def create( self, trans, visualization_title="", visualization_slug="", visualization_annotation="", visualization_dbkey="",
visualization_type="" ):
"""
Creates a new visualization or returns a form for creating visualization.
"""
visualization_title_err = visualization_slug_err = visualization_annotation_err = ""
if trans.request.method == "POST":
rval = self.create_visualization( trans, title=visualization_title,
slug=visualization_slug,
annotation=visualization_annotation,
dbkey=visualization_dbkey,
type=visualization_type )
if isinstance( rval, dict ):
# Found error creating viz.
visualization_title_err = rval[ 'title_err' ]
visualization_slug_err = rval[ 'slug_err' ]
else:
# Successfully created viz.
return trans.response.send_redirect( web.url_for(controller='visualization', action='list' ) )
viz_type_options = [ ( t, t ) for t in self.viz_types ]
return trans.show_form(
web.FormBuilder( web.url_for(controller='visualization', action='create'), "Create new visualization", submit_text="Submit" )
.add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err )
.add_select( "visualization_type", "Type", options=viz_type_options, error=None )
.add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err,
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_select( "visualization_dbkey", "Visualization DbKey/Build", value=visualization_dbkey, options=trans.app.genomes.get_dbkeys( trans, chrom_info=True ), error=None)
.add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err,
help="A description of the visualization; annotation is shown alongside published visualizations."),
template="visualization/create.mako" )
def reset_password(self, trans, email=None, **kwd):
error = ''
reset_user = trans.app.model.User.get_by(email=email)
user = trans.get_user()
if reset_user:
if user and user.id != reset_user.id:
error = "You may only reset your own password"
else:
chars = string.letters + string.digits
new_pass = ""
for i in range(15):
new_pass = new_pass + choice(chars)
mail = os.popen("%s -t" % self.app.config.sendmail_path, 'w')
mail.write(
"To: %s\nFrom: no-reply@%s\nSubject: Galaxy Password Reset\n\nYour password has been reset to \"%s\" (no quotes)."
% (email, trans.request.remote_addr, new_pass))
if mail.close():
return trans.show_ok_message(
"Failed to reset password! If this problem persist, submit a bug report."
)
reset_user.set_password_cleartext(new_pass)
reset_user.flush()
trans.log_event("User reset password: %s" % email)
return trans.show_ok_message(
"Password has been reset and emailed to: %s." % email)
elif email != None:
error = "The specified user does not exist"
return trans.show_form(
web.FormBuilder("/user/reset_password",
"Reset Password",
submit_text="Submit").add_text("email",
"Email",
value=email,
error=error))
def create(self,
trans,
email='',
password='',
confirm='',
subscribe=False):
email_error = password_error = confirm_error = None
if email:
if len(email) == 0 or "@" not in email or "." not in email:
email_error = "Please enter a real email address"
elif len(email) > 255:
email_error = "Email address exceeds maximum allowable length"
elif len(trans.app.model.User.select_by(email=email)) > 0:
email_error = "User with that email already exists"
elif len(password) < 6:
password_error = "Please use a password of at least 6 characters"
elif password != confirm:
confirm_error = "Passwords do not match"
else:
user = trans.app.model.User(email=email)
user.set_password_cleartext(password)
user.flush()
trans.set_user(user)
trans.log_event("User new")
trans.log_event("User logged in")
#subscribe user to email list
if subscribe:
mail = os.popen("%s -t" % self.app.config.sendmail_path,
'w')
mail.write(
"To: %s\nFrom: %s\nSubject: Join Mailing List\n\nJoin Mailing list."
% (self.app.config.mailing_join_addr, email))
if mail.close():
return trans.show_warn_message(
"Now logged in as " + user.email +
". However, subscribing to the mailing list has failed.",
refresh_frames=['masthead', 'history'])
return trans.show_ok_message(
"Now logged in as " + user.email,
refresh_frames=['masthead', 'history'])
return trans.show_form(
web.FormBuilder("/user/create",
"Create account",
submit_text="Create").add_text(
"email",
"Email address",
value=email,
error=email_error).add_password(
"password",
"Password",
value='',
error=password_error).add_password(
"confirm",
"Confirm password",
value='',
error=confirm_error).add_input(
"checkbox",
"Subscribe To Mailing List",
"subscribe",
value='subscribe'))
def login(self, trans, email='', password=''):
email_error = password_error = None
# Attempt login
if email or password:
user = trans.app.model.User.get_by(email=email)
if not user:
email_error = "No such user"
elif not user.check_password(password):
password_error = "Invalid password"
else:
trans.set_user(user)
trans.log_event("User logged in")
return trans.show_ok_message( "Now logged in as " + user.email, \
refresh_frames=['masthead', 'history'] )
return trans.show_form(
web.FormBuilder("/user/login", "Login",
submit_text="Login").add_text("email",
"Email address",
value=email,
error=email_error).
add_password(
"password",
"Password",
value='',
error=password_error,
help=
"<a href=\"/user/reset_password\">Forgot password? Reset here</a>"
))
def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ):
"""
Edit a page's attributes.
"""
encoded_id = id
id = trans.security.decode_id( id )
session = trans.sa_session
page = session.query( model.Page ).get( id )
user = trans.user
assert page.user == user
page_title_err = page_slug_err = page_annotation_err = ""
if trans.request.method == "POST":
if not page_title:
page_title_err = "Page name is required"
elif not page_slug:
page_slug_err = "Page id is required"
elif not self._is_valid_slug( page_slug ):
page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
elif page_slug != page.slug and trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first():
page_slug_err = "Page id must be unique"
elif not page_annotation:
page_annotation_err = "Page annotation is required"
else:
page.title = page_title
page.slug = page_slug
page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' )
self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
session.flush()
# Redirect to page list.
return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
else:
page_title = page.title
page_slug = page.slug
page_annotation = self.get_item_annotation_str( trans.sa_session, trans.user, page )
if not page_annotation:
page_annotation = ""
return trans.show_form(
web.FormBuilder( web.url_for(controller='page', action='edit', id=encoded_id ), "Edit page attributes", submit_text="Submit" )
.add_text( "page_title", "Page title", value=page_title, error=page_title_err )
.add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako" )
def create( self, trans, page_title="", page_slug="", page_annotation="" ):
"""
Create a new page
"""
user = trans.get_user()
page_title_err = page_slug_err = page_annotation_err = ""
if trans.request.method == "POST":
if not page_title:
page_title_err = "Page name is required"
elif not page_slug:
page_slug_err = "Page id is required"
elif not self._is_valid_slug( page_slug ):
page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first():
page_slug_err = "Page id must be unique"
else:
# Create the new stored page
page = model.Page()
page.title = page_title
page.slug = page_slug
page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' )
self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
page.user = user
# And the first (empty) page revision
page_revision = model.PageRevision()
page_revision.title = page_title
page_revision.page = page
page.latest_revision = page_revision
page_revision.content = ""
# Persist
session = trans.sa_session
session.add( page )
session.flush()
# Display the management page
## trans.set_message( "Page '%s' created" % page.title )
return trans.response.send_redirect( web.url_for(controller='page', action='list' ) )
return trans.show_form(
web.FormBuilder( web.url_for(controller='page', action='create'), "Create new page", submit_text="Submit" )
.add_text( "page_title", "Page title", value=page_title, error=page_title_err )
.add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
help="""A unique identifier that will be used for
public links to this page. A default is generated
from the page title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of the page; annotation is shown alongside published pages."),
template="page/create.mako" )
def edit( self, trans, id, visualization_title="", visualization_slug="", visualization_annotation="" ):
"""
Edit a visualization's attributes.
"""
visualization = self.get_visualization( trans, id, check_ownership=True )
session = trans.sa_session
visualization_title_err = visualization_slug_err = visualization_annotation_err = ""
if trans.request.method == "POST":
if not visualization_title:
visualization_title_err = "Visualization name is required"
elif not visualization_slug:
visualization_slug_err = "Visualization id is required"
elif not self._is_valid_slug( visualization_slug ):
visualization_slug_err = "Visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
elif visualization_slug != visualization.slug and trans.sa_session.query( model.Visualization ).filter_by( user=visualization.user, slug=visualization_slug, deleted=False ).first():
visualization_slug_err = "Visualization id must be unique"
else:
visualization.title = visualization_title
visualization.slug = visualization_slug
if visualization_annotation != "":
visualization_annotation = sanitize_html( visualization_annotation, 'utf-8', 'text/html' )
self.add_item_annotation( trans.sa_session, trans.get_user(), visualization, visualization_annotation )
session.flush()
# Redirect to visualization list.
return trans.response.send_redirect( web.url_for(controller='visualization', action='list' ) )
else:
visualization_title = visualization.title
# Create slug if it's not already set.
if visualization.slug is None:
self.create_item_slug( trans.sa_session, visualization )
visualization_slug = visualization.slug
visualization_annotation = self.get_item_annotation_str( trans.sa_session, trans.user, visualization )
if not visualization_annotation:
visualization_annotation = ""
return trans.show_form(
web.FormBuilder( web.url_for(controller='visualization', action='edit', id=id ), "Edit visualization attributes", submit_text="Submit" )
.add_text( "visualization_title", "Visualization title", value=visualization_title, error=visualization_title_err )
.add_text( "visualization_slug", "Visualization identifier", value=visualization_slug, error=visualization_slug_err,
help="""A unique identifier that will be used for
public links to this visualization. A default is generated
from the visualization title, but can be edited. This field
must contain only lowercase letters, numbers, and
the '-' character.""" )
.add_text( "visualization_annotation", "Visualization annotation", value=visualization_annotation, error=visualization_annotation_err,
help="A description of the visualization; annotation is shown alongside published visualizations."),
template="visualization/create.mako" )
def get_config_form(self):
type_hints = odict.odict()
type_hints["list"] = "List of Datasets"
type_hints["paired"] = "Dataset Pair"
type_hints["list:paired"] = "List of Dataset Pairs"
type_input = web.framework.DatalistInput(
name="collection_type",
label="Collection Type",
value=self.state["collection_type"],
extra_attributes=dict(refresh_on_change='true'),
options=type_hints)
form = web.FormBuilder(title=self.name).add_text(
"name", "Name", value=self.state['name'])
form.inputs.append(type_input)
return self.trans.fill_template("workflow/editor_generic_form.mako",
module=self,
form=form)
def change_password(self,
trans,
old_pass='',
new_pass='',
conf_pass='',
**kwd):
old_pass_err = new_pass_err = conf_pass_err = ''
user = trans.get_user()
if not user:
trans.response.send_redirect("/user/login")
if not user.check_password(old_pass):
old_pass_err = "Invalid password"
elif len(new_pass) < 6:
new_pass_err = "Please use a password of at least 6 characters"
elif new_pass != conf_pass:
conf_pass_err = "New passwords do not match."
else:
user.set_password_cleartext(new_pass)
user.flush()
trans.log_event("User change password")
return trans.show_ok_message("Password has been changed for " +
user.email)
return trans.show_form(
web.FormBuilder("/user/change_password",
"Change Password",
submit_text="Submit").add_password(
"old_pass",
"Old Password",
value='',
error=old_pass_err).add_password(
"new_pass",
"New Password",
value='',
error=new_pass_err).add_password(
"conf_pass",
"Confirm Password",
value='',
error=conf_pass_err))
def change_email(self, trans, email='', conf_email='', password='', **kwd):
email_err = conf_email_err = pass_err = ''
user = trans.get_user()
if not user:
trans.response.send_redirect("/user/login")
if not user.check_password(password):
pass_err = "Invalid password"
elif len(email) == 0 or "@" not in email or "." not in email:
email_err = "Please enter a real email address"
elif len(email) > 255:
email_err = "Email address exceeds maximum allowable length"
elif len(trans.app.model.User.select_by(email=email)) > 0:
email_err = "User with that email already exists"
elif email != conf_email:
conf_email_err = "Email addresses do not match."
else:
user.email = email
user.flush()
trans.log_event("User change email")
return trans.show_ok_message(
"Email has been changed to: " + user.email,
refresh_frames=['masthead', 'history'])
return trans.show_form(
web.FormBuilder("/user/change_email",
"Change Email",
submit_text="Submit").add_text(
"email", "Email", value=email,
error=email_err).add_text(
"conf_email",
"Confirm Email",
value='',
error=conf_email_err).add_password(
"password",
"Password",
value='',
error=pass_err))
def get_config_form( self ):
form = web.FormBuilder( title=self.name ) \
.add_text( "name", "Name", value=self.state['name'] )
return self.trans.fill_template( "workflow/editor_generic_form.mako",
module=self, form=form )
