from __future__ import absolute_import, division, print_function import os import string import resource import codecs import requests import random from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset from db import webqtlDatabaseFunction from utility import webqtlUtil from utility import hmac from utility.authentication_tools import check_resource_availability from utility.tools import GN2_BASE_URL, GN_VERSION from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info Redis = get_redis_conn() from wqflask import app import simplejson as json from MySQLdb import escape_string as escape from pprint import pformat as pf from flask import Flask, g, request, url_for, redirect, make_response, render_template from utility.logger import getLogger logger = getLogger(__name__ ) def create_trait(**kw): assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name"; permitted = True 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"; self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc. 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) self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet 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 != 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 self.data.items(): if sample_data.value != None: if not include_variance or sample_data.variance != 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" return formatted @property def alias_fmt(self): '''Return a text formatted alias''' alias = 'Not available' if self.alias: alias = string.replace(self.alias, ";", " ") alias = string.join(string.split(alias), ", ") 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 == 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): trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases) 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 trait_ob.data.iteritems() }]) 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 if response.strip() == "no-access": trait.view = False return trait else: trait_info = json.loads(response) except: resource_info = get_resource_info(resource_id) if resource_info: default_permissions = resource_info['default_mask']['data'] else: default_permissions = webqtlConfig.DEFAULT_PRIVILEGES if 'view' not in default_permissions: trait.view = False return trait if dataset.type == 'Publish': query = """ SELECT PublishXRef.Id, Publication.PubMed_ID, Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users, Publication.Authors, Publication.Title, Publication.Abstract, Publication.Journal, Publication.Volume, Publication.Pages, Publication.Month, Publication.Year, PublishXRef.Sequence, Phenotype.Units, PublishXRef.comments FROM PublishXRef, Publication, Phenotype, PublishFreeze WHERE PublishXRef.Id = %s AND Phenotype.Id = PublishXRef.PhenotypeId AND Publication.Id = PublishXRef.PublicationId AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId 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 = string.join(dataset.display_fields,',Geno.') 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, (string.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(trait_info[i], basestring): # holder = holder.encode('latin1') 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 trait.confidential: 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 = "" trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace") 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 = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8') target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': description_display = description_string else: description_display = trait.symbol if (len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 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 trait.locus_chr != "" and trait.locus_mb != "": trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb)) if trait.lrs != "": trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs else: raise KeyError, `trait.name`+' information is not found in the database.' return trait