def test_download_raw_data(self):
# it's possible that one of the tests is deleting the raw data
# so we will make sure that the files exists so this test passes
study = Study(1)
all_files = [x['fp'] for a in study.artifacts()
for x in a.filepaths]
for fp in all_files:
if not exists(fp):
with open(fp, 'w') as f:
f.write('')
response = self.get('/download_raw_data/1')
self.assertEqual(response.code, 200)
exp = (
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
'2125826711 58 /protected/raw_data/'
'1_s_G1_L001_sequences_barcodes.fastq.gz '
'raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/1_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n')
self.assertRegex(response.body.decode('ascii'), exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
# now, let's make sure that when artifacts are public AND the
# public_raw_download any user can download the files
study.public_raw_download = True
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
# 7 is an uploaded biom, which should now be available but as it's a
# biom, only the prep info file will be retrieved
Artifact(7).visibility = 'public'
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n')
self.assertRegex(response.body.decode('ascii'), exp)
def test_download_raw_data(self):
# it's possible that one of the tests is deleting the raw data
# so we will make sure that the files exists so this test passes
study = Study(1)
all_files = [x['fp'] for a in study.artifacts()
for x in a.filepaths]
for fp in all_files:
if not exists(fp):
with open(fp, 'w') as f:
f.write('')
response = self.get('/download_raw_data/1')
self.assertEqual(response.code, 200)
exp = (
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
'2125826711 58 /protected/raw_data/'
'1_s_G1_L001_sequences_barcodes.fastq.gz '
'raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/1_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n')
self.assertRegex(response.body.decode('ascii'), exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
# now, let's make sure that when artifacts are public AND the
# public_raw_download any user can download the files
study.public_raw_download = True
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
# 7 is an uploaded biom, which should now be available but as it's a
# biom, only the prep info file will be retrieved
Artifact(7).visibility = 'public'
BaseHandler.get_current_user = Mock(
return_value=User("*****@*****.**"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n')
self.assertRegex(response.body.decode('ascii'), exp)
def study_patch_request(user_id,
study_id,
req_op,
req_path,
req_value=None,
req_from=None):
"""Modifies an attribute of the study object
Parameters
----------
user_id : int
The id of the user performing the patch operation
study_id : int
The id of the study on which we will be performing the patch operation
req_op : str
The operation to perform on the study
req_path : str
The attribute to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str, str}
A dictionary with the following keys:
- status: str, whether if the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
return {'status': 'error', 'message': 'Incorrect path parameter'}
attribute = req_path[0]
# Check if the user actually has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
study = Study(study_id)
if attribute == 'tags':
message = study.update_tags(User(user_id), req_value)
return {'status': 'success', 'message': message}
elif attribute == 'specimen_id_column':
try:
study.specimen_id_column = req_value
return {
'status': 'success',
'message': 'Successfully updated specimen id column'
}
except (QiitaDBLookupError, QiitaDBColumnError) as e:
return {'status': 'error', 'message': str(e)}
elif attribute == 'toggle_public_raw_download':
try:
study.public_raw_download = not study.public_raw_download
return {
'status': 'success',
'message': 'Successfully updated public_raw_download'
}
except (QiitaDBLookupError, QiitaDBColumnError) as e:
return {'status': 'error', 'message': str(e)}
else:
# We don't understand the attribute so return an error
return {
'status':
'error',
'message':
'Attribute "%s" not found. '
'Please, check the path parameter' % attribute
}
else:
return {
'status':
'error',
'message':
'Operation "%s" not supported. '
'Current supported operations: replace' % req_op
}
