def tabulate_entities(query_list, date_ranges, text_words, mesh_terms, author):
dates = []
log = []
author_articles = defaultdict(list)
counts = defaultdict(list)
keyword_counts = defaultdict(list)
for from_date, to_date in date_ranges:
dates.append(pd.Timestamp(from_date))
for item in query_list:
query_param = (
{'author_name': item} if author else {'journal_name': item})
# Query totals (w/o keywords)
item_query = get_expression(
from_date=from_date, to_date=to_date, **query_param)
item_articles = get_search_count(item_query)
item_count = len(item_articles)
query = get_expression(
text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date,
**query_param)
articles = get_search_count(query)
keyword_count = len(articles)
log.append("{query}\n{count}".format(
query=item_query, count=item_count))
log.append("{query}\n{count}".format(
query=query, count=keyword_count))
if author:
author_articles[item].extend(item_articles)
# Get search count data for each Query (w/ keywords)
counts[item].append(item_count)
keyword_counts[item].append(keyword_count)
index = pd.Index(dates, name='dates')
search_counts = pd.DataFrame(counts, index=index)
keyword_search_counts = pd.DataFrame(keyword_counts, index=index)
return dict(
search_counts=search_counts,
keyword_search_counts=keyword_search_counts,
author_articles=author_articles,
log=log)
def tabulate_keywords(date_ranges, text_words, mesh_terms):
counts = defaultdict(list)
dates = []
log = []
for from_date, to_date in date_ranges:
query = get_expression(
text_terms=text_words, mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date)
articles = get_search_count(query)
count = len(articles)
log.append("{query}\n{count}".format(query=query, count=count))
dates.append(pd.Timestamp(from_date))
counts['count'].append(count)
index = pd.Index(dates, name='dates')
search_counts = pd.DataFrame(counts, index=index)
return dict(search_counts=search_counts, log=log)
def tabulate(query_list, date_ranges, text_words, mesh_terms, search_journals):
search_counts = {}
queries = []
query_totals = []
# O(n*y) for n=len(query_list) and y=len(date_ranges)
if len(query_list) > 0:
for item in query_list:
total = 'Total Article Count [' + item + ']'
partial = 'Keyword Article Count [' + item + ']'
search_counts[partial] = []
search_counts[total] = []
# search_counts[item] = {'partial':[], 'total':[]}
for from_date, to_date in date_ranges:
# Query totals (w/o keywords)
if search_journals:
item_expression = get_expression(journal_name=item,
from_date=from_date,
to_date=to_date)
else:
item_expression = get_expression(author_name=item,
from_date=from_date,
to_date=to_date)
item_count = get_search_count(item_expression)
search_counts[total].append(item_count)
print('Total - ' + item_expression)
print(str(item_count) + '\n')
query_totals.append('Total - ' + item_expression + '\n' +
str(item_count))
# Get search count data for each Query (w/ keywords)
if search_journals:
expression = get_expression(journal_name=item,
text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date,
to_date=to_date)
else:
expression = get_expression(author_name=item,
text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date,
to_date=to_date)
count = get_search_count(expression)
search_counts[partial].append(count)
# Log is printed to standard output and file
print(expression)
print(str(count) + '\n')
queries.append(expression + '\n' + str(count))
else:
search_counts['Counts'] = []
for from_date, to_date in date_ranges:
expression = get_expression(text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date,
to_date=to_date)
count = get_search_count(expression)
search_counts['Counts'].append(count)
# Log is printed to standard output and file
print(expression)
print(str(count) + '\n')
queries.append(expression + '\n' + str(count))
return dict(search_counts=search_counts,
queries='\n\n'.join(queries),
query_totals='\n\n'.join(query_totals))
def tabulate(query_list, date_ranges, text_words, mesh_terms, isAuthor):
# O(n*y) for n=len(query_list) and y=len(date_ranges)
author_articles = defaultdict(list)
sc = []
if query_list:
sc = [('from', 'to', 'name', 'count', 'count w/ keywords')]
for from_date, to_date in date_ranges:
for item in query_list:
query_param = ({'author_name': item} if isAuthor
else {'journal_name': item})
# Query totals (w/o keywords)
item_expression = get_expression(
from_date=from_date, to_date=to_date, **query_param)
expression = get_expression(
text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date,
**query_param)
with query() as cursor:
search_list = [(item_expression,), (expression,)]
item_articles= [str(article[0]) for article in cursor.execute("""SELECT article from
articles where query=? """,
(item_expression,)
).fetchall()]
keyword_articles = cursor.execute("""SELECT article from
articles where query=?
""",
(expression,)
).fetchall()
keyword_count = len(keyword_articles)
item_count = len(item_articles)
if not item_count:
item_articles = get_search_count(item_expression)
item_count = len(item_articles)
insert_articles = [(item_expression, article)
for article in item_articles]
with query() as cursor:
cursor.executemany("""INSERT INTO
articles(query, article)
values(?, ?)""", insert_articles)
if isAuthor:
author_articles[item].extend(item_articles)
# Get search count data for each Query (w/ keywords)
if not keyword_count:
keyword_articles = get_search_count(expression)
keyword_count = len(keyword_articles)
with query() as cursor:
insert_articles = [(expression, article)
for article in keyword_articles]
cursor.executemany("""INSERT INTO
articles(query, article)
values(?, ?)""", insert_articles)
sc.append((from_date, to_date, item,
item_count, keyword_count))
else:
sc = [('from', 'to', 'count')]
for from_date, to_date in date_ranges:
expression = get_expression(
text_terms=text_words, mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date)
with query() as cursor:
count = len(cursor.execute("""SELECT article from articles
where query = ?""",
(expression,)).fetchall())
if not count:
articles = get_search_count(expression)
count = len(articles)
with query() as cursor:
insert_articles = [(expression, article)
for article in articles]
cursor.executemany("""INSERT INTO articles(query, article)
values(?, ?)""", list_articles)
sc.append((from_date, to_date, count))
return dict(search_counts=sc, author_articles=author_articles)
def tabulate(query_list, date_ranges, text_words, mesh_terms, search_journals):
search_counts = {}
queries = []
query_totals = []
# O(n*y) for n=len(query_list) and y=len(date_ranges)
if len(query_list) > 0:
for item in query_list:
total = 'Total Article Count [' + item + ']'
partial = 'Keyword Article Count [' + item + ']'
search_counts[partial] = []
search_counts[total] = []
# search_counts[item] = {'partial':[], 'total':[]}
for from_date, to_date in date_ranges:
# Query totals (w/o keywords)
if search_journals:
item_expression = get_expression(
journal_name=item,
from_date=from_date, to_date=to_date)
else:
item_expression = get_expression(
author_name=item,
from_date=from_date, to_date=to_date)
item_count = get_search_count(item_expression)
search_counts[total].append(item_count)
print('Total - ' + item_expression)
print(str(item_count) + '\n')
query_totals.append(
'Total - ' + item_expression + '\n' + str(item_count))
# Get search count data for each Query (w/ keywords)
if search_journals:
expression = get_expression(
journal_name=item, text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date)
else:
expression = get_expression(
author_name=item, text_terms=text_words,
mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date)
count = get_search_count(expression)
search_counts[partial].append(count)
# Log is printed to standard output and file
print(expression)
print(str(count) + '\n')
queries.append(expression + '\n' + str(count))
else:
search_counts['Counts'] = []
for from_date, to_date in date_ranges:
expression = get_expression(
text_terms=text_words, mesh_terms=mesh_terms,
from_date=from_date, to_date=to_date)
count = get_search_count(expression)
search_counts['Counts'].append(count)
# Log is printed to standard output and file
print(expression)
print(str(count) + '\n')
queries.append(expression + '\n' + str(count))
return dict(
search_counts=search_counts,
queries='\n\n'.join(queries),
query_totals='\n\n'.join(query_totals))
def test_retstart():
expression = 'Reshma%20Jagsi[author]'
articles_list_20 = get_search_count(expression, retmax=20)
articles_list_100 = get_search_count(expression, retmax=1000)
assert len(articles_list_20) == len(articles_list_100)
def test_retstart():
expression = 'Reshma%20Jagsi[author]'
articles_list_20 = get_search_count(expression, retmax=20)
articles_list_100 = get_search_count(expression, retmax=1000)
assert len(articles_list_20) == len(articles_list_100)
