misused is not informative in terms of what the problem actually was.

1 reply

eblondel Sep 26, 2022
Maintainer

getCoverage is in principle enabled to add more OWS vendor params through ... In your case the coverage was considered as vendor but ignored with no crs was specified. Because of the not named param, it was considered as latest param in the sequence of formal named param defined in the function. Depending on what you provided, the coverage Id was assigned either to format, gridbaseCRS, etc... breaking the underlying WCS coverage request. I've added more info on main argument types, but I will add controls over types in R code. In that case, the first argument is a bbox, if not NULL, it should be a matrix. Having this control would break a call like $getCoverage(coverage....) where coverage is not a matrix.

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Error when using summary$getCoverage() with `crs = NULL` (the default) #94

annakrystalli
Aug 29, 2022

Replies: 4 comments 1 reply

annakrystalli
Aug 29, 2022
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annakrystalli
Sep 7, 2022
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eblondel
Sep 26, 2022
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annakrystalli
Sep 26, 2022
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eblondel Sep 26, 2022
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