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 HaploGroupPairwiseGeneticDist(Entity):
"""
2009-4-16
genetic distance between each haplogroup pair
"""
haplo_group1 = ManyToOne('HaploGroup',
colname='haplo_group_id1',
ondelete='CASCADE',
onupdate='CASCADE')
haplo_group2 = ManyToOne('HaploGroup',
colname='haplo_group_id2',
ondelete='CASCADE',
onupdate='CASCADE')
mismatch_rate = Field(Float)
no_of_mismatches = Field(Integer)
no_of_non_NA_pairs = Field(Integer)
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_pairwise_genetic_dist',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
using_table_options(UniqueConstraint('haplo_group_id1', 'haplo_group_id2'))
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 SNPsABAlleleMapping(Entity):
snp = ManyToOne('SNPs',
colname='snps_id',
ondelete='CASCADE',
onupdate='CASCADE')
allele_A_nt = Field(String(2))
allele_B_nt = Field(String(2))
tg_snps_name = Field(String(200))
NA_rate = Field(Float)
no_of_NAs = Field(Integer)
no_of_totals = Field(Integer)
relative_NA_rate = Field(Float)
relative_no_of_NAs = Field(Integer)
relative_no_of_totals = Field(Integer)
mismatch_rate = Field(Float)
no_of_mismatches = Field(Integer)
no_of_non_NA_pairs = Field(Integer)
readme = ManyToOne("README",
colname='readme_id',
ondelete='CASCADE',
onupdate='CASCADE')
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='snps_ab_allele_mapping',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Organism(Entity):
genus = Field(String(30))
species = Field(String(30))
using_options(tablename='organism',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class HistoricoSeminario(Entity):
using_options(tablename='historico_seminario')
item_id = Field(String(500))
objeto = Field(String(100))
url = Field(String(700))
user_id = Field(String(500))
texto = Field(String(500))
datetime = Field(DateTime, default=datetime.now)
class CadastroComite(Entity):
"""Cadastro de dados para participar do comite de transito"""
using_options(tablename='cadastro_comite')
nome = Field(String(500,convert_unicode=True))
email = Field(String(500,convert_unicode=True))
telefone = Field(String(500,convert_unicode=True))
cidade = Field(String(500,convert_unicode=True))
creation_date = Field(DateTime, default=datetime.now)
class Purpose(Entity):
using_options(tablename='purpose')
id = Field(Integer, primary_key=True)
email = Field(String(50), default='')
name = Field(String(225), default='')
description = Field(Text, default='')
user_id = Field(Integer, default=0)
class Extraction(Entity):
namelabel = Field(String(25))
datesubmitted = Field(DateTime, default=datetime.now)
notes = Field(String(255))
using_options(tablename='extraction',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
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 Site(Entity):
address = ManyToOne("Address",
colname='addressid',
ondelete='CASCADE',
onupdate='CASCADE')
name = Field(String(100))
description = Field(String(500))
using_options(tablename='site', metadata=__metadata__, session=__session__)
using_table_options(mysql_engine='InnoDB')
class Country(Entity):
name = Field(String(100))
abbr = Field(String(10))
capital = Field(Text)
latitude = Field(Float)
longitude = Field(Float)
using_options(tablename='country',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Team(Entity):
using_options(tablename='team')
id = Field(Integer, primary_key=True)
name = Field(String(255), default='')
password = Field(String(255), default='')
sign_up = Field(DateTime, default=datetime.datetime.now)
last_login = Field(DateTime, default=datetime.datetime.now)
last_modifed = Field(DateTime, default=datetime.datetime.now)
idea = ManyToOne('Idea')
class LinkColaborativo(Entity):
"""Links enviados pelos jornalistas no Seminário da Crise"""
using_options(tablename='link_colaborativo')
nome = Field(String(100))
email = Field(String(500))
link = Field(String(700))
site = Field(String(100))
clicks = Field(Integer)
imagem = Field(String(700))
datetime = Field(DateTime, default=datetime.now)
class Cross(Entity):
maternalid = Field(Integer)
paternalid = Field(Integer)
name = Field(String(40))
barcode = Field(String(25))
generation = Field(Integer)
using_options(tablename='crosses',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class SeqInfo(Entity):
platename = Field(String(40))
experiment = Field(String(40))
chip = Field(String(40))
experiment_type = Field(String(40))
ms_name = Field(String(40))
creation_date = Field(DateTime, default=datetime.now)
using_options(tablename='seqinfo',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Submitter(Entity):
first = Field(String(50))
last = Field(String(50))
organization = Field(String(50))
email = Field(String(50))
created = Field(DateTime, default=datetime.now)
modified = Field(DateTime)
using_options(tablename='submitter',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class SNPset(Entity):
name = Field(String(200), nullable=False, unique=True)
description = Field(String(4000))
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='snpset',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Delnode(Entity):
"""
2012.6.6
"""
tax_id = Field(Integer, unique=True) # -- taxonomy database division 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='delnode')
using_table_options(mysql_engine='InnoDB')
class README(Entity):
#2008-08-07
title = Field(String(2000))
description = Field(String(60000))
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='readme',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class SNPs(Entity):
organism = ManyToOne("Organism",
colname='organismid',
ondelete='CASCADE',
onupdate='CASCADE')
snpid = Field(String(20), unique=True)
dir = Field(String(1))
chromosome = Field(Integer)
position = Field(Integer)
refcall = Field(String(1))
using_options(tablename='snps', metadata=__metadata__, session=__session__)
using_table_options(mysql_engine='InnoDB')
class UserFollow(Entity):
"""Controle dos usuários que seguem as obras do monitoramento"""
using_options(tablename='user_follow')
# id = Field(Integer, primary_key=True)
user = ManyToOne('User')
obra_id = Field(Integer)
mode = Field(String(15,convert_unicode=True))
datetime = Field(DateTime, default=datetime.now)
facebook_id = Field(String(500,convert_unicode=True))
twitter_id = Field(String(500,convert_unicode=True))
email = Field(String(500,convert_unicode=True))
class Accession(Entity):
population_obj = ManyToOne('Population', colname='population')
region_obj = ManyToOne('Region', colname='region')
description = Field(Text)
name = Field(String(20))
origin = Field(String(50))
created = Field(DateTime, default=datetime.now)
modified = Field(DateTime)
number = Field(String(10))
using_options(tablename='accession',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Strain(Entity):
"""
2009-9-22
add 'replicate' into the unique constraint.
change type of replicate from boolean to integer
"""
ecotype = ManyToOne("Ecotype",
colname='ecotypeid',
ondelete='CASCADE',
onupdate='CASCADE')
extraction = ManyToOne("Extraction",
colname='extractionid',
ondelete='CASCADE',
onupdate='CASCADE')
seqinfo1 = ManyToOne("SeqInfo",
colname='seqinfoid1',
ondelete='CASCADE',
onupdate='CASCADE')
seqinfo2 = ManyToOne("SeqInfo",
colname='seqinfoid2',
ondelete='CASCADE',
onupdate='CASCADE')
seqinfo3 = ManyToOne("SeqInfo",
colname='seqinfoid3',
ondelete='CASCADE',
onupdate='CASCADE')
seqinfo4 = ManyToOne("SeqInfo",
colname='seqinfoid4',
ondelete='CASCADE',
onupdate='CASCADE')
plateid = Field(String(25))
wellid = Field(String(3))
replicate = Field(Integer)
contaminant_type = ManyToOne("%s.ContaminantType" % __name__,
colname='contaminant_type_id',
ondelete='CASCADE',
onupdate='CASCADE')
call_qc_ls = OneToMany("%s.CallQC" % __name__)
ecotypeid_strainid2tg_ecotypeid = OneToOne("EcotypeIDStrainID2TGEcotypeID",
inverse="strain")
created_by = Field(String(128))
updated_by = Field(String(128))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='strain',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
using_table_options(
UniqueConstraint('ecotypeid', 'plateid', 'wellid', 'replicate'))
class ContaminantType(Entity):
"""
2008-08-11
"""
short_name = Field(String(100), unique=True)
description = Field(Text)
created_by = Field(String(200))
updated_by = Field(String(200))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='contaminant_type',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
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 Division(Entity):
"""
2012.6.6
"""
id = Field(Integer, primary_key=True) # -- taxonomy database division id
code = Field(Text) # -- GenBank division code (three characters)
# e.g. BCT, PLN, VRT, MAM, PRI...
name = Field(Text)
comments = Field(Text)
created_by = Field(String(256))
updated_by = Field(String(256))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='division')
using_table_options(mysql_engine='InnoDB')
class Gencode(Entity):
"""
"""
id = Field(Integer, primary_key=True) # -- GenBank genetic code id
abbreviation = Field(Text) # -- genetic code name abbreviation
name = Field(Text) # -- genetic code name
code = Field(Text) #-- translation table for this genetic code
starts = Field(Text) # -- start codons for this genetic code
comment = Field(Text)
created_by = Field(String(256))
updated_by = Field(String(256))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='gencode')
using_table_options(mysql_engine='InnoDB')
class GeographicIntegrity(Entity):
"""
2009-3-31
a table storing different qualities of Geographic/GPS information associated with each ecotype
"""
short_name = Field(String(40), unique=True)
description = Field(String(8192))
created_by = Field(String(200))
updated_by = Field(String(200))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='geographic_integrity',
metadata=__metadata__,
session=__session__)
using_table_options(mysql_engine='InnoDB')
class Merged(Entity):
"""
2012.6.6
"""
old_tax_id = Field(Integer) #-- id of nodes which has been merged
new_tax = ManyToOne('%s.Node' % __name__,
colname='new_tax_id',
ondelete='CASCADE',
onupdate='CASCADE')
#-- id of nodes which is result of merging
created_by = Field(String(256))
updated_by = Field(String(256))
date_created = Field(DateTime, default=datetime.now)
date_updated = Field(DateTime)
using_options(tablename='merged')
using_table_options(mysql_engine='InnoDB')
