[SERVER-13735] “Malformed geometry” error when creating a geosphere index for a valid MultiPolygon Created: 25/Apr/14  Updated: 10/Dec/14  Resolved: 09/Jul/14

Status: Closed
Project: Core Server
Component/s: Geo
Affects Version/s: 2.6.0
Fix Version/s: None

Type: Bug Priority: Major - P3
Reporter: Carst Vaartjes Assignee: Siyuan Zhou
Resolution: Done Votes: 3
Labels: None
Remaining Estimate: Not Specified
Time Spent: Not Specified
Original Estimate: Not Specified

Issue Links:
Depends
Related
related to SERVER-14508 Better error messages from GeoJSON pa... Closed
is related to SERVER-14467 Capture S2 debug log messages Closed
Operating System: ALL
Participants:

 Description   

Hi,

Please see: http://stackoverflow.com/questions/23290114/mongodb-malformed-geometry-when-creating-a-geosphere-index?noredirect=1#comment35654181_23290114

It's a reproducible error for a GeoJSON that should be valid (it is based on output from PostGIS and validates with GeoJSONLint)

Mongodb 2.6
Pymongo 2.7
Ubuntu 12.04LTS 64bit

Kind regards,

Carst



 Comments   
Comment by Tiago Brito [X] [ 10/Nov/14 ]

I would like to have that option too.

Comment by eszter [ 05/Nov/14 ]

Thanks siyuan.zhou@10gen.com.
Actually I know that there are several self intersecting polygons in my dataset, and I am looking for an option where I could index the dataset anyway, e.g. by ignoring the invalid polygons. Deleting them is unfortunately not an option.

Comment by Siyuan Zhou [ 04/Nov/14 ]

eszter - if you look into the "errmsg", you will find "... Polygon isn't valid: Duplicate edge: loop 11, edge 14 and loop 6, edge 1 ...", which means a edge is shared by two different holes in a polygon. By looking into your data, we know it is

[12.0341076, 48.9307188] - [12.0340341, 48.9306908]

Comment by eszter [ 04/Nov/14 ]

Thanks siyuan.zhou@10gen.com for getting back to us.
I am currently using the version 2.7.8
This is the ensureIndex command I'm using:

        db.multipolygons.ensureIndex({geometry: "2dsphere"}) 

The error message:

     {
        "createdCollectionAutomatically" : false,
        "numIndexesBefore" : 1,
        "errmsg" : "exception: Can't extract geo keys: (..) ", 
        "code" : 16755,
        "ok" : 0

The geometry:

  { "type": "Feature", "properties": { "osm_id": "2602552", "osm_way_id": null, "name": "Kurpark", "type": "multipolygon", "aeroway": null, "amenity": null, "admin_level": null, "barrier": null, "boundary": null, "building": null, "craft": null, "geological": null, "historic": null, "land_area": null, "landuse": null, "leisure": "park", "man_made": null, "military": null, "natural": null, "office": null, "place": null, "shop": null, "sport": null, "tourism": "attraction", "other_tags": null }, "geometry": { "type": "MultiPolygon", "coordinates": [ [ [ [ 12.0308269, 48.9291539 ], [ 12.0305836, 48.9290533 ], [ 12.0302835, 48.92949 ], [ 12.030673, 48.9297361 ], [ 12.0311582, 48.9299831 ], [ 12.0327085, 48.9306112 ], [ 12.0334071, 48.9308868 ], [ 12.0339852, 48.9311278 ], [ 12.035182, 48.9317209 ], [ 12.0360286, 48.9321679 ], [ 12.0362144, 48.9322084 ], [ 12.0364541, 48.9323458 ], [ 12.036747, 48.9325243 ], [ 12.0368184, 48.9325684 ], [ 12.0369869, 48.9326708 ], [ 12.037208, 48.9328549 ], [ 12.0375615, 48.9326368 ], [ 12.037561, 48.93223 ], [ 12.0374824, 48.9322301 ], [ 12.0374822, 48.9320819 ], [ 12.0375715, 48.9320818 ], [ 12.0375712, 48.9318639 ], [ 12.0377907, 48.9318638 ], [ 12.0379803, 48.9316199 ], [ 12.0380092, 48.9312492 ], [ 12.0379334, 48.9312471 ], [ 12.0378675, 48.9312454 ], [ 12.0374241, 48.9315065 ], [ 12.0372324, 48.931383 ], [ 12.0377502, 48.9310731 ], [ 12.0376389, 48.9309949 ], [ 12.0370828, 48.9309874 ], [ 12.0370866, 48.9308085 ], [ 12.037754, 48.9308185 ], [ 12.0377579, 48.9307228 ], [ 12.0374778, 48.9304985 ], [ 12.037662, 48.9303826 ], [ 12.0380417, 48.9306547 ], [ 12.0382718, 48.9305161 ], [ 12.0384228, 48.9304369 ], [ 12.0383401, 48.9302766 ], [ 12.0382761, 48.9301483 ], [ 12.0382451, 48.9300814 ], [ 12.0382304, 48.930044 ], [ 12.0381472, 48.9300581 ], [ 12.0380739, 48.9298721 ], [ 12.0376825, 48.9297077 ], [ 12.0374466, 48.9296316 ], [ 12.0374046, 48.9296249 ], [ 12.037392, 48.9296419 ], [ 12.0373493, 48.9298059 ], [ 12.037328, 48.9298779 ], [ 12.0365691, 48.9298086 ], [ 12.0365765, 48.9297269 ], [ 12.0365847, 48.9295814 ], [ 12.0366184, 48.9294048 ], [ 12.0359592, 48.9294127 ], [ 12.0351298, 48.9293738 ], [ 12.0350232, 48.9294207 ], [ 12.034835, 48.9294257 ], [ 12.0341202, 48.9294454 ], [ 12.0336794, 48.9293511 ], [ 12.033371, 48.9292908 ], [ 12.0329828, 48.9291376 ], [ 12.0326037, 48.9289221 ], [ 12.0324915, 48.9285037 ], [ 12.0317044, 48.9283987 ], [ 12.0308269, 48.9291539 ] ], [ [ 12.0315786, 48.9294684 ], [ 12.0319286, 48.9295365 ], [ 12.032386, 48.9296255 ], [ 12.0329414, 48.9297337 ], [ 12.0334685, 48.9299755 ], [ 12.0337073, 48.9298971 ], [ 12.0340008, 48.9298298 ], [ 12.0341192, 48.9298023 ], [ 12.0348386, 48.9295665 ], [ 12.0347974, 48.9294574 ], [ 12.0341128, 48.9294817 ], [ 12.0337161, 48.9294229 ], [ 12.0334352, 48.9294008 ], [ 12.0334412, 48.9293725 ], [ 12.0334481, 48.9293403 ], [ 12.0333505, 48.9293198 ], [ 12.0329585, 48.9291629 ], [ 12.0325843, 48.9289555 ], [ 12.0323091, 48.9289924 ], [ 12.0318543, 48.9291391 ], [ 12.0317247, 48.9292489 ], [ 12.0315786, 48.9294684 ] ], [ [ 12.0323802, 48.9301001 ], [ 12.032566, 48.9299041 ], [ 12.0323147, 48.9298012 ], [ 12.0321289, 48.9299973 ], [ 12.0323802, 48.9301001 ] ], [ [ 12.0344007, 48.929739 ], [ 12.0346381, 48.9300108 ], [ 12.0347249, 48.9300073 ], [ 12.0347812, 48.9299953 ], [ 12.0348307, 48.9299733 ], [ 12.0348504, 48.9299541 ], [ 12.0348735, 48.9299087 ], [ 12.0349453, 48.9297836 ], [ 12.0349483, 48.9297074 ], [ 12.0348719, 48.929583 ], [ 12.0344007, 48.929739 ] ], [ [ 12.0361105, 48.9300764 ], [ 12.0362399, 48.9301313 ], [ 12.0362618, 48.930164 ], [ 12.0363075, 48.930181 ], [ 12.0363812, 48.9301771 ], [ 12.036415, 48.9301548 ], [ 12.0364289, 48.9301117 ], [ 12.036409, 48.9300869 ], [ 12.0363812, 48.9300594 ], [ 12.0363414, 48.9300568 ], [ 12.0363075, 48.9300633 ], [ 12.0362578, 48.9300503 ], [ 12.0362041, 48.9300319 ], [ 12.0361683, 48.9300202 ], [ 12.0361344, 48.930028 ], [ 12.0361145, 48.930045 ], [ 12.0361105, 48.9300764 ] ], [ [ 12.0369094, 48.9301669 ], [ 12.0369114, 48.9301922 ], [ 12.0369358, 48.9302124 ], [ 12.0369822, 48.9302189 ], [ 12.0370228, 48.9302024 ], [ 12.0370353, 48.9301772 ], [ 12.0370157, 48.9301473 ], [ 12.0369711, 48.9301355 ], [ 12.036929, 48.930146 ], [ 12.0369094, 48.9301669 ] ], [ [ 12.0334278, 48.9308868 ], [ 12.0339839, 48.9311134 ], [ 12.0342594, 48.9308503 ], [ 12.0343118, 48.9307965 ], [ 12.0341076, 48.9307188 ], [ 12.0340341, 48.9306908 ], [ 12.0337128, 48.9305698 ], [ 12.0334278, 48.9308868 ] ], [ [ 12.0361528, 48.9320564 ], [ 12.0361714, 48.9321035 ], [ 12.0362749, 48.9321157 ], [ 12.036328, 48.9320982 ], [ 12.0363493, 48.9321314 ], [ 12.0367847, 48.9320424 ], [ 12.0367475, 48.931957 ], [ 12.036705, 48.9319622 ], [ 12.0366493, 48.9318663 ], [ 12.0362245, 48.9319622 ], [ 12.0361298, 48.9319012 ], [ 12.0360864, 48.9318732 ], [ 12.0361077, 48.9318157 ], [ 12.0358077, 48.9316325 ], [ 12.0355873, 48.9316744 ], [ 12.0355735, 48.9317075 ], [ 12.0355475, 48.9318209 ], [ 12.0357493, 48.9319273 ], [ 12.0357838, 48.9319238 ], [ 12.036044, 48.9320965 ], [ 12.0361156, 48.9320477 ], [ 12.0361528, 48.9320564 ] ], [ [ 12.031546, 48.9291268 ], [ 12.0313573, 48.9290537 ], [ 12.0314627, 48.9289363 ], [ 12.0316513, 48.9290094 ], [ 12.0316146, 48.9290503 ], [ 12.031546, 48.9291268 ] ], [ [ 12.0308666, 48.92935 ], [ 12.0309838, 48.9292519 ], [ 12.0313407, 48.9294358 ], [ 12.0312235, 48.9295339 ], [ 12.0308666, 48.92935 ] ], [ [ 12.0313454, 48.9296843 ], [ 12.0313055, 48.9297282 ], [ 12.030448, 48.9293544 ], [ 12.0306448, 48.9291527 ], [ 12.0306926, 48.9291728 ], [ 12.0305319, 48.9293394 ], [ 12.0313454, 48.9296843 ] ], [ [ 12.0314034, 48.9297724 ], [ 12.0314444, 48.9297265 ], [ 12.0316426, 48.9298141 ], [ 12.0318621, 48.9296019 ], [ 12.0319218, 48.929628 ], [ 12.0318833, 48.9296681 ], [ 12.0318714, 48.9296612 ], [ 12.0316815, 48.9298504 ], [ 12.0317107, 48.9298635 ], [ 12.0316802, 48.9298966 ], [ 12.0326572, 48.9303196 ], [ 12.0329068, 48.9300545 ], [ 12.0342064, 48.9305246 ], [ 12.0342515, 48.9305411 ], [ 12.0341076, 48.9307188 ], [ 12.0340341, 48.9306908 ], [ 12.0341406, 48.9305601 ], [ 12.0337452, 48.9304188 ], [ 12.0329574, 48.9301358 ], [ 12.0326985, 48.9304158 ], [ 12.0321369, 48.9301731 ], [ 12.0315385, 48.9299159 ], [ 12.0315979, 48.9298565 ], [ 12.0314034, 48.9297724 ] ], [ [ 12.0327156, 48.9306035 ], [ 12.031166, 48.9299757 ], [ 12.030682, 48.9297293 ], [ 12.030302, 48.9294892 ], [ 12.0304502, 48.929367 ], [ 12.0313038, 48.9298112 ], [ 12.031212, 48.9299161 ], [ 12.0313281, 48.9298363 ], [ 12.031531, 48.9299234 ], [ 12.0321298, 48.9301807 ], [ 12.0327028, 48.9304284 ], [ 12.0329623, 48.9301478 ], [ 12.0337268, 48.9304224 ], [ 12.0336251, 48.9305477 ], [ 12.0336935, 48.930573 ], [ 12.0334027, 48.9308746 ], [ 12.0327156, 48.9306035 ] ], [ [ 12.0345978, 48.9311783 ], [ 12.0347515, 48.9310359 ], [ 12.0343249, 48.9308795 ], [ 12.0342706, 48.9308587 ], [ 12.0339946, 48.9311267 ], [ 12.0344172, 48.9313253 ], [ 12.0351808, 48.9317146 ], [ 12.0352661, 48.9316429 ], [ 12.0353404, 48.9315845 ], [ 12.0353106, 48.9315126 ], [ 12.0345978, 48.9311783 ] ], [ [ 12.0348851, 48.9310159 ], [ 12.0353913, 48.9312082 ], [ 12.0351982, 48.9313792 ], [ 12.0347448, 48.9311655 ], [ 12.0348851, 48.9310159 ] ] ] ] } }

Comment by Siyuan Zhou [ 03/Nov/14 ]

eszter, Beck and Magnus Gudmundsson - When indexing and inserting malformed geometries, the detailed error message should be reported since 2.7.7. Please try the latest version of 2.7 for the error details.

eszter - Could you please post the self-intersecting polygon data, the ensureIndex command and the error message here?

Magnus Gudmundsson, I am not able to reproduce your issue with the following script. Running against latest 2.7 version could give you more details, if it returns an error.

> db.err.ensureIndex({loc: "2dsphere"})
{
	"createdCollectionAutomatically" : true,
	"numIndexesBefore" : 1,
	"numIndexesAfter" : 2,
	"ok" : 1
}
> db.err.insert({"loc" : {"type" : "LineString", "coordinates" : [[121.4440576, 31.3075648 ], [121.443392, 31.3187488 ] ] } })
WriteResult({ "nInserted" : 1 })
> db.version()
2.6.5

Comment by Magnus Gudmundsson [X] [ 03/Nov/14 ]

I am also getting this error
Running Mongo 2.6.5

This is geo I am trying to insert:
{
"type": "LineString",
"coordinates": [
[
121.4440576,
31.3075648
],

[
121.443392,
31.3187488
]
]
}
it validates ok in http://geojsonlint.com/

Comment by david henningson [X] [ 31/Oct/14 ]

Also getting the error 16755 Can't extract geo keys from object, malformed geometry?
Mongo 2.6.4

Not sure from Ramon's post how this is a work around fix ... ?

If Foursquare is using Mongo to store their geospatial files, wondering how they are solving this problem, as surely they must be experiencing the same issue?

Comment by Ramon Fernandez Marina [ 30/Oct/14 ]

eszter, there's currently no way to skip self-intersecting polygons when building a geo index. Since the "Loop is not valid" message appears on insert(), one possible approach could be to re-insert all your documents into a new collection:

db.foo.find().forEach(function(d){db.bar.insert(d)})

Comment by eszter [ 30/Oct/14 ]

I have the same problem, I have several self-intersecting polygons in my collection so the indexing fails. Is there a way to skip these polygons and continue the indexing process?
Btw Siyuan Zhou : I am using the version 2.7.8 and I don't see the "Loop is not valid: [ ... ]" message..

Comment by Siyuan Zhou [ 15/Oct/14 ]

han.zava - Latest 2.7 version will give a more detailed error message.

...
Loop is not valid: [ ... ] 
Edges 4 and 7 cross. Edge locations in degrees: [114.0950930, 38.1135710]-[114.1043080, 38.1349120] and [114.1007960, 38.1306860]-[114.1002990, 38.1253730]

GeoJSONLint can visualize this GeoJSON. You can find the cross clearly.

Comment by zava [ 15/Oct/14 ]

I am also have this error

insert data

{ "code" : "130107000000" , "name" : "井陉矿区" , "parent" : "130100000000" , "level" : 4 , "cid" : 3511594003 ,
"latlngs" :

{ "type" : "MultiPolygon" , "coordinates" : [ [ [ [ 114.082128 , 38.083284] , [ 114.086436 , 38.095766] , [ 114.101448 , 38.102633] , [ 114.094794 , 38.107047] , [ 114.095093 , 38.113571] , [ 114.104308 , 38.134912] , [ 114.096598 , 38.134343] , [ 114.100796 , 38.130686] , [ 114.100299 , 38.125373] , [ 114.092243 , 38.116892] , [ 114.07353 , 38.111964] , [ 114.06433 , 38.117874] , [ 114.061132 , 38.112942] , [ 114.053055 , 38.114859] , [ 114.030268 , 38.111621] , [ 114.005167 , 38.102554] , [ 113.998606 , 38.095973] , [ 113.987816 , 38.064941] , [ 114.000219 , 38.057744] , [ 114.006912 , 38.042172] , [ 114.038053 , 38.031357] , [ 114.050343 , 38.024079] , [ 114.077266 , 38.04758] , [ 114.077178 , 38.07165] , [ 114.09851 , 38.072457] , [ 114.109236 , 38.078426] , [ 114.100544 , 38.081483] , [ 114.08488 , 38.079734] , [ 114.082128 , 38.083284]]]]}

exception

insertDocument :: caused by :: 16755 Can't extract geo keys from object, malformed geometry?: { _id: ObjectId('543e0111d740d2280b00002b'), code: "130107000000", name: "井陉矿区", parent: "130100000000", level: 4.0, cid: 3511594003.0, latlngs: { type: "MultiPolygon", coordinates: [ [ [ [ 114.082128, 38.083284 ], [ 114.086436, 38.095766 ], [ 114.101448, 38.102633 ], [ 114.094794, 38.107047 ], [ 114.095093, 38.113571 ], [ 114.104308, 38.134912 ], [ 114.096598, 38.134343 ], [ 114.100796, 38.130686 ], [ 114.100299, 38.125373 ], [ 114.092243, 38.116892 ], [ 114.07353, 38.111964 ], [ 114.06433, 38.117874 ], [ 114.061132, 38.112942 ], [ 114.053055, 38.114859 ], [ 114.030268, 38.111621 ], [ 114.005167, 38.102554 ], [ 113.998606, 38.095973 ], [ 113.987816, 38.064941 ], [ 114.000219, 38.057744 ], [ 114.006912, 38.042172 ], [ 114.038053, 38.031357 ], [ 114.050343, 38.024079 ], [ 114.077266, 38.04758 ], [ 114.077178, 38.07165 ], [ 114.09851, 38.072457 ], [ 114.109236, 38.078426 ], [ 114.100544, 38.081483 ], [ 114.084

Comment by David Hows [ 08/Jul/14 ]

Hi Markus,

That polygon is invalid according to the GeoJson Spec as there are duplicated vertices, which indicate that there is an overlap in your polygon. Please be aware that the geojsonlint website does not perform a full validation of a GeoJson polygon.

When loaded into the S2 engine that we use for polygon construction internally I find the following.

2014-07-08T09:47:26.049+1000 [conn4] S2 LOGGED: Duplicate vertices: 783 and 898

Looking at the polygon on the linter, it looks like there is supposed to be a "hole" in the right hand side of the polygon. This should be a separate "inner ring" which is to be "subtracted" from the first. Please see the Polygon section of the GeoJson spec, which details how this is to be implemented.

Regards,
David

Comment by Markus J Doetsch [X] [ 07/Jul/14 ]

+1

also valid, according to geojsonlint

{ "type" : "Polygon", "coordinates" : [ [ [ 18.0717700014988, 59.3171999977099 ], [ 18.0717911981462, 59.3171576097491 ], [ 18.0719285739094, 59.3168828527036 ], [ 18.071930000434, 59.3168800005332 ], [ 18.0720607583085, 59.3166184680486 ], [ 18.072078564714, 59.3165828577971 ], [ 18.0720839833518, 59.3165720261453 ], [ 18.0721000066015, 59.3165400005764 ], [ 18.0721046113657, 59.3165374798044 ], [ 18.0721650616961, 59.3165044204975 ], [ 18.0721705387244, 59.3165014243559 ], [ 18.0722098525945, 59.3164799200639 ], [ 18.0722146684627, 59.3164780933147 ], [ 18.0722395589826, 59.3164686661869 ], [ 18.0722618812191, 59.3164698364986 ], [ 18.0722683113599, 59.3164745910901 ], [ 18.0722756209514, 59.3164800034938 ], [ 18.072276420452, 59.3164882978967 ], [ 18.0722769953738, 59.3164943286882 ], [ 18.0722773223605, 59.3164977406048 ], [ 18.0722777239075, 59.3165018690097 ], [ 18.0722772298341, 59.3165123610051 ], [ 18.072280865316, 59.3165079983561 ], [ 18.0722837381283, 59.3165035220218 ], [ 18.0722904233906, 59.3164931212465 ], [ 18.0722988388082, 59.3164855062028 ], [ 18.0723106947733, 59.3164747799535 ], [ 18.0723174590874, 59.3164686661869 ], [ 18.0723296653955, 59.3164576245485 ], [ 18.0723398118666, 59.3164484454131 ], [ 18.0723647535905, 59.3164259005037 ], [ 18.0723972573324, 59.3164076270187 ], [ 18.0724208767362, 59.3163991276881 ], [ 18.0724721696406, 59.3163806740345 ], [ 18.0725497283856, 59.3163294391474 ], [ 18.0726358040578, 59.3162725735445 ], [ 18.0726928884009, 59.3162546098618 ], [ 18.0727130367144, 59.3162482696014 ], [ 18.072738086236, 59.3162365627391 ], [ 18.0727662798612, 59.3162000999032 ], [ 18.0727829939154, 59.3161784826517 ], [ 18.0728074640238, 59.3161614994596 ], [ 18.072826599936, 59.3161576428509 ], [ 18.0728401357506, 59.3161549638989 ], [ 18.0728641620913, 59.3161546012961 ], [ 18.0728770645937, 59.3161544050963 ], [ 18.0728799014733, 59.316154691603 ], [ 18.0728826134872, 59.3161549638989 ], [ 18.0729025282387, 59.3161569712793 ], [ 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Comment by A. Jesse Jiryu Davis [ 25/Jun/14 ]

Both siyuan's and wutzebaer's polygons are self-intersecting. Based on the frequency of reports it may be worth detecting self-intersection and making a special error message for it.

Comment by Peter [ 25/Jun/14 ]

same problems here
http://stackoverflow.com/questions/24375649/mongodb-sphere-index-rejects-my-object

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Generated at Thu Feb 08 03:32:42 UTC 2024 using Jira 9.7.1#970001-sha1:2222b88b221c4928ef0de3161136cc90c8356a66.