diff --git a/spacy/cli/convert.py b/spacy/cli/convert.py index 2ffbeb458..f4bddac39 100644 --- a/spacy/cli/convert.py +++ b/spacy/cli/convert.py @@ -2,24 +2,27 @@ from pathlib import Path from wasabi import Printer import srsly import re +import sys -from .converters import conllu2json, iob2json, conll_ner2json -from .converters import ner_jsonl2json +from ..tokens import DocBin +from ..gold.converters import iob2docs, conll_ner2docs, json2docs # Converters are matched by file extension except for ner/iob, which are # matched by file extension and content. To add a converter, add a new # entry to this dict with the file extension mapped to the converter function # imported from /converters. + CONVERTERS = { - "conllubio": conllu2json, - "conllu": conllu2json, - "conll": conllu2json, - "ner": conll_ner2json, - "iob": iob2json, - "jsonl": ner_jsonl2json, + #"conllubio": conllu2docs, TODO + #"conllu": conllu2docs, TODO + #"conll": conllu2docs, TODO + "ner": conll_ner2docs, + "iob": iob2docs, + "json": json2docs, } + # File types FILE_TYPES = ("json", "jsonl", "msg") FILE_TYPES_STDOUT = ("json", "jsonl") @@ -27,89 +30,58 @@ FILE_TYPES_STDOUT = ("json", "jsonl") def convert( # fmt: off - input_file: ("Input file", "positional", None, str), - output_dir: ("Output directory. '-' for stdout.", "positional", None, str) = "-", - file_type: (f"Type of data to produce: {FILE_TYPES}", "option", "t", str, FILE_TYPES) = "json", + input_path: ("Input file or directory", "positional", None, Path), + output_dir: ("Output directory.", "positional", None, Path), + file_type: (f"Type of data to produce: {FILE_TYPES}", "option", "t", str, FILE_TYPES) = "spacy", n_sents: ("Number of sentences per doc (0 to disable)", "option", "n", int) = 1, seg_sents: ("Segment sentences (for -c ner)", "flag", "s") = False, model: ("Model for sentence segmentation (for -s)", "option", "b", str) = None, morphology: ("Enable appending morphology to tags", "flag", "m", bool) = False, merge_subtokens: ("Merge CoNLL-U subtokens", "flag", "T", bool) = False, converter: (f"Converter: {tuple(CONVERTERS.keys())}", "option", "c", str) = "auto", - ner_map_path: ("NER tag mapping (as JSON-encoded dict of entity types)", "option", "N", Path) = None, + ner_map: ("NER tag mapping (as JSON-encoded dict of entity types)", "option", "N", Path) = None, lang: ("Language (if tokenizer required)", "option", "l", str) = None, # fmt: on ): """ - Convert files into JSON format for use with train command and other - experiment management functions. If no output_dir is specified, the data - is written to stdout, so you can pipe them forward to a JSON file: - $ spacy convert some_file.conllu > some_file.json + Convert files into json or DocBin format for use with train command and other + experiment management functions. """ + cli_args = locals() no_print = output_dir == "-" + output_dir = Path(output_dir) if output_dir != "-" else "-" msg = Printer(no_print=no_print) - input_path = Path(input_file) - if file_type not in FILE_TYPES_STDOUT and output_dir == "-": - # TODO: support msgpack via stdout in srsly? - msg.fail( - f"Can't write .{file_type} data to stdout", - "Please specify an output directory.", - exits=1, + verify_cli_args(msg, **cli_args) + converter = _get_converter(msg, converter, input_path) + ner_map = srsly.read_json(ner_map) if ner_map is not None else None + for input_loc in walk_directory(input_path): + input_data = input_loc.open("r", encoding="utf-8").read() + # Use converter function to convert data + func = CONVERTERS[converter] + docs = func( + input_data, + n_sents=n_sents, + seg_sents=seg_sents, + append_morphology=morphology, + merge_subtokens=merge_subtokens, + lang=lang, + model=model, + no_print=no_print, + ner_map=ner_map, ) - if not input_path.exists(): - msg.fail("Input file not found", input_path, exits=1) - if output_dir != "-" and not Path(output_dir).exists(): - msg.fail("Output directory not found", output_dir, exits=1) - input_data = input_path.open("r", encoding="utf-8").read() - if converter == "auto": - converter = input_path.suffix[1:] - if converter == "ner" or converter == "iob": - converter_autodetect = autodetect_ner_format(input_data) - if converter_autodetect == "ner": - msg.info("Auto-detected token-per-line NER format") - converter = converter_autodetect - elif converter_autodetect == "iob": - msg.info("Auto-detected sentence-per-line NER format") - converter = converter_autodetect - else: - msg.warn( - "Can't automatically detect NER format. Conversion may not succeed. See https://spacy.io/api/cli#convert" - ) - if converter not in CONVERTERS: - msg.fail(f"Can't find converter for {converter}", exits=1) - ner_map = None - if ner_map_path is not None: - ner_map = srsly.read_json(ner_map_path) - # Use converter function to convert data - func = CONVERTERS[converter] - data = func( - input_data, - n_sents=n_sents, - seg_sents=seg_sents, - append_morphology=morphology, - merge_subtokens=merge_subtokens, - lang=lang, - model=model, - no_print=no_print, - ner_map=ner_map, - ) - if output_dir != "-": - # Export data to a file suffix = f".{file_type}" - output_file = Path(output_dir) / Path(input_path.parts[-1]).with_suffix(suffix) + subpath = input_loc.relative_to(input_path) + output_file = (output_dir / subpath).with_suffix(suffix) + if not output_file.parent.exists(): + output_file.parent.mkdir(parents=True) if file_type == "json": - srsly.write_json(output_file, data) - elif file_type == "jsonl": - srsly.write_jsonl(output_file, data) - elif file_type == "msg": - srsly.write_msgpack(output_file, data) - msg.good(f"Generated output file ({len(data)} documents): {output_file}") - else: - # Print to stdout - if file_type == "json": - srsly.write_json("-", data) - elif file_type == "jsonl": - srsly.write_jsonl("-", data) + data = docs2json(docs) + srsly.write_json(output_file, docs2json(docs)) + else: + data = DocBin(docs=docs).to_bytes() + with output_file.open("wb") as file_: + file_.write(data) + msg.good(f"Generated output file ({len(docs)} documents): {output_file}") def autodetect_ner_format(input_data): @@ -129,3 +101,102 @@ def autodetect_ner_format(input_data): if format_guesses["ner"] == 0 and format_guesses["iob"] > 0: return "iob" return None + + +def walk_directory(path): + if not path.is_dir(): + return [path] + paths = [path] + locs = [] + seen = set() + for path in paths: + if str(path) in seen: + continue + seen.add(str(path)) + if path.parts[-1].startswith("."): + continue + elif path.is_dir(): + paths.extend(path.iterdir()) + else: + locs.append(path) + return locs + + +def verify_cli_args( + msg, + input_path, + output_dir, + file_type, + n_sents, + seg_sents, + model, + morphology, + merge_subtokens, + converter, + ner_map, + lang +): + if converter == "ner" or converter == "iob": + input_data = input_path.open("r", encoding="utf-8").read() + converter_autodetect = autodetect_ner_format(input_data) + if converter_autodetect == "ner": + msg.info("Auto-detected token-per-line NER format") + converter = converter_autodetect + elif converter_autodetect == "iob": + msg.info("Auto-detected sentence-per-line NER format") + converter = converter_autodetect + else: + msg.warn( + "Can't automatically detect NER format. Conversion may not", + "succeed. See https://spacy.io/api/cli#convert" + ) + if file_type not in FILE_TYPES_STDOUT and output_dir == "-": + # TODO: support msgpack via stdout in srsly? + msg.fail( + f"Can't write .{file_type} data to stdout", + "Please specify an output directory.", + exits=1, + ) + if not input_path.exists(): + msg.fail("Input file not found", input_path, exits=1) + if output_dir != "-" and not Path(output_dir).exists(): + msg.fail("Output directory not found", output_dir, exits=1) + if input_path.is_dir(): + input_locs = walk_directory(input_path) + if len(input_locs) == 0: + msg.fail("No input files in directory", input_path, exits=1) + file_types = list(set([loc.suffix[1:] for loc in input_locs])) + if len(file_types) >= 2: + file_types = ",".join(file_types) + msg.fail("All input files must be same type", file_types, exits=1) + if converter == "auto": + converter = file_types[0] + else: + converter = input_path.suffix[1:] + if converter not in CONVERTERS: + msg.fail(f"Can't find converter for {converter}", exits=1) + return converter + + +def _get_converter(msg, converter, input_path): + if input_path.is_dir(): + input_path = walk_directory(input_path)[0] + if converter == "auto": + converter = input_path.suffix[1:] + if converter == "ner" or converter == "iob": + with input_path.open() as file_: + input_data = file_.read() + converter_autodetect = autodetect_ner_format(input_data) + if converter_autodetect == "ner": + msg.info("Auto-detected token-per-line NER format") + converter = converter_autodetect + elif converter_autodetect == "iob": + msg.info("Auto-detected sentence-per-line NER format") + converter = converter_autodetect + else: + msg.warn( + "Can't automatically detect NER format. " + "Conversion may not succeed. " + "See https://spacy.io/api/cli#convert" + ) + return converter diff --git a/spacy/cli/converters/__init__.py b/spacy/cli/converters/__init__.py deleted file mode 100644 index e44ad407d..000000000 --- a/spacy/cli/converters/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from .conllu2json import conllu2json # noqa: F401 -from .iob2json import iob2docs # noqa: F401 -from .conll_ner2json import conll_ner2json # noqa: F401 -from .jsonl2docs import ner_jsonl2json # noqa: F401 diff --git a/spacy/cli/converters/jsonl2json.py b/spacy/cli/converters/jsonl2json.py deleted file mode 100644 index 8639a11b9..000000000 --- a/spacy/cli/converters/jsonl2json.py +++ /dev/null @@ -1,51 +0,0 @@ -import srsly - -from ...gold import docs_to_json -from ...util import get_lang_class, minibatch - - -def ner_jsonl2docs(input_data, lang=None, n_sents=10, use_morphology=False, **_): - if lang is None: - raise ValueError("No --lang specified, but tokenization required") - docs = [] - input_examples = [srsly.json_loads(line) for line in input_data.strip().split("\n")] - nlp = get_lang_class(lang)() - sentencizer = nlp.create_pipe("sentencizer") - for i, batch in enumerate(minibatch(input_examples, size=n_sents)): - docs = [] - # TODO: Should we be merging these? We're disrespecting the n_sents - # currently. - for record in batch: - raw_text = record["text"] - if "entities" in record: - ents = record["entities"] - else: - ents = record["spans"] - ents = [(e["start"], e["end"], e["label"]) for e in ents] - doc = nlp.make_doc(raw_text) - sentencizer(doc) - spans = [doc.char_span(s, e, label=L) for s, e, L in ents] - doc.ents = _cleanup_spans(spans) - docs.append(doc) - return docs - - -def _cleanup_spans(spans): - output = [] - seen = set() - for span in spans: - if span is not None: - # Trim whitespace - while len(span) and span[0].is_space: - span = span[1:] - while len(span) and span[-1].is_space: - span = span[:-1] - if not len(span): - continue - for i in range(span.start, span.end): - if i in seen: - break - else: - output.append(span) - seen.update(range(span.start, span.end)) - return output diff --git a/spacy/gold/converters/__init__.py b/spacy/gold/converters/__init__.py new file mode 100644 index 000000000..0a1242fb4 --- /dev/null +++ b/spacy/gold/converters/__init__.py @@ -0,0 +1,6 @@ +from .iob2docs import iob2docs # noqa: F401 +from .conll_ner2docs import conll_ner2docs # noqa: F401 +from .json2docs import json2docs + +# TODO: Update this one +#from .conllu2docs import conllu2docs # noqa: F401 diff --git a/spacy/cli/converters/conll_ner2json.py b/spacy/gold/converters/conll_ner2docs.py similarity index 99% rename from spacy/cli/converters/conll_ner2json.py rename to spacy/gold/converters/conll_ner2docs.py index 8d4139bde..7042bd7d6 100644 --- a/spacy/cli/converters/conll_ner2json.py +++ b/spacy/gold/converters/conll_ner2docs.py @@ -7,7 +7,7 @@ from ...vocab import Vocab from ...util import load_model -def conll_ner2doc( +def conll_ner2docs( input_data, n_sents=10, seg_sents=False, model=None, no_print=False, **kwargs ): """ diff --git a/spacy/cli/converters/conllu2json.py b/spacy/gold/converters/conllu2json.py similarity index 100% rename from spacy/cli/converters/conllu2json.py rename to spacy/gold/converters/conllu2json.py diff --git a/spacy/cli/converters/iob2json.py b/spacy/gold/converters/iob2docs.py similarity index 97% rename from spacy/cli/converters/iob2json.py rename to spacy/gold/converters/iob2docs.py index 2addc1af4..7901569fa 100644 --- a/spacy/cli/converters/iob2json.py +++ b/spacy/gold/converters/iob2docs.py @@ -3,7 +3,7 @@ from wasabi import Printer from ...gold import iob_to_biluo, tags_to_entities from ...util import minibatch from .util import merge_sentences -from .conll_ner2json import n_sents_info +from .conll_ner2docs import n_sents_info def iob2docs(input_data, n_sents=10, no_print=False, *args, **kwargs): diff --git a/spacy/gold/converters/json2docs.py b/spacy/gold/converters/json2docs.py new file mode 100644 index 000000000..98219bb04 --- /dev/null +++ b/spacy/gold/converters/json2docs.py @@ -0,0 +1,38 @@ +import tempfile +import contextlib +import shutil +from pathlib import Path +from ..gold_io import read_json_file +from ..example import annotations2doc +from ..example import _fix_legacy_dict_data, _parse_example_dict_data +from ...util import load_model +from ...lang.xx import MultiLanguage + +@contextlib.contextmanager +def make_tempdir(): + d = Path(tempfile.mkdtemp()) + yield d + shutil.rmtree(str(d)) + + +def json2docs( + input_data, + model=None, + **kwargs +): + nlp = load_model(model) if model is not None else MultiLanguage() + docs = [] + with make_tempdir() as tmp_dir: + json_path = Path(tmp_dir) / "data.json" + with (json_path).open("w") as file_: + file_.write(input_data) + for json_annot in read_json_file(json_path): + example_dict = _fix_legacy_dict_data(json_annot) + tok_dict, doc_dict = _parse_example_dict_data(example_dict) + doc = annotations2doc( + nlp.vocab, + tok_dict, + doc_dict + ) + docs.append(doc) + return docs diff --git a/spacy/gold/converters/util.py b/spacy/gold/converters/util.py new file mode 100644 index 000000000..ed9c84203 --- /dev/null +++ b/spacy/gold/converters/util.py @@ -0,0 +1,5 @@ +def merge_sentences(docs, n_sents): + merged = [] + for group in minibatch(docs, size=n_sents): + raise NotImplementedError + return merged diff --git a/spacy/tokens/_serialize.py b/spacy/tokens/_serialize.py index 7bf3faab3..3072787ae 100644 --- a/spacy/tokens/_serialize.py +++ b/spacy/tokens/_serialize.py @@ -9,6 +9,19 @@ from ..attrs import SPACY, ORTH, intify_attr from ..errors import Errors +ALL_ATTRS = ( + "ORTH", + "TAG", + "HEAD", + "DEP", + "SENT_START", + "ENT_IOB", + "ENT_TYPE", + "LEMMA", + "MORPH" +) + + class DocBin(object): """Pack Doc objects for binary serialization. @@ -39,7 +52,7 @@ class DocBin(object): document from the DocBin. """ - def __init__(self, attrs=None, store_user_data=False, docs=[]): + def __init__(self, attrs=ALL_ATTRS, store_user_data=False, docs=[]): """Create a DocBin object to hold serialized annotations. attrs (list): List of attributes to serialize. 'orth' and 'spacy' are @@ -49,7 +62,6 @@ class DocBin(object): DOCS: https://spacy.io/api/docbin#init """ - attrs = attrs or [] attrs = sorted([intify_attr(attr) for attr in attrs]) self.attrs = [attr for attr in attrs if attr != ORTH and attr != SPACY] self.attrs.insert(0, ORTH) # Ensure ORTH is always attrs[0] @@ -60,7 +72,7 @@ class DocBin(object): self.strings = set() self.store_user_data = store_user_data for doc in docs: - self.add(docs) + self.add(doc) def __len__(self): """RETURNS: The number of Doc objects added to the DocBin."""