def tokenize_wikimedia_jsonl(jsonl_in: pathlib.Path, jsonl_out: pathlib.Path,
sub_process_count: int) -> None:
"""
Tokenizes all the articles into the standard form: one sentence per line, paragraphs have a blank line between them.
Parameters
----------
jsonl_in : pathlib.Path
The JSONL containing all the articles
jsonl_out : pathlib.Path
The JSONL containing all the articles after tokenization
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=_collect_articles,
extract_args=(jsonl_in),
transform=_tokenize_article,
save=_save_articles_to_jsonl,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def extract_csv_from_jsonl(jsonl_in: pathlib.Path, csv_out: pathlib.Path,
extract: t.List[str],
sub_process_count: int) -> None:
"""
Extracts a `CSV` file from a `JSONL` file.
Parameters
----------
jsonl_in : pathlib.Path
The JSONL containing all the documents
csv_out : pathlib.Path
The CSV file containing all the documents
extract : List[str]
The name(s) of the elements to extract
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if csv_out.exists():
csv_out.unlink()
worker = mpb.EPTS(extract=u.list_jsonl_documents,
extract_args=(jsonl_in),
transform=_extract_document,
transform_init=_passthrough,
transform_init_args=(extract),
save=_save_documents,
save_args=(csv_out, extract),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def combine_txt_to_jsonl(folder_in: pathlib.Path, jsonl_out: pathlib.Path,
sub_process_count: int) -> None:
"""
Combines a folder of `TXT` files into a single `JSONL` file.
Parameters
----------
folder_in : pathlib.Path
Folder containing the source documents
jsonl_out : pathlib.Path
JSONL containing the aggregated corpus
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=u.list_folder_documents,
extract_args=(folder_in, u.is_txt_document),
transform=_process_document,
save=_save_documents_to_jsonl,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def convert_txt(folder_in: pathlib.Path, folder_out: pathlib.Path, stem: str,
max_lines: int, sub_process_count: int) -> None:
"""
Convert a folder of `TXT` files into a folder of _bigger_ `TXT` files.
Parameters
----------
folder_in : pathlib.Path
Folder containing the source documents
folder_out : pathlib.Path
The folder containing all the aggreated documents
stem : str
The output file's stem
max_lines : int
The number of lines per file
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
folder_out.mkdir(parents=True, exist_ok=True)
worker = mpb.EPTS(extract=u.list_folder_documents,
extract_args=(folder_in, u.is_txt_document),
transform=_process_document,
save=_save_documents,
save_args=(folder_out, stem, max_lines),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def convert_jsonl(jsonl_in: pathlib.Path, jsonl_out: pathlib.Path,
keep: t.List[str], sub_process_count: int) -> None:
"""
Converts a `JSONL` file into a _smaller_ `JSONL` file by keeping only some elements.
Parameters
----------
jsonl_in : pathlib.Path
The JSONL containing all the documents
jsonl_out : pathlib.Path
The JSONL file containing all the documents
keep : List[str]
The name(s) of the elements to keep
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=u.list_jsonl_documents,
extract_args=(jsonl_in),
transform=_convert_document,
transform_init=_passthrough,
transform_init_args=(keep),
save=_save_documents,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def wikimedia_to_json(mediawiki_in: pathlib.Path, jsonl_out: pathlib.Path,
sub_process_count: int) -> None:
"""
Converts a Wikimedia dump file to a JSONL file containing all the articles minus any wiki markup.
Articles that contain no text are removed.
Disambiguation articles are removed.
Parameters
----------
mediawiki_in : pathlib.Path
The XML dump file from Wikimedia
jsonl_file : pathlib.Path
JSONL containing all the wikimedia articles
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=_collect_articles,
extract_args=(mediawiki_in),
transform=_parse_article,
save=_save_articles_to_jsonl,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def extract_txt_from_jsonl(jsonl_in: pathlib.Path, folder_out: pathlib.Path,
id_element: str, extract: t.List[str],
sub_process_count: int) -> None:
"""
Extracts a folder of `TXT` files from a `JSONL` file.
Parameters
----------
jsonl_in : pathlib.Path
The JSONL containing all the documents
folder_out : pathlib.Path
The folder containing all the documents after being extracted
id_element : str
The name of the element to use as a file name
extract : List[str]
The name(s) of the elements to extract
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
folder_out.mkdir(parents=True, exist_ok=True)
worker = mpb.EPTS(extract=u.list_jsonl_documents,
extract_args=(jsonl_in),
transform=_save_txt_document,
transform_init=_passthrough,
transform_init_args=(str(folder_out), id_element,
extract),
save=u.drain_iterator,
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def merge_json_folders(folders_in: t.List[pathlib.Path],
folder_out: pathlib.Path,
sub_process_count: int) -> None:
"""
Merges _several_ folders of `JSON` files into a _single_ folder of `JSON` files based on their file name.
Parameters
----------
folders_in : List[pathlib.Path]
Folders containing the documents to merge
folder_out : pathlib.Path
Folder containing the merged documents
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
folder_out.mkdir(parents=True, exist_ok=True)
worker = mpb.EPTS(extract=u.list_merged_folder_documents,
extract_args=(folders_in, u.is_json_document),
transform=_merge_documents,
transform_init=_passthrough,
transform_init_args=(str(folder_out)),
save=u.drain_iterator,
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def oas_to_jsonl(folder_in: pathlib.Path, jsonl_out: pathlib.Path,
sub_process_count: int) -> None:
"""
Converts the PMC OAS folders to a JSONL file containing all the articles minus any markup.
Articles that contain no body are removed.
Parameters
----------
folder_in : pathlib.Path
The root of the JATS folders
jsonl_out : pathlib.Path
JSONL containing all the wikimedia articles
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=_collect_articles,
extract_args=(folder_in),
transform=_parse_article_safe,
save=_save_articles_to_jsonl,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
def tokenize_jsonl(jsonl_in: pathlib.Path, jsonl_out: pathlib.Path,
id_element: str, tokens: t.List[t.Tuple[str, str]],
sub_process_count: int) -> None:
"""
Tokenizes all the files into the standard form: one sentence per line, paragraphs have a blank line between them.
Parameters
----------
jsonl_in : pathlib.Path
The JSONL containing all the files
jsonl_out : pathlib.Path
The JSONL containing all the files after tokenization
id_element : str
The name of the element used for correlation between processed files
tokens : List[(str,str)]
Run the algorithm over these elements
sub_process_count : int
The number of sub processes used to transformation from in to out formats
"""
if jsonl_out.exists():
jsonl_out.unlink()
worker = mpb.EPTS(extract=_collect_documents,
extract_args=(jsonl_in),
transform=_tokenize_document,
transform_init=_passthrough,
transform_init_args=(id_element, tokens),
save=_save_documents_to_jsonl,
save_args=(jsonl_out),
worker_count=sub_process_count,
show_progress=True)
worker.start()
worker.join()
