def test_get_content():
"Test that content querries are correctly formed."
db = get_db_with_pubmed_content()
tr_list = db.select_all(db.TextRef)
id_dict = get_id_dict(tr_list)
readers = get_readers()
tc_query_1 = rdb.get_content_query(id_dict, readers, db=db,
force_read=False)
N_exp = db.filter_query(db.TextContent).count()
N_1 = tc_query_1.count()
assert N_1 == N_exp,\
"Expected %d results in our query, got %d." % (N_exp, N_1)
# This tests both that tcid and trid are recognized, and that we really
# are getting just a subset of the content.
test_tcs_2 = tc_query_1.limit(2).all()
small_id_dict = {'tcid': [test_tcs_2[0].id],
'trid': [test_tcs_2[1].text_ref_id]}
tc_query_2 = rdb.get_content_query(small_id_dict, readers, db=db)
N_2 = tc_query_2.count()
assert N_2 == 2, "Expected 2 items in query, but got %d." % N_2
# Now test the 'all' feature.
tc_query_3 = rdb.get_content_query('all', readers, db=db)
N_3 = tc_query_3.count()
assert N_3 == N_1, \
"Expected to get %d items in query, but got %d." % (N_1, N_3)
# Test response to empyt dict.
assert rdb.get_content_query({}, readers, db=db) is None, \
"Expected None when passing no ids."
def test_read_db():
"Test the low level make_db_readings functionality with various settings."
# Prep the inputs.
db = get_db_with_pubmed_content()
complete_tr_list = db.select_all(db.TextRef)
id_dict = get_id_dict(complete_tr_list)
readers = get_readers('SPARSER')
# Run the reading with default batch size, no force_fulltext, and
# no force_read
reading_output_1 = rdb.make_db_readings(id_dict, readers, db=db)
N1 = len(reading_output_1)
N1_exp = len(readers)*db.filter_query(db.TextContent).count()
assert N1 == N1_exp, \
'Expected %d readings, but got %d.' % (N1_exp, N1)
rdb.upload_readings(reading_output_1, db=db) # setup for later test.
N1_db = len(db.select_all(db.Readings))
assert N1_db == N1, \
'Expected %d readings to be copied to db, only %d found.' % (N1, N1_db)
# Run the reading with default batch size, no force_fulltext, but with
# force_read = True (this hould produce new readings.)
reading_output_2 = rdb.make_db_readings(id_dict, readers, db=db,
force_read=True)
N2 = len(reading_output_2)
assert N1 == N2, "Got %d readings from run 1 but %d from run 2." % (N1, N2)
# Run the reading with default batch size, no force_fulltext, but without
# force_read = True (this should NOT produce new readings.)
old_readings = rdb.get_db_readings(id_dict, readers, db=db)
reading_output = rdb.make_db_readings(id_dict, readers, db=db)
assert len(reading_output) == 0, "Got new readings when force_read=False."
assert len(old_readings) == N1, \
"Did not get old readings when force_read=False."
def test_multiproc_statements():
"Test the multiprocessing creation of statements."
db = get_db_with_pubmed_content()
readers = get_readers()
tc_list = db.select_all(db.TextContent)
id_dict = {'tcid': [tc.id for tc in tc_list]}
outputs = rdb.make_db_readings(id_dict, readers, db=db)
stmts = make_statements(outputs, 2)
assert len(stmts)
def test_sparser_parallel_one_batch():
"Test that sparser runs with multiple procs with batches of 1."
db = get_db_with_pubmed_content()
sparser_reader = SparserReader(n_proc=2)
tc_list = db.select_all(db.TextContent)
result = sparser_reader.read([process_content(tc) for tc in tc_list],
verbose=True, n_per_proc=1)
N_exp = len(tc_list)
N_res = len(result)
assert N_exp == N_res, \
"Expected to get %d results, but got %d." % (N_exp, N_res)
def test_sparser_parallel():
"Test running sparser in parallel."
db = get_db_with_pubmed_content()
sparser_reader = SparserReader(n_proc=2)
tc_list = db.select_all(db.TextContent)
result = sparser_reader.read([process_content(tc) for tc in tc_list],
verbose=True, log=True)
N_exp = len(tc_list)
N_res = len(result)
assert N_exp == N_res, \
"Expected to get %d results, but got %d." % (N_exp, N_res)
def test_produce_readings():
"Comprehensive test of the high level production of readings."
# Prep the inputs.
db = get_db_with_pubmed_content()
complete_tr_list = db.select_all(db.TextRef)
id_dict = get_id_dict(complete_tr_list)
# Test with just sparser for tollerable speeds.
reader_list = get_readers('SPARSER')
# Test the read_mode='none' option (should yield nothing, because there
# aren't any readings yet.)
outputs_0 = rdb.produce_readings(id_dict, reader_list, verbose=True, db=db,
read_mode='none')
assert len(outputs_0) == 0
# Test just getting a pickle file (Nothing should be posted to the db.).
pkl_file = 'test_db_res.pkl'
outputs_1 = rdb.produce_readings(id_dict, reader_list, verbose=True, db=db,
no_upload=True, pickle_file=pkl_file)
N_out = len(outputs_1)
N_exp = len(reader_list)*db.filter_query(db.TextContent).count()
assert N_out == N_exp, "Expected %d readings, got %d." % (N_exp, N_out)
assert path.exists(pkl_file), "Pickle file not created."
with open(pkl_file, 'rb') as f:
N_pkl = len(pickle.load(f))
assert N_pkl == N_exp, \
"Expected %d readings in pickle, got %d." % (N_exp, N_out)
N_readings = db.filter_query(db.Readings).count()
assert N_readings == 0, \
"There shouldn't be any readings yet, but found %d." % N_readings
# Test reading and insert to the database.
rdb.produce_readings(id_dict, reader_list, verbose=True, db=db)
N_db = db.filter_query(db.Readings).count()
assert N_db == N_exp, "Excpected %d readings, got %d." % (N_exp, N_db)
# Test reading again, without read_mode='all'
outputs_2 = rdb.produce_readings(id_dict, reader_list, verbose=True, db=db)
assert len(outputs_2) == N_exp, \
"Got %d readings, expected %d." % (len(outputs_2), N_exp)
assert all([rd.reading_id is not None for rd in outputs_2])
# Test with read_mode='none' again.
outputs_3 = rdb.produce_readings(id_dict, reader_list, verbose=True, db=db,
read_mode='none')
assert len(outputs_3) == N_exp
assert all([rd.reading_id is not None for rd in outputs_3])
# Test the read_mode='all'.
outputs_4 = rdb.produce_readings(id_dict, reader_list, verbose=True, db=db,
read_mode='all')
assert len(outputs_4) == N_exp
assert all([rd.reading_id is None for rd in outputs_4])
def test_multi_batch_run():
"Test that reading works properly with multiple batches run."
db = get_db_with_pubmed_content()
readers = get_readers()
tc_list = db.select_all(db.TextContent)
id_dict = {'tcid': [tc.id for tc in tc_list]}
outputs = rdb.make_db_readings(id_dict, readers,
batch_size=len(tc_list)//2, db=db)
# This should catch any repeated readings.
rdb.upload_readings(outputs, db=db)
num_readings = db.filter_query(db.Readings).count()
assert num_readings == 2*len(tc_list), \
"Expected %d readings, only found %d." % (2*len(tc_list), num_readings)
def test_reading_content_insert():
"Test the content primary through-put of make_db_readings."
db = get_db_with_pubmed_content()
print("Test reading")
tc_list = db.select_all(db.TextContent)
readers = get_readers()
reading_output = []
for reader in readers:
reading_output += reader.read([process_content(tc) for tc in tc_list],
verbose=True)
expected_output_len = len(tc_list)*len(readers)
assert len(reading_output) == expected_output_len, \
("Not all text content successfully read."
"Expected %d outputs, but got %d.") % (expected_output_len,
len(reading_output))
print("Test reading insert")
rdb.upload_readings(reading_output, db=db)
r_list = db.select_all(db.Readings)
def is_complete_match(r_list, reading_output):
return all([any([rd.matches(r) for r in r_list])
for rd in reading_output])
assert is_complete_match(r_list, reading_output), \
"Not all reading output posted."
rdb.upload_readings(reading_output, db=db)
assert is_complete_match(r_list, reading_output), \
"Uniqueness constraints failed."
print("Test enrichement")
assert all([rd.reading_id is None for rd in reading_output]), \
"No readings should have reading_ids already."
rdb._enrich_reading_data(reading_output, db=db)
assert all([rd.reading_id is not None for rd in reading_output]),\
"Some reading data objects didn't have reading_ids after enrichment."
print("Test making statements")
stmts = rdb.produce_statements(reading_output, db=db)
assert len(stmts), 'No statements created.'
db_stmts = db.select_all(db.Statements)
assert len(db_stmts) == len(stmts), \
"Only %d/%d statements added." % (len(db_stmts), len(stmts))
assert len(db.select_all(db.Agents)), "No agents added."
