def test_add_value(self):
if exists(self.addition_path):
remove(self.addition_path)
csv_m = CSVManager(self.addition_path)
csv_m.add_value("doi:10.1108/jd-12-2013-0166",
"orcid:0000-0003-0530-4305")
csv_m.add_value("doi:10.7717/peerj.4375", "orcid:0000-0003-1613-5981")
csv_m.add_value("doi:10.1108/jd-12-2013-0166",
"orcid:0000-0001-5506-523X")
self.assertDictEqual(
csv_m.data, {
"doi:10.1108/jd-12-2013-0166":
{"orcid:0000-0003-0530-4305", "orcid:0000-0001-5506-523X"},
"doi:10.7717/peerj.4375": {"orcid:0000-0003-1613-5981"}
})
def process(input_dir, output_dir):
if not exists(output_dir):
makedirs(output_dir)
citing_doi_with_no_date = set()
valid_doi = CSVManager(output_dir + sep + "valid_doi.csv")
id_date = CSVManager(output_dir + sep + "id_date.csv")
id_issn = CSVManager(output_dir + sep + "id_issn.csv")
id_orcid = CSVManager(output_dir + sep + "id_orcid.csv")
doi_manager = DOIManager(valid_doi)
issn_manager = ISSNManager()
orcid_manager = ORCIDManager()
all_files, opener = get_all_files(input_dir)
len_all_files = len(all_files)
# Read all the JSON file in the Crossref dump to create the main information of all the indexes
print("\n\n# Add valid DOIs from Crossref metadata")
for file_idx, file in enumerate(all_files, 1):
with opener(file) as f:
print("Open file %s of %s" % (file_idx, len_all_files))
try:
data = load(f)
# When using tar.gz file or zip file a stream of byte is returned by the opener. Thus,
# it must be converted into an utf-8 string before loading it into a JSON.
except TypeError:
utf8reader = codecs.getreader("utf-8")
data = load(utf8reader(f))
if "items" in data:
for obj in data['items']:
if "DOI" in obj:
citing_doi = doi_manager.normalise(obj["DOI"], True)
doi_manager.set_valid(citing_doi)
if id_date.get_value(citing_doi) is None:
citing_date = Citation.check_date(build_pubdate(obj))
if citing_date is not None:
id_date.add_value(citing_doi, citing_date)
if citing_doi in citing_doi_with_no_date:
citing_doi_with_no_date.remove(citing_doi)
else:
citing_doi_with_no_date.add(citing_doi)
if id_issn.get_value(citing_doi) is None:
if "type" in obj:
cur_type = obj["type"]
if cur_type is not None and "journal" in cur_type and "ISSN" in obj:
cur_issn = obj["ISSN"]
if cur_issn is not None:
for issn in [issn_manager.normalise(issn) for issn in cur_issn]:
if issn is not None:
id_issn.add_value(citing_doi, issn)
if id_orcid.get_value(citing_doi) is None:
if "author" in obj:
cur_author = obj['author']
if cur_author is not None:
for author in cur_author:
if "ORCID" in author:
orcid = orcid_manager.normalise(author["ORCID"])
if orcid is not None:
id_orcid.add_value(citing_doi, orcid)
# Do it again for updating the dates of the cited DOIs, if these are valid
print("\n\n# Check cited DOIs from Crossref reference field")
doi_date = {}
for file_idx, file in enumerate(all_files, 1):
with opener(file) as f:
print("Open file %s of %s" % (file_idx, len_all_files))
data = load(f)
if "items" in data:
for obj in data['items']:
if "DOI" in obj and "reference" in obj:
for ref in obj['reference']:
if "DOI" in ref:
cited_doi = doi_manager.normalise(ref["DOI"], True)
if doi_manager.is_valid(cited_doi) and id_date.get_value(cited_doi) is None:
if cited_doi not in doi_date:
doi_date[cited_doi] = []
cited_date = Citation.check_date(build_pubdate(ref))
if cited_date is not None:
doi_date[cited_doi].append(cited_date)
if cited_doi in citing_doi_with_no_date:
citing_doi_with_no_date.remove(cited_doi)
# Add the date to the DOI if such date is the most adopted one in the various references.
# In case two distinct dates are used the most, select the older one.
for doi in doi_date:
count = Counter(doi_date[doi])
if len(count):
top_value = count.most_common(1)[0][1]
selected_dates = []
for date in count:
if count[date] == top_value:
selected_dates.append(date)
best_date = sorted(selected_dates)[0]
id_date.add_value(doi, best_date)
else:
id_date.add_value(doi, "")
# Add emtpy dates for the remaining DOIs
for doi in citing_doi_with_no_date:
id_date.add_value(doi, "")