def import_articles(filename):
'''
Used to import a file directly into the database
'''
num_to_insert = 500
article_list = []
article_cols = [
'id',
'external_id',
'source',
'orig_file',
'journal',
'print_issn',
'e_issn',
'journal_unique_id',
'year',
'article_type',
'article_section',
'authors',
'author_emails',
'author_affiliations',
'keywords',
'title',
'abstract',
'vol',
'issue',
'page',
'pmid',
'pmc_id',
'doi',
'fulltext_url',
'time',
]
with gzip.open(filename) as f:
reader = csv.reader(f, delimiter="\t")
count = 0
for row in reader:
if reader.line_num == 1:
headers = row
headers = map(convert, headers)
if (headers[0] == '#article_id'):
headers[0] = 'id'
elif len(article_list) >= num_to_insert:
Article.objects.bulk_create(article_list)
print "bulk updating %s articles" % (len(article_list))
article_list = []
else:
line_dict = {}
line_dict = dict(zip(headers, row))
article_dict = sub_dict_remove_strict(
line_dict, article_cols)
if line_dict:
raise Exception('Unidentified column in file')
# convert int columns from string to int
ints = ['year', 'page', 'pmid', 'pmc_id']
for field in ints:
if (article_dict[field] == ''):
article_dict[field] = None
else:
article_dict[field] = int(article_dict[field])
# convert timestamp to time object
try:
if (article_dict['time'] == ''):
article_dict['time'] = None
else:
article_dict['time'] = time.strftime("%Y-%m-%d %T", time.strptime(article_dict['time']))
except Exception as e:
print e
print article_dict['time']
# append article to list to be bulk created
count += 1
article_list.append(Article(**article_dict))
Article.objects.bulk_create(article_list)
def import_tsv_old(sample, filename):
headers = None
# num_to_insert = 100
# clonotype_list = []
# amino_acid_list = []
# recombination_list = []
reader = csv.reader(open(filename, 'r'), delimiter="\t")
recombination_cols = ['nucleotide',
'v_family_name',
'v_gene_name',
'v_ties',
'd_gene_name',
'j_gene_name',
'j_ties',
'sequence_status',
'v_deletion',
'd5_deletion',
'd3_deletion',
'j_deletion',
'n2_insertion',
'n1_insertion',
'v_index',
'n1_index',
'n2_index',
'd_index',
'j_index',
'cdr3_length',
]
amino_acid_cols = ['amino_acid']
clonotype_cols = [
'sequence_id',
'container',
'normalized_frequency',
'normalized_copy',
'raw_frequency',
'copy',
]
for row in reader:
if reader.line_num == 1:
headers = row
headers = map(convert, headers)
else:
line_dict = {}
line_dict = dict(zip(headers, row))
# split into clonotype, recombination and amino acid dicts
amino_acid_dict = sub_dict_remove_strict(
line_dict, amino_acid_cols)
recombination_dict = sub_dict_remove_strict(
line_dict, recombination_cols)
clonotype_dict = sub_dict_remove_strict(
line_dict, clonotype_cols)
# throw error if any leftover columns
if line_dict:
raise Exception('Unidentified column in file')
if clonotype_dict['normalized_frequency'] == '':
raise Exception('Normalized_frequency cannot be null')
if not amino_acid_dict['amino_acid'] == '':
# Fix discrepancies between column and model fields
amino_acid_dict['sequence'] = amino_acid_dict['amino_acid']
del amino_acid_dict['amino_acid']
aa, created = AminoAcid.objects.get_or_create(
**amino_acid_dict)
# aa.samples.add(sample)
# aa.save()
r, created = Recombination.objects.get_or_create(
amino_acid=aa, **recombination_dict)
else:
r, created = Recombination.objects.get_or_create(
**recombination_dict)
clonotype_dict['recombination'] = r
clonotype_dict['sample'] = sample
Clonotype.objects.create(**clonotype_dict)
