diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/data_set.py | 214 |
1 files changed, 109 insertions, 105 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 7531ac81..39296f6a 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -659,12 +659,8 @@ class DataSet: "Dataset {} is not yet available in GeneNetwork.".format(self.name)) pass - - - def chunk_dataset(self, dataset, n): - results = {} query = """ @@ -677,10 +673,7 @@ class DataSet: # should cache this - traits_name_dict= dict(g.db.execute(query).fetchall()) - - - + traits_name_dict = dict(g.db.execute(query).fetchall()) for i in range(0, len(dataset), n): matrix = list(dataset[i:i + n]) @@ -716,50 +709,50 @@ class DataSet: FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = '{}' - and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids),self.name) + and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name) - query_results=list(g.db.execute(query).fetchall()) + query_results = list(g.db.execute(query).fetchall()) - data_results=self.chunk_dataset(query_results, len(sample_ids)) - self.trait_data=data_results + data_results = self.chunk_dataset(query_results, len(sample_ids)) + self.trait_data = data_results def get_trait_data(self, sample_list=None): if sample_list: - self.samplelist=sample_list + self.samplelist = sample_list else: - self.samplelist=self.group.samplelist + 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=""" + 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] + 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=[] + 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" + dataset_type = "Phenotype" else: - dataset_type=self.type - temp=['T%s.value' % item for item in sample_ids_step] + 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)) + query = "SELECT {}XRef.Id,".format(escape(self.type)) else: - query="SELECT {}.Name,".format(escape(dataset_type)) - data_start_pos=1 + query = "SELECT {}.Name,".format(escape(dataset_type)) + data_start_pos = 1 query += ', '.join(temp) query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type, self.type, @@ -788,27 +781,27 @@ class DataSet: """.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() + results = g.db.execute(query).fetchall() trait_sample_data.append(results) - trait_count=len(trait_sample_data[0]) - self.trait_data=collections.defaultdict(list) + 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] + 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 PhenotypeDataSet(DataSet): - DS_NAME_MAP['Publish']='PhenotypeDataSet' + DS_NAME_MAP['Publish'] = 'PhenotypeDataSet' def setup(self): # Fields in the database table - self.search_fields=['Phenotype.Post_publication_description', + self.search_fields = ['Phenotype.Post_publication_description', 'Phenotype.Pre_publication_description', 'Phenotype.Pre_publication_abbreviation', 'Phenotype.Post_publication_abbreviation', @@ -821,7 +814,7 @@ class PhenotypeDataSet(DataSet): 'PublishXRef.Id'] # Figure out what display_fields is - self.display_fields=['name', 'group_code', + self.display_fields = ['name', 'group_code', 'pubmed_id', 'pre_publication_description', 'post_publication_description', @@ -839,7 +832,7 @@ class PhenotypeDataSet(DataSet): 'sequence', 'units', 'comments'] # Fields displayed in the search results table header - self.header_fields=['Index', + self.header_fields = ['Index', 'Record', 'Description', 'Authors', @@ -848,9 +841,9 @@ class PhenotypeDataSet(DataSet): 'Max LRS Location', 'Additive Effect'] - self.type='Publish' + self.type = 'Publish' - self.query_for_group=''' + self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM @@ -870,13 +863,13 @@ class PhenotypeDataSet(DataSet): if not this_trait.haveinfo: this_trait.retrieve_info(get_qtl_info=True) - description=this_trait.post_publication_description + 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="" + this_trait.description_display = "" continue # for now, because no authorization features if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait( @@ -884,46 +877,46 @@ class PhenotypeDataSet(DataSet): userName=self.userName, authorized_users=this_trait.authorized_users): - description=this_trait.pre_publication_description + description = this_trait.pre_publication_description if len(description) > 0: - this_trait.description_display=description.strip() + this_trait.description_display = description.strip() else: - this_trait.description_display="" + this_trait.description_display = "" if not this_trait.year.isdigit(): - this_trait.pubmed_text="N/A" + this_trait.pubmed_text = "N/A" else: - this_trait.pubmed_text=this_trait.year + this_trait.pubmed_text = this_trait.year if this_trait.pubmed_id: - this_trait.pubmed_link=webqtlConfig.PUBMEDLINK_URL % 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" + this_trait.LRS_score_repr = "N/A" + this_trait.LRS_location_repr = "N/A" if this_trait.lrs: - query=""" + 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) logger.sql(query) - result=g.db.execute(query).fetchone() + result = g.db.execute(query).fetchone() if result: if result[0] and result[1]: - LRS_Chr=result[0] - LRS_Mb=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' % ( + 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=""" + query = """ SELECT Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2 FROM @@ -941,34 +934,34 @@ class PhenotypeDataSet(DataSet): Strain.Name """ logger.sql(query) - results=g.db.execute(query, (trait, self.id)).fetchall() + results = g.db.execute(query, (trait, self.id)).fetchall() return results class GenotypeDataSet(DataSet): - DS_NAME_MAP['Geno']='GenotypeDataSet' + DS_NAME_MAP['Geno'] = 'GenotypeDataSet' def setup(self): # Fields in the database table - self.search_fields=['Name', + self.search_fields = ['Name', 'Chr'] # Find out what display_fields is - self.display_fields=['name', + self.display_fields = ['name', 'chr', 'mb', 'source2', 'sequence'] # Fields displayed in the search results table header - self.header_fields=['Index', + self.header_fields = ['Index', 'ID', 'Location'] # Todo: Obsolete or rename this field - self.type='Geno' + self.type = 'Geno' - self.query_for_group=''' + self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM @@ -987,11 +980,11 @@ class GenotypeDataSet(DataSet): this_trait.retrieveInfo() if this_trait.chr and this_trait.mb: - this_trait.location_repr='Chr%s: %.6f' % ( + this_trait.location_repr = 'Chr%s: %.6f' % ( this_trait.chr, float(this_trait.mb)) def retrieve_sample_data(self, trait): - query=""" + query = """ SELECT Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2 FROM @@ -1008,7 +1001,7 @@ class GenotypeDataSet(DataSet): Strain.Name """ logger.sql(query) - results=g.db.execute(query, + results = g.db.execute(query, (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait, self.name)).fetchall() return results @@ -1022,11 +1015,11 @@ class MrnaAssayDataSet(DataSet): platform and is far too specific. ''' - DS_NAME_MAP['ProbeSet']='MrnaAssayDataSet' + DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet' def setup(self): # Fields in the database table - self.search_fields=['Name', + self.search_fields = ['Name', 'Description', 'Probe_Target_Description', 'Symbol', @@ -1036,7 +1029,7 @@ class MrnaAssayDataSet(DataSet): 'RefSeq_TranscriptId'] # Find out what display_fields is - self.display_fields=['name', 'symbol', + self.display_fields = ['name', 'symbol', 'description', 'probe_target_description', 'chr', 'mb', 'alias', 'geneid', @@ -1056,7 +1049,7 @@ class MrnaAssayDataSet(DataSet): 'flag'] # Fields displayed in the search results table header - self.header_fields=['Index', + self.header_fields = ['Index', 'Record', 'Symbol', 'Description', @@ -1067,9 +1060,9 @@ class MrnaAssayDataSet(DataSet): 'Additive Effect'] # Todo: Obsolete or rename this field - self.type='ProbeSet' + self.type = 'ProbeSet' - self.query_for_group=''' + self.query_for_group = ''' SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM @@ -1087,7 +1080,7 @@ class MrnaAssayDataSet(DataSet): # Note: setting trait_list to [] is probably not a great idea. if not trait_list: - trait_list=[] + trait_list = [] for this_trait in trait_list: @@ -1095,33 +1088,33 @@ class MrnaAssayDataSet(DataSet): this_trait.retrieveInfo(QTL=1) if not this_trait.symbol: - this_trait.symbol="N/A" + this_trait.symbol = "N/A" # XZ, 12/08/2008: description # XZ, 06/05/2009: Rob asked to add probe target description - description_string=str( + description_string = str( str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string=str( + 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 + description_display = description_string else: - description_display=this_trait.symbol + 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() + description_display = description_display + '; ' + target_string.strip() # Save it for the jinja2 template - this_trait.description_display=description_display + this_trait.description_display = description_display if this_trait.chr and this_trait.mb: - this_trait.location_repr='Chr%s: %.6f' % ( + this_trait.location_repr = 'Chr%s: %.6f' % ( this_trait.chr, float(this_trait.mb)) # Get mean expression value - query=( + query = ( """select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet where ProbeSetXRef.ProbeSetFreezeId = %s and ProbeSet.Id = ProbeSetXRef.ProbeSetId and @@ -1131,38 +1124,38 @@ class MrnaAssayDataSet(DataSet): # logger.debug("query is:", pf(query)) logger.sql(query) - result=g.db.execute(query).fetchone() + result = g.db.execute(query).fetchone() - mean=result[0] if result else 0 + mean = result[0] if result else 0 if mean: - this_trait.mean="%2.3f" % 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' + 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=""" + 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() + 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, 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=""" + query = """ SELECT Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2 FROM @@ -1183,19 +1176,19 @@ class MrnaAssayDataSet(DataSet): Strain.Name """ % (escape(trait), escape(self.name)) logger.sql(query) - results=g.db.execute(query).fetchall() + results = g.db.execute(query).fetchall() # logger.debug("RETRIEVED RESULTS HERE:", results) return results def retrieve_genes(self, column_name): - query=""" + 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() + results = g.db.execute(query).fetchall() return dict(results) @@ -1203,40 +1196,51 @@ class MrnaAssayDataSet(DataSet): class TempDataSet(DataSet): '''Temporary user-generated data set''' - DS_NAME_MAP['Temp']='TempDataSet' + DS_NAME_MAP['Temp'] = 'TempDataSet' def setup(self): - self.search_fields=['name', + self.search_fields = ['name', 'description'] - self.display_fields=['name', + self.display_fields = ['name', 'description'] - self.header_fields=['Name', + self.header_fields = ['Name', 'Description'] - self.type='Temp' + self.type = 'Temp' # Need to double check later how these are used - self.id=1 - self.fullname='Temporary Storage' - self.shortname='Temp' + self.id = 1 + self.fullname = 'Temporary Storage' + self.shortname = 'Temp' def geno_mrna_confidentiality(ob): - dataset_table=ob.type + "Freeze" + dataset_table = ob.type + "Freeze" # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table)) - query='''SELECT Id, Name, FullName, confidentiality, + query = '''SELECT Id, Name, FullName, confidentiality, AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name) logger.sql(query) - result=g.db.execute(query) + result = g.db.execute(query) + + (dataset_id, + name, + full_name, + confidential, + authorized_users) = result.fetchall()[0] + + if confidential: + return True +uery) + result = g.db.execute(query) (dataset_id, name, full_name, confidential, - authorized_users)=result.fetchall()[0] + authorized_users) = result.fetchall()[0] if confidential: return True |