def index():
"""
Main landing page
"""
studies = current_user.get_studies()
timepoint_count = Timepoint.query.count()
study_count = Study.query.count()
site_count = Site.query.count()
return render_template('index.html',
studies=studies,
timepoint_count=timepoint_count,
study_count=study_count,
site_count=site_count)
def index():
"""
Main landin page
"""
# studies = db_session.query(Study).order_by(Study.nickname).all()
studies = current_user.get_studies()
session_count = Session.query.count()
study_count = Study.query.count()
site_count = Site.query.count()
return render_template('index.html',
studies=studies,
session_count=session_count,
study_count=study_count,
site_count=site_count)
def scan(scan_id=None):
"""
Default view for a single scan
"""
if scan_id is None:
flash('Invalid scan')
return redirect(url_for('index'))
# Check the user has permission to see this study
studies = current_user.get_studies()
scan = Scan.query.get(scan_id)
if not current_user.has_study_access(scan.session.study):
flash('Not authorised')
return redirect(url_for('index'))
# form for updating the study blacklist.csv on the filesystem
bl_form = ScanBlacklistForm()
# form used for updating the analysis comments
scancomment_form = ScanCommentForm()
if not bl_form.is_submitted():
# this isn't an update so just populate the blacklist form with current values from the database
# these should be the same as in the filesystem
bl_form.scan_id = scan_id
bl_form.bl_comment.data = scan.bl_comment
if bl_form.validate_on_submit():
# going to make an update to the blacklist
# update the scan object in the database with info from the form
# updating the databse object automatically syncronises blacklist.csv on the filesystem
# see models.py
scan.bl_comment = bl_form.bl_comment.data
try:
db.session.add(scan)
db.session.commit()
flash("Blacklist updated")
return redirect(url_for('session', session_id=scan.session_id))
except SQLAlchemyError as err:
logger.error('Scan blacklist update failed:{}'.format(str(err)))
flash('Update failed, admins have been notified, please try again')
return render_template('scan.html',
studies=studies,
scan=scan,
blacklist_form=bl_form,
scancomment_form=scancomment_form)
def users():
"""
View that lists all users
"""
if not current_user.is_admin:
flash('You are not authorised')
return redirect(url_for('user'))
users = User.query.all()
user_forms = []
for user in users:
form = UserForm()
form.user_id.data = user.id
form.realname.data = user.realname
form.is_admin.data = user.is_admin
form.has_phi.data = user.has_phi
study_ids = [str(study.id) for study in user.studies]
form.studies.data = study_ids
user_forms.append(form)
return render_template('users.html',
studies=current_user.get_studies(),
user_forms=user_forms)
def session(session_id=None, delete=False, flag_finding=False):
"""
Default view for a single session_id
If called as http://srv-dashboard/session/<session_id>/delete/True it will
delete the session from the database
"""
if session_id is None:
return redirect('index')
session = Session.query.get(session_id)
if not current_user.has_study_access(session.study):
flash('Not authorised')
return redirect(url_for('index'))
try:
# Update open issue ID if necessary
# this is necessary because GitHub may timeout a user without telling us
token = flask_session['active_token']
except:
flash('It appears you\'ve been idle too long; please sign in again.')
return redirect(url_for('login'))
try:
# check to see if any issues have been posted on github for this session
gh = Github(token)
# Due to the way GitHub search API works, splitting session name into separate search terms will find a session
# regardless of repeat number, and will not match other sessions with the same study/site
open_issues = gh.search_issues(
"{} in:title repo:TIGRLab/admin state:open".format(
str(session.name).replace("_", " ")))
if open_issues.totalCount:
session.gh_issue = open_issues[0].number
else:
session.gh_issue = None
db.session.commit()
except:
flash("Error searching for session's GitHub issue.")
if delete:
try:
if not current_user.is_admin:
flash('You dont have permission to do that')
raise Exception
db.session.delete(session)
db.session.commit()
flash('Deleted session:{}'.format(session.name))
return redirect(
url_for('study', study_id=session.study_id, active_tab='qc'))
except Exception:
flash('Failed to delete session:{}'.format(session.name))
if flag_finding:
try:
incident = IncidentalFinding()
incident.session_id = session.id
incident.user_id = current_user.id
db.session.add(incident)
db.session.commit()
flash('Finding flagged.')
return redirect(url_for('session', session_id=session.id))
except:
logger.error('Failed flagging finding for session:{}'.format(
session.id))
flash('Failed flagging finding. Admins have been notified')
studies = current_user.get_studies()
form = SessionForm(obj=session)
# This form deals with the checklist comments.
# Updating the checklist in the database causes checklist.csv to be updated
# see models.py
scancomment_form = ScanCommentForm()
if form.validate_on_submit():
# form has been submitted
session.cl_comment = form.cl_comment.data
try:
db.session.add(session)
db.session.commit()
flash('Session updated')
return redirect(
url_for('study', study_id=session.study_id, active_tab='qc'))
except SQLAlchemyError as err:
logger.error('Session update failed:{}'.format(str(err)))
flash('Update failed, admins have been notified, please try again')
form.populate_obj(session)
return render_template('session.html',
studies=studies,
study=session.study,
session=session,
form=form,
scancomment_form=scancomment_form)