def editTypeLot(dbtype, item_id):
"""Edit item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
editedItem = (session.query(eval(dbtype.capitalize()+'Lot'))
.filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != editedItem.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
maxablot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
maxtoxinlot = (session.query(CytotoxinLot)
.order_by(desc(CytotoxinLot.id)).first().id)
if request.method == 'POST':
# set date attribute of query object with request form data
try:
editedItem.date = (datetime.strptime(request.form['date'].replace('-', ' '), '%Y %m %d'))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
for column in table.columns:
if column.name in ('id', 'date', 'antibody_id',
'cytotoxin_id', 'adc_id', 'user_id'):
pass # don't modify item identifier
# set attribute of query object with request form data
else:
setattr(editedItem, column.name, request.form[column.name])
session.add(editedItem)
session.commit()
flash('%s Lot Edited' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('edit-type-lot.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
editedItem=editedItem, maxablot=maxablot,
maxtoxinlot=maxtoxinlot)
def getUserID(email):
"""Get user's id in the db using its e-mail address"""
try:
user = session.query(User).filter_by(email=email).one()
return user.id
except:
return None
def createTypeLot(dbtype, item_id):
"""Create new item within the category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
return redirect(url_for(dbtype))
# get property names from table, check maximum lot# from ab and cytotoxin
table = Table('%s_lot' % dbtype, meta, autoload=True, autoload_with=engine)
maxablot = (session.query(AntibodyLot)
.order_by(desc(AntibodyLot.id)).first().id)
maxtoxinlot = (session.query(CytotoxinLot)
.order_by(desc(CytotoxinLot.id)).first().id)
originID = (session.query(eval(dbtype.capitalize()))
.filter_by(id=item_id).one().user_id)
user_id = getUserID(login_session['email'])
if request.method == 'POST':
# instantiate new object
new = eval(dbtype.capitalize()+'Lot')()
for field in request.form:
# set date attribute of new object with request form data
if field == 'date':
try:
setattr(new, field, datetime.strptime(request.form[field].replace('-', ' '), '%Y %m %d'))
# in some cases users can input 6 digit year, catch this error
except ValueError as detail:
print 'Handling run-time error: ', detail
flash('Invalid date detected. Please type the date in '
'format: MM/DD/YYYY')
return redirect(url_for(dbtype))
# set attribute of new object with request form data
if hasattr(new, field):
setattr(new, field, request.form[field])
setattr(new, dbtype+'_id', item_id)
setattr(new, 'user_id', user_id)
session.add(new)
session.commit()
flash('%s Lot Created' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
return render_template('create-type-lot.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
maxablot=maxablot, maxtoxinlot=maxtoxinlot,
originID=originID,
userID=getUserID(login_session['email']))
def set_category(dbtype):
"""Provide category/item data to pass onto html templates"""
# define object and object lots
obj = eval(dbtype.capitalize())
items = eval(dbtype.capitalize()+'Lot')
# query the object items and object lots items
cat = session.query(obj).order_by(obj.name).all()
lots = session.query(items).all()
# create a dict to associate object id with its respective object lot items
lotdict = {}
for x in range(1, session.query(obj).count()+1):
lotdict[x] = (session.query(items)
.filter(getattr(items, dbtype+'_id') == x)
.order_by(items.date).all())
return (cat, lotdict, lots)
def createUser(name, email, picture):
user = User(name=name, email=email)
session.add(user)
session.commit()
newUserID = session.query(User).filter_by(email=email).one().id
if picture.startswith("https"):
attach_picture_url(User, newUserID, picture)
else:
attach_picture(User, newUserID, picture)
def antibodylot():
total = []
for x in range(1, 6):
lotlist = []
antibodies = session.query(AntibodyLot).filter(AntibodyLot.antibody_id == x).all()
for antibody in antibodies:
lotlist.append(antibody.id)
total.append(lotlist)
return total
def cytotoxinlot():
total = []
for x in range(1, 6):
lotlist = []
cytotoxins = session.query(CytotoxinLot).filter(CytotoxinLot.cytotoxin_id == x).all()
for cytotoxin in cytotoxins:
lotlist.append(cytotoxin.id)
total.append(lotlist)
return total
def createUser(login_session):
"""Create a new user in the db using user info in the login_session"""
newUser = User(name=login_session['username'], email=login_session[
'email'])
session.add(newUser)
session.commit()
user = session.query(User).filter_by(email=login_session['email']).one()
attach_picture_url(User, user.id, login_session['picture'])
return user.id
def get_picture_url(dbtype, item_id):
"""Redirect stored image url within the db to an organized url for
Antibody/Cytotoxin/Adc.html to access
"""
item = session.query(eval(dbtype.capitalize())).filter_by(id=item_id).one()
with store_context(fs_store):
try:
picture_url = item.picture.locate()
except IOError:
print "No picture found for lot# %s" % str(item_id)
picture_url = ''
return render_template('img.html', item=item,
picture_url=picture_url, dbtype=dbtype)
def editType(dbtype, item_id):
"""Edit the category (within 3 pre-defined type) in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to edit
editedItem = (session.query(eval(dbtype.capitalize()))
.filter_by(id=item_id).one())
# make sure user is authorized to edit this item
if login_session['user_id'] != editedItem.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
# get property names from table
table = Table(dbtype, meta, autoload=True, autoload_with=engine)
if request.method == 'POST':
for column in table.columns:
if column.name in ('id', 'user_id'):
pass # don't modify item id# and user_id#
else:
# set attribute of query object with request form data
setattr(editedItem, column.name, request.form[column.name])
session.add(editedItem)
session.commit()
flash('%s Edited' % dbtype.capitalize())
# upload image
image = request.files['picture']
if image and allowed_file(image.filename):
with store_context(fs_store):
editedItem.picture.from_file(image)
# prevent user uploading unsupported file type
elif image and not allowed_file(image.filename):
flash('Unsupported file detected. No image has been uploaded.')
return redirect(url_for(dbtype))
else:
return render_template('edit-type.html', dbtype=dbtype,
columns=table.columns, item_id=item_id,
editedItem=editedItem)
def attach_picture_url(table, item_id, location):
"""
A helper function used in populator.py to upload picture to the db from web
Args:
table: The category which the picture belongs to
item_id: The category's id number which the picture should be
uploaded to
location: a web url of where the picture is found
Returns:
None
"""
try:
item = session.query(table).filter_by(id=item_id).one()
with store_context(fs_store):
item.picture.from_file(urlopen(location))
session.commit()
except Exception:
session.rollback()
raise
def delete(dbtype, item_id):
"""Delete either the item or category in the database"""
# check login status
if 'email' not in login_session:
flash('Sorry, the page you tried to access is for members only. '
'Please sign in first.')
abort(401)
# query the item user wants to delete
deleteItem = (session.query(eval(dbtype[0].upper()+dbtype[1:]))
.filter_by(id=item_id).one())
# make sure user is authorized to delete this item
if login_session['user_id'] != deleteItem.user_id:
flash('You are not authorized to modify items you did not create. '
'Please create your own item in order to modify it.')
return redirect(url_for(dbtype))
if request.method == 'POST':
try:
session.delete(deleteItem)
session.commit()
# handling legacy error when delete invovled cascade-delete
except IntegrityError as detail:
print 'Handling run-time error: ', detail
session.rollback()
flash('Delete Operation Failed')
return redirect(url_for('home'))
if dbtype.endswith('Lot'):
flash('%s Lot Deleted' % dbtype[:-3].capitalize())
return redirect(url_for(dbtype[:-3]))
else:
flash('%s Deleted' % dbtype.capitalize())
return redirect(url_for(dbtype))
else:
pass
def antibodyJSON():
"""Create an JSON endpoint with all antibody categories"""
antibodies = session.query(Antibody).all()
return jsonify(Antibodies=[i.serialize for i in antibodies])
def getUserInfo(user_id):
"""Get user object in the db using its user_id"""
user = session.query(User).filter_by(id=user_id).one()
return user
def adcLotJSON():
"""Create an JSON endpoint with all items within the ADC categories"""
lots = session.query(AdcLot).all()
return jsonify(Adc_Lots=[i.serialize for i in lots])
def cytotoxinLotJSON():
"""Create an JSON endpoint with all items within the cytotoxin categories"""
lots = session.query(CytotoxinLot).all()
return jsonify(Cytotoxin_Lots=[i.serialize for i in lots])
def adcJSON():
"""Create an JSON endpoint with all ADC categories"""
adcs = session.query(Adc).all()
return jsonify(Adcs=[i.serialize for i in adcs])
def cytotoxinJSON():
"""Create an JSON endpoint with all cytotoxin categories"""
cytotoxins = session.query(Cytotoxin).all()
return jsonify(Cytotoxins=[i.serialize for i in cytotoxins])
def collectionLots(dbtype):
"""Create an XML endpoint with all items within the categories available"""
collections = session.query(eval(dbtype.capitalize()+'Lot')).all()
return render_template('collections-lot.xml', dbtype=dbtype,
collections=collections)
def collections(dbtype):
"""Create an XML endpoint with all categories"""
collections = session.query(eval(dbtype.capitalize())).all()
return render_template('collections.xml', dbtype=dbtype,
collections=collections)