def delete_prep_template(self, study, user, callback):
"""Delete the selected prep template
Parameters
----------
study : Study
The current study object
user : User
The current user object
callback : function
The callback function to call with the results once the processing
is done
"""
prep_template_id = int(self.get_argument('prep_template_id'))
prep_id = PrepTemplate(prep_template_id).raw_data
try:
PrepTemplate.delete(prep_template_id)
msg = ("Prep template %d has been deleted" % prep_template_id)
msg_level = "success"
prep_id = None
except Exception as e:
msg = ("Couldn't remove prep template: %s" % str(e))
msg_level = "danger"
callback((msg, msg_level, 'prep_template_tab', prep_id, None))
def delete_prep_template(self, study, user, callback):
"""Delete the selected prep template
Parameters
----------
study : Study
The current study object
user : User
The current user object
callback : function
The callback function to call with the results once the processing
is done
"""
prep_template_id = int(self.get_argument('prep_template_id'))
prep_id = PrepTemplate(prep_template_id).raw_data
try:
PrepTemplate.delete(prep_template_id)
msg = ("Prep template %d has been deleted" % prep_template_id)
msg_level = "success"
prep_id = None
except Exception as e:
msg = ("Couldn't remove prep template: %s" % str(e))
msg_level = "danger"
callback((msg, msg_level, 'raw_data_tab', prep_id, None))
def remove_add_study_template(self, raw_data, study_id, fp_rsp):
"""Replace prep templates, raw data, and sample template with a new one
"""
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
SampleTemplate.create(load_template_to_dataframe(fp_rsp),
Study(study_id))
remove(fp_rsp)
def remove_add_study_template(self, raw_data, study_id, fp_rsp):
"""Replace prep templates, raw data, and sample template with a new one
"""
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
SampleTemplate.create(load_template_to_dataframe(fp_rsp),
Study(study_id))
remove(fp_rsp)
def remove_add_study_template(self, raw_data, study_id, fp_rsp, data_type, is_mapping_file):
"""Replace prep templates, raw data, and sample template with a new one
"""
if is_mapping_file and data_type == "":
raise ValueError("Please, choose a data type if uploading a QIIME " "mapping file")
for rd in raw_data():
rd = RawData(rd)
for pt in rd.prep_templates:
if PrepTemplate.exists(pt):
PrepTemplate.delete(pt)
if SampleTemplate.exists(study_id):
SampleTemplate.delete(study_id)
if is_mapping_file:
create_templates_from_qiime_mapping_file(fp_rsp, Study(study_id), int(data_type))
else:
SampleTemplate.create(load_template_to_dataframe(fp_rsp), Study(study_id))
remove(fp_rsp)