class Category(Entity):
using_options(tablename='category')
name = Field(Unicode, primary_key=True)
code_sous_cat = Field(Unicode)
path = Field(Unicode)
url = Field(Unicode)
videos = OneToMany('Video')
config = ManyToMany('Config', inverse='categories')
config_availables = ManyToMany('Config', inverse='categories_availables')
def __init__(self, name, dir_user, code_sous_cat, url, create_path=False):
self.name = unicode(name)
if dir_user:
self.path = os.path.join(unicode(dir_user), self.name)
self.code_sous_cat = unicode(code_sous_cat)
self.url = unicode(url)
self.videos = []
if create_path and not os.path.exists(self.path):
try:
os.makedirs(self.path)
except Exception, e:
print "%s ne peut être créé" % self.path
exit(2)
class Group(Entity):
group_id = Field(Integer, primary_key=True)
group_name = Field(Unicode(16), unique=True)
display_name = Field(Unicode(255))
created = Field(DateTime, default=datetime.now)
users = ManyToMany('User', inverse='groups')
permissions = ManyToMany('Permission', inverse='groups')
using_options(tablename='tg_group')
class nmap_host(Entity):
# host attributes
checked = Field(String)
os_match = Field(String)
os_accuracy = Field(String)
ip = Field(String)
ipv4 = Field(String)
ipv6 = Field(String)
macaddr = Field(String)
status = Field(String)
hostname = Field(String)
vendor = Field(String)
uptime = Field(String)
lastboot = Field(String)
distance = Field(String)
state = Field(String)
count = Field(String)
# host relationships
os = ManyToMany('nmap_os')
ports = ManyToMany('nmap_port')
def __init__(self,
os_match='',
os_accuracy='',
ip='',
ipv4='',
ipv6='',
macaddr='',
status='',
hostname='',
vendor='',
uptime='',
lastboot='',
distance='',
state='',
count=''):
self.checked = 'False'
self.os_match = os_match
self.os_accuracy = os_accuracy
self.ip = ip
self.ipv4 = ipv4
self.ipv6 = ipv6
self.macaddr = macaddr
self.status = status
self.hostname = hostname
self.vendor = vendor
self.uptime = uptime
self.lastboot = lastboot
self.distance = distance
self.state = state
self.count = count
class Config(Entity):
using_options(tablename='config')
dir_user = Field(Unicode)
player = Field(Unicode)
blacklist = ManyToMany('Download', inverse='blacklist')
categories_availables = ManyToMany('Category')
categories = ManyToMany('Category')
def __init__(self, dir_user, player):
self.dir_user = unicode(dir_user)
self.player = unicode(player)
self.categories_availables = []
self.categories = []
self.blacklist = []
class HaploGroup(Entity):
"""
2009-3-30
table to store the haplotype groups generated from Alex
"""
short_name = Field(String(40), unique=True)
ref_ecotype = ManyToOne(
"Ecotype",
colname='ref_ecotypeid',
ondelete='CASCADE',
onupdate='CASCADE') #the ecotype with the best reference genotype.
latitude = Field(Float)
longitude = Field(Float)
max_snp_typing_error_rate = Field(Float)
comment = Field(String(8192))
ecotypes = ManyToMany("Ecotype",
tablename='haplo_group2ecotype',
ondelete='CASCADE',
onupdate='CASCADE')
created_by = Field(String(200))
updated_by = Field(String(200))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='haplo_group',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
using_table_options(UniqueConstraint('short_name', 'ref_ecotypeid'))
class DataCard(Entity):
'''Card mapper'''
using_options(tablename='card')
title = Field(UnicodeText)
index = Field(Integer)
creation_date = Field(DateTime, default=datetime.datetime.utcnow)
column = ManyToOne('DataColumn')
# feature data to move to card extensions
members = ManyToMany('DataUser')
def update(self, other):
self.title = other.title
self.index = other.index
session.flush()
# Methods for data belonging to card extensions
def remove_member(self, datauser):
if datauser in self.members:
self.members.remove(datauser)
@property
def archived(self):
return self.column.archive
class DataLabel(Entity):
"""Label mapper
"""
using_options(tablename='label')
title = Field(Unicode(255))
color = Field(Unicode(255))
board = ManyToOne('DataBoard')
cards = ManyToMany('DataCard', tablename='label_cards__card_labels')
index = Field(Integer)
def copy(self):
new_data = DataLabel(title=self.title,
color=self.color,
index=self.index)
return new_data
def remove(self, card):
self.cards.remove(card)
def add(self, card):
self.cards.append(card)
@classmethod
def get_by_card(cls, card):
q = cls.query
q = q.filter(cls.cards.contains(card))
return q.order_by(cls.index)
class DataLabel(Entity):
"""Label mapper
"""
using_options(tablename='label')
title = Field(Unicode(255))
color = Field(Unicode(255))
board = ManyToOne('DataBoard')
cards = ManyToMany('DataCard', tablename='label_cards__card_labels')
index = Field(Integer)
def copy(self, parent):
new_data = DataLabel(title=self.title,
color=self.color,
index=self.index,
board=parent)
session.flush()
return new_data
@classmethod
def get_by_card(cls, card):
q = cls.query
q = q.filter(cls.cards.contains(card))
return q.all()
@classmethod
def add_to_card(cls, card, id):
label = cls.get(id)
if not card in label.cards:
label.cards.append(card)
@classmethod
def remove_from_card(cls, card, id):
label = cls.get(id)
if card in label.cards:
label.cards.remove(card)
class Download(Entity):
using_options(tablename='download')
url = Field(Unicode, primary_key=True)
category = ManyToOne('Category')
name = Field(Unicode)
path = Field(Unicode)
date = Field(Unicode)
description = Field(Unicode)
blacklist = ManyToMany('Config', inverse='blacklist')
def __init__(self, url, category, name, description, date=None):
self.url = unicode(url)
self.category = category
self.description = unicode(description)
self.name = unicode(name)
self.name = self.name.replace(' ', '_').replace('/', '-')
self.date = unicode(date)
self.path = unicode(os.path.join(self.category.path,
self.name + '.ts'))
def rm(self):
try:
print self.path
os.remove(self.path)
except:
print "cannot remove"
pass
class Citation(Entity):
"""
2012.6.6
"""
cit_id = Field(Integer) #- the unique id of citation
cit_key = Field(Text) # -- citation key
pubmed_id = Field(
Integer) # -- unique id in PubMed database (0 if not in PubMed)
medline_id = Field(
Integer) # -- unique id in MedLine database (0 if not in MedLine)
url = Field(Text) # -- URL associated with citation
text = Field(Text) #-- any text (usually article name and authors).
#-- The following characters are escaped in this text by a backslash:
#-- newline (appear as "\n"),
#-- tab character ("\t"),
#-- double quotes ('\"'),
#-- backslash character ("\\").
tax_list = ManyToMany("Node",
tablename='citation2node',
local_colname='citation_id')
# -- list of node ids separated by a single space
created_by = Field(String(256))
updated_by = Field(String(256))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='citation')
using_table_options(mysql_engine='InnoDB')
class Movie(Entity):
title = Field(Unicode(60))
description = Field(Unicode(512))
releasedate = Field(DateTime)
director = ManyToOne('Director', inverse='movies')
actors = ManyToMany('Actor', inverse='movies', tablename='movie_casting')
using_options(tablename='movies')
class Permission(Entity):
"""A relationship that determines what each Group can do"""
using_options(tablename="permission", auto_primarykey="permission_id")
permission_name = Field(Unicode(16), unique=True)
groups = ManyToMany("Group")
class sys_groups(Entity):
gid = Field(Integer, primary_key=True)
groupname = Field(String(30), required=True)
group_password = Field(String(64), required=True)
users = OneToMany('sys_users')
groupusers = ManyToMany('sys_users', tablename='sys_groupmembers')
using_options(tablename='sys_groups')
using_table_options(mysql_engine='InnoDB')
class Host(Entity):
using_options(tablename='hosts')
ip = Field(String)
hostnames = ManyToMany('Hostname')
def __init__(self, ip=None, hostnames=[]):
self.ip = ip
self.hostnames = hostnames
class Hostname(Entity):
using_options(tablename='hostnames')
hostname = Field(String)
hosts = ManyToMany('Host')
def __init__(self, hostname=None, hosts=[]):
self.hostname = hostname
self.hosts = hosts
class DataLabel(Entity):
"""Label mapper
"""
using_options(tablename='label')
title = Field(Unicode(255))
color = Field(Unicode(255))
board = ManyToOne('DataBoard')
cards = ManyToMany('DataCard')
index = Field(Integer)
class Ecotype(Entity):
"""
2009-3-30
add column haplo_groups.
"""
donor = ManyToOne("Person",
colname='donorid',
ondelete='CASCADE',
onupdate='CASCADE')
collector = ManyToOne("Person",
colname='collectorid',
ondelete='CASCADE',
onupdate='CASCADE')
site = ManyToOne("Site",
colname='siteid',
ondelete='CASCADE',
onupdate='CASCADE')
trip = ManyToOne("Trip",
colname='tripid',
ondelete='CASCADE',
onupdate='CASCADE')
organism = ManyToOne("Organism",
colname='organismid',
ondelete='CASCADE',
onupdate='CASCADE')
cross = ManyToOne("Cross",
colname='crossid',
ondelete='CASCADE',
onupdate='CASCADE')
name = Field(String(50))
alias = Field(String(50))
description = Field(String(270))
barcode = Field(String(14))
stockparent = Field(String(10))
nativename = Field(String(50))
collectiondate = Field(DateTime)
latitude = Field(Float)
longitude = Field(Float)
locationquality = Field(Integer)
elevation = Field(String(5))
dnastatus = Field(Integer)
bulkstatus = Field(Integer)
bulkdate = Field(DateTime)
labderived = Field(Boolean)
incompleteplex = Field(Integer)
haplo_groups = ManyToMany("HaploGroup",
tablename='haplo_group2ecotype',
ondelete='CASCADE',
onupdate='CASCADE')
geographic_integrity = ManyToOne("GeographicIntegrity",
colname='geographic_integrity_id',
ondelete='CASCADE',
onupdate='CASCADE')
using_options(tablename='ecotype',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Comentario(Entity):
data = Field(DateTime)
autor = Field(Unicode)
autor_url = Field(Unicode)
instituicao = Field(Unicode)
contribuicao = Field(Unicode)
justificativa = Field(Unicode)
opiniao = Field(Unicode)
proposta = Field(Unicode)
tags = ManyToMany(Tag, inverse='comentarios')
paragrafo = ManyToOne(Paragrafo)
class Group(Entity):
"""An ultra-simple group definition."""
using_options(tablename="group", auto_primarykey="group_id")
group_name = Field(Unicode(16), unique=True)
display_name = Field(Unicode(255))
created = Field(DateTime, default=datetime.now)
users = ManyToMany("User")
permissions = ManyToMany(
"Permission",
inverse="groups",
tablename="group_permission",
local_colname="group_id",
remote_colname="permission_id",
)
class Tag(Entity):
using_options(tablename='tags')
name = Field(Unicode(60), required=True)
movies = ManyToMany('Movie')
def __unicode__(self):
return self.name
class Admin(EntityAdmin):
form_size = (400,200)
list_display = ['name']
form_display = ['name', 'movies']
lines_per_row = 2
class nmap_port(Entity):
port_id = Field(String)
protocol = Field(String)
state = Field(String)
host = ManyToOne('nmap_host')
service = ManyToOne('nmap_service')
script = ManyToMany('nmap_script')
def __init__(self, port_id, protocol, state, host, service=''):
self.port_id = port_id
self.protocol = protocol
self.state = state
self.host = host
self.service = service
class Station(Entity):
name = Field(String(256))
url = Field(String(256))
bitrate = ManyToOne('Bitrate')
stream = ManyToOne('Stream')
genres = ManyToMany('Genre')
def __init__(self, **kwars):
for key, value in kwars.items():
setattr(self, key, value)
def __repr__(self):
return '<Station %s>' % (self.name)
class User(Entity):
user_id = Field(Integer, primary_key=True)
user_name = Field(Unicode(16), unique=True)
email_address = Field(Unicode(255), unique=True)
display_name = Field(Unicode(255))
password = Field(Unicode(40))
created = Field(DateTime, default=datetime.now)
groups = ManyToMany('Group', inverse='users')
using_options(tablename='tg_user')
@property
def permissions(self):
perms = set()
for g in self.groups:
perms = perms | set(g.permissions)
return perms
class Node(Entity):
"""
2012.6.6
taxonomy node and its parent node
"""
tax_id = Field(Integer, unique=True,
primary_key=True) #-- node id in GenBank taxonomy database
parent_tax_id = Field(
Integer) #2012.6.7 some parent taxonomy node might not exist at all.
#parent_tax = ManyToOne('%s.Node'%__name__, colname='parent_tax_id', ondelete='CASCADE', onupdate='CASCADE')
rank = Field(Text) #-- rank of this node (superkingdom, kingdom, ...)
embl_code = Field(Text) #-- locus-name prefix; not unique
division = ManyToOne('%s.Division' % __name__,
colname='division_id',
ondelete='CASCADE',
onupdate='CASCADE')
#see division.dmp file
inherited_div_flag = Field(
Integer) # (1 or 0) -- 1 if node inherits division from parent
genetic_code = ManyToOne('%s.Gencode' % __name__,
colname='genetic_code_id',
ondelete='CASCADE',
onupdate='CASCADE')
# -- see gencode.dmp file
inherited_GC_flag = Field(
Integer) #(1 or 0) -- 1 if node inherits genetic code from parent
mitochondrial_genetic_code = ManyToOne('%s.Gencode'%__name__, colname='mitochondrial_genetic_code_id', \
ondelete='CASCADE', onupdate='CASCADE')
# -- see gencode.dmp file
inherited_MGC_flag = Field(
Integer
) #(1 or 0) # -- 1 if node inherits mitochondrial gencode from parent
GenBank_hidden_flag = Field(
Integer
) # (1 or 0) -- 1 if name is suppressed in GenBank entry lineage
hidden_subtree_root_flag = Field(
Integer) #(1 or 0) -- 1 if this subtree has no sequence data yet
comments = Field(Text)
citation_list = ManyToMany("Citation",
tablename='citation2node',
local_colname='tax_id')
created_by = Field(String(256))
updated_by = Field(String(256))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='node')
using_table_options(mysql_engine='InnoDB')
class Contrib(Entity):
"""Mapper for the `contrib' entity
"""
using_options(shortnames=True)
title = Field(String(256))
content = Field(String(600))
original = Field(String(600), default='')
status = Field(Boolean, default=False)
enabled = Field(Boolean, default=True)
parent = Field(Integer, default=0)
moderation = Field(Boolean, default=False)
user = ManyToOne('User')
creation_date = Field(DateTime, default=datetime.now)
children = ManyToMany('Contrib')
theme = Field(Enum(
u'cuidado', u'familia', u'emergencia',
u'medicamentos', u'regional'
))
class CallMethod(Entity):
"""
2009-5-19
add ManyToMany relationship towards Accession
"""
short_name = Field(String(100), nullable=False, unique=True)
method_description = Field(String(8000))
data_description = Field(String(8000))
comment = Field(String(8000))
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
accession_ls = ManyToMany("Accession",
tablename='accession2call_method',
ondelete='CASCADE',
onupdate='CASCADE')
using_options(tablename='call_method',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Accession(Entity):
"""
2009-5-19
add ManyToMany relationship towards CallMethod
"""
name = Field(String(100), nullable=False, unique=True)
ecotype_id = Field(Integer)
duplicate = Field(Integer)
accession_2010_id = Field(Integer)
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
call_method_ls = ManyToMany("CallMethod",
tablename='accession2call_method',
ondelete='CASCADE',
onupdate='CASCADE')
using_options(tablename='accession',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class DataCard(Entity):
'''Card mapper'''
using_options(tablename='card')
title = Field(UnicodeText)
index = Field(Integer)
creation_date = Field(DateTime, default=datetime.datetime.utcnow)
column = ManyToOne('DataColumn')
# feature data to move to card extensions
members = ManyToMany('DataUser')
def copy(self, parent):
new_data = DataCard(title=self.title,
column=parent)
session.flush()
return new_data
# Methods for data belonging to card extensions
def make_cover(self, asset):
"""
"""
DataCard.get(self.id).cover = asset.data
def remove_cover(self):
"""
"""
DataCard.get(self.id).cover = None
def remove_member(self, datauser):
if datauser in self.members:
self.members.remove(datauser)
@property
def archived(self):
return self.column.archive
class User(Entity):
"""Reasonably basic User definition. Probably would want additional
attributes.
"""
using_options(tablename="tg_user", auto_primarykey="user_id")
user_name = Field(Unicode(16), required=True, unique=True)
email_address = Field(Unicode(255), required=True, unique=True)
display_name = Field(Unicode(255))
created = Field(DateTime, default=datetime.now)
_password = Field(Unicode(40), colname="password", required=True)
groups = ManyToMany(
"Group",
inverse="users",
tablename="tg_user_group",
local_colname="group_id",
remote_colname="user_id",
)
def _set_password(self, password):
"""encrypts password on the fly"""
self._password = self.__encrypt_password(password)
def _get_password(self):
"""returns password"""
return self._password
password = descriptor = property(_get_password, _set_password)
def __encrypt_password(self, password):
"""Hash the given password with SHA1."""
if isinstance(password, unicode):
password_8bit = password.encode('UTF-8')
else:
password_8bit = password
hashed_password = sha1()
hashed_password.update(password_8bit)
hashed_password = hashed_password.hexdigest()
# make sure the hased password is an UTF-8 object at the end of the
# process because SQLAlchemy _wants_ a unicode object for Unicode columns
if not isinstance(hashed_password, unicode):
hashed_password = hashed_password.decode('UTF-8')
return hashed_password
def validate_password(self, password):
"""Check the password against existing credentials.
this method _MUST_ return a boolean.
@param password: the password that was provided by the user to
try and authenticate. This is the clear text version that we will
need to match against the (possibly) encrypted one in the database.
@type password: unicode object
"""
return self.password == self.__encrypt_password(password)
class A(Entity):
cs = ManyToMany('..db1.c.C')
