def scan_comment(scan_id):
"""
View for adding scan comments
"""
form = ScanCommentForm()
form.user_id = current_user.id
form.scan_id = scan_id
scan = Scan.query.get(scan_id)
session = scan.session
if not current_user.has_study_access(session.study):
flash('Not authorised')
return redirect(url_for('index'))
if form.validate_on_submit():
try:
scancomment = ScanComment()
scancomment.scan_id = scan_id
scancomment.user_id = current_user.id
scancomment.analysis_id = form.analyses.data
scancomment.excluded = form.excluded.data
scancomment.comment = form.comment.data
db.session.add(scancomment)
db.session.commit()
flash('Scan comment added')
except:
flash('Failed adding comment')
return redirect(url_for('session', session_id=session.id))
def create_issue(session_id, issue_title="", issue_body=""):
"""
Post a session issue to github, returns to the session view
"""
session = Session.query.get(session_id)
if not current_user.has_study_access(session.study):
flash("Not authorised")
return redirect(url_for('index'))
token = flask_session['active_token']
if issue_title and issue_body:
try:
gh = Github(token)
repo = gh.get_user("TIGRLab").get_repo("Admin")
iss = repo.create_issue(issue_title, issue_body)
session.gh_issue = iss.number
db.session.commit()
flash("Issue '{}' created!".format(issue_title))
except:
flash(
"Issue '{}' was not created successfully.".format(issue_title))
else:
flash("Please enter both an issue title and description.")
return (redirect(url_for('session', session_id=session.id)))
def todo(study_id=None):
"""
Runs the datman binary dm-qc-todo.py and returns the results
as a json object
"""
if study_id:
study = Study.query.get(study_id)
study_name = study.nickname
else:
study_name = None
if not current_user.has_study_access(study_id):
flash('Not authorised')
return redirect(url_for('index'))
# todo_list = utils.get_todo(study_name)
try:
todo_list = utils.get_todo(study_name)
except utils.TimeoutError:
# should do something nicer here
todo_list = {'error': 'timeout'}
except RuntimeError as e:
todo_list = {'error': 'runtime:{}'.format(e)}
except:
todo_list = {'error': 'other'}
return jsonify(todo_list)
def get_timepoint(study_id, timepoint_id, current_user):
timepoint = Timepoint.query.get(timepoint_id)
if timepoint is None:
flash("Timepoint {} does not exist".format(timepoint_id))
raise RequestRedirect(url_for("main.index"))
if (not current_user.has_study_access(study_id, timepoint.site_id)
or not timepoint.belongs_to(study_id)):
flash("Not authorised to view {}".format(timepoint_id))
raise RequestRedirect(url_for("main.index"))
return timepoint
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 get_scan(scan_id, study_id, current_user, fail_url=None):
if not fail_url:
fail_url = url_for('main.index')
scan = Scan.query.get(scan_id)
if scan is None:
logger.error("User {} attempted to retrieve scan with ID {}. "
"Retrieval failed.".format(current_user, scan_id))
flash("Scan does not exist.")
raise RequestRedirect(fail_url)
timepoint = scan.session.timepoint
if (not current_user.has_study_access(study_id, timepoint.site_id)
or not timepoint.belongs_to(study_id)):
flash("Not authorized to view {}".format(scan.name))
raise RequestRedirect(fail_url)
return scan
def study(study_id=None, active_tab=None):
"""
This is the main view for a single study.
The page is a tabulated view, I would have done this differently given
another chance.
"""
if not current_user.has_study_access(study_id):
flash('Not authorised')
return redirect(url_for('index'))
# get the list of metrics to be displayed in the graph pages from the study config
display_metrics = app.config['DISPLAY_METRICS']
# get the study object from the database
study = Study.query.get(study_id)
# this is used to update the readme text file
form = StudyOverviewForm()
if form.validate_on_submit():
# form has been submitted check for changes
# simple MD seems to replace \n with \r\n
form.readme_txt.data = form.readme_txt.data.replace('\r', '')
# also strip blank lines at the start and end as these are
# automatically stripped when the form is submitted
if not form.readme_txt.data.strip() == study.read_me:
study.read_me = form.readme_txt.data
study.save()
form.readme_txt.data = study.read_me
form.study_id.data = study_id
return render_template('study.html',
metricnames=study.get_valid_metric_names(),
study=study,
form=form,
active_tab=active_tab,
display_metrics=display_metrics)
def session_by_name(session_name=None):
"""
Basically just a helper view, converts a session name to a sesssion_id
and returns the session view
"""
if session_name is None:
return redirect('/index')
# Strip any file extension or qc_ prefix
session_name = session_name.replace('qc_', '')
session_name = os.path.splitext(session_name)[0]
q = Session.query.filter(Session.name == session_name)
if q.count() < 1:
flash('Session not found')
return redirect(url_for('index'))
session = q.first()
if not current_user.has_study_access(session.study):
flash('Not authorised')
return redirect(url_for('index'))
return redirect(url_for('session', session_id=session.id))
def scan_blacklist(scan_id):
"""
View for adding scan comments
"""
form = ScanBlacklistForm()
form.scan_id = scan_id
scan = Scan.query.get(scan_id)
session = scan.session
if not current_user.has_study_access(session.study):
flash('Not authorised')
return redirect(url_for('index'))
if form.validate_on_submit():
try:
scan.bl_comment = form.bl_comment.data
db.session.commit()
flash('Scan blacklisted')
except:
flash('Failed blacklisting scan')
return redirect(url_for('session', session_id=session.id))
def study(study_id=None, active_tab=None):
"""
This is the main view for a single study.
The page is a tabulated view, I would have done this differently given
another chance.
"""
if study_id is None:
return redirect('/index')
#study_id = current_user.get_studies()[0].id
# get the study object from the database
study = Study.query.get(study_id)
if not current_user.has_study_access(study):
flash('Not authorised')
return redirect(url_for('index'))
# this is used to update the readme text file
form = StudyOverviewForm()
# load the study config
cfg = dm.config.config()
try:
cfg.set_study(study.nickname)
except KeyError:
abort(500)
# Get the contents of the study README,md file fro the file system
readme_path = os.path.join(cfg.get_study_base(), 'README.md')
try:
with codecs.open(readme_path, encoding='utf-8', mode='r') as myfile:
data = myfile.read()
except IOError:
data = ''
if form.validate_on_submit():
# form has been submitted check for changes
# simple MD seems to replace \n with \r\n
form.readme_txt.data = form.readme_txt.data.replace('\r', '')
# also strip blank lines at the start and end as these are
# automatically stripped when the form is submitted
if not form.readme_txt.data.strip() == data.strip():
# form has been updated so make a backup anf write back to file
timestamp = datetime.datetime.now().strftime('%Y%m%d%H%m')
base, ext = os.path.splitext(readme_path)
backup_file = base + '_' + timestamp + ext
try:
shutil.copyfile(readme_path, backup_file)
except (IOError, os.error, shutil.Error), why:
logger.error(
'Failed to backup readme for study {} with excuse {}'.
format(study.nickname, why))
abort(500)
with codecs.open(readme_path, encoding='utf-8',
mode='w') as myfile:
myfile.write(form.readme_txt.data)
data = form.readme_txt.data
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)
