def get_continuation_studies():
user = data_utils.get_current_user()
profiles = Profile().get_for_user(user.id)
output = list()
for p in profiles:
output.append({"value": p.title, "label": p._id})
return output
def _get_dataverse(self, profile_id):
# create new dataverse if none already exists
u = data_utils.get_current_user()
# create new dataverse if none exists already
dv_details = Profile().check_for_dataverse_details(profile_id)
if not dv_details:
# dataverse = connection.create_dataverse(dv_alias, '{0} {1}'.format(u.first_name, u.last_name), u.email)
dv_details = self._create_dataverse(profile_id)
Profile().add_dataverse_details(profile_id, dv_details)
return dv_details
def save_record(self, auto_fields=dict(), **kwargs):
if not kwargs.get("target_id", str()):
repo = kwargs.pop("repository", str())
for k, v in dict(repository=repo,
status=False,
complete='false',
is_cg=str(repo == "cg_core"),
user_id=data_utils.get_current_user().id,
date_created=data_utils.get_datetime()).items():
auto_fields[self.get_qualified_field(k)] = v
return super(Submission, self).save_record(auto_fields, **kwargs)
def view_user_info(request):
user = data_utils.get_current_user()
# op = Orcid().get_orcid_profile(user)
d = SocialAccount.objects.get(user_id=user.id)
op = json.loads(json.dumps(d.extra_data).replace("-", "_"))
repo_ids = user.userdetails.repo_submitter
repos = Repository().get_by_ids(repo_ids)
# data_dict = jsonpickle.encode(data_dict)
data_dict = {'orcid': op, "repos": repos}
return render(request, 'copo/user_info.html', data_dict)
def get_for_user(self, user=None):
if not user:
user = data_utils.get_current_user().id
docs = self.get_collection_handle().find({
"user_id":
user,
"deleted":
data_utils.get_not_deleted_flag()
}).sort([['_id', -1]])
if docs:
return docs
else:
return None
def isValidCredentials(self, user_id):
# check if token exists for user
token = Figshare().get_token_for_user(
user_id=data_utils.get_current_user().id)
if token:
# now check if token works
headers = {'Authorization': 'token ' + token['token']}
r = requests.get('https://api.figshare.com/v2/account/articles',
headers=headers)
if r.status_code == 200:
return True
else:
# we have an invalid token stored, so we should delete it and prompt the user for a new one
Figshare().delete_tokens_for_user(user_id=user_id)
return False
def get_profiles_status(self):
# this method examines all the profiles owned by the current user and returns
# the number of profiles which have been marked as dirty
issues = {}
issue_desc = []
issue_id = []
issues_count = 0
try:
user_id = data_utils.get_current_user().id
prof = Profiles.find({"user_id": user_id})
except AttributeError as e:
prof = []
# iterate profiles and find collections which are dirty
for p in prof:
try:
collections_ids = p['collections']
except:
issues_count += 1
context = {"profile_name": p['title'], "link": reverse('copo:view_copo_profile', args=[p["_id"]])}
issue_desc.append(STATUS_CODES['PROFILE_EMPTY'].format(**context))
break
# now get the corresponding collection_heads
collections_heads = Collections.find({'_id': {'$in': collections_ids}},
{'is_clean': 1, 'collection_details': 1})
# for c in collections_heads:
# try:
# if c['is_clean'] == 0:
# profile = Profile().get_profile_from_collection_id(c["_id"])
# issues_count += 1
# context = {}
# context["profile_name"] = p['title']
# context["link"] = reverse('copo:view_copo_profile', args=[profile["_id"]])
#
# # now work out why the collection is dirty
# if False:
# pass
# else:
# issue_desc.append(STATUS_CODES['PROFILE_NOT_DEPOSITED'].format(**context))
# except:
# pass
issues['issue_id_list'] = issue_id
issues['num_issues'] = issues_count
issues['issue_description_list'] = issue_desc
return issues
def get_shared_for_user(self, user=None):
# get profiles shared with user
if not user:
user = data_utils.get_current_user().id
groups = CopoGroup().Group.find({'member_ids': str(user)})
p_list = list()
for g in groups:
gp = dict(g)
p_list.extend(gp['shared_profile_ids'])
# remove duplicates
# p_list = list(set(p_list))
docs = self.get_collection_handle().find({
"_id": {
"$in": p_list
},
"deleted":
data_utils.get_not_deleted_flag()
})
out = list(docs)
for d in out:
d['shared'] = True
return out
def create_sra_person(self):
"""
creates an (SRA) person record and attach to profile
Returns:
"""
people = self.get_all_records()
sra_roles = list()
for record in people:
for role in record.get("roles", list()):
sra_roles.append(role.get("annotationValue", str()))
# has sra roles?
has_sra_roles = all(
x in sra_roles
for x in ['SRA Inform On Status', 'SRA Inform On Error'])
if not has_sra_roles:
try:
user = data_utils.get_current_user()
auto_fields = {
'copo.person.roles.annotationValue':
'SRA Inform On Status',
'copo.person.lastName': user.last_name,
'copo.person.firstName': user.first_name,
'copo.person.roles.annotationValue___0___1':
'SRA Inform On Error',
'copo.person.email': user.email
}
except Exception as e:
pass
else:
kwargs = dict()
self.save_record(auto_fields, **kwargs)
return
def get_tokens_for_user(request):
user = data_utils.get_current_user().id
# get Figshare Tokens
t = util.cursor_to_list(Figshare().get_figshare_tokens_for_user(user))
return HttpResponse(json_util.dumps({'figshare_tokens': t}))
def __call__(self, request):
# Code to be executed for each request before
# the view (and later middleware) are called.
url = request.get_full_path()
if url.startswith('/copo', 0, 5):
doc = Submission().get_incomplete_submissions_for_user(
request.user.id, figshare)
data_dict = dict()
token = None
if doc.count() > 0:
if 'code' in request.GET and 'state' in request.GET:
token_obtained = True
for d in doc:
if d.get('token_obtained') == 'false':
token_obtained = False
break
if not token_obtained:
# get new token from Figshare
code = request.GET.get('code')
client_id = FIGSHARE_CREDENTIALS['client_id']
token_url = FIGSHARE_API_URLS['authorization_token']
# now get token
data = {
'client_id': client_id,
'code': code,
'client_secret':
FIGSHARE_CREDENTIALS['client_secret'],
'grant_type': 'authorization_code',
'scope': 'all'
}
try:
r = requests.post(token_url, data)
data_dict = ast.literal_eval(
r.content.decode('utf-8'))
token = data_dict['token']
t = Figshare().put_token_for_user(
user_id=data_utils.get_current_user().id,
token=token)
if t:
# mark fighshare submissions for this user as token obtained
Submission().mark_all_token_obtained(
user_id=request.user.id)
# if all is well, the access token will be stored in FigshareSubmussionCollection
except Exception as e:
print(e)
else:
# retrieve token
token = Figshare().get_token_for_user(
user_id=data_utils.get_current_user().id)
# request.session['partial_submissions'] = doc
else:
request.session['partial_submissions'] = None
def do_analysis_xml(sub_id):
sub = Submission().get_record(sub_id)
dfs = list()
for d in sub["bundle"]:
dfs.append(DataFile().get_record(d))
df = dfs[0]
p = Profile().get_record(df["profile_id"])
analysis_set = Element("ANALYSIS_SET")
analysis = Element("ANALYSIS")
alias = make_alias(sub)
analysis.set("alias", alias + "_anaysis")
center_name = df["description"]["attributes"]["study_type"][
"study_analysis_center_name"]
analysis.set("analysis_center", center_name)
broker_name = df["description"]["attributes"]["study_type"]["study_broker"]
analysis.set("broker_name", broker_name)
analysis_date = df["description"]["attributes"]["study_type"][
"study_analysis_date"]
# ad = analysis_date.split('/')
# d = datetime.date(int(ad[2]), int(ad[1]), int(ad[0]))
# analysis.set("anlalysis_date", d)
# analysis_set.append(analysis)
title = Element("TITLE")
title.text = df["description"]["attributes"]["study_type"]["study_title"]
analysis.append(title)
description = Element("DESCRIPTION")
description.text = df["description"]["attributes"]["study_type"][
"study_description"]
analysis.append(description)
study_ref = Element("STUDY_REF")
study_ref.set("refname", str(sub["_id"]))
analysis.append(study_ref)
# TODO - Sample is not required for annotation submissions....ENA documentation saying it is is not correct. Will remove these stages from the wizard at some point
s_ref = get_sample_ref(df)
sample_ref = Element("SAMPLE_REF")
sample_ref.set("refname", s_ref)
# analysis.append(sample_ref)
analysis_type = Element("ANALYSIS_TYPE")
SubElement(analysis_type, "SEQUENCE_ANNOTATION")
analysis.append(analysis_type)
files = Element("FILES")
file = Element("FILE")
filename = df["name"]
file_hash = df["file_hash"]
fqfn = str(
sub_id) + '/' + data_utils.get_current_user().username + '/' + filename
file.set("filename", fqfn)
file.set("filetype", "tab")
file.set("checksum_method", "MD5")
file.set("checksum", file_hash)
file.set("unencrypted_checksum", file_hash)
files.append(file)
analysis.append(files)
attrs = Element("ANALYSIS_ATTRIBUTES")
for a in df["description"]["attributes"]["attach_study_samples"][
"attributes"]:
attr = Element("ANALYSIS_ATTRIBUTE")
tag = Element("TAG")
tag.text = a["name"]
value = Element("VALUE")
value.text = a["value"]
attr.append(tag)
attr.append(value)
attrs.append(attr)
analysis.append(attrs)
return prettify(analysis)
def generate_filename2(instance, filename):
partition = datetime.datetime.now().strftime("%H_%M_%S_%f")
filename = os.path.join(settings.UPLOAD_PATH, str(data_utils.get_current_user().id), partition, instance.filename)
return filename