diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 507 |
1 files changed, 226 insertions, 281 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 1457ba8d..178234fe 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -18,7 +18,24 @@ # # This module is used by GeneNetwork project (www.genenetwork.org) -from __future__ import absolute_import, print_function, division +from db.call import fetchall, fetchone, fetch1 +from utility.logger import getLogger +from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL +from db.gn_server import menu_main +from pprint import pformat as pf +from utility.db_tools import escape +from utility.db_tools import mescape +from utility.db_tools import create_in_clause +from maintenance import get_group_samplelists +from utility.tools import locate, locate_ignore_error, flat_files +from utility import gen_geno_ob +from utility import chunks +from utility.benchmark import Bench +from utility import webqtlUtil +from db import webqtlDatabaseFunction +from base import species +from base import webqtlConfig +from flask import Flask, g import os import math import string @@ -28,43 +45,24 @@ import codecs import json import requests import gzip -import cPickle as pickle +import pickle as pickle import itertools from redis import Redis -Redis = Redis() - -from flask import Flask, g -import reaper +r = Redis() -from base import webqtlConfig -from base import species -from db import webqtlDatabaseFunction -from utility import webqtlUtil -from utility.benchmark import Bench -from utility import chunks -from utility import gen_geno_ob -from utility.tools import locate, locate_ignore_error, flat_files - -from wqflask.api import gen_menu - -from maintenance import get_group_samplelists - -from MySQLdb import escape_string as escape -from pprint import pformat as pf -from db.gn_server import menu_main -from db.call import fetchall,fetchone,fetch1 - -from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL -from utility.logger import getLogger -logger = getLogger(__name__ ) +logger = getLogger(__name__) # Used by create_database to instantiate objects # Each subclass will add to this DS_NAME_MAP = {} -def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None): + +def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None): + if dataset_name == "Temp": + dataset_type = "Temp" + if not dataset_type: dataset_type = Dataset_Getter(dataset_name) @@ -75,9 +73,10 @@ def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, gro else: return dataset_class(dataset_name, get_samplelist) -class Dataset_Types(object): - def __init__(self): +class DatasetType: + + def __init__(self, redis_instance): """Create a dictionary of samples where the value is set to Geno, Publish or ProbeSet. E.g. @@ -92,14 +91,15 @@ Publish or ProbeSet. E.g. 'B139_K_1206_R': 'ProbeSet' ... """ + self.redis_instance = redis_instance self.datasets = {} - - data = Redis.get("dataset_structure") + data = self.redis_instance.get("dataset_structure") if data: self.datasets = json.loads(data) - else: #ZS: I don't think this should ever run unless Redis is emptied + else: # ZS: I don't think this should ever run unless Redis is emptied try: - data = json.loads(requests.get(GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout = 5).content) + data = json.loads(requests.get( + GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content) for species in data['datasets']: for group in data['datasets'][species]: for dataset_type in data['datasets'][species][group]: @@ -115,81 +115,71 @@ Publish or ProbeSet. E.g. except: pass - Redis.set("dataset_structure", json.dumps(self.datasets)) + self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) - # Set LOG_LEVEL_DEBUG=5 to see the following: - logger.debugf(5, "datasets",self.datasets) + def set_dataset_key(self, t, name): + """If name is not in the object's dataset dictionary, set it, and update + dataset_structure in Redis - def __call__(self, name): - if name not in self.datasets: - mrna_expr_query = """ - SELECT - ProbeSetFreeze.Id - FROM - ProbeSetFreeze - WHERE - ProbeSetFreeze.Name = "{0}" - """.format(name) - - results = g.db.execute(mrna_expr_query).fetchall() - if len(results): - self.datasets[name] = "ProbeSet" - Redis.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] + args: + t: Type of dataset structure which can be: 'mrna_expr', 'pheno', + 'other_pheno', 'geno' + name: The name of the key to inserted in the datasets dictionary + """ + sql_query_mapping = { + 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ + + """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """), + 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ + + """FROM InfoFiles, PublishFreeze, InbredSet """ + + """WHERE InbredSet.Name = '{}' AND """ + + """PublishFreeze.InbredSetId = InbredSet.Id AND """ + + """InfoFiles.InfoPageName = PublishFreeze.Name"""), + 'other_pheno': ("""SELECT PublishFreeze.Name """ + + """FROM PublishFreeze, InbredSet """ + + """WHERE InbredSet.Name = '{}' AND """ + + """PublishFreeze.InbredSetId = InbredSet.Id"""), + 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ + + """GenoFreeze.Name = "{}" """) + } + + dataset_name_mapping = { + "mrna_expr": "ProbeSet", + "pheno": "Publish", + "other_pheno": "Publish", + "geno": "Geno", + } + + group_name = name + if t in ['pheno', 'other_pheno']: group_name = name.replace("Publish", "") - pheno_query = """SELECT InfoFiles.GN_AccesionId - FROM InfoFiles, PublishFreeze, InbredSet - WHERE InbredSet.Name = '{0}' AND - PublishFreeze.InbredSetId = InbredSet.Id AND - InfoFiles.InfoPageName = PublishFreeze.Name""".format(group_name) - - results = g.db.execute(pheno_query).fetchall() - if len(results): - self.datasets[name] = "Publish" - Redis.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - #ZS: For when there isn't an InfoFiles ID; not sure if this and the preceding query are both necessary - other_pheno_query = """SELECT PublishFreeze.Name - FROM PublishFreeze, InbredSet - WHERE InbredSet.Name = '{}' AND - PublishFreeze.InbredSetId = InbredSet.Id""".format(group_name) - - results = g.db.execute(other_pheno_query).fetchall() - if len(results): - self.datasets[name] = "Publish" - Redis.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - geno_query = """ - SELECT - GenoFreeze.Id - FROM - GenoFreeze - WHERE - GenoFreeze.Name = "{0}" - """.format(name) - - results = g.db.execute(geno_query).fetchall() - if len(results): - self.datasets[name] = "Geno" - Redis.set("dataset_structure", json.dumps(self.datasets)) - return self.datasets[name] - - #ZS: It shouldn't ever reach this - return None - else: - return self.datasets[name] + results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone() + if results: + self.datasets[name] = dataset_name_mapping[t] + self.redis_instance.set("dataset_structure", json.dumps(self.datasets)) + return True + + return None + + def __call__(self, name): + + if name not in self.datasets: + for t in ["mrna_expr", "pheno", "other_pheno", "geno"]: + # This has side-effects, with the end result being a truth-y value + if(self.set_dataset_key(t, name)): + break + return self.datasets.get(name, None) # Return None if name has not been set + # Do the intensive work at startup one time only -Dataset_Getter = Dataset_Types() +Dataset_Getter = DatasetType(r) + def create_datasets_list(): if USE_REDIS: key = "all_datasets" - result = Redis.get(key) + result = r.get(key) if result: logger.debug("Redis cache hit") @@ -205,38 +195,25 @@ def create_datasets_list(): for dataset_type in type_dict: query = "SELECT Name FROM {}".format(type_dict[dataset_type]) for result in fetchall(query): - #The query at the beginning of this function isn't - #necessary here, but still would rather just reuse - #it logger.debug("type: {}\tname: - #{}".format(dataset_type, result.Name)) + # The query at the beginning of this function isn't + # necessary here, but still would rather just reuse + # it logger.debug("type: {}\tname: + # {}".format(dataset_type, result.Name)) dataset = create_dataset(result.Name, dataset_type) datasets.append(dataset) if USE_REDIS: - Redis.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*60) + r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL)) + r.expire(key, 60*60) return datasets -def create_in_clause(items): - """Create an in clause for mysql""" - in_clause = ', '.join("'{}'".format(x) for x in mescape(*items)) - in_clause = '( {} )'.format(in_clause) - return in_clause - - -def mescape(*items): - """Multiple escape""" - escaped = [escape(str(item)) for item in items] - #logger.debug("escaped is:", escaped) - return escaped - - class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" + def __init__(self, name): - json_data_fh = open(locate(name + ".json",'genotype/json')) + json_data_fh = open(locate(name + ".json", 'genotype/json')) markers = [] with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh: @@ -266,12 +243,12 @@ class Markers(object): logger.debug("length of self.markers:", len(self.markers)) logger.debug("length of p_values:", len(p_values)) - if type(p_values) is list: + if isinstance(p_values, list): # THIS IS only needed for the case when we are limiting the number of p-values calculated - #if len(self.markers) > len(p_values): + # if len(self.markers) > len(p_values): # self.markers = self.markers[:len(p_values)] - for marker, p_value in itertools.izip(self.markers, p_values): + for marker, p_value in zip(self.markers, p_values): if not p_value: continue marker['p_value'] = float(p_value) @@ -280,9 +257,9 @@ class Markers(object): marker['lrs_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) - #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 - elif type(p_values) is dict: + elif isinstance(p_values, dict): filtered_markers = [] for marker in self.markers: #logger.debug("marker[name]", marker['name']) @@ -295,18 +272,20 @@ class Markers(object): marker['lrs_value'] = 0 else: marker['lod_score'] = -math.log10(marker['p_value']) - #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values - marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61 + # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values + marker['lrs_value'] = - \ + math.log10(marker['p_value']) * 4.61 filtered_markers.append(marker) - #else: + # else: #logger.debug("marker {} NOT in p_values".format(i)) - #self.markers.remove(marker) + # self.markers.remove(marker) #del self.markers[i] self.markers = filtered_markers + class HumanMarkers(Markers): - def __init__(self, name, specified_markers = []): + def __init__(self, name, specified_markers=[]): marker_data_fh = open(flat_files('mapping') + '/' + name + '.bim') self.markers = [] for line in marker_data_fh: @@ -329,7 +308,6 @@ class HumanMarkers(Markers): #logger.debug("markers is: ", pf(self.markers)) - def add_pvalues(self, p_values): super(HumanMarkers, self).add_pvalues(p_values) @@ -342,12 +320,15 @@ class DatasetGroup(object): has multiple datasets associated with it. """ + def __init__(self, dataset, name=None): """This sets self.group and self.group_id""" if name == None: - self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group) + self.name, self.id, self.genetic_type = fetchone( + dataset.query_for_group) else: - self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name) + self.name, self.id, self.genetic_type = fetchone( + "SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name) if self.name == 'BXD300': self.name = "BXD" @@ -366,7 +347,8 @@ class DatasetGroup(object): def get_mapping_methods(self): - mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] + mapping_id = g.db.execute( + "select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0] if mapping_id == "1": mapping_names = ["GEMMA", "QTLReaper", "R/qtl"] elif mapping_id == "2": @@ -423,22 +405,23 @@ class DatasetGroup(object): result = None key = "samplelist:v3:" + self.name if USE_REDIS: - result = Redis.get(key) + result = r.get(key) if result is not None: self.samplelist = json.loads(result) else: logger.debug("Cache not hit") - genotype_fn = locate_ignore_error(self.name+".geno",'genotype') + genotype_fn = locate_ignore_error(self.name+".geno", 'genotype') if genotype_fn: - self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn) + self.samplelist = get_group_samplelists.get_samplelist( + "geno", genotype_fn) else: self.samplelist = None if USE_REDIS: - Redis.set(key, json.dumps(self.samplelist)) - Redis.expire(key, 60*5) + r.set(key, json.dumps(self.samplelist)) + r.expire(key, 60*5) def all_samples_ordered(self): result = [] @@ -448,32 +431,29 @@ class DatasetGroup(object): def read_genotype_file(self, use_reaper=False): '''Read genotype from .geno file instead of database''' - #genotype_1 is Dataset Object without parents and f1 - #genotype_2 is Dataset Object with parents and f1 (not for intercross) + # genotype_1 is Dataset Object without parents and f1 + # genotype_2 is Dataset Object with parents and f1 (not for intercross) #genotype_1 = reaper.Dataset() # reaper barfs on unicode filenames, so here we ensure it's a string if self.genofile: - if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData - full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype')) + if "RData" in self.genofile: # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData + full_filename = str( + locate(self.genofile.split(".")[0] + ".geno", 'genotype')) else: full_filename = str(locate(self.genofile, 'genotype')) else: full_filename = str(locate(self.name + '.geno', 'genotype')) - - if use_reaper: - genotype_1 = reaper.Dataset() - genotype_1.read(full_filename) - else: - genotype_1 = gen_geno_ob.genotype(full_filename) + genotype_1 = gen_geno_ob.genotype(full_filename) if genotype_1.type == "group" and self.parlist: - genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1) + genotype_2 = genotype_1.add( + Mat=self.parlist[0], Pat=self.parlist[1]) # , F1=_f1) else: genotype_2 = genotype_1 - #determine default genotype object + # determine default genotype object if self.incparentsf1 and genotype_1.type != "intercross": genotype = genotype_2 else: @@ -484,27 +464,21 @@ class DatasetGroup(object): return genotype -def datasets(group_name, this_group = None): + +def datasets(group_name, this_group=None): key = "group_dataset_menu:v2:" + group_name - logger.debug("key is2:", key) dataset_menu = [] - logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH) - logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH)) the_results = fetchall(''' (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name FROM PublishFreeze,InbredSet WHERE PublishFreeze.InbredSetId = InbredSet.Id and InbredSet.Name = '%s' - and PublishFreeze.public > %s - and PublishFreeze.confidentiality < 1 ORDER BY PublishFreeze.Id ASC) UNION (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name FROM GenoFreeze, InbredSet WHERE GenoFreeze.InbredSetId = InbredSet.Id - and InbredSet.Name = '%s' - and GenoFreeze.public > %s - and GenoFreeze.confidentiality < 1) + and InbredSet.Name = '%s') UNION (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue @@ -512,16 +486,15 @@ def datasets(group_name, this_group = None): and ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id and InbredSet.Name like %s - and ProbeSetFreeze.public > %s - and ProbeSetFreeze.confidentiality < 1 ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC) - ''' % (group_name, webqtlConfig.PUBLICTHRESH, - group_name, webqtlConfig.PUBLICTHRESH, - "'" + group_name + "'", webqtlConfig.PUBLICTHRESH)) + ''' % (group_name, + group_name, + "'" + group_name + "'")) sorted_results = sorted(the_results, key=lambda kv: kv[0]) - pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown + # ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown + pheno_inserted = False geno_inserted = False for dataset_item in sorted_results: tissue_name = dataset_item[0] @@ -529,13 +502,16 @@ def datasets(group_name, this_group = None): dataset_short = dataset_item[2] if tissue_name in ['#PublishFreeze', '#GenoFreeze']: if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'): - dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)])) + dataset_menu.insert( + 0, dict(tissue=None, datasets=[(dataset, dataset_short)])) pheno_inserted = True elif pheno_inserted and tissue_name == '#GenoFreeze': - dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)])) + dataset_menu.insert( + 1, dict(tissue=None, datasets=[(dataset, dataset_short)])) geno_inserted = True else: - dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)])) + dataset_menu.append( + dict(tissue=None, datasets=[(dataset, dataset_short)])) else: tissue_already_exists = False for i, tissue_dict in enumerate(dataset_menu): @@ -548,11 +524,11 @@ def datasets(group_name, this_group = None): dataset_menu[i]['datasets'].append((dataset, dataset_short)) else: dataset_menu.append(dict(tissue=tissue_name, - datasets=[(dataset, dataset_short)])) + datasets=[(dataset, dataset_short)])) if USE_REDIS: - Redis.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) - Redis.expire(key, 60*5) + r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL)) + r.expire(key, 60*5) if this_group != None: this_group._datasets = dataset_menu @@ -560,6 +536,7 @@ def datasets(group_name, this_group = None): else: return dataset_menu + class DataSet(object): """ DataSet class defines a dataset in webqtl, can be either Microarray, @@ -567,7 +544,7 @@ class DataSet(object): """ - def __init__(self, name, get_samplelist = True, group_name = None): + def __init__(self, name, get_samplelist=True, group_name=None): assert name, "Need a name" self.name = name @@ -575,22 +552,23 @@ class DataSet(object): self.shortname = None self.fullname = None self.type = None - self.data_scale = None #ZS: For example log2 + self.data_scale = None # ZS: For example log2 self.setup() - if self.type == "Temp": #Need to supply group name as input if temp trait - self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype + if self.type == "Temp": # Need to supply group name as input if temp trait + # sets self.group and self.group_id and gets genotype + self.group = DatasetGroup(self, name=group_name) else: self.check_confidentiality() self.retrieve_other_names() - self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype + # sets self.group and self.group_id and gets genotype + self.group = DatasetGroup(self) self.accession_id = self.get_accession_id() if get_samplelist == True: - self.group.get_samplelist() + self.group.get_samplelist() self.species = species.TheSpecies(self) - def get_desc(self): """Gets overridden later, at least for Temp...used by trait's get_given_name""" return None @@ -637,29 +615,26 @@ class DataSet(object): """ - try: if self.type == "ProbeSet": query_args = tuple(escape(x) for x in ( - str(webqtlConfig.PUBLICTHRESH), self.name, self.name, self.name)) self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1(""" -SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name -FROM ProbeSetFreeze, ProbeFreeze, Tissue -WHERE ProbeSetFreeze.public > %s -AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id -AND ProbeFreeze.TissueId = Tissue.Id -AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') - """ % (query_args),"/dataset/"+self.name+".json", - lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"]) + SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name + FROM ProbeSetFreeze, ProbeFreeze, Tissue + WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id + AND ProbeFreeze.TissueId = Tissue.Id + AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s') + """ % (query_args), "/dataset/"+self.name+".json", + lambda r: (r["id"], r["name"], r["full_name"], + r["short_name"], r["data_scale"], r["tissue"]) ) else: query_args = tuple(escape(x) for x in ( (self.type + "Freeze"), - str(webqtlConfig.PUBLICTHRESH), self.name, self.name, self.name)) @@ -668,12 +643,12 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre self.id, self.name, self.fullname, self.shortname = fetchone(""" SELECT Id, Name, FullName, ShortName FROM %s - WHERE public > %s AND - (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)) + WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s') + """ % (query_args)) except TypeError: - logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name)) + logger.debug( + "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass def get_trait_data(self, sample_list=None): @@ -713,7 +688,7 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre else: query = "SELECT {}.Name,".format(escape(dataset_type)) data_start_pos = 1 - query += string.join(temp, ', ') + query += ', '.join(temp) query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, self.type)) @@ -731,7 +706,7 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre and {}.Id = {}XRef.{}Id order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.name, - dataset_type, self.type, dataset_type, dataset_type)) + dataset_type, self.type, dataset_type, dataset_type)) else: query += """ WHERE {}XRef.{}FreezeId = {}Freeze.Id @@ -739,13 +714,9 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre and {}.Id = {}XRef.{}Id order by {}.Id """.format(*mescape(self.type, self.type, self.type, self.type, - self.name, dataset_type, self.type, self.type, dataset_type)) + self.name, dataset_type, self.type, self.type, dataset_type)) - #logger.debug("trait data query: ", query) - - logger.sql(query) results = g.db.execute(query).fetchall() - #logger.debug("query results:", results) trait_sample_data.append(results) trait_count = len(trait_sample_data[0]) @@ -759,6 +730,7 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre self.trait_data[trait_name] += ( trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) + class PhenotypeDataSet(DataSet): DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' @@ -768,16 +740,16 @@ class PhenotypeDataSet(DataSet): # Fields in the database table self.search_fields = ['Phenotype.Post_publication_description', - 'Phenotype.Pre_publication_description', - 'Phenotype.Pre_publication_abbreviation', - 'Phenotype.Post_publication_abbreviation', - 'PublishXRef.mean', - 'Phenotype.Lab_code', - 'Publication.PubMed_ID', - 'Publication.Abstract', - 'Publication.Title', - 'Publication.Authors', - 'PublishXRef.Id'] + 'Phenotype.Pre_publication_description', + 'Phenotype.Pre_publication_abbreviation', + 'Phenotype.Post_publication_abbreviation', + 'PublishXRef.mean', + 'Phenotype.Lab_code', + 'Publication.PubMed_ID', + 'Publication.Abstract', + 'Publication.Title', + 'Publication.Authors', + 'PublishXRef.Id'] # Figure out what display_fields is self.display_fields = ['name', 'group_code', @@ -799,13 +771,13 @@ class PhenotypeDataSet(DataSet): # Fields displayed in the search results table header self.header_fields = ['Index', - 'Record', - 'Description', - 'Authors', - 'Year', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Record', + 'Description', + 'Authors', + 'Year', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] self.type = 'Publish' @@ -823,7 +795,7 @@ class PhenotypeDataSet(DataSet): # (Urgently?) Need to write this pass - def get_trait_info(self, trait_list, species = ''): + def get_trait_info(self, trait_list, species=''): for this_trait in trait_list: if not this_trait.haveinfo: @@ -831,9 +803,9 @@ class PhenotypeDataSet(DataSet): description = this_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 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 this_trait.confidential: this_trait.description_display = "" continue # for now, because no authorization features @@ -858,7 +830,7 @@ class PhenotypeDataSet(DataSet): if this_trait.pubmed_id: this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id - #LRS and its location + # LRS and its location this_trait.LRS_score_repr = "N/A" this_trait.LRS_location_repr = "N/A" @@ -878,7 +850,8 @@ class PhenotypeDataSet(DataSet): LRS_Mb = result[1] this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb)) + this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % ( + LRS_Chr, float(LRS_Mb)) def retrieve_sample_data(self, trait): query = """ @@ -945,12 +918,13 @@ class GenotypeDataSet(DataSet): this_trait.retrieveInfo() if this_trait.chr and this_trait.mb: - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) ) + this_trait.location_repr = 'Chr%s: %.6f' % ( + this_trait.chr, float(this_trait.mb)) def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2 + Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2 FROM (GenoData, GenoFreeze, Strain, Geno, GenoXRef) left join GenoSE on @@ -1014,14 +988,14 @@ class MrnaAssayDataSet(DataSet): # Fields displayed in the search results table header self.header_fields = ['Index', - 'Record', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] + 'Record', + 'Symbol', + 'Description', + 'Location', + 'Mean', + 'Max LRS', + 'Max LRS Location', + 'Additive Effect'] # Todo: Obsolete or rename this field self.type = 'ProbeSet' @@ -1037,7 +1011,6 @@ class MrnaAssayDataSet(DataSet): ProbeSetFreeze.Name = "%s" ''' % escape(self.name) - def check_confidentiality(self): return geno_mrna_confidentiality(self) @@ -1055,10 +1028,12 @@ class MrnaAssayDataSet(DataSet): if not this_trait.symbol: this_trait.symbol = "N/A" - #XZ, 12/08/2008: description - #XZ, 06/05/2009: Rob asked to add probe target description - description_string = unicode(str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = unicode(str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') + # XZ, 12/08/2008: description + # XZ, 06/05/2009: Rob asked to add probe target description + description_string = str( + str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') + target_string = str( + str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') if len(description_string) > 1 and description_string != 'None': description_display = description_string @@ -1073,11 +1048,12 @@ class MrnaAssayDataSet(DataSet): this_trait.description_display = description_display if this_trait.chr and this_trait.mb: - this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb)) + this_trait.location_repr = 'Chr%s: %.6f' % ( + this_trait.chr, float(this_trait.mb)) - #Get mean expression value + # Get mean expression value query = ( - """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet + """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and ProbeSet.Name = '%s' @@ -1093,11 +1069,11 @@ class MrnaAssayDataSet(DataSet): if mean: this_trait.mean = "%2.3f" % mean - #LRS and its location + # LRS and its location this_trait.LRS_score_repr = 'N/A' this_trait.LRS_location_repr = 'N/A' - #Max LRS and its Locus location + # Max LRS and its Locus location if this_trait.lrs and this_trait.locus: query = """ select Geno.Chr, Geno.Mb from Geno, Species @@ -1111,18 +1087,22 @@ class MrnaAssayDataSet(DataSet): if result: lrs_chr, lrs_mb = result this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb)) + this_trait.LRS_location_repr = 'Chr%s: %.6f' % ( + lrs_chr, float(lrs_mb)) return trait_list def retrieve_sample_data(self, trait): query = """ SELECT - Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id, Strain.Name2 + Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2 FROM (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef) left join ProbeSetSE on (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId) + left join NStrain on + (NStrain.DataId = ProbeSetData.Id AND + NStrain.StrainId = ProbeSetData.StrainId) WHERE ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND @@ -1173,47 +1153,12 @@ class TempDataSet(DataSet): self.shortname = 'Temp' - @staticmethod - def handle_pca(desc): - if 'PCA' in desc: - # Todo: Modernize below lines - desc = desc[desc.rindex(':')+1:].strip() - else: - desc = desc[:desc.index('entered')].strip() - return desc - - def get_desc(self): - query = 'SELECT description FROM Temp WHERE Name=%s' % self.name - logger.sql(query) - g.db.execute(query) - desc = g.db.fetchone()[0] - desc = self.handle_pca(desc) - return desc - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id - FROM - TempData, Temp, Strain - WHERE - TempData.StrainId = Strain.Id AND - TempData.Id = Temp.DataId AND - Temp.name = '%s' - Order BY - Strain.Name - """ % escape(trait.name) - - logger.sql(query) - results = g.db.execute(query).fetchall() - - def geno_mrna_confidentiality(ob): dataset_table = ob.type + "Freeze" #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) query = '''SELECT Id, Name, FullName, confidentiality, - AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table,ob.name) + AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) logger.sql(query) result = g.db.execute(query) |