[R-sig-Geo] Error reading spatialite table with sf::st_read

Sat Mar 5 16:29:46 CET 2022

On 04/03/2022 13:36, Edzer Pebesma wrote:
> Loic,
>
> I agree with Barry that there is a (logic) bug there, leading to a 
> confusing error message. The problem seems the DBI driver failing to 
> interpret a binary column ("blob") as wkb, which is needed when taking 
> this path:
>
>
> > tb = dbReadTable(con, "olinda1")
> > head(tb)
>   ogc_fid    id      cd_geocodi   tipo   cd_geocodb    nm_bair v014 
> GEOMETRY
> 1       1 28801 260960005000001 URBANO 260960005020 Ouro Preto 1119 
> blob[484 B]
> 2       2 28802 260960005000002 URBANO 260960005020 Ouro Preto 1267 
> blob[532 B]
> 3       3 28803 260960005000003 URBANO 260960005020 Ouro Preto 557 
> blob[276 B]
> 4       4 28804 260960005000004 URBANO 260960005020 Ouro Preto 709 
> blob[468 B]
> 5       5 28805 260960005000005 URBANO 260960005020 Ouro Preto 1045 
> blob[452 B]
> 6       6 28806 260960005000006 URBANO 260960005020 Ouro Preto 727 
> blob[388 B]
> > st_as_sfc(tb$GEOMETRY)
> wkbType: 30078980
> Error in CPL_read_wkb(x, EWKB, spatialite) :
>   unsupported wkbType dim in switch
>
> so there seems to be something special with spatialite's WKB, which is 
> not recognized by sf's WKB reader. Reading ?st_as_sfc:

I'm certainly no expert in WKB, but I did notice on the spatialite group 
list the following thread:

https://groups.google.com/g/spatialite-users/c/fJSlg6qGUfc

where Sandro explains that the spatialite "geom" column is NOT in 
standard WKB...

>
> > st_as_sfc(tb$GEOMETRY, spatialite = TRUE)
> Geometry set for 470 features
> Geometry type: POLYGON
> Dimension:     XY
> Bounding box:  xmin: -34.91692 ymin: -8.044467 xmax: -34.82779 ymax: 
> -7.954672
> CRS:           NA
> First 5 geometries:
> POLYGON ((-34.86406 -7.992488, -34.86397 -7.992...
> POLYGON ((-34.86129 -7.989947, -34.86087 -7.989...
> POLYGON ((-34.85856 -7.992407, -34.85899 -7.992...
> POLYGON ((-34.85752 -7.994827, -34.85722 -7.994...
> POLYGON ((-34.8582 -7.997543, -34.858 -7.996937...
> Warning message:
> In CPL_crs_from_input(x) :
>   GDAL Error 1: PROJ: proj_create_from_database: crs not found
>
> This can no doubt be made more automatic (e.g. by adding a spatialite 
> argument to st_read.DBIObject), but the the question remains why, when
>
> x = st_read('/tmp/olinda1.sqlite')
>
> works OK, that couldn't be used instead?
>
> Many regards,
>
>
> On 03/03/2022 19:19, Barry Rowlingson wrote:
>> Looks like that error might be generated about here:
>> https://github.com/r-spatial/sf/blob/5dde39c8261dc6b202e6cde9d41ad3bf0f46aa3a/R/db.R#L134 
>>
>>
>> where the code does:
>>
>> try(sfc <- st_as_sfc(tbl[[i]]), silent = TRUE)
>> if (!inherits(sfc, "try-error")) {
>> tbl[[i]] = sfc
>> success = TRUE
>> }
>>
>> If the first "try" fails then `sfc` doesn't get created and so the error
>> happens on `if(!inherits(sfc,....)`.
>>
>> The code is looping over columns trying to find a valid geometry column,
>> but not trapping this error properly. A bug, I think. Feel free to 
>> report
>> as an issue.
>>
>> However I don't think that gets us out of the woods - that code only 
>> talks
>> about PostGIS databases, but it gets called for any object of class
>> DBIObject, which your SQLite connection object is:
>>
>>   > inherits(con,"DBIObject")
>>   [1] TRUE
>>
>> Perhaps that method should be something like st_read.PGConnection if it
>> only works on PostGIS databases? Experimenting with bits of that 
>> function
>> don't get me the geometry from my test spatialite DB anyway, and I think
>> its due to it being PostGIS-specific. I kept getting empty geometries.
>>
>> But why not read the Spatialite directly without going through DBI?  
>> Here's
>> a test I made of some points:
>>
>>> d = st_read("/tmp/olinda1.sqlite","pts")
>> Reading layer `pts' from data source `/tmp/olinda1.sqlite' using driver
>> `SQLite'
>> Simple feature collection with 1000 features and 1 field
>> Geometry type: POINT
>> Dimension:     XY
>> Bounding box:  xmin: 234250 ymin: -198750 xmax: 909750 ymax: 502750
>> CRS:           unknown
>>
>> THe CRS is printed as unknown but the WKT is there. Maybe this is a 
>> funny
>> CRS I was using for testing or something:
>>
>>> st_crs(d)
>> Coordinate Reference System:
>>    User input: unknown
>>    wkt:
>> PROJCRS["unknown",
>>      BASEGEOGCRS["GCS_unknown",
>> DATUM["D_Unknown_based_on_Australian_Natl_S_Amer_1969_ellipsoid",
>> ELLIPSOID["Australian_Natl_S_Amer_1969",6378160,298.25,
>>                  LENGTHUNIT["metre",1,
>>
>> and you can add SQL queries to `st_read` if that;s part of your 
>> motivation
>> for using a spatial file database:
>>
>>> d = st_read("/tmp/olinda1_no.sqlite", query="select * from pts where
>> pampa_srtm>300")
>> Reading query `select * from pts where pampa_srtm>300' from data source
>> `/tmp/olinda1_no.sqlite' using driver `SQLite'
>> Simple feature collection with 189 features and 1 field
>>
>> Barry
>>
>> On Thu, Mar 3, 2022 at 4:48 PM DUTRIEUX Loic 
>> <Loic.DUTRIEUX using ec.europa.eu>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> When trying to read data contained in a sqlite table with the full
>>> spatialite options (see what FORMAT=SPATIALITE implies here -->
>>> https://gdal.org/drivers/vector/sqlite.html), I get a
>>> wkbType: 30078980 Error in inherits(sfc, "try-error") : object 'sfc' 
>>> not
>>> found.
>>>
>>> See the example below:
>>>
>>> # In bash
>>> ogr2ogr -F SQLITE -dsco SPATIALITE=YES /tmp/olinda1.sqlite
>>> ~/R/x86_64-pc-linux-gnu-library/4.0/sf/shape/olinda1.shp
>>>
>>> # In R
>>> library(sf)
>>> library(DBI)
>>>
>>> con <- dbConnect(RSQLite::SQLite(), '/tmp/olinda1.sqlite')
>>> st_read(con, query='select * from olinda1;')
>>>
>>>
>>> If I create the database without the SPATIALITE=YES creation option
>>> (geometries encoded as WKB), reading with sf partly works (no CRS) 
>>> but then
>>> I lose the spatialite functionalities. Any suggestion?
>>>
>>> Kind regards,
>>> Loïc
>>>
>>> _______________________________________________
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>>> R-sig-Geo using r-project.org
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>>>
>>
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>>
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>
-- 
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918