def get(self, method, lookup, rdb):
''' Lookup the user by the uid '''
if method == 'uid':
uid = lookup
elif method == 'username':
uid = self.getUID(lookup, rdb)
results = r.table('users').get(uid).run(rdb)
data = results
if data:
self.email = results['email']
self.uid = results['id']
self.username = results['username']
self.status = results['status']
self.company = results['company']
self.contact = results['contact']
self.acttype = results['acttype']
self.stripeid = results['stripeid']
self.stripe = results['stripe']
self.subplans = results['subplans']
self.payments = results['payments']
self.subscription = results['subscription']
self.creation_time = results['creation_time']
self.confirmed = results['confirmed']
## Identify number of monitors and reactions
monitor = Monitor()
reaction = Reaction()
self.monitorCount = monitor.count(self.uid, rdb)
self.reactionCount = reaction.count(self.uid, rdb)
return self
else:
return None
def test_getRID_works(self):
# Ensure that getRID() works as expected.
timestamp = str(datetime.datetime.now())
new_timestamp = timestamp.replace(":", "")
with self.client:
self.client.post(
'/login',
data=dict(email="*****@*****.**", password="******"),
follow_redirects=True
)
self.client.post(
'/dashboard/reactions/enotify',
data=dict(name=new_timestamp, trigger=1,
frequency=1, email="*****@*****.**",
send_true=True),
follow_redirects=True
)
user = User()
user_id = user.getUID('*****@*****.**', g.rdb_conn)
get_reaction_id = Reaction()
response = get_reaction_id.getRID(
new_timestamp+':'+user_id, g.rdb_conn)
results = r.table('reactions').filter(
{'name': new_timestamp}).run(g.rdb_conn)
for result in results:
reaction_id = result['id']
break
self.assertEqual(response, reaction_id)
def test_getRID_works(self):
# Ensure that getRID() works as expected.
timestamp = str(datetime.datetime.now())
new_timestamp = timestamp.replace(":", "")
with self.client:
self.client.post(
'/login',
data=dict(email="*****@*****.**", password="******"),
follow_redirects=True
)
self.client.post(
'/dashboard/reactions/enotify',
data=dict(name=new_timestamp, trigger=1,
frequency=1, email="*****@*****.**",
send_true=True),
follow_redirects=True
)
user = User()
user_id = user.getUID('*****@*****.**', g.rdb_conn)
get_reaction_id = Reaction()
response = get_reaction_id.getRID(
new_timestamp+':'+user_id, g.rdb_conn)
results = r.table('reactions').filter(
{'name': new_timestamp}).run(g.rdb_conn)
for result in results:
reaction_id = result['id']
break
self.assertEqual(response, reaction_id)
def delreaction_page(rid):
'''
Dashboard Delete Domains:
This will delete a domain based on url parameters
'''
verify = verifyLogin(app.config['SECRET_KEY'],
app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
if user.status != "active":
pass
else:
appliedcount = 0
results = r.table('monitors').filter({
'uid': user.uid
}).run(g.rdb_conn)
for x in results:
if rid in x['data']['reactions']:
appliedcount = appliedcount + 1
if appliedcount < 1:
# Delete the Reaction
reaction = Reaction(rid)
result = reaction.deleteReaction(user.uid, rid, g.rdb_conn)
if result:
flash('Reaction was successfully deleted', 'success')
else:
flash('Reaction was not deleted', 'danger')
else:
flash(
'You must first detach this reaction from all monitors before deleting',
'danger')
return redirect(url_for('member.dashboard_page'))
def delreaction_page(rid):
'''
Dashboard Delete Domains:
This will delete a domain based on url parameters
'''
verify = verifyLogin(
app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
if user.status != "active":
pass
else:
appliedcount = 0
results = r.table('monitors').filter(
{'uid': user.uid}).run(g.rdb_conn)
for x in results:
if rid in x['data']['reactions']:
appliedcount = appliedcount + 1
if appliedcount < 1:
# Delete the Reaction
reaction = Reaction(rid)
result = reaction.deleteReaction(user.uid, rid, g.rdb_conn)
if result:
flash('Reaction was successfully deleted.', 'success')
else:
flash('Reaction was not deleted.', 'danger')
else:
flash('You must first detach this reaction \
from all monitors before deleting.', 'danger')
return redirect(url_for('member.dashboard_page'))
def get(self, method, lookup, rdb):
''' Lookup the user by the uid '''
if method == 'uid':
uid = lookup
elif method == 'username':
uid = self.getUID(lookup, rdb)
results = r.table('users').get(uid).run(rdb)
data = results
if data:
self.email = results['email']
self.uid = results['id']
self.username = results['username']
self.status = results['status']
self.company = results['company']
self.contact = results['contact']
self.acttype = results['acttype']
self.stripeid = results['stripeid']
self.stripe = results['stripe']
self.subplans = results['subplans']
self.payments = results['payments']
self.subscription = results['subscription']
self.creation_time = results['creation_time']
self.confirmed = results['confirmed']
## Identify number of monitors and reactions
monitor = Monitor()
reaction = Reaction()
self.monitorCount = monitor.count(self.uid, rdb)
self.reactionCount = reaction.count(self.uid, rdb)
return self
else:
return None
def get(self, method, lookup, rdb):
""" Lookup the user by the uid """
if method == "uid":
uid = lookup
elif method == "username":
uid = self.getUID(lookup, rdb)
results = r.table("users").get(uid).run(rdb)
data = results
if data:
self.email = results["email"]
self.uid = results["id"]
self.username = results["username"]
self.status = results["status"]
self.company = results["company"]
self.contact = results["contact"]
self.acttype = results["acttype"]
self.stripeid = results["stripeid"]
self.stripe = results["stripe"]
self.subplans = results["subplans"]
self.payments = results["payments"]
self.subscription = results["subscription"]
self.creation_time = results["creation_time"]
self.confirmed = results["confirmed"]
## Identify number of monitors and reactions
monitor = Monitor()
reaction = Reaction()
self.monitorCount = monitor.count(self.uid, rdb)
self.reactionCount = reaction.count(self.uid, rdb)
return self
else:
return None
def unassign(self):
if self.assignee is None:
return
self.set_status(ReportStatus.NEW)
self.client.flows[self.assignee.id].remove(self.review_flow)
self.assignee = None
self.review_flow = None
assignReaction = Reaction("✋",
click_handler=self.reaction_attempt_assign,
once_per_message=False)
for msg in self._channel_messages:
if msg[1]: # Check if message is "assignable"
asyncio.create_task(assignReaction.register_message(msg[0]))
def _parse_reaction(line, all_species, parameters, reactions, tables):
line_split_arrow = line.split('=>')
if len(line_split_arrow) != 2:
raise InvalidLine(
f"Syntax error on line '{line}': There can only be one reaction per line. In a reaction, "
f"the reactants and products are separated by the arrow '=>'.")
left_side = line_split_arrow[0]
line_split_excl = line_split_arrow[1].split('!')
if len(line_split_excl) != 2:
raise InvalidLine(
f"Syntax error on line '{line}': Each reaction must have its rate specified. The rate "
f"specification goes after the single exclamation mark '!'. The exclamation mark '!' "
f"must not be used elsewhere.")
right_side = line_split_excl[0]
rate_spec = line_split_excl[1]
reaction = Reaction(_parse_species(left_side, all_species),
_parse_species(right_side, all_species))
_parse_rate(reaction, rate_spec, tables,
parameters) # fills attributes rate_fun and table_name
reaction.scale(
parameters) # # scale the rate function: using the 'ratio' parameter
reactions.append(reaction)
def addreaction_page(rname):
verify = verifyLogin(
app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.config = app.config
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/reactions/' + rname
tmpl = 'reactions/create.html'
data['js_bottom'] = ['reactions/base.js']
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__(
"reactionforms." + rname, globals(),
locals(), ['ReactForm'], -1)
form = reform.ReactForm(request.form)
if request.method == 'POST':
if form.validate():
reaction = Reaction()
reaction.config = app.config
reaction.name = form.name.data
reaction.trigger = form.trigger.data
reaction.frequency = form.frequency.data
reaction.uid = user.uid
reaction.rtype = rname
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
reaction.data = tmpdata
if reaction.count(user.uid, g.rdb_conn) < data['rlimit']:
results = reaction.createReaction(g.rdb_conn)
else:
results = "toomany"
if results == "exists":
print("/dashboard/reactions/{0} - \
Reaction creation failed: exists".format(rname))
flash('{0} seems to already exist. Try using a \
different name.'.format(reaction.name), 'danger')
elif results == "edit noexists":
print("/dashboard/reactions/{0} - Reaction \
edit failed: doesn't exist".format(rname))
flash('{0} cannot be edited as it does not \
exist.'.format(reaction.name), 'danger')
elif results == "edit true":
print("/dashboard/reactions/{0} - \
Reaction edit successful".format(rname))
flash('Reaction successfully edited: {0}.'.format(
reaction.name), 'success')
elif results == "edit failed":
print("/dashboard/reactions/{0} - \
Reaction edit failed: unknown".format(rname))
flash('Reaction not successfully edited: {0}.'.format(
reaction.name), 'danger')
elif results == "toomany":
print("/dashboard/reactions/{0} - \
Reaction creation failed: too many".format(rname))
flash('Could not create reaction: \
Too many reactions already created.', 'danger')
elif results is False:
print("/dashboard/reactions/{0} - \
Reaction creation failed: unknown".format(rname))
flash('Could not create reaction.', 'danger')
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
print("/dashboard/reactions/{0} - \
Reaction creation successful".format(rname))
flash('Reaction "{0}" successfully added.'.format(
reaction.name), 'success')
else:
print("/dashboard/reactions/{0} - \
Reaction creation failed: form invalid".format(rname))
flash('Form is not valid.', 'success')
page = render_template(tmpl, data=data, form=form)
return page
else:
flash('Please Login.', 'warning')
return redirect(url_for('user.login_page'))
def editreact_page(rname, rid):
''' This is a generic edit page for reactions '''
verify = verifyLogin(
app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.config = app.config
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/edit-reactions/' + rname + '/' + rid
tmpl = 'reactions/create.html'
data['js_bottom'] = ['reactions/base.js', ]
data['edit'] = True
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__(
"reactionforms." + rname, globals(),
locals(), ['ReactForm'], -1)
form = reform.ReactForm(request.form)
reaction = Reaction()
reaction.config = app.config
# If Edit get information
reaction.get("rid", rid, g.rdb_conn)
if reaction.uid == user.uid:
data['reaction'] = {
'rid': reaction.rid,
'name': reaction.name,
'trigger': reaction.trigger,
'frequency': reaction.frequency,
'uid': reaction.uid,
'rtype': reaction.rtype,
'data': reaction.data
}
data['selects'] = []
for item in form.__iter__():
if item.type == "SelectField" or \
item.type == "SelectMultipleField":
item.default = data['reaction']['data'][item.name]
tmpl = 'reactions/create.html'
if request.method == 'POST':
if form.validate():
reaction2 = Reaction()
reaction2.config = app.config
reaction2.rid = reaction.rid
reaction2.name = form.name.data
reaction2.trigger = form.trigger.data
reaction2.frequency = form.frequency.data
reaction2.lastrun = reaction.lastrun
reaction2.uid = user.uid
reaction2.rtype = reaction.rtype
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
if item.type == "SelectField" or\
item.type == "SelectMultipleField":
item.default = item.data
reaction2.data = tmpdata
data['reaction'] = {
'rid': reaction2.rid,
'name': reaction2.name,
'trigger': reaction2.trigger,
'frequency': reaction2.frequency,
'uid': reaction2.uid,
'rtype': reaction2.rtype,
'data': reaction2.data
}
if reaction.uid == user.uid:
results = reaction2.editReaction(g.rdb_conn)
else:
results = False
print("/dashboard/reactions/{0} - \
Reaction edit failed: not owner".format(rname))
flash("It doesn't appear that you own this reaction.",
'danger')
if results == "exists":
print("/dashboard/reactions/{0} - \
Reaction edit failed: exists".format(rname))
flash('This reaction seems to already exist. \
Try using a different name.', 'danger')
elif results == "edit noexists":
print("/dashboard/reactions/{0} - \
Reaction edit failed: exists".format(rname))
flash('This reaction can not be edited \
as it does not exist.', 'danger')
elif results == "edit true":
print("/dashboard/reactions/{0} - \
Reaction edit successful".format(rname))
flash('Reaction successfully edited.', 'success')
elif results == "edit failed":
print("/dashboard/reactions/{0} - \
Reaction edit failed: unknown".format(rname))
flash('Reaction not successfully edited.', 'danger')
elif results is False:
print("/dashboard/reactions/{0} - \
Reaction edit failed: unknown".format(rname))
flash('Could not create reaction.', 'danger')
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
print("/dashboard/reactions/{0} - \
Reaction edit success".format(rname))
flash('Reaction "{0}" successfully \
added.'.format(reaction2.name), 'danger')
else:
print("/dashboard/reactions/{0} - \
Reaction edit failed: form invalid".format(rname))
flash('Form is not valid.', 'danger')
form.process()
page = render_template(tmpl, data=data, form=form)
return page
else:
flash('Please Login.', 'warning')
return redirect(url_for('user.login_page'))
def addreaction_page(rname):
verify = verifyLogin(app.config['SECRET_KEY'],
app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/reactions/' + rname
tmpl = 'reactions/' + rname + '.html'
data['js_bottom'] = ['reactions/base.js', 'reactions/' + rname + '.js']
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__("reactionforms." + rname, globals(), locals(),
['ReactForm'], -1)
form = reform.ReactForm(request.form)
if request.method == 'POST':
if form.validate():
reaction = Reaction()
reaction.name = form.name.data
reaction.trigger = form.trigger.data
reaction.frequency = form.frequency.data
reaction.uid = user.uid
reaction.rtype = rname
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
reaction.data = tmpdata
if reaction.count(user.uid, g.rdb_conn) < data['rlimit']:
results = reaction.createReaction(g.rdb_conn)
else:
results = "toomany"
if results == "exists":
data[
'msg'] = "This reaction seems to already exist, try using a different name: %s" % reaction.name
print(
"/dashboard/reactions/%s - Reaction creation failed: exists"
) % rname
data['error'] = True
elif results == "edit noexists":
data[
'msg'] = "This reaction can not be edited as it does not exist: %s" % reaction.name
print(
"/dashboard/reactions/%s - Reaction edit failed: doesnt exist"
) % rname
data['error'] = True
elif results == "edit true":
data[
'msg'] = "Reaction successfully edited: %s" % reaction.name
print(
"/dashboard/reactions/%s - Reaction edit successful"
) % rname
data['error'] = False
elif results == "edit false":
data[
'msg'] = "Reaction not successfully edited: %s" % reaction.name
print(
"/dashboard/reactions/%s - Reaction edit failed: unknown"
) % rname
data['error'] = True
elif results == "toomany":
data[
'msg'] = "Could not create reaction: Too many reactions already created [%d]" % data[
'rlimit']
print(
"/dashboard/reactions/%s - Reaction creation failed: too many"
) % rname
data['error'] = True
elif results is False:
data['msg'] = "Could not create reaction"
print(
"/dashboard/reactions/%s - Reaction creation failed: unknown"
) % rname
data['error'] = True
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
data[
'msg'] = 'Reaction "%s" successfully added' % reaction.name
print(
"/dashboard/reactions/%s - Reaction creation successful"
) % rname
data['error'] = False
else:
data['msg'] = "Form is not valid"
print(
"/dashboard/reactions/%s - Reaction creation failed: form invalid"
) % rname
data['error'] = True
page = render_template(tmpl, data=data, form=form)
return page
else:
return redirect(url_for('user.login_page'))
def editreact_page(rname, rid):
''' This is a generic edit page for reactions '''
verify = verifyLogin(app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/edit-reactions/' + rname + '/' + rid
tmpl = 'reactions/index.html'
data['js_bottom'] = [ 'reactions/base.js', 'reactions/' + rname + '.js' ]
data['edit'] = True
## Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'mod-subscription.html'
else:
reform = __import__("reactionforms." + rname, globals(), locals(), ['ReactForm'], -1)
form = reform.ReactForm(request.form)
reaction = Reaction()
## If Edit get information
reaction.get("rid", rid, g.rdb_conn)
if reaction.uid == user.uid:
data['reaction'] = {
'rid': reaction.rid,
'name': reaction.name,
'trigger': reaction.trigger,
'frequency': reaction.frequency,
'uid': reaction.uid,
'rtype': reaction.rtype,
'data': reaction.data
}
data['selects'] = []
for item in form.__iter__():
if item.type == "SelectField" or item.type == "SelectMultipleField":
item.default = data['reaction']['data'][item.name]
tmpl = 'reactions/' + rname + '.html'
if request.method == 'POST':
if form.validate():
reaction2 = Reaction()
reaction2.rid = reaction.rid
reaction2.name = form.name.data
reaction2.trigger = form.trigger.data
reaction2.frequency = form.frequency.data
reaction2.uid = user.uid
reaction2.rtype = reaction.rtype
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
if item.type == "SelectField" or item.type == "SelectMultipleField":
item.default = item.data
reaction2.data = tmpdata
data['reaction'] = {
'rid': reaction2.rid,
'name': reaction2.name,
'trigger': reaction2.trigger,
'frequency': reaction2.frequency,
'uid': reaction2.uid,
'rtype': reaction2.rtype,
'data': reaction2.data
}
if reaction.uid == user.uid:
results = reaction2.editReaction(g.rdb_conn)
else:
results = False
data['msg'] = "I Doesn't appear that you own this reaction"
print("/dashboard/reactions/%s - Reaction edit failed: not owner") % rname
data['error'] = True
if results == "exists":
data['msg'] = "This reaction seems to already exist, try using a different name: %s" % reaction2.name
print("/dashboard/reactions/%s - Reaction edit failed: exists") % rname
data['error'] = True
elif results == "edit noexists":
data['msg'] = "This reaction can not be edited as it does not exist: %s" % reaction2.name
print("/dashboard/reactions/%s - Reaction edit failed: exists") % rname
data['error'] = True
elif results == "edit true":
data['msg'] = "Reaction successfully edited: %s" % reaction2.name
print("/dashboard/reactions/%s - Reaction edit successful") % rname
data['error'] = False
elif results == "edit false":
data['msg'] = "Reaction not successfully edited: %s" % reaction2.name
print("/dashboard/reactions/%s - Reaction edit failed: unknown") % rname
data['error'] = True
elif results == False:
data['msg'] = "Could not create reaction"
print("/dashboard/reactions/%s - Reaction edit failed: unknown") % rname
data['error'] = True
else:
stathat.ez_count(app.config['STATHAT_EZ_KEY'], app.config['ENVNAME'] + ' Reaction Added', 1)
data['msg'] = 'Reaction "%s" successfully added' % reaction2.name
print("/dashboard/reactions/%s - Reaction edit success") % rname
data['error'] = False
else:
data['msg'] = "Form is not valid"
print("/dashboard/reactions/%s - Reaction edit failed: form invalid") % rname
data['error'] = True
form.process()
page = render_template(tmpl, data=data, form=form)
return page
else:
return redirect(url_for('login_page'))
def addreaction_page(rname):
verify = verifyLogin(
app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/reactions/' + rname
tmpl = 'reactions/' + rname + '.html'
data['js_bottom'] = ['reactions/base.js', 'reactions/' + rname + '.js']
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__(
"reactionforms." + rname, globals(),
locals(), ['ReactForm'], -1)
form = reform.ReactForm(request.form)
if request.method == 'POST':
if form.validate():
reaction = Reaction()
reaction.name = form.name.data
reaction.trigger = form.trigger.data
reaction.frequency = form.frequency.data
reaction.uid = user.uid
reaction.rtype = rname
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
reaction.data = tmpdata
if reaction.count(user.uid, g.rdb_conn) < data['rlimit']:
results = reaction.createReaction(g.rdb_conn)
else:
results = "toomany"
if results == "exists":
print("/dashboard/reactions/{0} - \
Reaction creation failed: exists".format(rname))
flash('{0} seems to already exist. Try using a \
different name.'.format(reaction.name), 'danger')
elif results == "edit noexists":
print("/dashboard/reactions/{0} - Reaction \
edit failed: doesn't exist".format(rname))
flash('{0} cannot be edited as it does not \
exist.'.format(reaction.name), 'danger')
elif results == "edit true":
print("/dashboard/reactions/{0} - \
Reaction edit successful".format(rname))
flash('Reaction successfully edited: {0}.'.format(
reaction.name), 'success')
elif results == "edit failed":
print("/dashboard/reactions/{0} - \
Reaction edit failed: unknown".format(rname))
flash('Reaction not successfully edited: {0}.'.format(
reaction.name), 'danger')
elif results == "toomany":
print("/dashboard/reactions/{0} - \
Reaction creation failed: too many".format(rname))
flash('Could not create reaction: \
Too many reactions already created.', 'danger')
elif results is False:
print("/dashboard/reactions/{0} - \
Reaction creation failed: unknown".format(rname))
flash('Could not create reaction.', 'danger')
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
print("/dashboard/reactions/{0} - \
Reaction creation successful".format(rname))
flash('Reaction "{0}" successfully added.'.format(
reaction.name), 'success')
else:
print("/dashboard/reactions/{0} - \
Reaction creation failed: form invalid".format(rname))
flash('Form is not valid.', 'success')
page = render_template(tmpl, data=data, form=form)
return page
else:
flash('Please Login.', 'warning')
return redirect(url_for('user.login_page'))
def addreaction_page(rname):
verify = verifyLogin(
app.config['SECRET_KEY'], app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/reactions/' + rname
tmpl = 'reactions/' + rname + '.html'
data['js_bottom'] = ['reactions/base.js', 'reactions/' + rname + '.js']
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__(
"reactionforms." + rname, globals(),
locals(), ['ReactForm'], -1)
form = reform.ReactForm(request.form)
if request.method == 'POST':
if form.validate():
reaction = Reaction()
reaction.name = form.name.data
reaction.trigger = form.trigger.data
reaction.frequency = form.frequency.data
reaction.uid = user.uid
reaction.rtype = rname
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
reaction.data = tmpdata
if reaction.count(user.uid, g.rdb_conn) < data['rlimit']:
results = reaction.createReaction(g.rdb_conn)
else:
results = "toomany"
if results == "exists":
data['msg'] = "This reaction seems to already exist, try using a different name: %s" % reaction.name
print("/dashboard/reactions/%s - Reaction creation failed: exists") % rname
data['error'] = True
elif results == "edit noexists":
data['msg'] = "This reaction can not be edited as it does not exist: %s" % reaction.name
print("/dashboard/reactions/%s - Reaction edit failed: doesnt exist") % rname
data['error'] = True
elif results == "edit true":
data['msg'] = "Reaction successfully edited: %s" % reaction.name
print("/dashboard/reactions/%s - Reaction edit successful") % rname
data['error'] = False
elif results == "edit false":
data['msg'] = "Reaction not successfully edited: %s" % reaction.name
print("/dashboard/reactions/%s - Reaction edit failed: unknown") % rname
data['error'] = True
elif results == "toomany":
data['msg'] = "Could not create reaction: Too many reactions already created [%d]" % data['rlimit']
print("/dashboard/reactions/%s - Reaction creation failed: too many") % rname
data['error'] = True
elif results is False:
data['msg'] = "Could not create reaction"
print("/dashboard/reactions/%s - Reaction creation failed: unknown") % rname
data['error'] = True
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
data['msg'] = 'Reaction "%s" successfully added' % reaction.name
print("/dashboard/reactions/%s - Reaction creation successful") % rname
data['error'] = False
else:
data['msg'] = "Form is not valid"
print("/dashboard/reactions/%s - Reaction creation failed: form invalid") % rname
data['error'] = True
page = render_template(tmpl, data=data, form=form)
return page
else:
return redirect(url_for('user.login_page'))
def genReactionScheme(visc, visc2):
return [
Reaction('S0 + I <-> S1', k_emmision
), #excitation (this works if we redefine I as being I/I_sat)
Reaction('S1 <-> S0',
k_emmision), #emmission - we ignore the emitted photon
Reaction('S1 <-> T1', 6.6e-1), #intersystem crossing
Reaction('T1 <-> S0', 5e-5), #radiationless deactivation
Reaction('2T1 <-> T1 + S0', 5e2 / visc2), #triplet quenching
Reaction('T1 + S0 <-> 2S0', 5e1 / visc2), #triplet quenching
Reaction('2T1 <-> R + X', 6e2 / visc2), #electron transfer
Reaction('T1 + S0 <-> R + X', 6e2 / visc2), #electron transfer
Reaction('T1 + X <-> S0 + X', 1e3 / visc2,
catalysts=['X']), #quenching by X
Reaction('T1 + R <-> S0 + R', 1e3 / visc2,
catalysts=['R']), #quenching by R
Reaction('T1 + O2 <-> S0 + O2',
1.56e3 / visc), #physical quenching by 02
Reaction('T1 + O2 <-> X + HO2',
1.4e2 / visc), #chemical quenching by 02
Reaction('T1 + q <-> S0 + q', k10 / visc), #quencher
Reaction('T1 + q <-> R + qo', k11 / visc),
Reaction(
'R + q <-> S0 + q', k12 / visc
), #should nominally be a reaction with qo, but cannot determine rate constant for this - instead assume that q and qo are in some form of equilibrium and use the relationship to q
Reaction('X + q <-> S0 + qo', k13 / visc),
Reaction('X <-> P',
k14 / visc), #postulated permanent bleaching pathway
Reaction('R <-> P',
k15 / visc), #postulated permanent bleaching pathway
Reaction(
'R + O2 <-> S0 + HO2', 5e2 / visc
), #oxidation of R by 02 - rate constant from [kaske & linquist `64]
]
def editreact_page(rname, rid):
''' This is a generic edit page for reactions '''
verify = verifyLogin(app.config['SECRET_KEY'],
app.config['COOKIE_TIMEOUT'], request.cookies)
if verify:
user = User()
user.get('uid', verify, g.rdb_conn)
data = startData(user)
data['active'] = 'dashboard'
data['url'] = '/dashboard/edit-reactions/' + rname + '/' + rid
tmpl = 'reactions/index.html'
data['js_bottom'] = ['reactions/base.js', 'reactions/' + rname + '.js']
data['edit'] = True
# Check Users Status
if user.status != "active":
data['url'] = '/dashboard/mod-subscription'
tmpl = 'member/mod-subscription.html'
else:
reform = __import__("reactionforms." + rname, globals(), locals(),
['ReactForm'], -1)
form = reform.ReactForm(request.form)
reaction = Reaction()
# If Edit get information
reaction.get("rid", rid, g.rdb_conn)
if reaction.uid == user.uid:
data['reaction'] = {
'rid': reaction.rid,
'name': reaction.name,
'trigger': reaction.trigger,
'frequency': reaction.frequency,
'uid': reaction.uid,
'rtype': reaction.rtype,
'data': reaction.data
}
data['selects'] = []
for item in form.__iter__():
if item.type == "SelectField" or \
item.type == "SelectMultipleField":
item.default = data['reaction']['data'][item.name]
tmpl = 'reactions/' + rname + '.html'
if request.method == 'POST':
if form.validate():
reaction2 = Reaction()
reaction2.rid = reaction.rid
reaction2.name = form.name.data
reaction2.trigger = form.trigger.data
reaction2.frequency = form.frequency.data
reaction2.lastrun = reaction.lastrun
reaction2.uid = user.uid
reaction2.rtype = reaction.rtype
tmpdata = {}
for item in form.__iter__():
tmpdata[item.name] = item.data
if item.type == "SelectField" or\
item.type == "SelectMultipleField":
item.default = item.data
reaction2.data = tmpdata
data['reaction'] = {
'rid': reaction2.rid,
'name': reaction2.name,
'trigger': reaction2.trigger,
'frequency': reaction2.frequency,
'uid': reaction2.uid,
'rtype': reaction2.rtype,
'data': reaction2.data
}
if reaction.uid == user.uid:
results = reaction2.editReaction(g.rdb_conn)
else:
results = False
data[
'msg'] = "It doesn't appear that you own this reaction"
print(
"/dashboard/reactions/%s - Reaction edit failed: not owner"
) % rname
data['error'] = True
if results == "exists":
data[
'msg'] = "This reaction seems to already exist, try using a different name: %s" % reaction2.name
print(
"/dashboard/reactions/%s - Reaction edit failed: exists"
) % rname
data['error'] = True
elif results == "edit noexists":
data[
'msg'] = "This reaction can not be edited as it does not exist: %s" % reaction2.name
print(
"/dashboard/reactions/%s - Reaction edit failed: exists"
) % rname
data['error'] = True
elif results == "edit true":
data[
'msg'] = "Reaction successfully edited: %s" % reaction2.name
print(
"/dashboard/reactions/%s - Reaction edit successful"
) % rname
data['error'] = False
elif results == "edit false":
data[
'msg'] = "Reaction not successfully edited: %s" % reaction2.name
print(
"/dashboard/reactions/%s - Reaction edit failed: unknown"
) % rname
data['error'] = True
elif results is False:
data['msg'] = "Could not create reaction"
print(
"/dashboard/reactions/%s - Reaction edit failed: unknown"
) % rname
data['error'] = True
else:
stathat.ez_count(
app.config['STATHAT_EZ_KEY'],
app.config['ENVNAME'] + ' Reaction Added', 1)
data[
'msg'] = 'Reaction "%s" successfully added' % reaction2.name
print("/dashboard/reactions/%s - Reaction edit success"
) % rname
data['error'] = False
else:
data['msg'] = "Form is not valid"
print(
"/dashboard/reactions/%s - Reaction edit failed: form invalid"
) % rname
data['error'] = True
form.process()
page = render_template(tmpl, data=data, form=form)
return page
else:
return redirect(url_for('user.login_page'))
def _populate(self):
"""Populate with reactions.
Arguments:
None
Returns:
None
Populates:
self
"""
# try to
try:
# read in the configurationn
yam = self._acquire(self.yam)
# unpack yam
species, reactions, bonds, forces = yam['species'], yam[
'reactions'], yam['bonds'], yam['repulsions']
# convert bonds to dictionary
species = {record['chemical']: record for record in species}
bonds = {record['bond']: record for record in bonds}
forces = {record['repulsion']: record for record in forces}
# update each species with its energy
for chemical, record in species.items():
# calculate attractions and repulsions, and update energy
attractions = sum(
[bonds[bond]['energy'] for bond in self._bind(chemical)])
repulsions = sum([
forces[force]['energy']
for force in self._repulse(chemical)
])
record.update({'energy': attractions + repulsions})
# for each reaction
for reaction in reactions:
# unpack reaction
electrophile, nucleophile = reaction['electrophile'], reaction[
'nucleophile']
reactant, product, leaver = reaction['reactant'], reaction[
'product'], reaction['leaver']
catalysis = reaction['catalysis']
# get bond energies of reactants
chemicals = (nucleophile, reactant)
reactants = sum([
bonds[bond]['energy'] for chemical in chemicals
for bond in self._bind(chemical)
])
reactants += sum([
forces[force]['energy'] for chemical in chemicals
for force in self._repulse(chemical)
])
# get bond energies of transition state
chemicals = (nucleophile, electrophile, leaver)
transition = sum([
bonds[bond]['energy'] for chemical in chemicals
for bond in self._bind(chemical)
])
transition += sum([
forces[force]['energy'] for chemical in chemicals
for force in self._repulse(chemical)
])
# get bond energies of products
chemicals = (product, leaver)
products = sum([
bonds[bond]['energy'] for chemical in chemicals
for bond in self._bind(chemical)
])
products += sum([
forces[force]['energy'] for chemical in chemicals
for force in self._repulse(chemical)
])
# calculate the forward and backward reection rates
forward = math.exp(-(catalysis + transition - reactants))
backward = math.exp(-(catalysis + transition - products))
# create reaction instance
energies = (reactants, transition + catalysis, products)
member = Reaction(reaction, forward, backward, energies)
self.append(member)
# add attributes
self.species = species
self.bonds = bonds
self.forces = forces
# add list of chemicals
chemicals = list(species.keys())
chemicals.sort()
self.chemicals = chemicals
# unless not found
except (KeyError, FileNotFoundError):
# print warning
self._print('no yams!, generating...')
# generate from text
text = self.yam.replace('yaml', 'txt')
self._generate(text)
return None
