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Diffstat (limited to 'gn3/base/data_set.py')
| -rw-r--r-- | gn3/base/data_set.py | 882 |
1 files changed, 0 insertions, 882 deletions
diff --git a/gn3/base/data_set.py b/gn3/base/data_set.py deleted file mode 100644 index 01913f2..0000000 --- a/gn3/base/data_set.py +++ /dev/null @@ -1,882 +0,0 @@ - -import json -import math -import collections -import requests -from redis import Redis -from flask import g -from gn3.utility.db_tools import escape -from gn3.utility.db_tools import mescape -from gn3.utility.db_tools import create_in_clause -from gn3.utility.tools import locate_ignore_error -from gn3.db.calls import fetch1 -from gn3.db.calls import fetchone -from gn3.db.webqtlDatabaseFunction import retrieve_species -from gn3.utility import chunks - -from gn3.utility import get_group_samplelists -from gn3.base.species import TheSpecies -r = Redis() - -# should probably move this to its own configuration files - -USE_REDIS = True - -# todo move to config file -GN2_BASE_URL = "https://genenetwork.org/" - -DS_NAME_MAP = {} - -# pylint: disable-all -#todo file not linted -# pylint: disable=C0103 - - - -def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None): - - if dataset_name == "Temp": - dataset_type = "Temp" - - if dataset_type is None: - dataset_type = Dataset_Getter(dataset_name) - dataset_ob = DS_NAME_MAP[dataset_type] - dataset_class = globals()[dataset_ob] - - if dataset_type == "Temp": - results = dataset_class(dataset_name, get_samplelist, group_name) - - else: - results = dataset_class(dataset_name, get_samplelist) - - return results - - -class DatasetType: - def __init__(self, redis_instance): - self.redis_instance = redis_instance - self.datasets = {} - - data = self.redis_instance.get("dataset_structure") - if data: - self.datasets = json.loads(data) - - else: - - try: - - data = json.loads(requests.get( - GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content) - - # todo:Refactor code below n^4 loop - - for species in data["datasets"]: - for group in data["datasets"][species]: - for dataset_type in data['datasets'][species][group]: - for dataset in data['datasets'][species][group][dataset_type]: - - short_dataset_name = dataset[1] - if dataset_type == "Phenotypes": - new_type = "Publish" - - elif dataset_type == "Genotypes": - new_type = "Geno" - else: - new_type = "ProbeSet" - - self.datasets[short_dataset_name] = new_type - - except Exception as e: - raise e - - self.redis_instance.set( - "dataset_structure", json.dumps(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 - - 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", "") - - 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"]: - - if(self.set_dataset_key(t, name)): - # This has side-effects, with the end result being a truth-y value - break - - return self.datasets.get(name, None) - - -# Do the intensive work at startup one time only -# could replace the code below -Dataset_Getter = DatasetType(r) - - -class DatasetGroup: - """ - Each group has multiple datasets; each species has multiple groups. - - For example, Mouse has multiple groups (BXD, BXA, etc), and each group - 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) - - else: - 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" - - self.f1list = None - - self.parlist = None - - self.get_f1_parent_strains() - - # remove below not used in correlation - - self.mapping_id, self.mapping_names = self.get_mapping_methods() - - self.species = retrieve_species(self.name) - - def get_f1_parent_strains(self): - try: - # should import ParInfo - raise e - # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py; - f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name] - except Exception as e: - f1 = f12 = maternal = paternal = None - - if f1 and f12: - self.f1list = [f1, f12] - - if maternal and paternal: - self.parlist = [maternal, paternal] - - def get_mapping_methods(self): - 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": - mapping_names = ["GEMMA"] - - elif mapping_id == "3": - mapping_names = ["R/qtl"] - - elif mapping_id == "4": - mapping_names = ["GEMMA", "PLINK"] - - else: - mapping_names = [] - - return mapping_id, mapping_names - - def get_samplelist(self): - result = None - key = "samplelist:v3:" + self.name - if USE_REDIS: - result = r.get(key) - - if result is not None: - - self.samplelist = json.loads(result) - - else: - # logger.debug("Cache not hit") - # should enable logger - genotype_fn = locate_ignore_error(self.name+".geno", 'genotype') - if genotype_fn: - self.samplelist = get_group_samplelists.get_samplelist( - "geno", genotype_fn) - - else: - self.samplelist = None - - if USE_REDIS: - r.set(key, json.dumps(self.samplelist)) - r.expire(key, 60*5) - - -class DataSet: - """ - DataSet class defines a dataset in webqtl, can be either Microarray, - Published phenotype, genotype, or user input dataset(temp) - - """ - - def __init__(self, name, get_samplelist=True, group_name=None): - - assert name, "Need a name" - self.name = name - self.id = None - self.shortname = None - self.fullname = None - self.type = None - self.data_scale = None # ZS: For example log2 - - self.setup() - - 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() - # 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.species = TheSpecies(self) - - def get_desc(self): - """Gets overridden later, at least for Temp...used by trait's get_given_name""" - return None - - - def get_accession_id(self): - if self.type == "Publish": - results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where - InbredSet.Name = %s and - PublishFreeze.InbredSetId = InbredSet.Id and - InfoFiles.InfoPageName = PublishFreeze.Name and - PublishFreeze.public > 0 and - PublishFreeze.confidentiality < 1 order by - PublishFreeze.CreateTime desc""", (self.group.name)).fetchone() - elif self.type == "Geno": - results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where - InbredSet.Name = %s and - GenoFreeze.InbredSetId = InbredSet.Id and - InfoFiles.InfoPageName = GenoFreeze.ShortName and - GenoFreeze.public > 0 and - GenoFreeze.confidentiality < 1 order by - GenoFreeze.CreateTime desc""", (self.group.name)).fetchone() - else: - results = None - - if results != None: - return str(results[0]) - else: - return "None" - - def retrieve_other_names(self): - """This method fetches the the dataset names in search_result. - - If the data set name parameter is not found in the 'Name' field of - the data set table, check if it is actually the FullName or - ShortName instead. - - This is not meant to retrieve the data set info if no name at - all is passed. - - """ - - try: - if self.type == "ProbeSet": - query_args = tuple(escape(x) for x in ( - 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.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"), - self.name, - self.name, - self.name)) - - self.tissue = "N/A" - self.id, self.name, self.fullname, self.shortname = fetchone(""" - SELECT Id, Name, FullName, ShortName - FROM %s - WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s') - """ % (query_args)) - - except TypeError as e: - logger.debug( - "Dataset {} is not yet available in GeneNetwork.".format(self.name)) - pass - - def get_trait_data(self, sample_list=None): - if sample_list: - self.samplelist = sample_list - else: - self.samplelist = self.group.samplelist - - if self.group.parlist != None and self.group.f1list != None: - if (self.group.parlist + self.group.f1list) in self.samplelist: - self.samplelist += self.group.parlist + self.group.f1list - - query = """ - SELECT Strain.Name, Strain.Id FROM Strain, Species - WHERE Strain.Name IN {} - and Strain.SpeciesId=Species.Id - and Species.name = '{}' - """.format(create_in_clause(self.samplelist), *mescape(self.group.species)) - # logger.sql(query) - results = dict(g.db.execute(query).fetchall()) - sample_ids = [results[item] for item in self.samplelist] - - # MySQL limits the number of tables that can be used in a join to 61, - # so we break the sample ids into smaller chunks - # Postgres doesn't have that limit, so we can get rid of this after we transition - chunk_size = 50 - number_chunks = int(math.ceil(len(sample_ids) / chunk_size)) - trait_sample_data = [] - for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks): - if self.type == "Publish": - dataset_type = "Phenotype" - else: - dataset_type = self.type - temp = ['T%s.value' % item for item in sample_ids_step] - if self.type == "Publish": - query = "SELECT {}XRef.Id,".format(escape(self.type)) - else: - query = "SELECT {}.Name,".format(escape(dataset_type)) - data_start_pos = 1 - query += ', '.join(temp) - query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, - self.type, - self.type)) - - for item in sample_ids_step: - query += """ - left join {}Data as T{} on T{}.Id = {}XRef.DataId - and T{}.StrainId={}\n - """.format(*mescape(self.type, item, item, self.type, item, item)) - - if self.type == "Publish": - query += """ - WHERE {}XRef.InbredSetId = {}Freeze.InbredSetId - and {}Freeze.Name = '{}' - 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)) - else: - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - 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)) - - results = g.db.execute(query).fetchall() - trait_sample_data.append(results) - - trait_count = len(trait_sample_data[0]) - self.trait_data = collections.defaultdict(list) - - # put all of the separate data together into a dictionary where the keys are - # trait names and values are lists of sample values - for trait_counter in range(trait_count): - trait_name = trait_sample_data[0][trait_counter][0] - for chunk_counter in range(int(number_chunks)): - self.trait_data[trait_name] += ( - trait_sample_data[chunk_counter][trait_counter][data_start_pos:]) - - -class MrnaAssayDataSet(DataSet): - ''' - An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait - - This used to be called ProbeSet, but that term only refers specifically to the Affymetrix - platform and is far too specific. - - ''' - DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet' - - def setup(self): - # Fields in the database table - self.search_fields = ['Name', - 'Description', - 'Probe_Target_Description', - 'Symbol', - 'Alias', - 'GenbankId', - 'UniGeneId', - 'RefSeq_TranscriptId'] - - # Find out what display_fields is - self.display_fields = ['name', 'symbol', - 'description', 'probe_target_description', - 'chr', 'mb', - 'alias', 'geneid', - 'genbankid', 'unigeneid', - 'omim', 'refseq_transcriptid', - 'blatseq', 'targetseq', - 'chipid', 'comments', - 'strand_probe', 'strand_gene', - 'proteinid', 'uniprotid', - 'probe_set_target_region', - 'probe_set_specificity', - 'probe_set_blat_score', - 'probe_set_blat_mb_start', - 'probe_set_blat_mb_end', - 'probe_set_strand', - 'probe_set_note_by_rw', - 'flag'] - - # Fields displayed in the search results table header - self.header_fields = ['Index', - 'Record', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] - - # Todo: Obsolete or rename this field - self.type = 'ProbeSet' - - self.query_for_group = ''' - SELECT - InbredSet.Name, InbredSet.Id, InbredSet.GeneticType - FROM - InbredSet, ProbeSetFreeze, ProbeFreeze - WHERE - ProbeFreeze.InbredSetId = InbredSet.Id AND - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Name = "%s" - ''' % escape(self.name) - - def check_confidentiality(self): - return geno_mrna_confidentiality(self) - - def get_trait_info(self, trait_list=None, species=''): - - # Note: setting trait_list to [] is probably not a great idea. - if not trait_list: - trait_list = [] - - for this_trait in trait_list: - - if not this_trait.haveinfo: - this_trait.retrieveInfo(QTL=1) - - 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 = 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 - else: - description_display = this_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 - 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)) - - # Get mean expression value - query = ( - """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet - where ProbeSetXRef.ProbeSetFreezeId = %s and - ProbeSet.Id = ProbeSetXRef.ProbeSetId and - ProbeSet.Name = '%s' - """ % (escape(str(this_trait.dataset.id)), - escape(this_trait.name))) - - #logger.debug("query is:", pf(query)) - logger.sql(query) - result = g.db.execute(query).fetchone() - - mean = result[0] if result else 0 - - if mean: - this_trait.mean = "%2.3f" % mean - - # LRS and its location - this_trait.LRS_score_repr = 'N/A' - this_trait.LRS_location_repr = 'N/A' - - # Max LRS and its Locus location - if this_trait.lrs and this_trait.locus: - query = """ - select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '{}' and - Geno.Name = '{}' and - Geno.SpeciesId = Species.Id - """.format(species, this_trait.locus) - logger.sql(query) - result = g.db.execute(query).fetchone() - - 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)) - - return trait_list - - def retrieve_sample_data(self, trait): - query = """ - SELECT - 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 - ProbeSetFreeze.Name = '%s' AND - ProbeSetXRef.DataId = ProbeSetData.Id AND - ProbeSetData.StrainId = Strain.Id - Order BY - Strain.Name - """ % (escape(trait), escape(self.name)) - # logger.sql(query) - results = g.db.execute(query).fetchall() - #logger.debug("RETRIEVED RESULTS HERE:", results) - return results - - def retrieve_genes(self, column_name): - query = """ - select ProbeSet.Name, ProbeSet.%s - from ProbeSet,ProbeSetXRef - where ProbeSetXRef.ProbeSetFreezeId = %s and - ProbeSetXRef.ProbeSetId=ProbeSet.Id; - """ % (column_name, escape(str(self.id))) - # logger.sql(query) - results = g.db.execute(query).fetchall() - - return dict(results) - - -class TempDataSet(DataSet): - '''Temporary user-generated data set''' - - DS_NAME_MAP['Temp'] = 'TempDataSet' - - def setup(self): - self.search_fields = ['name', - 'description'] - - self.display_fields = ['name', - 'description'] - - self.header_fields = ['Name', - 'Description'] - - self.type = 'Temp' - - # Need to double check later how these are used - self.id = 1 - self.fullname = 'Temporary Storage' - self.shortname = 'Temp' - - -class PhenotypeDataSet(DataSet): - DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' - - def setup(self): - - #logger.debug("IS A PHENOTYPEDATASET") - - # 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'] - - # Figure out what display_fields is - self.display_fields = ['name', 'group_code', - 'pubmed_id', - 'pre_publication_description', - 'post_publication_description', - 'original_description', - 'pre_publication_abbreviation', - 'post_publication_abbreviation', - 'mean', - 'lab_code', - 'submitter', 'owner', - 'authorized_users', - 'authors', 'title', - 'abstract', 'journal', - 'volume', 'pages', - 'month', 'year', - 'sequence', 'units', 'comments'] - - # Fields displayed in the search results table header - self.header_fields = ['Index', - 'Record', - 'Description', - 'Authors', - 'Year', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] - - self.type = 'Publish' - - self.query_for_group = ''' - SELECT - InbredSet.Name, InbredSet.Id, InbredSet.GeneticType - FROM - InbredSet, PublishFreeze - WHERE - PublishFreeze.InbredSetId = InbredSet.Id AND - PublishFreeze.Name = "%s" - ''' % escape(self.name) - - def check_confidentiality(self): - # (Urgently?) Need to write this - pass - - def get_trait_info(self, trait_list, species=''): - for this_trait in trait_list: - - if not this_trait.haveinfo: - this_trait.retrieve_info(get_qtl_info=True) - - 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 this_trait.confidential: - this_trait.description_display = "" - continue # todo for now, because no authorization features - - if not webqtlUtil.has_access_to_confidentail_phenotype_trait( - privilege=self.privilege, - userName=self.userName, - authorized_users=this_trait.authorized_users): - - description = this_trait.pre_publication_description - - if len(description) > 0: - this_trait.description_display = description.strip() - else: - this_trait.description_display = "" - - if not this_trait.year.isdigit(): - this_trait.pubmed_text = "N/A" - else: - this_trait.pubmed_text = this_trait.year - - if this_trait.pubmed_id: - this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id - - # LRS and its location - this_trait.LRS_score_repr = "N/A" - this_trait.LRS_location_repr = "N/A" - - if this_trait.lrs: - query = """ - select Geno.Chr, Geno.Mb from Geno, Species - where Species.Name = '%s' and - Geno.Name = '%s' and - Geno.SpeciesId = Species.Id - """ % (species, this_trait.locus) - - result = g.db.execute(query).fetchone() - - if result: - if result[0] and result[1]: - LRS_Chr = result[0] - 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)) - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2 - FROM - (PublishData, Strain, PublishXRef, PublishFreeze) - left join PublishSE on - (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId) - left join NStrain on - (NStrain.DataId = PublishData.Id AND - NStrain.StrainId = PublishData.StrainId) - WHERE - PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND - PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND - PublishFreeze.Id = %s AND PublishData.StrainId = Strain.Id - Order BY - Strain.Name - """ - - results = g.db.execute(query, (trait, self.id)).fetchall() - return results - - -class GenotypeDataSet(DataSet): - DS_NAME_MAP['Geno'] = 'GenotypeDataSet' - - def setup(self): - # Fields in the database table - self.search_fields = ['Name', - 'Chr'] - - # Find out what display_fields is - self.display_fields = ['name', - 'chr', - 'mb', - 'source2', - 'sequence'] - - # Fields displayed in the search results table header - self.header_fields = ['Index', - 'ID', - 'Location'] - - # Todo: Obsolete or rename this field - self.type = 'Geno' - - self.query_for_group = ''' - SELECT - InbredSet.Name, InbredSet.Id, InbredSet.GeneticType - FROM - InbredSet, GenoFreeze - WHERE - GenoFreeze.InbredSetId = InbredSet.Id AND - GenoFreeze.Name = "%s" - ''' % escape(self.name) - - def check_confidentiality(self): - return geno_mrna_confidentiality(self) - - def get_trait_info(self, trait_list, species=None): - for this_trait in trait_list: - if not this_trait.haveinfo: - 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)) - - def retrieve_sample_data(self, trait): - query = """ - SELECT - Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2 - FROM - (GenoData, GenoFreeze, Strain, Geno, GenoXRef) - left join GenoSE on - (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId) - WHERE - Geno.SpeciesId = %s AND Geno.Name = %s AND GenoXRef.GenoId = Geno.Id AND - GenoXRef.GenoFreezeId = GenoFreeze.Id AND - GenoFreeze.Name = %s AND - GenoXRef.DataId = GenoData.Id AND - GenoData.StrainId = Strain.Id - Order BY - Strain.Name - """ - results = g.db.execute(query, - (webqtlDatabaseFunction.retrieve_species_id(self.group.name), - trait, self.name)).fetchall() - return results - - -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) - # - result = g.db.execute(query) - - (_dataset_id, - _name, - _full_name, - confidential, - _authorized_users) = result.fetchall()[0] - - if confidential: - return True |