empty spans and spans with no 'text' attribute

[ryanwesslen]

hi @stefan.bartell!

Thanks for your question and welcome to the Prodigy community

@stefan.bartell

The output of db-out when I save annotations produces empty spans and spans with no 'text' attribute, while when I used db-out before, spans were an empty list () or a list of dictionaries with a 'text' attribute (key).

This is a bit odd. Your annotated file has "answer":"accept" tags for each record, indicating they were accepted (saved), but yes, they should include your spans as a list of dictionaries, dictionary per span. For ner.manual, saved annotated spans will be in spans. See this link for what the data looks like for it.

When I did the steps below, everything worked out fine:

python3 -m prodigy ner.manual identify_dosage_non_dosage_validate_data_SB2 en_core_web_lg validate_data_dosage_annotations_SB2.jsonl --label non_dosage,dosage

Then annotated two spans, accepting them by clicking the Green "Accept" button.

Then on the next record, I clicked save at the top:

I can now go back to my terminal and shut down the server by pressing CTRL + C. When I do this, you can also confirm whether your annotation was saved in the CLI:

$ python3 -m prodigy ner.manual dosage_dataset en_core_web_lg data/validate_data_dosage_annotations_SB2.jsonl --label non_dosage,dosage
Using 2 label(s): non_dosage, dosage
Added dataset dosage_dataset to database SQLite.

✨  Starting the web server at http://localhost:8080 ...
Open the app in your browser and start annotating!

^C
✔ Saved 1 annotations to database SQLite
Dataset: dosage_dataset
Session ID: 2023-01-10_14-17-06

Now if I output out that file with db-out:

python3 -m prodigy db-out dosage_dataset > dosage.jsonl

I get:

{
  "text": "January 9 - 241 6 - 375mg split into 3 doses. 96m deadlift/back/shoulder session. 30m cardio. 7,872 steps. 1,640 calories at 17g (7g net) carbs, 93g fat, 128g protein. 1 5g water January 10 - 241 4 - 375mg split into 3 doses. 74m arms session. 30m cardio. 8,402 steps. 1,640 calories at 26g (15g net) carbs, 127g fat, 106g protein. 1 5g water Expected a weight drop by now so I hope it's just water retention as I've been religious with everything and eating has been on point. My circadian rhythms do usually ebb and flow where I'll get a \"whoosh\" weight drop every once in awhile. I'm gonna keep on, keepin' on.",
  "_input_hash": 1201376478,
  "_task_hash": -478339982,
  "_is_binary": false,
  "tokens": [
    {
      "text": "January",
      "start": 0,
      "end": 7,
      "id": 0,
      "ws": true
    },
    .
    .
    .
    {
      "text": ".",
      "start": 612,
      "end": 613,
      "id": 163,
      "ws": false
    }
  ],
  "_view_id": "ner_manual",
  "answer": "accept",
  "_timestamp": 1673378743,
  "spans": [
    {
      "start": 12,
      "end": 44,
      "token_start": 3,
      "token_end": 11,
      "label": "dosage"
    },
    {
      "start": 192,
      "end": 224,
      "token_start": 56,
      "token_end": 64,
      "label": "dosage"
    }
  ]
}

These are the two spans that were saved.

Now those spans do not include by default the raw span text. You can add this by modifying your db-out recipe:

spans.manual merge tokens using db-out

Hi @cheyanneb! So you're just looking to add the raw span text to each span dict? Thinking you could just add this to db-out: for eg in examples: for span in eg["spans"]: span['text'] = eg['text'][span['start']:span['end']] If you create a new flag argument (add_span_text) to turn this on or off (set off by default), you could run this from pathlib import Path from typing import Optional, Union import srsly from prodigy.components.db import connect from prodigy.util import m…

Can you double check that you annotated correctly (e.g., highlighting the spans, clicking Accept (green) button, and saving your annotations by clicking the Save Button)?