import re import click import pandas as pd from io import StringIO import os import xml.etree.ElementTree as ET @click.command() @click.argument('tsv-file', type=click.Path(exists=True), required=True, nargs=1) @click.argument('url-file', type=click.Path(exists=False), required=True, nargs=1) def extract_document_links(tsv_file, url_file): parts = extract_doc_links(tsv_file) urls = [part['url'] for part in parts] urls = pd.DataFrame(urls, columns=['url']) urls.to_csv(url_file, sep="\t", quoting=3, index=False) @click.command() @click.argument('tsv-file', type=click.Path(exists=True), required=True, nargs=1) @click.argument('annotated-tsv-file', type=click.Path(exists=False), required=True, nargs=1) def annotate_tsv(tsv_file, annotated_tsv_file): parts = extract_doc_links(tsv_file) annotated_parts = [] for part in parts: part_data = StringIO(part['header'] + part['text']) df = pd.read_csv(part_data, sep="\t", comment='#', quoting=3) df['url_id'] = len(annotated_parts) annotated_parts.append(df) df = pd.concat(annotated_parts) df.to_csv(annotated_tsv_file, sep="\t", quoting=3, index=False) def extract_doc_links(tsv_file): parts = [] header = None with open(tsv_file, 'r') as f: text = [] url = None for line in f: if header is None: header = "\t".join(line.split()) + '\n' continue urls = [url for url in re.findall(r'http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+', line)] if len(urls) > 0: if url is not None: parts.append({"url": url, 'header': header, 'text': "".join(text)}) text = [] url = urls[-1] else: if url is None: continue line = '\t'.join(line.split()) if line.count('\t') == 2: line = "\t" + line if line.count('\t') >= 3: text.append(line + '\n') continue if line.startswith('#'): continue if len(line) == 0: continue print('Line error: |', line, '|Number of Tabs: ', line.count('\t')) if url is not None: parts.append({"url": url, 'header': header, 'text': "".join(text)}) return parts @click.command() @click.argument('page-xml-file', type=click.Path(exists=True), required=True, nargs=1) @click.argument('tsv-out-file', type=click.Path(), required=True, nargs=1) @click.option('--image-url', type=str, default='') def page2tsv(page_xml_file, tsv_out_file, image_url): tree = ET.parse(page_xml_file) xmlns = tree.getroot().tag.split('}')[0].strip('{') urls = [] if os.path.exists(tsv_out_file): parts = extract_doc_links(tsv_out_file) urls = [part['url'] for part in parts] else: pd.DataFrame([], columns=['No.', 'TOKEN', 'NE-TAG', 'NE-EMB', 'GND-ID', 'url_id', 'left', 'right', 'top', 'bottom']). to_csv(tsv_out_file, sep="\t", quoting=3, index=False) tsv = [] for words in tree.findall('.//{%s}Word' % xmlns): for word in words.findall('.//{%s}Unicode' % xmlns): text = word.text for coords in words.findall('.//{%s}Coords' % xmlns): points = [int(pos) for p in coords.attrib['points'].split(' ') for pos in p.split(',')] left = points[0] right = points[2] top = points[1] bottom = points[5] tsv.append((0, text, 'O', 'O', '-', len(urls), left, right, top, bottom)) with open(tsv_out_file, 'a') as f: f.write('# ' + image_url + '\n') tsv = pd.DataFrame(tsv, columns=['No.', 'TOKEN', 'NE-TAG', 'NE-EMB', 'GND-ID', 'url_id', 'left', 'right', 'top', 'bottom']) tsv.to_csv(tsv_out_file, sep="\t", quoting=3, index=False, mode='a', header=False)