import requests
import simplejson as json
from wqflask import app
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from utility import hmac
from utility.authentication_tools import check_resource_availability
from utility.tools import GN2_BASE_URL
from utility.redis_tools import get_redis_conn, get_resource_id
from utility.db_tools import escape
from flask import g, request, url_for
from utility.logger import getLogger
logger = getLogger(__name__)
Redis = get_redis_conn()
def create_trait(**kw):
assert bool(kw.get('dataset')) != bool(
kw.get('dataset_name')), "Needs dataset ob. or name"
if kw.get('name'):
if kw.get('dataset_name'):
if kw.get('dataset_name') != "Temp":
dataset = create_dataset(kw.get('dataset_name'))
else:
dataset = kw.get('dataset')
if kw.get('dataset_name') != "Temp":
if dataset.type == 'Publish':
permissions = check_resource_availability(
dataset, kw.get('name'))
else:
permissions = check_resource_availability(dataset)
if "view" in permissions['data']:
the_trait = GeneralTrait(**kw)
if the_trait.dataset.type != "Temp":
the_trait = retrieve_trait_info(
the_trait,
the_trait.dataset,
get_qtl_info=kw.get('get_qtl_info'))
return the_trait
else:
return None
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
"""
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
assert bool(kw.get('dataset')) != bool(
kw.get('dataset_name')), "Needs dataset ob. or name"
# Trait ID, ProbeSet ID, Published ID, etc.
self.name = kw.get('name')
if kw.get('dataset_name'):
if kw.get('dataset_name') == "Temp":
temp_group = self.name.split("_")[2]
self.dataset = create_dataset(
dataset_name="Temp",
dataset_type="Temp",
group_name=temp_group)
else:
self.dataset = create_dataset(kw.get('dataset_name'))
else:
self.dataset = kw.get('dataset')
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
# Blat sequence, available for ProbeSet
self.sequence = kw.get('sequence')
self.data = kw.get('data', {})
self.view = True
# Sets defaults
self.locus = None
self.lrs = None
self.pvalue = None
self.mean = None
self.additive = None
self.num_overlap = None
self.strand_probe = None
self.symbol = None
self.display_name = self.name
self.LRS_score_repr = "N/A"
self.LRS_location_repr = "N/A"
if kw.get('fullname'):
name2 = value.split("::")
if len(name2) == 2:
self.dataset, self.name = name2
# self.cellid is set to None above
elif len(name2) == 3:
self.dataset, self.name, self.cellid = name2
# Todo: These two lines are necessary most of the time, but
# perhaps not all of the time So we could add a simple if
# statement to short-circuit this if necessary
if get_sample_info is not False:
self = retrieve_sample_data(self, self.dataset)
def export_informative(self, include_variance=0):
"""
export informative sample
mostly used in qtl regression
"""
samples = []
vals = []
the_vars = []
sample_aliases = []
for sample_name, sample_data in list(self.data.items()):
if sample_data.value is not None:
if not include_variance or sample_data.variance is not None:
samples.append(sample_name)
vals.append(sample_data.value)
the_vars.append(sample_data.variance)
sample_aliases.append(sample_data.name2)
return samples, vals, the_vars, sample_aliases
@property
def description_fmt(self):
"""Return a text formated description"""
if self.dataset.type == 'ProbeSet':
if self.description:
formatted = self.description
if self.probe_target_description:
formatted += "; " + self.probe_target_description
else:
formatted = "Not available"
elif self.dataset.type == 'Publish':
if self.confidential:
formatted = self.pre_publication_description
else:
formatted = self.post_publication_description
else:
formatted = "Not available"
if isinstance(formatted, bytes):
formatted = formatted.decode("utf-8")
return formatted
@property
def alias_fmt(self):
"""Return a text formatted alias"""
alias = 'Not available'
if getattr(self, "alias", None):
alias = self.alias.replace(";", " ")
alias = ", ".join(alias.split())
return alias
@property
def wikidata_alias_fmt(self):
"""Return a text formatted alias"""
alias = 'Not available'
if self.symbol:
human_response = requests.get(
GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
mouse_response = requests.get(
GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
other_response = requests.get(
GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
if human_response and mouse_response and other_response:
alias_list = json.loads(human_response.content) + json.loads(
mouse_response.content) + \
json.loads(other_response.content)
filtered_aliases = []
seen = set()
for item in alias_list:
if item in seen:
continue
else:
filtered_aliases.append(item)
seen.add(item)
alias = "; ".join(filtered_aliases)
return alias
@property
def location_fmt(self):
"""Return a text formatted location
While we're at it we set self.location in case we need it
later (do we?)
"""
if self.chr and self.mb:
self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
elif self.chr:
self.location = 'Chr %s @ Unknown position' % (self.chr)
else:
self.location = 'Not available'
fmt = self.location
# XZ: deal with direction
if self.strand_probe == '+':
fmt += (' on the plus strand ')
elif self.strand_probe == '-':
fmt += (' on the minus strand ')
return fmt
def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist is None:
samplelist = []
if dataset.type == "Temp":
results = Redis.get(trait.name).split()
else:
results = dataset.retrieve_sample_data(trait.name)
# Todo: is this necessary? If not remove
trait.data.clear()
if results:
if dataset.type == "Temp":
all_samples_ordered = dataset.group.all_samples_ordered()
for i, item in enumerate(results):
try:
trait.data[all_samples_ordered[i]] = webqtlCaseData(
all_samples_ordered[i], float(item))
except:
pass
else:
for item in results:
name, value, variance, num_cases, name2 = item
if not samplelist or (samplelist and name in samplelist):
# name, value, variance, num_cases)
trait.data[name] = webqtlCaseData(*item)
return trait
@app.route("/trait/get_sample_data")
def get_sample_data():
params = request.args
trait = params['trait']
dataset = params['dataset']
trait_ob = create_trait(name=trait, dataset_name=dataset)
if trait_ob:
trait_dict = {}
trait_dict['name'] = trait
trait_dict['db'] = dataset
trait_dict['type'] = trait_ob.dataset.type
trait_dict['group'] = trait_ob.dataset.group.name
trait_dict['tissue'] = trait_ob.dataset.tissue
trait_dict['species'] = trait_ob.dataset.group.species
trait_dict['url'] = url_for(
'show_trait_page', trait_id=trait, dataset=dataset)
trait_dict['description'] = trait_ob.description_display
if trait_ob.dataset.type == "ProbeSet":
trait_dict['symbol'] = trait_ob.symbol
trait_dict['location'] = trait_ob.location_repr
elif trait_ob.dataset.type == "Publish":
if trait_ob.pubmed_id:
trait_dict['pubmed_link'] = trait_ob.pubmed_link
trait_dict['pubmed_text'] = trait_ob.pubmed_text
return json.dumps([trait_dict, {key: value.value for
key, value in list(
trait_ob.data.items())}])
else:
return None
def jsonable(trait):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
dataset = create_dataset(dataset_name=trait.dataset.name,
dataset_type=trait.dataset.type,
group_name=trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
symbol=trait.symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
mean=trait.mean,
location=trait.location_repr,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
elif dataset.type == "Publish":
if trait.pubmed_id:
return dict(name=trait.name,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
else:
return dict(name=trait.name,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
elif dataset.type == "Geno":
return dict(name=trait.name,
dataset=dataset.name,
dataset_name=dataset.shortname,
location=trait.location_repr
)
else:
return dict()
def jsonable_table_row(trait, dataset_name, index):
"""Return a list suitable for json and intended to be displayed in a table
Actual turning into json doesn't happen here though"""
dataset = create_dataset(dataset_name)
if dataset.type == "ProbeSet":
if trait.mean == "":
mean = "N/A"
else:
mean = "%.3f" % round(float(trait.mean), 2)
if trait.additive == "":
additive = "N/A"
else:
additive = "%.3f" % round(float(trait.additive), 2)
return ['',
index,
''+str(trait.name)+'',
trait.symbol,
trait.description_display,
trait.location_repr,
mean,
trait.LRS_score_repr,
trait.LRS_location_repr,
additive]
elif dataset.type == "Publish":
if trait.additive == "":
additive = "N/A"
else:
additive = "%.2f" % round(float(trait.additive), 2)
if trait.pubmed_id:
return ['',
index,
''+str(trait.name)+'',
trait.description_display,
trait.authors,
'' + trait.pubmed_text + '',
trait.LRS_score_repr,
trait.LRS_location_repr,
additive]
else:
return ['',
index,
''+str(trait.name)+'',
trait.description_display,
trait.authors,
trait.pubmed_text,
trait.LRS_score_repr,
trait.LRS_location_repr,
additive]
elif dataset.type == "Geno":
return ['',
index,
''+str(trait.name)+'',
trait.location_repr]
else:
return dict()
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
resource_id, g.user_session.user_id)
else:
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
resource_id, g.user_session.user_id, trait.name)
try:
response = requests.get(the_url).content
trait_info = json.loads(response)
except: # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
if dataset.type == 'Publish':
query = """
SELECT
PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
CAST(Phenotype.Pre_publication_description AS BINARY),
CAST(Phenotype.Post_publication_description AS BINARY),
CAST(Phenotype.Original_description AS BINARY),
CAST(Phenotype.Pre_publication_abbreviation AS BINARY),
CAST(Phenotype.Post_publication_abbreviation AS BINARY), PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
CAST(Publication.Authors AS BINARY), CAST(Publication.Title AS BINARY), CAST(Publication.Abstract AS BINARY),
CAST(Publication.Journal AS BINARY), Publication.Volume, Publication.Pages,
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
# XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
# XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif dataset.type == 'ProbeSet':
display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
display_fields_string = 'ProbeSet.' + display_fields_string
query = """
SELECT %s
FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
WHERE
ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSetFreeze.Name = '%s' AND
ProbeSet.Name = '%s'
""" % (escape(display_fields_string),
escape(dataset.name),
escape(str(trait.name)))
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
# XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif dataset.type == 'Geno':
display_fields_string = ',Geno.'.join(dataset.display_fields)
display_fields_string = 'Geno.' + display_fields_string
query = """
SELECT %s
FROM Geno, GenoFreeze, GenoXRef
WHERE
GenoXRef.GenoFreezeId = GenoFreeze.Id AND
GenoXRef.GenoId = Geno.Id AND
GenoFreeze.Name = '%s' AND
Geno.Name = '%s'
""" % (escape(display_fields_string),
escape(dataset.name),
escape(trait.name))
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
else: # Temp type
query = """SELECT %s FROM %s WHERE Name = %s"""
logger.sql(query)
trait_info = g.db.execute(query,
','.join(dataset.display_fields),
dataset.type, trait.name).fetchone()
if trait_info:
trait.haveinfo = True
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
if isinstance(holder, bytes):
holder = holder.decode("utf-8", errors="ignore")
setattr(trait, field, holder)
if dataset.type == 'Publish':
if trait.group_code:
trait.display_name = trait.group_code + "_" + str(trait.name)
trait.confidential = 0
if trait.pre_publication_description and not trait.pubmed_id:
trait.confidential = 1
description = trait.post_publication_description
# If the dataset is confidential and the user has access to confidential
# phenotype traits, then display the pre-publication description instead
# of the post-publication description
if not trait.pubmed_id:
trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
else:
trait.abbreviation = trait.post_publication_abbreviation
if description:
trait.description_display = description.strip()
else:
trait.description_display = ""
if not trait.year.isdigit():
trait.pubmed_text = "N/A"
else:
trait.pubmed_text = trait.year
if trait.pubmed_id:
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
if dataset.type == 'ProbeSet' and dataset.group:
description_string = trait.description
target_string = trait.probe_target_description
if str(description_string or "") != "" and description_string != 'None':
description_display = description_string
else:
description_display = trait.symbol
if (str(description_display or "") != "" and
description_display != 'N/A' and
str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
trait.description_display = description_display
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
trait.location_repr = 'Chr%s: %.6f' % (
trait.chr, float(trait.mb))
elif dataset.type == "Geno":
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
trait.location_repr = 'Chr%s: %.6f' % (
trait.chr, float(trait.mb))
if get_qtl_info:
# LRS and its location
trait.LRS_score_repr = "N/A"
trait.LRS_location_repr = "N/A"
trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
FROM
ProbeSetXRef, ProbeSet
WHERE
ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
ProbeSet.Name = "{}" AND
ProbeSetXRef.ProbeSetFreezeId ={}
""".format(trait.name, dataset.id)
logger.sql(query)
trait_qtl = g.db.execute(query).fetchone()
if trait_qtl:
trait.locus, trait.lrs, trait.pvalue, trait.mean, trait.additive = trait_qtl
if trait.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '{}' and
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(dataset.group.species, trait.locus)
logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
trait.locus_chr = result[0]
trait.locus_mb = result[1]
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
if dataset.type == 'Publish':
query = """
SELECT
PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive
FROM
PublishXRef, PublishFreeze
WHERE
PublishXRef.Id = %s AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
PublishFreeze.Id =%s
""" % (trait.name, dataset.id)
logger.sql(query)
trait_qtl = g.db.execute(query).fetchone()
if trait_qtl:
trait.locus, trait.lrs, trait.additive = trait_qtl
if trait.locus:
query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '{}' and
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(dataset.group.species, trait.locus)
logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
trait.locus_chr = result[0]
trait.locus_mb = result[1]
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.lrs = trait.additive = ""
if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
trait.locus_chr, float(trait.locus_mb))
if str(trait.lrs or "") != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
raise KeyError(repr(trait.name) +
' information is not found in the database.')
return trait