def submit_newcourse():
""" create new course """
#print_debug('submit_newcourse: {}'.format(request.form))
name = request.form['name'] # e.g. "Intro Programming"
path = request.form[
'path'] # should have form term/folder e.g. fall2018/cs1
copyfrom = request.form['copyfrom'] # e.g. "fall2017/cs1"
startdate = path_to_startdate(path)
title = name_to_htmltitle(name)
print_debug(' submit_newcourse: name = "{}"'.format(name))
print_debug(' path = "{}"'.format(path))
print_debug(' copyfrom = "{}"'.format(copyfrom))
newcourse = Course.create_course(name,
path,
start=startdate,
name_as_title=title,
copyfrom=copyfrom)
for name in request.form['faculty'].split(','):
try:
faculty = Person.get(username=name.strip())
except:
faculty = None
if not faculty:
try:
faculty = Person.get(username=name.strip())
except:
faculty = None
if faculty:
today = str(Time())[:10]
newcourse.enroll(faculty, 'faculty', today, create_work=False)
return newcourse.url
def login():
form = LoginForm()
if form.validate_on_submit():
getPass = Get_password(form.email.data)
if getPass == None:
flash('Login Unsuccessful. Please check username and password',
'danger')
return redirect(url_for('login'))
if bcrypt.check_password_hash(getPass, form.password.data) is True:
flash('You have been logged in!', 'success')
session['user'] = form.email.data
session['time'] = Time(form.email.data)
# print(session.get('time'))
return redirect(url_for('lounge'))
else:
flash('Login Unsuccessful. Please check username and password',
'danger')
return render_template('login.html',
time=session.get('time'),
user_email=session.get("user"),
title='Login',
form=form,
enable=8)
def parse_sampling_time(object_):
"""Parse an object into a sampling time.
Parameters
----------
object_ : datetime.datetime, model.Sample
The object to be parsed into a Time object, representing the sampling
time.
"""
# Parse from datetime-like object
try:
time = Time.from_datetime(object_)
except AttributeError:
time = None
else:
return time
# Parse from model.Sample
try:
sample_date = object_.sample_date
sample_time = object_.sample_time
default_date = datetime.date(1, 1, 1)
default_time = datetime.time(0, 0, 0)
if sample_date and sample_time:
timestamp = datetime.datetime.combine(sample_date, sample_time)
elif sample_date:
timestamp = datetime.datetime.combine(sample_date, default_time)
elif sample_time:
timestamp = datetime.datetime.combine(default_date, sample_time)
else:
# Sample object has no date or time
return None
time = Time.from_datetime(timestamp)
except AttributeError:
time = None
else:
return time
return time
def submit_edit():
""" handle file edit form """
# ... including student work pages.
# invoked from handle_post()
# the form text data is in the form dict key, i.e. request.form['edit_text']
# print_debug(' submit_edit: request.form : {}'.format(request.form.items()))
#
# request.form will look something like
# { 'submit_edit' : u'save page', # submit button
# 'edit_text' : u'page content\r\n===\r\n etc' # textarea
# }
#
# If this is a work page, then update the Work database object.
# (The Work object is created in Page.get_from_path)
if request.page.is_work:
now = str(Time()) # string with current time
with db.atomic():
if request.page.user_role.name == 'faculty':
page = request.page
page.work.faculty_modified = now
# If checkbox for 'submitted' and that didn't have a value,
# then set it - used to mark work as submitted,
# i.e. student emails work & faculty submits.
if "submitted_checkbox" in request.form \
and not page.work.submitted:
due = Time(page.work_due)
print_debug(" submit_edit: due = {}".format(str(due)))
if "on_time_checkbox" in request.form:
due.shift_minutes(-5)
else:
due.shift_minutes(5)
page.work.submitted = str(due)
print_debug(" submit_edit: submitted set to {}".format( \
page.work.submitted))
if 'grade' in request.form:
page.work.grade = str(request.form['grade'])
else:
request.page.work.student_modified = now
if not request.page.work.submitted:
request.page.work.submitted = now
request.page.work.save()
# Save the page content to a file and to git.
bytes_written = request.page.write_content(request.form['edit_text'])
print_debug(' submit_edit: bytes_written = {}'.format(bytes_written))
git.add_and_commit(request.page)
return request.base_url # ... and reload it without ?action=edit
def load_times(file_user):
for row in (open(file_user)):
row = row.strip()
monday, tuesday, wednesday, thursday, friday, saturday, sunday, morning, late_morning, early_night, late_night = row.split(
",")
time_preference = Time(monday=monday,
tuesday=tuesday,
wednesday=wednesday,
thursday=thursday,
friday=friday,
saturday=saturday,
sunday=sunday,
morning=morning,
late_morning=late_morning,
early_night=early_night,
late_night=late_night)
db.session.add(time_preference)
db.session.commit()
def do_before_request():
""" initialize database and session """
# See http://docs.peewee-orm.com/en/latest/peewee/database.html .
# This gives "connection already open" error if in console.
# The current (kludgy) fix is to test for the console explicitly.
if not in_console():
db.connect()
#print " db={}".format(db)
#print " request={}".format(request)
# See PERMANENT_SESSION_LIFETIME in env/settings.py
session.permanent = True
# site settings
g.debug = umber_debug
g.contact_url = contact_url
g.about_url = about_url
g.help_url = help_url
g.umber_url = umber_url
g.markup_url = markup_url
g.site_url = site_url
g.now = Time()
def parse_sample_time(row, datetime_col):
datetime = row[datetime_col]
return Time.from_datetime(datetime)
class SampleParserTest(unittest.TestCase):
sample_test_file = './data/test_data/samp_metadata/sample1.txt'
row = OrderedDict([
('sample_name', '317.F10'), ('age', '22'), ('age_unit', 'years'),
('altitude', '0'), ('anatomical_body_site', 'FMA:Palm'),
('anonymized_name', 'F10'), ('body_habitat', 'UBERON:skin'),
('body_product', 'UBERON:sebum'),
('body_site', 'UBERON:zone of skin of hand'),
('collection_date', '11/12/2006'),
('country', 'GAZ:United States of America'), ('depth', '0'),
('description', 'human skin metagenome'), ('dna_extracted', 'true'),
('dominant_hand', ''), ('elevation', '1591.99'),
('env_biome', 'ENVO:human-associated habitat'),
('env_feature', 'ENVO:human-associated habitat'),
('host_common_name', 'human'), ('host_subject_id', 'F1'),
('host_taxid', '9606'), ('latitude', '40'), ('longitude', '-105'),
('palm_size', ''), ('physical_specimen_remaining', 'false'),
('public', 'true'), ('qiita_study_id', '317'),
('sample_type', 'XXQIITAXX'), ('sex', 'female'),
('time_since_last_wash', '0'),
('title',
'The influence of sex handedness and washing on the diversity of hand surface bacteriaS1_V160'
)
])
dayfirst_dict = {'collection_date': False}
# TODO Update details of source (when necessary)
source1 = Source(name='qiita',
type_='Database (Public)',
url='https://qiita.ucsd.edu/study/description/0')
experiment1 = Experiment(source=source1, orig_study_id='317')
subject1 = Subject(
source=source1,
orig_study_id='317',
orig_subject_id='F1',
sex='female',
country='United States of America',
race=None,
csection=None,
disease=None,
dob=None,
)
subject2 = Subject(
source=source1,
orig_study_id='317',
orig_subject_id='F2',
sex='female',
country='United States of America',
race=None,
csection=None,
disease=None,
dob=None,
)
sampling_site = SamplingSite(
uberon_habitat_term='UBERON:skin',
uberon_product_term='UBERON:sebum',
uberon_site_term='UBERON:zone of skin of hand',
env_biom_term='ENVO:human-associated habitat',
env_feature_term='ENVO:human-associated habitat')
sampling_time = Time(timestamp=datetime.datetime(2006, 11, 12),
uncertainty=None,
date=datetime.date(2006, 11, 12),
time=None,
year=2006,
month=11,
day=12,
hour=None,
minute=None,
second=None,
season='autumn')
sample1 = Sample(source=source1,
orig_study_id='317',
orig_subject_id='F1',
orig_sample_id='317.F10',
age_units=ureg.years,
age=22.0,
latitude=40.0,
longitude=-105.0,
elevation=1591.99,
height_units=ureg.metres,
height=None,
weight_units=ureg.kilograms,
weight=None,
bmi=None,
sample_date=datetime.date(2006, 11, 12),
sample_time=None,
sampling_site=sampling_site,
sampling_time=sampling_time)
sample2 = Sample(source=source1,
orig_study_id='317',
orig_subject_id='F1',
orig_sample_id='317.F12',
age_units=ureg.years,
age=22.0,
latitude=40.0,
longitude=-105.0,
elevation=1591.99,
height_units=ureg.metres,
height=None,
weight_units=ureg.kilograms,
weight=None,
bmi=None,
sample_date=datetime.date(2006, 11, 12),
sample_time=None,
sampling_site=sampling_site,
sampling_time=sampling_time)
sample3 = Sample(source=source1,
orig_study_id='317',
orig_subject_id='F2',
orig_sample_id='317.F20',
age_units=ureg.years,
age=None,
latitude=40.0,
longitude=-105.0,
elevation=1591.99,
height_units=ureg.metres,
height=None,
weight_units=ureg.kilograms,
weight=None,
bmi=None,
sample_date=datetime.date(2006, 11, 12),
sample_time=None,
sampling_site=sampling_site,
sampling_time=sampling_time)
# Not necessary to establish these relationships for purpose of
# test_parse_objects:
sample1._subject = subject1
sample2._subject = subject1
sample3._subject = subject2
subject1._samples = {sample1, sample2}
subject2._samples = {sample3}
experiment1._subjects = {subject1, subject2}
experiment1._samples = {sample1, sample2, sample3}
def test_parse_objects(self):
experiment_ids = parse_objects(self.sample_test_file)
self.assertIn('317', experiment_ids)
experiment = experiment_ids['317']
self.assertEqual(self.experiment1, experiment)
self.assertIn(self.subject1, experiment.subjects)
self.assertIn(self.subject2, experiment.subjects)
self.assertIn(self.sample1, experiment.samples)
self.assertIn(self.sample2, experiment.samples)
self.assertIn(self.sample3, experiment.samples)
# TODO: We will have to test without the source keyword at some point.
def test_parse_sample(self):
self.maxDiff = None
blacklist_attrs = [
'_sa_instance_state', 'source', 'counts', '_experiments',
'_subject', '_preparations'
]
sample = parse_sample(self.row,
self.dayfirst_dict,
source=self.source1)
sample_attrs = set((key, value)
for key, value in sample.__dict__.items()
if key not in blacklist_attrs)
expected_attrs = set((key, value)
for key, value in self.sample1.__dict__.items()
if key not in blacklist_attrs)
self.assertEqual(sample_attrs, expected_attrs)
self.assertEqual(sample.source, self.source1)
self.assertEqual(sample.counts, self.sample1.counts)
# When sample is parsed, it is not yet associated with subject/experiments
self.assertEqual(sample._subject, None)
self.assertEqual(sample._experiments, set())
self.assertEqual(sample._preparations, set())
def test_parse_subject(self):
self.maxDiff = None
blacklist_attrs = [
'_sa_instance_state', 'source', 'counts', 'perturbation_facts',
'_experiments', '_samples', '_perturbations'
]
subject = parse_subject(self.row, source=self.source1)
subject_attrs = set((key, value)
for key, value in subject.__dict__.items()
if key not in blacklist_attrs)
expected_attrs = set((key, value)
for key, value in self.subject1.__dict__.items()
if key not in blacklist_attrs)
self.assertEqual(subject_attrs, expected_attrs)
self.assertEqual(subject.source, self.source1)
self.assertEqual(subject.counts, self.subject1.counts)
self.assertEqual(subject.perturbation_facts,
self.subject1.perturbation_facts)
# When subject is parsed, it is not yet associated with samples/experiments
self.assertEqual(subject._experiments, set())
self.assertEqual(subject._samples, set())
self.assertEqual(subject._perturbations, set())
def test_parse_processing(self):
self.maxDiff = None
processing1 = Processing(parent=None,
parameter_values='{}',
orig_prep_id='577',
orig_proc_id='2593')
processing2 = Processing(parent=processing1,
parameter_values='{'
'"barcode_type":"golay_12",'
'"command":"Split libraries (QIIMEq2 1.9.1)",'
'"disable_bc_correction":"False",'
'"disable_primers":"False",'
'"generated on":"2016-01-14 17:01",'
'"input_data":"2593",'
'"max_ambig":"6",'
'"max_barcode_errors":"1.5",'
'"max_homopolymer":"6",'
'"max_primer_mismatch":"0",'
'"max_seq_len":"1000",'
'"min_qual_score":"25",'
'"min_seq_len":"200",'
'"qual_score_window":"0",'
'"reverse_primer_mismatches":"0",'
'"reverse_primers":"disable",'
'"trim_seq_length":"False",'
'"truncate_ambi_bases":"False"'
'}',
orig_prep_id='577',
orig_proc_id='310')
processing3 = Processing(
parent=processing2,
parameter_values='{'
'"command":"Pick closed-reference OTUs (QIIMEq2 1.9.1)",'
'"generated on":"2015-06-30 14:06",'
'"input_data":"310",'
'"reference-seq":"/databases/gg/13_8/rep_set/97_otus.fasta",'
'"reference-tax":"/databases/gg/13_8/taxonomy/97_otu_taxonomy.txt",'
'"similarity":"0.97",'
'"sortmerna_coverage":"0.97",'
'"sortmerna_e_value":"1",'
'"sortmerna_max_pos":"10000",'
'"threads":"1"'
'}',
orig_prep_id='577',
orig_proc_id='2594')
expected_processings = {
'2593': processing1,
'310': processing2,
'2594': processing3
}
processings = parse_processings('./data/test_data/proc1.json')
# TODO: Implement workflows and parents as mocks?
blacklist_attrs = ['_sa_instance_state', 'workflows', 'parent']
for proc_id, processing in processings.items():
self.assertIn(proc_id, expected_processings)
processing_attrs = set(
(key, value) for key, value in processing.__dict__.items()
if key not in blacklist_attrs)
expected_attrs = set(
(key, value) for key, value in
expected_processings[proc_id].__dict__.items()
if key not in blacklist_attrs)
self.assertEqual(processing_attrs, expected_attrs)
with app.app_context():
for k, v in data.hours.items():
hour = Hour(code=k, name=v)
db.session.add(hour)
for k, v in data.week.items():
day = Day(code=k, name=v)
db.session.add(day)
for k, v in data.goals.items():
goal = Goal(code=k, name=v)
db.session.add(goal)
for k, v in data.times.items():
time = Time(code=k, name=v)
db.session.add(time)
for t in data.teachers:
teacher = Teacher(id=t['id'],
name=t['name'],
about=t['about'],
rating=t['rating'],
picture=t['picture'],
price=t['price'],
free=t['free'])
db.session.add(teacher)
for g in t['goals']:
new_goal = Goal.query.filter(Goal.code == g).first()
teacher.goals.append(new_goal)
def new_show_page_process():
user_id = session.get("user_id")
monday = request.json.get("monday")
tuesday = request.json.get("tuesday")
wednesday = request.json.get("wednesday")
thursday = request.json.get("thursday")
friday = request.json.get("friday")
saturday = request.json.get("saturday")
sunday = request.json.get("sunday")
morning = request.json.get("morning")
late_morning = request.json.get("late_morning")
early_night = request.json.get("early_night")
late_night = request.json.get("late_night")
new_time = Time(monday=monday,
tuesday=tuesday,
wednesday=wednesday,
thursday=thursday,
friday=friday,
saturday=saturday,
sunday=sunday,
morning=morning,
late_morning=late_morning,
early_night=early_night,
late_night=late_night)
db.session.add(new_time)
db.session.commit()
db.session.refresh(new_time)
berkeley = request.json.get("berkeley")
burlingame = request.json.get("burlingame")
daly_city = request.json.get("daly_city")
dublin = request.json.get("dublin")
emeryville = request.json.get("emeryville")
palo_alto = request.json.get("palo_alto")
san_francisco = request.json.get("san_francisco")
san_jose = request.json.get("san_jose")
santa_clara = request.json.get("santa_clara")
sunnyvale = request.json.get("sunnyvale")
new_location = Location(berkeley=berkeley,
burlingame=burlingame,
daly_city=daly_city,
dublin=dublin,
emeryville=emeryville,
palo_alto=palo_alto,
san_francisco=san_francisco,
san_jose=san_jose,
santa_clara=santa_clara,
sunnyvale=sunnyvale)
db.session.add(new_location)
db.session.commit()
db.session.refresh(new_location)
show_name = request.json.get("show_name")
show_type = request.json.get("show_type")
show_url = request.json.get("show_url")
show_amount_people = request.json.get("show_amount_people")
show_dressing_room = request.json.get("show_dressing_room")
show_length = request.json.get("show_length")
show_location_preferred = request.json.get("show_location_preferred")
show_ticket_price = request.json.get("show_ticket_price")
show_rent = request.json.get("show_rent")
new_show = Show(user_id=user_id,
show_name=show_name,
show_type=show_type,
show_url=show_url,
show_amount_people=show_amount_people,
show_dressing_room=show_dressing_room,
show_length=show_length,
location_id=new_location.location_id,
show_ticket_price=show_ticket_price,
time_id=new_time.time_id,
show_rent=show_rent)
db.session.add(new_show)
db.session.commit()
db.session.refresh(new_show)
show_rarking = adding_ranking("show", new_show.show_id)
user = User.query.filter_by(user_id=user_id).first()
return jsonify(user_fname=user.user_fname,
monday=monday,
tuesday=tuesday,
wednesday=wednesday,
thursday=thursday,
friday=friday,
saturday=saturday,
sunday=sunday,
morning=morning,
late_morning=late_morning,
early_night=early_night,
late_night=late_night,
show_name=show_name,
show_type=show_type,
show_url=show_url,
show_amount_people=show_amount_people,
show_dressing_room=show_dressing_room,
show_length=show_length,
show_ticket_price=show_ticket_price,
show_rent=show_rent,
show_id=new_show.show_id,
berkeley=berkeley,
burlingame=burlingame,
daly_city=daly_city,
dublin=dublin,
emeryville=emeryville,
palo_alto=palo_alto,
san_francisco=san_francisco,
san_jose=san_jose,
santa_clara=santa_clara,
sunnyvale=sunnyvale)
def venue_page_process():
"""Process new venue"""
user_id = session.get("user_id")
user = User.query.filter_by(user_id=user_id).first()
monday = request.json.get("monday")
tuesday = request.json.get("tuesday")
wednesday = request.json.get("wednesday")
thursday = request.json.get("thursday")
friday = request.json.get("friday")
saturday = request.json.get("saturday")
sunday = request.json.get("sunday")
morning = request.json.get("morning")
late_morning = request.json.get("late_morning")
early_night = request.json.get("early_night")
late_night = request.json.get("late_night")
venue_name = request.json.get("venue_name")
venue_url = request.json.get("venue_url")
venue_email = request.json.get("venue_email")
venue_address = request.json.get("venue_address")
venue_city = request.json.get("venue_city")
venue_type = request.json.get("venue_type")
venue_backspace = request.json.get("venue_backspace")
venue_capacity = request.json.get("venue_capacity")
venue_license = request.json.get("venue_license")
venue_rent = request.json.get("venue_rent")
check_venue_info = Venue.query.filter_by(
venue_address=venue_address).first()
if check_venue_info:
return jsonify("venue_already_register")
else:
new_time = Time(monday=monday,
tuesday=tuesday,
wednesday=wednesday,
thursday=thursday,
friday=friday,
saturday=saturday,
sunday=sunday,
morning=morning,
late_morning=late_morning,
early_night=early_night,
late_night=late_night)
db.session.add(new_time)
db.session.commit()
db.session.refresh(new_time)
new_venue = Venue(user_id=user_id,
venue_name=venue_name,
venue_url=venue_url,
venue_email=venue_email,
venue_address=venue_address,
venue_city=venue_city,
venue_type=venue_type,
venue_backspace=venue_backspace,
venue_capacity=venue_capacity,
venue_license=venue_license,
time_id=new_time.time_id,
venue_rent=venue_rent)
db.session.add(new_venue)
db.session.commit()
db.session.refresh(new_venue)
venue_rarking = adding_ranking("venue", new_venue.venue_id)
return jsonify(time_id=new_time.time_id,
monday=new_time.monday,
tuesday=new_time.tuesday,
wednesday=new_time.wednesday,
thursday=new_time.thursday,
friday=new_time.friday,
saturday=new_time.saturday,
sunday=new_time.sunday,
morning=new_time.morning,
late_morning=new_time.late_morning,
early_night=new_time.early_night,
late_night=new_time.late_night,
venue_id=new_venue.venue_id,
venue_name=new_venue.venue_name,
venue_url=new_venue.venue_url,
venue_email=new_venue.venue_email,
venue_address=new_venue.venue_address,
venue_city=new_venue.venue_city,
venue_type=new_venue.venue_type,
venue_backspace=new_venue.venue_backspace,
venue_capacity=new_venue.venue_capacity,
venue_license=new_venue.venue_license,
venue_rent=new_venue.venue_rent)