def sample_template_overview_handler_get_request(study_id, user):
# Check if the current user has access to the sample template
sample_template_checks(study_id, user)
# Check if the sample template exists
exists = SampleTemplate.exists(study_id)
# The following information should always be provided:
# The files that have been uploaded to the system and can be a
# sample template file
files = [
f for _, f in get_files_from_uploads_folders(study_id)
if f.endswith(('txt', 'tsv'))
]
# If there is a job associated with the sample information, the job id
job = None
job_info = r_client.get(SAMPLE_TEMPLATE_KEY_FORMAT % study_id)
if job_info:
job = loads(job_info)['job_id']
# Specific information if it exists or not:
data_types = []
st_fp_id = None
old_files = []
num_samples = 0
num_cols = 0
if exists:
# If it exists we need to provide:
# The id of the sample template file so the user can download it and
# the list of old filepaths
st = SampleTemplate(study_id)
all_st_files = st.get_filepaths()
# The current sample template file is the first one in the list
# (pop(0)) and we are interested only in the id ([0])
st_fp_id = all_st_files.pop(0)[0]
# For the old filepaths we are only interested in their basename
old_files = [basename(fp) for _, fp in all_st_files]
# The number of samples - this is a space efficient way of counting
# the number of samples. Doing len(list(st.keys())) creates a list
# that we are not using
num_samples = sum(1 for _ in st.keys())
# The number of columns
num_cols = len(st.categories())
else:
# It doesn't exist, we also need to provide the data_types in case
# the user uploads a QIIME mapping file
data_types = sorted(data_types_get_req()['data_types'])
return {
'exists': exists,
'uploaded_files': files,
'data_types': data_types,
'user_can_edit': Study(study_id).can_edit(user),
'job': job,
'download_id': st_fp_id,
'old_files': old_files,
'num_samples': num_samples,
'num_columns': num_cols
}
def sample_template_overview_handler_get_request(study_id, user):
# Check if the current user has access to the sample template
sample_template_checks(study_id, user)
# Check if the sample template exists
exists = SampleTemplate.exists(study_id)
# The following information should always be provided:
# The files that have been uploaded to the system and can be a
# sample template file
files = [f for _, f, _ in get_files_from_uploads_folders(study_id)
if f.endswith(('txt', 'tsv', 'xlsx'))]
# If there is a job associated with the sample information, the job id
job = None
job_info = r_client.get(SAMPLE_TEMPLATE_KEY_FORMAT % study_id)
if job_info:
job = loads(job_info)['job_id']
# Specific information if it exists or not:
data_types = []
st_fp_id = None
old_files = []
num_samples = 0
num_cols = 0
if exists:
# If it exists we need to provide:
# The id of the sample template file so the user can download it and
# the list of old filepaths
st = SampleTemplate(study_id)
all_st_files = st.get_filepaths()
# The current sample template file is the first one in the list
# (pop(0)) and we are interested only in the id ([0])
st_fp_id = all_st_files.pop(0)[0]
# For the old filepaths we are only interested in their basename
old_files = [basename(fp) for _, fp in all_st_files]
# The number of samples - this is a space efficient way of counting
# the number of samples. Doing len(list(st.keys())) creates a list
# that we are not using
num_samples = sum(1 for _ in st.keys())
# The number of columns
num_cols = len(st.categories())
else:
# It doesn't exist, we also need to provide the data_types in case
# the user uploads a QIIME mapping file
data_types = sorted(data_types_get_req()['data_types'])
return {'exists': exists,
'uploaded_files': files,
'data_types': data_types,
'user_can_edit': Study(study_id).can_edit(user),
'job': job,
'download_id': st_fp_id,
'old_files': old_files,
'num_samples': num_samples,
'num_columns': num_cols}
def sample_template_filepaths_get_req(study_id, user_id):
"""Returns all the filepaths attached to the sample template
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
Returns
-------
dict
Filepaths in the form
{'status': status,
'message': msg,
'filepaths': filepaths}
status can be success, warning, or error depending on result
message has the warnings or errors
filepaths is a list of tuple of int and str
All files in the sample template, as [(id, URL), ...]
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(study_id, user_id)
if access_error:
return access_error
try:
template = SampleTemplate(int(study_id))
except QiitaDBUnknownIDError as e:
return {'status': 'error',
'message': str(e)}
return {'status': 'success',
'message': '',
'filepaths': template.get_filepaths()
}
def sample_template_filepaths_get_req(study_id, user_id):
"""Returns all the filepaths attached to the sample template
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
Returns
-------
dict
Filepaths in the form
{'status': status,
'message': msg,
'filepaths': filepaths}
status can be success, warning, or error depending on result
message has the warnings or errors
filepaths is a list of tuple of int and str
All files in the sample template, as [(id, URL), ...]
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(study_id, user_id)
if access_error:
return access_error
try:
template = SampleTemplate(int(study_id))
except QiitaDBUnknownIDError as e:
return {'status': 'error', 'message': str(e)}
return {
'status': 'success',
'message': '',
'filepaths': template.get_filepaths()
}
