def post_delete(id):
post = db_session.query(Post).get(id)
if post is None:
abort(404)
db_session.delete(post)
db_session.commit()
return redirect(url_for('index'))
def test_source_is_deleted_while_logged_in(self, logger):
"""If a source is deleted by a journalist when they are logged in,
a NoResultFound will occur. The source should be redirected to the
index when this happens, and a warning logged."""
with self.client as client:
codename = new_codename(client, session)
resp = client.post('login', data=dict(codename=codename),
follow_redirects=True)
# Now the journalist deletes the source
filesystem_id = crypto_util.hash_codename(codename)
crypto_util.delete_reply_keypair(filesystem_id)
source = Source.query.filter_by(filesystem_id=filesystem_id).one()
db_session.delete(source)
db_session.commit()
# Source attempts to continue to navigate
resp = client.post('/lookup', follow_redirects=True)
self.assertEqual(resp.status_code, 200)
self.assertIn('Submit documents for the first time', resp.data)
self.assertNotIn('logged_in', session.keys())
self.assertNotIn('codename', session.keys())
logger.assert_called_once_with(
"Found no Sources when one was expected: "
"No row was found for one()")
def delete_user(args):
"""Deletes a journalist or administrator from the application."""
username = _get_username_to_delete()
try:
selected_user = Journalist.query.filter_by(username=username).one()
except NoResultFound:
print('ERROR: That user was not found!')
return 0
# Confirm deletion if user is found
if not _get_delete_confirmation(selected_user.username):
return 0
# Try to delete user from the database
try:
db_session.delete(selected_user)
db_session.commit()
except Exception as e:
# If the user was deleted between the user selection and confirmation,
# (e.g., through the web app), we don't report any errors. If the user
# is still there, but there was a error deleting them from the
# database, we do report it.
try:
Journalist.query.filter_by(username=username).one()
except NoResultFound:
pass
else:
raise e
print('User "{}" successfully deleted'.format(username))
return 0
def categories_list():
#if errors detected
errors = []
#saved?
saved = False
if request.method == 'POST':
categories = []
saved = True
for field in request.form:
if field.startswith('title'):
not_needed, category_id = field.split('-')
categories.append(category_id)
for category_id in categories:
category = Category.query.get(int(category_id))
category.title = escape(request.form['title-' + category_id])
category.description = escape(request.form['description-' + category_id])
try:
db_session.add(category)
db_session.commit()
except exc.SQLAlchemyError:
db_session.rollback()
errors += ['Error saving category #{0}\n'.format(category.id)]
saved = False
if request.form['new-title']:
category = Category(escape(request.form['new-title']), escape(request.form['new-description']))
try:
db_session.add(category)
db_session.commit()
except exc.SQLAlchemyError:
db_session.rollback()
errors += ['Error with new category']
saved = False
category_to_delete = request.values.get('delete', False)
if category_to_delete:
category = Category.query.get(int(category_to_delete))
db_session.delete(category)
db_session.commit()
return redirect(url_for('categories_list'))
categories = Category.query.all()
prop = dict()
prop.update(default)
prop['categories'] = categories
prop['saved'] = saved
prop['errors'] = errors
return render_template('admin/categories_list.html', **prop)
def bulk_delete(sid, items_selected):
for item in items_selected:
item_path = store.path(sid, item.filename)
worker.enqueue(store.secure_unlink, item_path)
db_session.delete(item)
db_session.commit()
flash("Submission{} deleted.".format("s" if len(items_selected) > 1 else ""), "notification")
return redirect(url_for("col", sid=sid))
def delete_task(task_id, group_id):
print "taskid = " + task_id
print "group_id = " + group_id
query_result = db_session.query(models.Task).filter(models.Task.id==int(task_id)).first()
if query_result:
db_session.delete(query_result)
db_session.commit()
updated_query = db_session.query(models.Task).filter(models.Task.group_id==int(group_id)).order_by(models.Task.date).all()
return utils.list_to_json('tasks', updated_query)
return utils.error_json_message("invalid task id")
def delete_collection(source_id):
# Delete the source's collection of submissions
worker.enqueue(store.delete_source_directory, source_id)
# Delete the source's reply keypair
crypto_util.delete_reply_keypair(source_id)
# Delete their entry in the db
source = get_source(source_id)
db_session.delete(source)
db_session.commit()
def bulk_delete(filesystem_id, items_selected):
for item in items_selected:
item_path = store.path(filesystem_id, item.filename)
worker.enqueue(srm, item_path)
db_session.delete(item)
db_session.commit()
flash(ngettext("Submission deleted.",
"{num} submissions deleted.".format(
num=len(items_selected)),
len(items_selected)), "notification")
return redirect(url_for('col.col', filesystem_id=filesystem_id))
def delete_collection(filesystem_id):
# Delete the source's collection of submissions
job = worker.enqueue(srm, store.path(filesystem_id))
# Delete the source's reply keypair
crypto_util.delete_reply_keypair(filesystem_id)
# Delete their entry in the db
source = get_source(filesystem_id)
db_session.delete(source)
db_session.commit()
return job
def del_entry(view,id):
if view=='books':
entry = db_session.query(Book).filter(Book.id==id).first()
else:
entry = db_session.query(Author).filter(Author.id==id).first()
if entry:
db_session.delete(entry)
db_session.commit()
flash('%s successfuly removed from database' % entry.name)
else:
flash('No entry with id = %d' % id)
return redirect(url_for('admin_show_entries',pagin = app.config['PAGIN'], page=1, view=view))
def delete_user(user_id):
user = Journalist.query.get(user_id)
if user:
db_session.delete(user)
db_session.commit()
flash(gettext("Deleted user '{user}'").format(
user=user.username), "notification")
else:
current_app.logger.error(
"Admin {} tried to delete nonexistent user with pk={}".format(
g.user.username, user_id))
abort(404)
return redirect(url_for('admin.index'))
def clients_list():
clients = Client.query.all()
client_to_delete = request.values.get('delete', False)
if client_to_delete:
client = Client.query.get(int(client_to_delete))
db_session.delete(client)
db_session.commit()
return redirect(url_for('clients_list'))
prop = dict()
prop.update(default)
prop['clients'] = clients
return render_template('admin/clients_list.html', **prop)
def projects_list():
""" Projects list
"""
project_to_delete = request.values.get('delete', False)
if project_to_delete:
project = Project.query.get(int(project_to_delete))
db_session.delete(project)
db_session.commit()
return redirect(url_for('projects_list'))
projects = Project.query.all()
prop = dict()
prop.update(default)
prop['projects'] = projects
return render_template('admin/projects_list.html', **prop)
def mutate(self, info, orgCode):
import utils
if utils.isAllowAccess():
result = OrgDelete()
from db_models.orgSelection import isOrgByOrgCodeExist, selectOrgByOrgCode
if isOrgByOrgCodeExist(orgCode):
toDeleteOrg = selectOrgByOrgCode(orgCode)
db_session.delete(toDeleteOrg)
db_session.commit()
result.status = True
result.msg = "Delete organziation by orgCode '{}' success.".format(
orgCode)
else:
result.msg = "Org by this orgCode '{}' is not exist.".format(
orgCode)
return result
def mutate(self, info, peopleCode):
import utils
if utils.isAllowAccess():
msg = ''
status = False
from mutation_people import isPeopleByPCodeExist, selectPeopleByPCode
if isPeopleByPCodeExist(peopleCode, info):
delettingPeople = selectPeopleByPCode(peopleCode, info)
db_session.delete(delettingPeople)
db_session.commit()
status = True
msg = 'delete pCode\'s {} success.'.format(peopleCode)
else:
msg = 'This pCode\'s {} is not exist'.format(peopleCode)
return DeletePeople(peopleCode=peopleCode, msg=msg, status=status)
def get(self, qty):
# Firstly, delete old entries
while EntryModel.query.first():
entry = EntryModel.query.first()
db_session.delete(entry)
db_session.commit()
# Create some new entries for every method call
for idx in range(qty):
header = get_header(idx)
publisher = get_publisher(idx)
content = get_content(idx)
link = get_link(idx)
n_days_ago = get_num_days_ago(idx)
img = get_base64_img(idx)
entry = EntryModel(header, publisher, content, link, n_days_ago,
img)
db_session.add(entry)
db_session.commit()
return EntryModel.query.limit(qty).all()
def delete_user(): # pragma: no cover
"""Deletes a journalist or administrator from the application."""
# Select user to delete
username = raw_input('Username to delete: ')
try:
selected_user = Journalist.query.filter_by(username=username).one()
except NoResultFound:
print('ERROR: That user was not found!')
return 0
# Confirm deletion if user is found
confirmation = raw_input('Are you sure you want to delete user '
'{} (y/n)?'.format(selected_user))
if confirmation.lower() != 'y':
print('Confirmation not received: user "{}" was NOT '
'deleted'.format(username))
return 0
# Try to delete user from the database
try:
db_session.delete(selected_user)
db_session.commit()
except:
# If the user was deleted between the user selection and confirmation,
# (e.g., through the web app), we don't report any errors. If the user
# is still there, but there was a error deleting them from the
# database, we do report it.
try:
selected_user = Journalist.query.filter_by(username=username).one()
except NoResultFound:
pass
else:
raise
print('User "{}" successfully deleted'.format(username))
return 0
def delete(id):
item = Items.query.filter(Items.id == id).one()
db_session.delete(item)
db_session.commit()
return redirect(url_for('index'))
def delete(self, order_id):
order = OrderModel.query.filter_by(id=order_id).first()
db_session.delete(order)
db_session.commit()
return '', 204
def delete(id):
categories = Categories.query.filter(Categories.id == id).one()
db_session.delete(categories)
db_session.commit()
return redirect(url_for('category.new'))
def admin_delete_user(user_id):
user = Journalist.query.get(user_id)
db_session.delete(user)
db_session.commit()
return redirect(url_for('admin_index'))
def admin_delete_user(user_id):
user = Journalist.query.get(user_id)
db_session.delete(user)
db_session.commit()
return redirect(url_for("admin_index"))
from db import db_session from models import User user = User.query.first() db_session.delete(user) db_session.commit()
def crawl(pubmed_id_f, cutoff, start_at=0, overwrite=False):
# collect papers to parse
pubmed_ids = list()
with open(pubmed_id_f) as f:
pubmed_ids = [int(line.strip()) for line in f]
# download GWC data for each paper
for pmid in pubmed_ids:
if pmid < start_at: continue
# overwrite previous associations:
if overwrite:
assocs = db_session.query(Association).join(Association.paper).filter(Paper.pubmed_id==pmid).filter(Association.source=='gwas_central').all()
if assocs:
for a in assocs: db_session.delete(a)
db_session.commit()
# create/load paper
paper = db_session.query(Paper).filter(Paper.pubmed_id==pmid).first()
if not paper:
paper = Paper(pubmed_id=pmid)
db_session.add(paper)
db_session.commit()
# get study identifier
gwcid = pmid2gwcid(pmid)
if not gwcid: continue
# get list of results
try:
results = gwcid2results(gwcid)
except ValueError:
print 'ERROR!'
continue
phenotypes = dict()
snps = dict()
for result in results:
rsid, resultset_id, resultset_link, pvalue, neglog_pvalue = result
if neglog_pvalue < cutoff: continue
# if phenotype is not known, retrieve it
if resultset_id not in phenotypes:
phenotype_name = res2phen(resultset_id, resultset_link)
phenotype = Phenotype(name=phenotype_name, source='gwas_central')
phenotypes[resultset_id] = phenotype
db_session.add(phenotype)
db_session.commit()
else:
phenotype = phenotypes[resultset_id]
# create snp
if rsid not in snps:
snp = db_session.query(SNP).filter(SNP.rs_id==rsid).first()
if not snp:
snp = SNP(rs_id=rsid)
db_session.add(snp)
db_session.commit()
else:
snp = snps[rsid]
# create association
db_session.add(Association(
snp=snp,
phenotype=phenotype,
paper=paper,
pvalue=pvalue,
source='gwas_central'
))
print 'Extracted association:', paper.pubmed_id, phenotype.name, snp.rs_id, pvalue
db_session.commit()
