def post(self, study_id):
study_id = int(study_id)
user = User(self.current_user)
try:
study = Study(study_id)
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %d does not exist" % study_id)
else:
check_access(User(self.current_user), study,
raise_error=True)
# vars to add sample template
msg = ''
msg_level = ''
tab_to_display = ''
sample_template = self.get_argument('sample_template', None)
# vars to add raw data
filetype = self.get_argument('filetype', None)
previous_raw_data = self.get_argument('previous_raw_data', None)
# vars to add prep template
add_prep_template = self.get_argument('add_prep_template', None)
raw_data_id = self.get_argument('raw_data_id', None)
data_type_id = self.get_argument('data_type_id', None)
make_public = self.get_argument('make_public', False)
make_sandbox = self.get_argument('make_sandbox', False)
approve_study = self.get_argument('approve_study', False)
request_approval = self.get_argument('request_approval', False)
investigation_type = self.get_argument('investigation-type', None)
user_defined_investigation_type = self.get_argument(
'user-defined-investigation-type', None)
new_investigation_type = self.get_argument('new-investigation-type',
None)
# None Selected is the equivalent to the user not specifying the info
# thus we should make the investigation_type None
if investigation_type == "" or investigation_type == "None Selected":
investigation_type = None
# to update investigation type
update_investigation_type = self.get_argument(
'update_investigation_type', None)
edit_investigation_type = self.get_argument('edit-investigation-type',
None)
edit_user_defined_investigation_type = self.get_argument(
'edit-user-defined-investigation-type', None)
edit_new_investigation_type = self.get_argument(
'edit-new-investigation-type', None)
# None Selected is the equivalent to the user not specifying the info
# thus we should make the investigation_type None
if edit_investigation_type == "" or \
edit_investigation_type == "None Selected":
edit_investigation_type = None
msg_level = 'success'
if sample_template:
# processing sample templates
_, base_fp = get_mountpoint("uploads")[0]
fp_rsp = join(base_fp, str(study_id), sample_template)
if not exists(fp_rsp):
raise HTTPError(400, "This file doesn't exist: %s" % fp_rsp)
try:
# deleting previous uploads and inserting new one
yield Task(self.remove_add_study_template,
study.raw_data,
study_id, fp_rsp)
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError, KeyError,
CParserError, QiitaDBDuplicateHeaderError) as e:
msg = html_error_message % ('parsing the sample template:',
basename(fp_rsp), str(e))
self.display_template(study, msg, "danger")
return
msg = ("The sample template '%s' has been added" %
sample_template)
tab_to_display = ""
elif request_approval:
study.status = 'awaiting_approval'
msg = "Study sent to admin for approval"
tab_to_display = ""
elif make_public:
msg = ''
study.status = 'public'
msg = "Study set to public"
tab_to_display = ""
elif make_sandbox:
msg = ''
study.status = 'sandbox'
msg = "Study reverted to sandbox"
tab_to_display = ""
elif approve_study:
# make sure user is admin, then make full private study
if user.level == 'admin' or not \
qiita_config.require_approval:
study.status = 'private'
msg = "Study approved"
tab_to_display = ""
elif filetype or previous_raw_data:
# adding blank raw data
if filetype and previous_raw_data:
msg = ("You can not specify both a new raw data and a "
"previouly used one")
elif filetype:
try:
RawData.create(filetype, [study])
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError, KeyError,
CParserError) as e:
msg = html_error_message % ("creating a new raw data "
"object for study:",
str(study.id), str(e))
self.display_template(study, msg, "danger")
return
msg = ""
else:
raw_data = [RawData(rd) for rd in previous_raw_data]
study.add_raw_data(raw_data)
msg = ""
tab_to_display = ""
elif add_prep_template and raw_data_id and data_type_id:
# adding prep templates
if investigation_type == 'Other' and \
user_defined_investigation_type == 'New Type':
investigation_type = new_investigation_type
# this is a new user defined investigation type so store it
ontology = Ontology(convert_to_id('ENA', 'ontology'))
ontology.add_user_defined_term(investigation_type)
elif investigation_type == 'Other' and \
user_defined_investigation_type != 'New Type':
investigation_type = user_defined_investigation_type
raw_data_id = int(raw_data_id)
_, base_path = get_mountpoint("uploads")[0]
fp_rpt = join(base_path, str(study_id), add_prep_template)
if not exists(fp_rpt):
raise HTTPError(400, "This file doesn't exist: %s" % fp_rpt)
try:
# inserting prep templates
yield Task(self.remove_add_prep_template, fp_rpt, raw_data_id,
study, data_type_id, investigation_type)
except (TypeError, QiitaDBColumnError, QiitaDBExecutionError,
QiitaDBDuplicateError, IOError, ValueError,
CParserError) as e:
msg = html_error_message % ("parsing the prep template: ",
basename(fp_rpt), str(e))
self.display_template(study, msg, "danger",
str(raw_data_id))
return
msg = "Your prep template was added"
tab_to_display = str(raw_data_id)
elif update_investigation_type:
# updating the prep template investigation type
pt = PrepTemplate(update_investigation_type)
investigation_type = edit_investigation_type
# figure out whether to add it as a user defined term or not
if edit_investigation_type == 'Other' and \
edit_user_defined_investigation_type == 'New Type':
investigation_type = edit_new_investigation_type
# this is a new user defined investigation type so store it
ontology = Ontology(convert_to_id('ENA', 'ontology'))
ontology.add_user_defined_term(investigation_type)
elif investigation_type == 'Other' and \
user_defined_investigation_type != 'New Type':
investigation_type = edit_user_defined_investigation_type
try:
pt.investigation_type = investigation_type
except QiitaDBColumnError as e:
msg = html_error_message % (", invalid investigation type: ",
investigation_type, str(e))
self.display_template(study, msg, "danger",
str(pt.raw_data))
return
msg = "The prep template has been updated!"
tab_to_display = str(pt.raw_data)
else:
msg = ("Error, did you select a valid uploaded file or are "
"passing the correct parameters?")
msg_level = 'danger'
tab_to_display = ""
self.display_template(study, msg, msg_level, tab_to_display)
