def build_xml(article_id, article=None, jats_config=None, add_comment=True):
"generate xml from an article object"
if not jats_config:
jats_config = parse_raw_config(raw_config(None))
if not article:
article = build_article_from_csv(article_id, jats_config)
if not hasattr(article, "manuscript"):
LOGGER.info("could not build article for %s", article_id)
return None
article_xml = ArticleXML(article, jats_config, add_comment)
if hasattr(article_xml, "root"):
LOGGER.info("generated xml for %s", article_id)
return article_xml
return None
def build_article_from_csv(article_id, jats_config=None):
"build article objects populated with csv data"
if not jats_config:
jats_config = parse_raw_config(raw_config(None))
article, error_count, error_messages = parse.build_article(article_id)
if article:
return article
LOGGER.warning(
"the following article did not have enough components and " +
"xml was not generated %s",
article_id,
)
LOGGER.warning("warning count was %s", error_count)
if error_messages:
LOGGER.warning(", ".join(error_messages))
return False
def test_parse_raw_config(self):
"test parsing a raw config of all the different value types"
# override the library values
conf.BOOLEAN_VALUES = ["test_boolean"]
conf.INT_VALUES = ["test_int"]
conf.LIST_VALUES = ["test_list"]
# build a config object
config = configparser.ConfigParser(interpolation=None)
config["DEFAULT"]["test_boolean"] = "True"
config["DEFAULT"]["test_int"] = "42"
config["DEFAULT"]["test_list"] = "[1,1,2,3,5]"
# parse the raw config for coverage
config_dict = conf.parse_raw_config(config["DEFAULT"])
# assert some things
self.assertIsNotNone(config_dict)
self.assertEqual(config_dict.get("test_boolean"), True)
self.assertEqual(config_dict.get("test_int"), 42)
self.assertEqual(config_dict.get("test_list"), [1, 1, 2, 3, 5])
def build_xml_to_disk(article_id,
article=None,
jats_config=None,
add_comment=True):
"generate xml from an article object and write to disk"
if not jats_config:
jats_config = parse_raw_config(raw_config(None))
if not article:
article = build_article_from_csv(article_id, jats_config)
article_xml = build_xml(article_id, article, jats_config, add_comment)
if article_xml and hasattr(article_xml, "root"):
filename = jats_config.get("xml_filename_pattern").format(
manuscript=article.manuscript)
try:
output_dir = jats_config.get("target_output_dir")
write_xml_to_disk(article_xml, filename, output_dir)
LOGGER.info("xml written for %s", article_id)
print("written " + str(article_id))
return True
except IOError:
LOGGER.error("could not write xml for %s", article_id)
return False
LOGGER.error("could not generate xml to disk for %s", article_id)
return False
def build_config(config_section):
"build the config and override the output directory"
jats_config = parse_raw_config(raw_config(config_section))
jats_config["target_output_dir"] = TARGET_OUTPUT_DIR
return jats_config