def update_project_backend(language='en'):
file = request.files['update']
file_secure_name = secure_filename(file.filename)
project_name = request.form['project_name']
if file_secure_name.split('.') <= 0 or file_secure_name.split('.')[-1] != 'json':
if project_name:
return redirect(url_for('samples.samples_backend', language=language, project_name=project_name))
else:
return redirect(url_for('.projects_backend', language=language))
file.seek(0)
file.save(os.path.join(UPLOAD_FOLDER, file_secure_name))
if 'username' in session:
username = session['username']
user = User.objects.get(username=username)
count = CreatedProjects.objects(username=username, project_name=project_name).count()
if count <= 0 and not user['admin']:
return redirect(url_for('index.index_backend', language=language))
else:
mongo.db.samples.remove({'project_name': project_name})
os.system("mongoimport -c samples -d Biopedia --file %s" % file_secure_name)
os.system("rm -f %s" % file_secure_name)
return redirect(url_for('samples.samples_backend', language=language, name=project_name))
else:
return redirect(url_for('index.index_backend', language=language))
def profile_backend(language='en'):
if session['username']:
username = session['username']
user = User.objects.get(username=username)
starred_projects = StarredProjects.objects(username=username)
created_projects = CreatedProjects.objects(username=username)
if not user['admin']:
alert_message = request.args.get('alert_message', '')
alert_type = request.args.get('alert_type', '')
if alert_type:
return render_template('user.html', user=user, disp_user=user,
starred_projects=starred_projects,
created_projects=created_projects,
language=language, alert_message=alert_message,
alert_type=alert_type)
else:
return render_template('user.html', user=user, disp_user=user,
starred_projects=starred_projects,
created_projects=created_projects,
language=language)
else:
admin = user
username = request.args.get('username', '')
if username:
user = User.objects.get(username=username)
return render_template('user.html', user=admin, disp_user=user,
starred_projects=starred_projects,
created_projects=created_projects,
language=language)
else:
return redirect(url_for('index.index_backend'))
def delete_project_backend(language='en'):
if 'username' in session:
username = session['username']
user = User.objects.get(username=username)
project_name = request.args.get('projectname', '')
count = CreatedProjects.objects(username=username, project_name=project_name).count()
if count <= 0 and not user['admin']:
return redirect(url_for('index.index_backend', language=language))
else:
CreatedProjects.objects(project_name=project_name).delete()
StarredProjects.objects(project_name=project_name).delete()
mongo.db.projects.remove({'name': project_name})
mongo.db.samples.remove({'project_name': project_name})
mongo.db.fields.remove({'project_name': project_name})
mongo.db.mapping.remove({'project_name': project_name})
return redirect(url_for('.projects_backend', language=language))
else:
return redirect(url_for('index.index_backend', language=language))
def projects_backend(language='en'):
"""
Returns the projects page.
:param language: Defines the language ('en' or 'cn') used for the template.
:return: The rendered project.html template which contains all the projects for now.
/projects
"""
project_list = list(mongo.db.projects.find())
alertinfo = ''
if 'insert_error' in session and session['insert_error'] != '':
succeed = 'False'
alertinfo = session['insert_error']
session['insert_error'] = ''
else:
succeed = 'True'
session['insert_error'] = ''
print succeed
print session['insert_error']
if 'username' in session:
user = User.objects.get(username=session['username'])
for project in project_list:
project_name = project['name']
starred_project = StarredProjects.objects(username=user['username'], project_name=project_name).count()
created_project = CreatedProjects.objects(username=user['username'], project_name=project_name).count()
if starred_project > 0:
project['star'] = True
else:
project['star'] = False
if created_project > 0:
project['delete'] = True
else:
project['delete'] = False
return render_template('projects.html',language=language, project_list=project_list, user=user, succeed=succeed,
alertinfo=alertinfo)
return render_template('projects.html', language=language, project_list=project_list, succeed=succeed,
alertinfo=alertinfo)
def projects_insert(language='en'):
"""
:param language:
:return:
"""
name = request.form['name']
environment = request.form['environment']
site = request.form['site']
sequence_type = request.form['sequence_type']
project_id = request.form['project_id']
num_of_total_sequences = request.form['num_of_total_sequences']
num_of_orfs = request.form['num_of_orfs']
num_of_samples = request.form['num_of_samples']
read_length = request.form['read_length']
platform = request.form['platform']
create_date = request.form['create_date']
update_date = request.form['update_date']
mapping_file = request.files['mapping']
mapping_file_secure_name = secure_filename(mapping_file.filename)
samples_file = request.files['samples']
samples_file_secure_name = secure_filename(samples_file.filename)
succeed = str(name) and environment and site and sequence_type and project_id and \
str(num_of_total_sequences).isdigit() and str(num_of_orfs).isdigit() and \
str(read_length).isdigit() and platform
if not succeed:
session['insert_error'] = 'Data format error!'
if mongo.db.projects.find({'name': name}).count() != 0:
if succeed:
session['insert_error'] = 'Project name already exists!'
succeed = False
if len(str(create_date).split('/'))==3 and str(create_date).split('/')[0].isdigit() and \
str(create_date).split('/')[1].isdigit() and str(create_date).split('/')[2].isdigit():
create_date = {'month': int(str(create_date).split('/')[0]),
'day': int(str(create_date).split('/')[1]),
'year': int(str(create_date).split('/')[2]) }
else:
if succeed:
session['insert_error'] = 'Date format error: MM/DD/YY'
succeed = False
if len(str(update_date).split('/'))==3 and str(update_date).split('/')[0].isdigit() and \
str(update_date).split('/')[1].isdigit() and str(update_date).split('/')[2].isdigit():
update_date = {'month': int(str(update_date).split('/')[0]),
'day': int(str(update_date).split('/')[1]),
'year': int(str(update_date).split('/')[2]) }
else:
if succeed:
session['insert_error'] = 'Date format error: MM/DD/YY'
succeed = False
if len(mapping_file_secure_name.split('.')) <=0 or mapping_file_secure_name.split('.')[-1] != 'csv' or \
len(samples_file_secure_name.split('.')) <= 0 or samples_file_secure_name.split('.')[-1] != 'json':
if succeed:
session['insert_error'] = 'File format error: mapping should be .csv and samples should be .json'
succeed = False
else:
fvalue = mapping_file.read()
mapping_file.seek(0)
mapping_file.save(os.path.join(UPLOAD_FOLDER, mapping_file_secure_name))
fvalue = samples_file.read()
samples_file.seek(0)
samples_file.save(os.path.join(UPLOAD_FOLDER, samples_file_secure_name))
try:
check_sample_legal(open(os.path.join(UPLOAD_FOLDER, samples_file_secure_name), "r").readlines(), name)
except:
if succeed:
session['insert_error'] = 'File data error: some sample in the file does not belong to the project'
succeed = False
if succeed:
proj_info = {
"name": name,
"environment": environment,
"site": site,
"sequence_type": sequence_type,
"project_id": project_id,
"num_of_total_sequences": int(num_of_total_sequences),
"num_of_orfs": int(num_of_orfs),
"num_of_samples": int(num_of_samples),
"read_length": read_length,
"platform": platform,
"create_date": create_date,
"update_date": update_date,
}
mongo.db.projects.save(proj_info)
os.system("mongoimport -c mapping -d Biopedia --file %s --type csv --headerline" % mapping_file_secure_name)
os.system("mongoimport -c samples -d Biopedia --file %s" % samples_file_secure_name)
os.system("rm -f %s" % mapping_file_secure_name)
os.system("rm -f %s" % samples_file_secure_name)
if mongo.db.samples.find({"project_name": name}).count() > 0:
samples = mongo.db.samples.find({"project_name": name})
fields = samples[0].keys()
fields.remove("project_name")
fields.remove("_id")
string_fields = []
default_fields = []
for field in fields:
# check if string
samples = mongo.db.samples.find({"project_name": name})
for sample in samples:
if sample[field] != 'NA':
try:
tmpeval = eval(str(sample[field]))
except Exception:
string_fields.append(field)
break
# create default
if field in default_default_fields:
default_fields.append(field)
mongo.db.fields.insert({"project_name": name, "default_fields": default_fields,
"string_fields": string_fields})
user = User.objects.get(username=session['username'])
project_name = name
created_project = CreatedProjects(username=user['username'], project_name=project_name)
created_project.save()
else:
mongo.db.projects.remove({"name": name})
if succeed:
session['insert_error'] = 'Samples failed!'
succeed = False
project_list = mongo.db.projects.find()
if 'username' in session:
user = User.objects.get(username=session['username'])
return redirect(url_for('projects.projects_backend', language=language))
