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getting seabed_substrate_1m layer from geology_seabed_substrate_maps fails in EMODnetWFS 2.0.0 #23
Comments
Thanks again for reporting this! (and for bearing with this experimental version of the package!). I will have a look at this first thing Monday morning. |
Hi Anna, Thanks for looking into this. Note that I added a small addition to the original post: the example for getting layers from chemistry works for me, so this it does not seem to be something general about the setup of my computer. |
Hello there @JanJaapPoos and thanks for your patience. I'm having really strange experiences looking into this error! > wfs <- emodnet_init_wfs_client(service="geology_seabed_substrate_maps")
✓ WFS client created succesfully
ℹ Service: 'https://drive.emodnet-geology.eu/geoserver/gtk/wfs'
ℹ Version: '2.0.0'
> test <- emodnet_get_layers(wfs = wfs, layers = "seabed_substrate_1m", reduce_layers = T)
Warning message:
In CPL_read_ogr(dsn, layer, query, as.character(options), quiet, :
GDAL Error 1: HTTP error code : 502 Here's the test object I get: Simple feature collection with 35816 features and 31 fields
Geometry type: MULTIPOLYGON
Dimension: XY
Bounding box: xmin: 747069.2 ymin: 347574.3 xmax: 7670427 ymax: 6622268
Projected CRS: ETRS89-extended / LCC Europe
First 10 features:
gml_id name id objectid code country data_holder contact scale original_scale original_grain_size
1 seabed_substrate_1m.1 1 1 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
2 seabed_substrate_1m.2 2 2 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
3 seabed_substrate_1m.3 3 3 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
4 seabed_substrate_1m.4 4 4 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
5 seabed_substrate_1m.5 5 5 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
6 seabed_substrate_1m.6 6 6 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
7 seabed_substrate_1m.7 7 7 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
8 seabed_substrate_1m.8 8 8 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
9 seabed_substrate_1m.9 9 9 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
10 seabed_substrate_1m.10 10 10 BE-003 Belgium RBINS vera.vanlancker@naturalsciences.be 1000000 0 Folk16
references
1 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
2 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
3 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
4 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
5 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
6 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
7 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
8 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
9 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
10 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
comments reclassification method sample_number original_substrate relation folk_16cl
1 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
2 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
3 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
4 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
5 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
6 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
7 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
8 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
9 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
10 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology. 1 1 0 0 6
folk_16cl_txt folk_7cl folk_7cl_txt folk_5cl folk_5cl_txt surface_feature shape_length shape_area conf_rs conf_s conf_d conf_tot
1 6. No data at this level 2 2. Sand 2 2. Sand 0.012192284 2.149613e-06 NA NA NA NA
2 6. No data at this level 2 2. Sand 2 2. Sand 0.003482063 4.213989e-08 NA NA NA NA
3 6. No data at this level 2 2. Sand 2 2. Sand 0.038381086 1.200432e-07 NA NA NA NA
4 6. No data at this level 2 2. Sand 2 2. Sand 0.083580831 7.006010e-05 NA NA NA NA
5 6. No data at this level 2 2. Sand 2 2. Sand 0.205756667 1.565305e-04 NA NA NA NA
6 6. No data at this level 2 2. Sand 2 2. Sand 0.139014139 4.262724e-05 NA NA NA NA
7 6. No data at this level 2 2. Sand 2 2. Sand 0.065356895 4.309050e-05 NA NA NA NA
8 6. No data at this level 2 2. Sand 2 2. Sand 0.297000687 3.275952e-05 NA NA NA NA
9 6. No data at this level 2 2. Sand 2 2. Sand 0.187015766 3.855894e-05 NA NA NA NA
10 6. No data at this level 2 2. Sand 2 2. Sand 0.120020756 1.209241e-05 NA NA NA NA
geometry
1 MULTIPOLYGON (((3550505 276...
2 MULTIPOLYGON (((3541775 276...
3 MULTIPOLYGON (((3541570 276...
4 MULTIPOLYGON (((3539852 277...
5 MULTIPOLYGON (((3536146 277...
6 MULTIPOLYGON (((3481646 278...
7 MULTIPOLYGON (((3489332 279...
8 MULTIPOLYGON (((3528872 278...
9 MULTIPOLYGON (((3520718 279...
10 MULTIPOLYGON (((3495594 279... As you can see however, I also got a warning which I believe is coming form the interaction between However, running your example in using library(EMODnetWFS)
wfs <- emodnet_init_wfs_client(service="geology_seabed_substrate_maps")
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Space required after the Public Identifier
#> SystemLiteral " or ' expected
#> SYSTEM or PUBLIC, the URI is missing
#> Entity 'nbsp' not defined
#> Error: 1: Space required after the Public Identifier
#> 2: SystemLiteral " or ' expected
#> 3: SYSTEM or PUBLIC, the URI is missing
#> 4: Entity 'nbsp' not defined
t0 <- Sys.time()
test <- emodnet_get_layers(wfs = wfs, layers = "seabed_substrate_1m", reduce_layers = T)
#> Error in emodnet_get_layers(wfs = wfs, layers = "seabed_substrate_1m", : object 'wfs' not found
Sys.time() - t0
#> Time difference of 0.003529072 secs
test
#> Error in eval(expr, envir, enclos): object 'test' not found Created on 2021-10-25 by the reprex package (v2.0.1) Oddly, now when I try to rerun on the console, I get the same error, even after restarting a new R session! 🤷♀️ Regardless of the odf and inconsistent behaviour described above, it seems the problem must have been introduced when implementing the recent filtering feature as using the version of the package at 11adf76 using I get data successfully with no warnings. library(EMODnetWFS)
wfs <- emodnet_init_wfs_client(service="geology_seabed_substrate_maps")
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Loading IANA mime types...
#> No encoding supplied: defaulting to UTF-8.
#> ✓ WFS client created succesfully
#> ℹ Service: 'https://drive.emodnet-geology.eu/geoserver/gtk/wfs'
#> ℹ Version: '2.0.0'
t0 <- Sys.time()
test <- emodnet_get_layers(wfs = wfs, layers = "seabed_substrate_1m", reduce_layers = T)
Sys.time() - t0
#> Time difference of 3.476063 mins
test
#> Simple feature collection with 35816 features and 30 fields
#> Geometry type: MULTISURFACE
#> Dimension: XY
#> Bounding box: xmin: 747069.2 ymin: 347574.3 xmax: 7670427 ymax: 6622268
#> CRS: +init=epsg:3034
#> First 10 features:
#> gml_id id objectid code country data_holder
#> 1 seabed_substrate_1m.1 1 1 BE-003 Belgium RBINS
#> 2 seabed_substrate_1m.2 2 2 BE-003 Belgium RBINS
#> 3 seabed_substrate_1m.3 3 3 BE-003 Belgium RBINS
#> 4 seabed_substrate_1m.4 4 4 BE-003 Belgium RBINS
#> 5 seabed_substrate_1m.5 5 5 BE-003 Belgium RBINS
#> 6 seabed_substrate_1m.6 6 6 BE-003 Belgium RBINS
#> 7 seabed_substrate_1m.7 7 7 BE-003 Belgium RBINS
#> 8 seabed_substrate_1m.8 8 8 BE-003 Belgium RBINS
#> 9 seabed_substrate_1m.9 9 9 BE-003 Belgium RBINS
#> 10 seabed_substrate_1m.10 10 10 BE-003 Belgium RBINS
#> contact scale original_scale
#> 1 [email protected] 1000000 0
#> 2 [email protected] 1000000 0
#> 3 [email protected] 1000000 0
#> 4 [email protected] 1000000 0
#> 5 [email protected] 1000000 0
#> 6 [email protected] 1000000 0
#> 7 [email protected] 1000000 0
#> 8 [email protected] 1000000 0
#> 9 [email protected] 1000000 0
#> 10 [email protected] 1000000 0
#> original_grain_size
#> 1 Folk16
#> 2 Folk16
#> 3 Folk16
#> 4 Folk16
#> 5 Folk16
#> 6 Folk16
#> 7 Folk16
#> 8 Folk16
#> 9 Folk16
#> 10 Folk16
#> references
#> 1 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 2 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 3 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 4 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 5 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 6 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 7 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 8 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 9 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> 10 Van Lancker, V. (2009). SediCURVE@SEA: a multiparameter sedimentdatabase in support of EIA at sea.
#> comments
#> 1 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 2 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 3 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 4 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 5 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 6 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 7 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 8 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 9 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> 10 Generalized from 250k scale to 1 M by GTK June 2016/EMODnet Geology.
#> reclassification method sample_number original_substrate relation folk_16cl
#> 1 1 1 0 0 6
#> 2 1 1 0 0 6
#> 3 1 1 0 0 6
#> 4 1 1 0 0 6
#> 5 1 1 0 0 6
#> 6 1 1 0 0 6
#> 7 1 1 0 0 6
#> 8 1 1 0 0 6
#> 9 1 1 0 0 6
#> 10 1 1 0 0 6
#> folk_16cl_txt folk_7cl folk_7cl_txt folk_5cl folk_5cl_txt
#> 1 6. No data at this level 2 2. Sand 2 2. Sand
#> 2 6. No data at this level 2 2. Sand 2 2. Sand
#> 3 6. No data at this level 2 2. Sand 2 2. Sand
#> 4 6. No data at this level 2 2. Sand 2 2. Sand
#> 5 6. No data at this level 2 2. Sand 2 2. Sand
#> 6 6. No data at this level 2 2. Sand 2 2. Sand
#> 7 6. No data at this level 2 2. Sand 2 2. Sand
#> 8 6. No data at this level 2 2. Sand 2 2. Sand
#> 9 6. No data at this level 2 2. Sand 2 2. Sand
#> 10 6. No data at this level 2 2. Sand 2 2. Sand
#> surface_feature conf_rs conf_s conf_d conf_tot shape_length shape_area
#> 1 NA NA NA NA 0.012192284 2.149613e-06
#> 2 NA NA NA NA 0.003482063 4.213989e-08
#> 3 NA NA NA NA 0.038381086 1.200432e-07
#> 4 NA NA NA NA 0.083580831 7.006010e-05
#> 5 NA NA NA NA 0.205756667 1.565305e-04
#> 6 NA NA NA NA 0.139014139 4.262724e-05
#> 7 NA NA NA NA 0.065356895 4.309050e-05
#> 8 NA NA NA NA 0.297000687 3.275952e-05
#> 9 NA NA NA NA 0.187015766 3.855894e-05
#> 10 NA NA NA NA 0.120020756 1.209241e-05
#> geom
#> 1 MULTISURFACE (POLYGON ((355...
#> 2 MULTISURFACE (POLYGON ((354...
#> 3 MULTISURFACE (POLYGON ((354...
#> 4 MULTISURFACE (POLYGON ((353...
#> 5 MULTISURFACE (POLYGON ((353...
#> 6 MULTISURFACE (POLYGON ((348...
#> 7 MULTISURFACE (POLYGON ((348...
#> 8 MULTISURFACE (POLYGON ((352...
#> 9 MULTISURFACE (POLYGON ((352...
#> 10 MULTISURFACE (POLYGON ((349...
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.1.0 (2021-05-18)
#> os macOS Big Sur 10.16
#> system x86_64, darwin17.0
#> ui X11
#> language (EN)
#> collate en_GB.UTF-8
#> ctype en_GB.UTF-8
#> tz Europe/London
#> date 2021-10-25
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
#> askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0)
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
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#> classInt 0.4-3 2020-04-07 [1] CRAN (R 4.1.0)
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#> EMODnetWFS * 2.0.0 2021-10-25 [1] Github (EMODnet/EMODnetWFS@11adf76)
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#>
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library Created on 2021-10-25 by the reprex package (v2.0.1) So I still haven't figured out and fixed the problem. Just wanted to report back what I've found so far (to record it in the issue too). Will update here with further progress. |
Hi @annakrystalli, Just to confirm that I also received the "HTTP error code : 502" once when I was trying to get data. It did not seem to be consistent, so I was thinking it was some unfortunate mishap in my connection. I am glad that you managed to reproduce the error. I will use the 11adf76 version as you suggest. Thanks for your efforts. |
Hi @JanJaapPoos So more confusion and inconsistency. I've now been able to download data twice last night and twice this morning from the servers using the latest version of the package (ie after running The consistent error about I also noticed that the first time I managed to download data, the object seemed to have a different CRS ( @JanJaapPoos, Can you please try again (with the latest package @salvafern do you have any ideas? It feels like we need to work on better communications with the server maintainers somehow. I'll open another issue for that. |
Yes it is likely that the server maintainers are changing things. I'll follow up in #24 . As an intermediate solution: What do you think about adding handlers for the errors? e.g. |
So we already do use |
Hi @annakrystalli , You're right, works fine for me too now. Some relevant info: crs according to st_crs() st_crs(test) Sessioninfo: sessionInfo() Matrix products: default locale: attached base packages: other attached packages: loaded via a namespace (and not attached): sf::sf_extSoftVersion() |
Thanks for the info @JanJaapPoos and so happy it's all working for you again. We really appreciate you taking the time to report errors to us and help us make the package (and underlying services better). And while the crs is technically the same, it's the expression that seemed to be different. I know there's been big changes in the geospatial software landscape in terms of expressing CRSs as a result of versions of the |
Just installed EMODnetWFS and getting the seabed_substrate_1m layer from geology_seabed_substrate_maps now fails. I think that it also failed for 1.0.0, but I am not sure. This is on windows, R3.6.1.
The error is thus "Space required after the Public Identifier". Some digging in emodnet_get_layers() reveals that this comes from a call to purrr::map2
debug: out <- purrr::map2(.x = layers, .y = cql_filter, ~ews_get_layer(.x,
wfs, cql_filter = .y), wfs, suppress_warnings) %>% stats::setNames(layers)
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Warning: Download of layer 'seabed_substrate_1m' failed: Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
at this time layers is a single string "seabed_substrate_1m" and cql_filter is NA. The version of purrr is:
Any pointers?
To add: getting layers from chemistry_marine_litter as per the example on the github main page works fine.
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