Fathomnet explorer search not returning all descendants

[Brian-RC-Kennedy]

When I log in and search a high level taxon like Cnidaria I get very few returns in this case, Cnidaria only returns 6 images. I am sure there way more than 6 images that contain Cnidarians and 6 is the largest number I can get. If I narrow to just worms or MBARI for provider I get 0 returns

[hohonuuli]

@Brian-RC-Kennedy Be default a search does an exact match. So you're only getting things that are explicitly labeled as "Cnidaria". You can extend the search to descendants by selecting a Taxaonomy provider (e.g. mbari).

[hohonuuli]

Side note for myself. Selecting "Cnidaria" with the "fathomnet" taxa provider hits this bug: fathomnet/fathomnet-rest-api#24.

Sanity check at https://fathomnet.org/worms/taxa/descendants/Cnidaria, which is where the data originates, works fine. When it gets munged through https://fathomnet.org/api/taxa/query/fathomnet/Cnidaria It returns:

{
    "_links": {
        "self": [
            {
                "href": "[/taxa/query/fathomnet/Cnidaria](https://fathomnet.org/taxa/query/fathomnet/Cnidaria)",
                "templated": false
            }
        ]
    },
    "_embedded": {
        "errors": [
            {
                "message": "Internal Server Error: Client 'fastworms': Error decoding HTTP response body: Error decoding JSON stream for type [FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Error decoding property [List children] of type [class org.fathomnet.services.taxa.FastWormsTaxaProvider$FWTaxa]: Maximum depth exceeded while deserializing. The maximum nesting depth can be increased, if necessary, using the micronaut.serde.maximum-nesting-depth config property."
            }
        ]
    },
    "message": "Internal Server Error"
}

Note that the max depth isn't actually being exceed while deserializing, as mentioned in the error. It looks like I'm hitting a bug between micronaut and the underlying netty server.

[hohonuuli]

More notes on the different taxa providers:

• mbari - MBARI's KB works fine. https://fathomnet.org/api/taxa/query/mbari/Cnidaria
• worms - The WoRMS API is way too slow to use for high level taxa (See https://fathomnet.org/api/taxa/query/worms/Cnidaria, it will timeout). That's out of our control.
• fathomnet - It processes a fairly large tree for Cnidraria (40834 names) and that's tanking when fathomnet deserializes it and tries to normalize the tree to fathom net's taxa structure. The call to https://fathomnet.org/worms/taxa/descendants/Cnidaria returns about 4.2MB of structured json data. Formatted it's about 300k lines

[Brian-RC-Kennedy]

@hohonuuli Thanks for the quick response. I can't get anything to show up even using MBARI as the provider and selecting all descendants. I am sorry if I am being dense and just missed something. I am using Chrome version 121.0.6167.160 on a Mac running 12.2.1 (21D62) in case there is a problem beyond me not understanding. This video is what I see when I try get all the descendants. Thanks

Fathomnet_search_bug.mp4

[hohonuuli]

@Brian-RC-Kennedy In your video, it looks like you're not giving the initial query (Cnidaria + mbari taxa provider) enough time to complete the request. On my very fast network, it takes almost 6 seconds to complete the Cnidaria request; you're requesting a very large chunk of information so be patient.

[Brian-RC-Kennedy]

@hohonuuli thank you I understand now. May I suggest a spinning wheel or something for the user to know when it is processing vs no results.

[hohonuuli]

May I suggest a spinning wheel or something for the user to know when it is processing vs no results.

You may. That's a great suggestion.

[hohonuuli]

@Brian-RC-Kennedy I've added your suggestion in issue #152