spaCy/spacy/cli/converters/iob2json.py

70 lines
2.3 KiB
Python
Raw Normal View History

2017-05-19 18:27:51 +00:00
# coding: utf8
from __future__ import unicode_literals
2018-12-18 12:58:30 +00:00
import re
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
from wasabi import Printer
2018-12-18 12:58:30 +00:00
2017-05-26 16:32:34 +00:00
from ...gold import iob_to_biluo
from ...util import minibatch
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
from .conll_ner2json import n_sents_info
2017-05-19 18:27:51 +00:00
💫 New JSON helpers, training data internals & CLI rewrite (#2932) * Support nowrap setting in util.prints * Tidy up and fix whitespace * Simplify script and use read_jsonl helper * Add JSON schemas (see #2928) * Deprecate Doc.print_tree Will be replaced with Doc.to_json, which will produce a unified format * Add Doc.to_json() method (see #2928) Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space. * Remove outdated test * Add write_json and write_jsonl helpers * WIP: Update spacy train * Tidy up spacy train * WIP: Use wasabi for formatting * Add GoldParse helpers for JSON format * WIP: add debug-data command * Fix typo * Add missing import * Update wasabi pin * Add missing import * 💫 Refactor CLI (#2943) To be merged into #2932. ## Description - [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi) - [x] use [`black`](https://github.com/ambv/black) for auto-formatting - [x] add `flake8` config - [x] move all messy UD-related scripts to `cli.ud` - [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO) ### Types of change enhancement ## Checklist <!--- Before you submit the PR, go over this checklist and make sure you can tick off all the boxes. [] -> [x] --> - [x] I have submitted the spaCy Contributor Agreement. - [x] I ran the tests, and all new and existing tests passed. - [x] My changes don't require a change to the documentation, or if they do, I've added all required information. * Update wasabi pin * Delete old test * Update errors * Fix typo * Tidy up and format remaining code * Fix formatting * Improve formatting of messages * Auto-format remaining code * Add tok2vec stuff to spacy.train * Fix typo * Update wasabi pin * Fix path checks for when train() is called as function * Reformat and tidy up pretrain script * Update argument annotations * Raise error if model language doesn't match lang * Document new train command
2018-11-30 19:16:14 +00:00
def iob2json(input_data, n_sents=10, *args, **kwargs):
2017-05-19 18:27:51 +00:00
"""
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
Convert IOB files with one sentence per line and tags separated with '|'
into JSON format for use with train cli. IOB and IOB2 are accepted.
Sample formats:
I|O like|O London|I-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|O like|O London|B-GPE and|O New|B-GPE York|I-GPE City|I-GPE .|O
I|PRP|O like|VBP|O London|NNP|I-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
I|PRP|O like|VBP|O London|NNP|B-GPE and|CC|O New|NNP|B-GPE York|NNP|I-GPE City|NNP|I-GPE .|.|O
2017-05-19 18:27:51 +00:00
"""
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
msg = Printer()
docs = read_iob(input_data.split("\n"))
if n_sents > 0:
n_sents_info(msg, n_sents)
docs = merge_sentences(docs, n_sents)
💫 New JSON helpers, training data internals & CLI rewrite (#2932) * Support nowrap setting in util.prints * Tidy up and fix whitespace * Simplify script and use read_jsonl helper * Add JSON schemas (see #2928) * Deprecate Doc.print_tree Will be replaced with Doc.to_json, which will produce a unified format * Add Doc.to_json() method (see #2928) Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space. * Remove outdated test * Add write_json and write_jsonl helpers * WIP: Update spacy train * Tidy up spacy train * WIP: Use wasabi for formatting * Add GoldParse helpers for JSON format * WIP: add debug-data command * Fix typo * Add missing import * Update wasabi pin * Add missing import * 💫 Refactor CLI (#2943) To be merged into #2932. ## Description - [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi) - [x] use [`black`](https://github.com/ambv/black) for auto-formatting - [x] add `flake8` config - [x] move all messy UD-related scripts to `cli.ud` - [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO) ### Types of change enhancement ## Checklist <!--- Before you submit the PR, go over this checklist and make sure you can tick off all the boxes. [] -> [x] --> - [x] I have submitted the spaCy Contributor Agreement. - [x] I ran the tests, and all new and existing tests passed. - [x] My changes don't require a change to the documentation, or if they do, I've added all required information. * Update wasabi pin * Delete old test * Update errors * Fix typo * Tidy up and format remaining code * Fix formatting * Improve formatting of messages * Auto-format remaining code * Add tok2vec stuff to spacy.train * Fix typo * Update wasabi pin * Fix path checks for when train() is called as function * Reformat and tidy up pretrain script * Update argument annotations * Raise error if model language doesn't match lang * Document new train command
2018-11-30 19:16:14 +00:00
return docs
2017-05-19 18:27:51 +00:00
def read_iob(raw_sents):
2017-05-19 18:27:51 +00:00
sentences = []
for line in raw_sents:
2017-05-19 18:27:51 +00:00
if not line.strip():
continue
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
tokens = [t.split('|') for t in line.split()]
2017-05-28 13:11:39 +00:00
if len(tokens[0]) == 3:
words, pos, iob = zip(*tokens)
elif len(tokens[0]) == 2:
2017-05-28 13:11:39 +00:00
words, iob = zip(*tokens)
💫 New JSON helpers, training data internals & CLI rewrite (#2932) * Support nowrap setting in util.prints * Tidy up and fix whitespace * Simplify script and use read_jsonl helper * Add JSON schemas (see #2928) * Deprecate Doc.print_tree Will be replaced with Doc.to_json, which will produce a unified format * Add Doc.to_json() method (see #2928) Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space. * Remove outdated test * Add write_json and write_jsonl helpers * WIP: Update spacy train * Tidy up spacy train * WIP: Use wasabi for formatting * Add GoldParse helpers for JSON format * WIP: add debug-data command * Fix typo * Add missing import * Update wasabi pin * Add missing import * 💫 Refactor CLI (#2943) To be merged into #2932. ## Description - [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi) - [x] use [`black`](https://github.com/ambv/black) for auto-formatting - [x] add `flake8` config - [x] move all messy UD-related scripts to `cli.ud` - [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO) ### Types of change enhancement ## Checklist <!--- Before you submit the PR, go over this checklist and make sure you can tick off all the boxes. [] -> [x] --> - [x] I have submitted the spaCy Contributor Agreement. - [x] I ran the tests, and all new and existing tests passed. - [x] My changes don't require a change to the documentation, or if they do, I've added all required information. * Update wasabi pin * Delete old test * Update errors * Fix typo * Tidy up and format remaining code * Fix formatting * Improve formatting of messages * Auto-format remaining code * Add tok2vec stuff to spacy.train * Fix typo * Update wasabi pin * Fix path checks for when train() is called as function * Reformat and tidy up pretrain script * Update argument annotations * Raise error if model language doesn't match lang * Document new train command
2018-11-30 19:16:14 +00:00
pos = ["-"] * len(words)
else:
2019-02-07 19:54:07 +00:00
raise ValueError(
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
"The sentence-per-line IOB/IOB2 file is not formatted correctly. Try checking whitespace and delimiters. See https://spacy.io/api/cli#convert"
2019-02-07 19:54:07 +00:00
)
2017-05-26 16:32:34 +00:00
biluo = iob_to_biluo(iob)
💫 New JSON helpers, training data internals & CLI rewrite (#2932) * Support nowrap setting in util.prints * Tidy up and fix whitespace * Simplify script and use read_jsonl helper * Add JSON schemas (see #2928) * Deprecate Doc.print_tree Will be replaced with Doc.to_json, which will produce a unified format * Add Doc.to_json() method (see #2928) Converts Doc objects to JSON using the same unified format as the training data. Method also supports serializing selected custom attributes in the doc._. space. * Remove outdated test * Add write_json and write_jsonl helpers * WIP: Update spacy train * Tidy up spacy train * WIP: Use wasabi for formatting * Add GoldParse helpers for JSON format * WIP: add debug-data command * Fix typo * Add missing import * Update wasabi pin * Add missing import * 💫 Refactor CLI (#2943) To be merged into #2932. ## Description - [x] refactor CLI To use [`wasabi`](https://github.com/ines/wasabi) - [x] use [`black`](https://github.com/ambv/black) for auto-formatting - [x] add `flake8` config - [x] move all messy UD-related scripts to `cli.ud` - [x] make converters function that take the opened file and return the converted data (instead of having them handle the IO) ### Types of change enhancement ## Checklist <!--- Before you submit the PR, go over this checklist and make sure you can tick off all the boxes. [] -> [x] --> - [x] I have submitted the spaCy Contributor Agreement. - [x] I ran the tests, and all new and existing tests passed. - [x] My changes don't require a change to the documentation, or if they do, I've added all required information. * Update wasabi pin * Delete old test * Update errors * Fix typo * Tidy up and format remaining code * Fix formatting * Improve formatting of messages * Auto-format remaining code * Add tok2vec stuff to spacy.train * Fix typo * Update wasabi pin * Fix path checks for when train() is called as function * Reformat and tidy up pretrain script * Update argument annotations * Raise error if model language doesn't match lang * Document new train command
2018-11-30 19:16:14 +00:00
sentences.append(
[
{"orth": w, "tag": p, "ner": ent}
for (w, p, ent) in zip(words, pos, biluo)
]
)
sentences = [{"tokens": sent} for sent in sentences]
paragraphs = [{"sentences": [sent]} for sent in sentences]
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
docs = [{"id": i, "paragraphs": [para]} for i, para in enumerate(paragraphs)]
2017-05-19 18:27:51 +00:00
return docs
2019-05-11 17:15:26 +00:00
def merge_sentences(docs, n_sents):
merged = []
for group in minibatch(docs, size=n_sents):
2019-05-11 17:15:26 +00:00
group = list(group)
first = group.pop(0)
to_extend = first["paragraphs"][0]["sentences"]
Updates/bugfixes for NER/IOB converters (#4186) * Updates/bugfixes for NER/IOB converters * Converter formats `ner` and `iob` use autodetect to choose a converter if possible * `iob2json` is reverted to handle sentence-per-line data like `word1|pos1|ent1 word2|pos2|ent2` * Fix bug in `merge_sentences()` so the second sentence in each batch isn't skipped * `conll_ner2json` is made more general so it can handle more formats with whitespace-separated columns * Supports all formats where the first column is the token and the final column is the IOB tag; if present, the second column is the POS tag * As in CoNLL 2003 NER, blank lines separate sentences, `-DOCSTART- -X- O O` separates documents * Add option for segmenting sentences (new flag `-s`) * Parser-based sentence segmentation with a provided model, otherwise with sentencizer (new option `-b` to specify model) * Can group sentences into documents with `n_sents` as long as sentence segmentation is available * Only applies automatic segmentation when there are no existing delimiters in the data * Provide info about settings applied during conversion with warnings and suggestions if settings conflict or might not be not optimal. * Add tests for common formats * Add '(default)' back to docs for -c auto * Add document count back to output * Revert changes to converter output message * Use explicit tabs in convert CLI test data * Adjust/add messages for n_sents=1 default * Add sample NER data to training examples * Update README * Add links in docs to example NER data * Define msg within converters
2019-08-29 10:04:01 +00:00
for sent in group:
2019-05-11 17:15:26 +00:00
to_extend.extend(sent["paragraphs"][0]["sentences"])
merged.append(first)
return merged