Label-studio: Prepopulating relations among entities for NER annotation doesn't work
Describe the bug
I'm using LabelStudio for a NER + Relations Among Entities task.
I want to pre-populate some relations to the annotation (using predictions). When I pre-populate entities, it shows up fine. However, when I try to pre-populate relations, I get the following error in my browser console:
Uncaught (in promise) Error: [mobx-state-tree] Can only store references to tree nodes or identifiers, got: 'undefined'
at be (mobx-state-tree.module.js:3662)
at new e (mobx-state-tree.module.js:6984)
at t.instantiate (mobx-state-tree.module.js:7243)
at mobx-state-tree.module.js:5734
at mobx-state-tree.module.js:5891
at Array.forEach (<anonymous>)
at t.forAllProps (mobx-state-tree.module.js:5890)
at t.initializeChildNodes (mobx-state-tree.module.js:5733)
at new t (mobx-state-tree.module.js:1442)
at ae (mobx-state-tree.module.js:3401)
Also, the spinner keeps spinning and nothing shows up in my browser.
This is the content of my tasks.json:
[
{
"id": 2,
"data": {
"text": "sales rep with highest sales for winkle"
},
"predictions": [
{
"result": [
{
"id": "anJaSFkP",
"from_name": "label",
"to_name": "text",
"type": "labels",
"normalization": "1P sales (Local Currency)",
"value": {
"start": 23,
"end": 28,
"text": "sales",
"labels": [
"Measure"
]
}
},
{
"id": "pBUYX3sZ",
"from_name": "label",
"to_name": "text",
"type": "labels",
"normalization": "Sales Representative",
"value": {
"start": 0,
"end": 9,
"text": "sales rep",
"labels": [
"Attribute"
]
}
},
{
"id": "L7o4xpaW",
"from_name": "label",
"to_name": "text",
"type": "labels",
"normalization": "Winkle~~Brand",
"value": {
"start": 33,
"end": 39,
"text": "winkle",
"labels": [
"Business Object"
]
}
},
{
"id": "TV7255ne",
"from_name": "label",
"to_name": "text",
"type": "labels",
"normalization": "TOP 1",
"value": {
"start": 15,
"end": 22,
"text": "highest",
"labels": [
"Rank"
]
}
},
/* THE RELATIONS BELOW IS THE PROBLEM */
{
"direction": "right",
"from_id": "TV7255ne",
"labels": [
"Rank-Attribute"
],
"to_id": "pBUYX3sZ",
"type": "relation"
},
{
"direction": "right",
"from_id": "TV7255ne",
"labels": [
"Rank-Measure"
],
"to_id": "anJaSFkP",
"type": "relation"
}
]
}
]
},
]
This is the content of my config.xml:
<View>
<Relations>
<Relation value="Period-Measure" />
<Relation value="Measure-Condition" />
<Relation value="Rank-Attribute" />
<Relation value="Rank-Periodicity" />
<Relation value="Rank-Attribute (Group)" />
<Relation value="Rank-Periodicity (Group)" />
<Relation value="Rank-Measure" />
</Relations>
<Labels name="label" toName="text">
<Label value="Measure" />
<Label value="Business Object" />
<Label value="Attribute" />
<Label value="Periodicity (Global)" />
<Label value="Periodicity (Rank)" />
<Label value="Temporal (Specific)" />
<Label value="Temporal (Range)" />
<Label value="Range (Start)" />
<Label value="Range (End)" />
<Label value="Condition Type" />
<Label value="Condition Value" />
<Label value="Rank" />
</Labels>
<Text name="text" value="$text" />
</View>
P.S. When I annotate the relation manually myself, the resulting JSON for that relation (in the completions folder is identical to what I have in the predictions list).
msamogh
All 17 comments
Hi! Sorry for long response, I'm trying to understand is this problem still exists, because we had a fix specifically for relations deserialisation, but we got another complain right after we deployed it.
I'll check it soon and come back with solution.
hlomzik
on 22 Jun 2020
Sure, no problem! Thank you very much!
msamogh
on 27 Jun 2020
Any update on this, @hlomzik?
msamogh
on 3 Jul 2020
@hlomzik Any update?
msamogh
on 15 Jul 2020
Hi everyone, I'm working "exactly" in the same direction, but have not started yet to create the "predictions". I'll be watching this thread with high interest and feed-back you on my own progress, if any.
Many thanks for your work and input.
paulakeen
on 15 Jul 2020
@msamogh @paulakeen I've just created a new project with your label config and imported your task (but there is incorrect comma at the end). And everything is work fine. I've used release 0.7.3.
makseq
on 16 Jul 2020
makseq
on 16 Jul 2020
I hope this problem is fixed in https://github.com/heartexlabs/label-studio/releases/tag/v0.7.4.
Feel free to open this issue if it is not.
makseq
on 13 Aug 2020
Hi @makseq,
I have the same issue with prepopulating relations among labels.
This is the content of my task.json:
{"602": {
"data": {
"text": "A 41-year-old African-American female with a past medical history of diabetes type II, hypertension, and hypercholesterolemia presents to pulmonary clinic for evaluation of shortness of breath. She has no history of childhood asthma; however, at age 26 she was diagnosed clinically with asthma based solely on symptoms during an unrelated hospitalization."
},
"id": 602,
"predictions": [
{
"result": [
{
"from_name": "label",
"id": "00",
"to_name": "text",
"type": "labels",
"value": {
"end": 77,
"labels": [
"medical_condition"
],
"start": 69,
"text": "diabetes"
}
},
{
"from_name": "label",
"id": "01",
"to_name": "text",
"type": "labels",
"value": {
"end": 99,
"labels": [
"medical_condition"
],
"start": 87,
"text": "hypertension"
}
},
{
"from_name": "label",
"id": "02",
"to_name": "text",
"type": "labels",
"value": {
"end": 192,
"labels": [
"medical_condition"
],
"start": 173,
"text": "shortness of breath"
}
},
{
"from_name": "label",
"id": "03",
"to_name": "text",
"type": "labels",
"value": {
"end": 233,
"labels": [
"medical_condition"
],
"start": 217,
"text": "childhood asthma"
}
},
{
"from_name": "label",
"id": "04",
"to_name": "text",
"type": "labels",
"value": {
"end": 253,
"labels": [
"age"
],
"start": 247,
"text": "age 26"
}
},
{
"from_name": "label",
"id": "05",
"to_name": "text",
"type": "labels",
"value": {
"end": 294,
"labels": [
"medical_condition"
],
"start": 288,
"text": "asthma"
}
},
{
"direction": "right",
"from_id": "03",
"labels": [
"has_age"
],
"to_id": "04",
"type": "relation"
}
]
}
]
}}
And this is the content of my config.xml:
<View>
<Relations>
<Relation value="has_date_time" />
<Relation value="has_age" />
<Relation value="has_severity" />
<Relation value="has_frequency" />
<Relation value="has_dosage" />
</Relations>
<Labels name="label" toName="text">
<Label value="TEMPORAL" background="red"/>
<Label value="age" background="darkorange"/>
<Label value="medical_condition" background="orange"/>
<Label value="severity" background="green"/>
<Label value="frequency" background="darkblue"/>
<Label value="treatment_medication" background="blue"/>
<Label value="dosage" background="purple"/>
</Labels>
<Text name="text" value="$text"/>
</View>
Including predictions for entities works perfectly fine. Including the relations does not work properly however. It is added as a predicted relation (see below on the right). The text does not show up in the UI anymore though and the following error shows up instead:
And it is the same for me: When I annotate the relation manually myself, the resulting JSON for that relation (in the completions folder is identical to what I have in the predictions list).
anja-wo
on 7 Dec 2020
@anja-wo Sorry for a long answer. What LS version do you use?
makseq
on 5 Jan 2021
@makseq I am facing the exact same problem as @anja-wo. The entities prediction work fine. But when I add relations, I get the 'TypeError: Cannot read property 'traverseTree' of null' on labelstudio. I'm using version 0.8.2.
shehryar-malik
on 8 Jan 2021
@makseq I'm also facing the same problem as that of @shehryar-malik and @anja-wo . I am using 0.8.2 version.
MNMaqsood
on 8 Jan 2021
@hlomzik Could you check this, please?
makseq
on 8 Jan 2021
I have the same issue. Can someone please advise when this will be resolved?
jrubensteinsp
on 10 Jan 2021
@jrubensteinsp Thanks for your report, we are working on it. I'll ping here, when we finish.
makseq
on 11 Jan 2021
Thanks Max. Do you have a RC we can test? Do you expect it in 0.8.3 or
0.9.0 and what's your best guess on an ETA?
Thanks
Jeff
On Sun, Jan 10, 2021 at 6:02 PM Max notifications@github.com wrote:
@jrubensteinsp https://github.com/jrubensteinsp Thanks for your report,
we are working on it. I'll ping here, when we finish.—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/heartexlabs/label-studio/issues/323#issuecomment-757559668,
or unsubscribe
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jrubensteinsp
on 11 Jan 2021
I hope it will be in 0.9.0 on this week :slightly_smiling_face:
makseq
on 11 Jan 2021
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