def output_pure_article(self, article, subject):
self.article = os.path.join(self.inPath, subject, article)
self.tree = Articles.parse_XML_no_Table(self.article)
self.body = self.get_article_body_text(self.tree)
self.sentences = self.tokenize_text(self.body)
self.doi = Articles.extract_element(self.tree, "front/article-meta/article-id")
if not os.path.exists(os.path.join(self.outPath, subject)):
sys.stderr.write("creating directory %s\n" % os.path.join(self.outPath, subject))
os.mkdir(os.path.join(self.outPath, subject))
self.write(os.path.join(self.outPath, subject))
def collect_files_by_DOI(DOI_dict, archive_dir, data_dir, raw_article_dir, updater = 200):
"""
iterates over all archived articles and copies files to subject dirs
if article DOIs are in the DOI list.
"""
archived_articles = generate_files(archive_dir)
article_trees = ((Articles.parse_XML(article), article) for article in archived_articles)
article_IDs = ((list(Articles.extract_element(tree[0],
"front/article-meta/article-id")), tree[1]) for tree in article_trees)
found_DOIs = dict(((key, {}) for key in settings.DOI_LISTS.keys()))
for n, ID in enumerate(article_IDs):
found_DOIs = check_and_copy_DOI(DOI_dict, ID, data_dir, raw_article_dir, found_DOIs)
if n % updater == 0:
sys.stderr.write( "%d files processed...\n" % n)
from pmcminer.ProcessFiles import Raw, Articles
from control import settings
def check_DOI_by_dict(DOI_dict, article_ID, data_dir, raw_article_dir):
"""generate subject, DOI and filename for PMC XML file"""
for subject in DOI_dict:
for item in article_ID[0]:
if item in DOI_dict[subject]:
yield (subject, item, article_ID[1])
DOIs = Raw.get_DOI_list(settings.DOI_LISTS)
archived_articles = Raw.generate_files(settings.ARCHIVE_DIR)
article_trees = ((Articles.parse_XML(article), article) for article in archived_articles)
article_IDs = ((list(Articles.extract_element(tree[0],
"front/article-meta/article-id")), tree[1]) for tree in article_trees)
check_dict = dict(((key, {}) for key in settings.DOI_LISTS.keys()))
#for ID in article_IDs:
for n, ID in enumerate(article_IDs):
checker = check_DOI_by_dict(DOIs, ID, settings.DATA_DIR, settings.RAW_ARTICLES_DIR)
for i in checker:
try:
check_dict[i[0]][i[1]].append(i[2])
except KeyError:
check_dict[i[0]][i[1]] = [i[2]]
if n % 500 == 0:
sys.stderr.write( "%d files processed...\n" % n)
