diff options
Diffstat (limited to 'gn3/base')
| -rw-r--r-- | gn3/base/__init__.py | 0 | ||||
| -rw-r--r-- | gn3/base/data_set.py | 882 | ||||
| -rw-r--r-- | gn3/base/mrna_assay_tissue_data.py | 94 | ||||
| -rw-r--r-- | gn3/base/species.py | 64 | ||||
| -rw-r--r-- | gn3/base/trait.py | 366 | ||||
| -rw-r--r-- | gn3/base/webqtlCaseData.py | 84 |
6 files changed, 0 insertions, 1490 deletions
diff --git a/gn3/base/__init__.py b/gn3/base/__init__.py deleted file mode 100644 index e69de29..0000000 --- a/gn3/base/__init__.py +++ /dev/null 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 diff --git a/gn3/base/mrna_assay_tissue_data.py b/gn3/base/mrna_assay_tissue_data.py deleted file mode 100644 index 0f51ade..0000000 --- a/gn3/base/mrna_assay_tissue_data.py +++ /dev/null @@ -1,94 +0,0 @@ - -# pylint: disable-all -import collections - -from flask import g - -from gn3.utility.db_tools import create_in_clause -from gn3.utility.db_tools import escape -from gn3.utility.bunch import Bunch - - -# from utility.logger import getLogger -# logger = getLogger(__name__ ) - -class MrnaAssayTissueData(object): - - def __init__(self, gene_symbols=None): - self.gene_symbols = gene_symbols - if self.gene_symbols == None: - self.gene_symbols = [] - - self.data = collections.defaultdict(Bunch) - - query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description - from ( - select Symbol, max(Mean) as maxmean - from TissueProbeSetXRef - where TissueProbeSetFreezeId=1 and ''' - - # Note that inner join is necessary in this query to get distinct record in one symbol group - # with highest mean value - # Due to the limit size of TissueProbeSetFreezeId table in DB, - # performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list) - if len(gene_symbols) == 0: - query += '''Symbol!='' and Symbol Is Not Null group by Symbol) - as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol - and t.Mean = x.maxmean; - ''' - else: - in_clause = create_in_clause(gene_symbols) - - # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower - query += ''' Symbol in {} group by Symbol) - as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol - and t.Mean = x.maxmean; - '''.format(in_clause) - - results = g.db.execute(query).fetchall() - - lower_symbols = [] - for gene_symbol in gene_symbols: - if gene_symbol != None: - lower_symbols.append(gene_symbol.lower()) - - for result in results: - symbol = result[0] - if symbol.lower() in lower_symbols: - symbol = symbol.lower() - - self.data[symbol].gene_id = result.GeneId - self.data[symbol].data_id = result.DataId - self.data[symbol].chr = result.Chr - self.data[symbol].mb = result.Mb - self.data[symbol].description = result.description - self.data[symbol].probe_target_description = result.Probe_Target_Description - - ########################################################################### - # Input: cursor, symbolList (list), dataIdDict(Dict) - # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair, - # key is symbol, value is one list of expression values of one probeSet; - # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type). - # Attention! All keys are lower case! - ########################################################################### - - def get_symbol_values_pairs(self): - id_list = [self.data[symbol].data_id for symbol in self.data] - - symbol_values_dict = {} - - if len(id_list) > 0: - query = """SELECT TissueProbeSetXRef.Symbol, TissueProbeSetData.value - FROM TissueProbeSetXRef, TissueProbeSetData - WHERE TissueProbeSetData.Id IN {} and - TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(create_in_clause(id_list)) - - results = g.db.execute(query).fetchall() - for result in results: - if result.Symbol.lower() not in symbol_values_dict: - symbol_values_dict[result.Symbol.lower()] = [result.value] - else: - symbol_values_dict[result.Symbol.lower()].append( - result.value) - - return symbol_values_dict diff --git a/gn3/base/species.py b/gn3/base/species.py deleted file mode 100644 index 9fb08fb..0000000 --- a/gn3/base/species.py +++ /dev/null @@ -1,64 +0,0 @@ - -# pylint: disable-all -import collections -from flask import g -from dataclasses import dataclass - -class TheSpecies: - def __init__(self, dataset=None, species_name=None): - if species_name is not None: - self.name = species_name - - self.chromosomes = Chromosomes(species=self.name) - - else: - self.dataset = dataset - self.chromosomes = Chromosomes(dataset=self.dataset) - - -class Chromosomes: - def __init__(self, dataset=None, species=None): - self.chromosomes = collections.OrderedDict() - - if species is not None: - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species - where - Chr_Length.SpeciesId = Species.SpeciesId AND - Species.Name = '%s' - Order by OrderId - """ % species.capitalize() - - else: - self.dataset = dataset - - query = """ - Select - Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet - where - Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = '%s' - Order by OrderId - """ % self.dataset.group.name - - # logger.sql(query) - - results = g.db.execute(query).fetchall() - - for item in results: - self.chromosomes[item.OrderId] = IndChromosome( - item.Name, item.Length) - - -# @dataclass -class IndChromosome: - def __init__(self,name,length): - self.name= name - self.length = length - - @property - def mb_length(self): - """Chromosome length in megabases""" - return self.length/ 1000000 - diff --git a/gn3/base/trait.py b/gn3/base/trait.py deleted file mode 100644 index f4be61c..0000000 --- a/gn3/base/trait.py +++ /dev/null @@ -1,366 +0,0 @@ - -# pylint: disable-all -from flask import g -from redis import Redis -from gn3.utility.db_tools import escape -from gn3.base.webqtlCaseData import webqtlCaseData - - -def check_resource_availability(dataset, name=None): - - # todo add code for this - # should probably work on this has to do with authentication - return {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']} - - -def create_trait(**kw): - # work on check resource availability deals with authentication - assert bool(kw.get("dataset")) != bool( - kw.get('dataset_name')), "Needs dataset ob. or name" - - assert bool(kw.get("name")), "Need trait 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 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 - - return None - - -class GeneralTrait: - def __init__(self, get_qtl_info=False, get_sample_info=True, **kw): - 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) - 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 - - 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 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 Exception as e: - 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) - - return trait - -def retrieve_trait_info(trait, dataset, get_qtl_info=False): - assert dataset, "Dataset doesn't exist" - - the_url = None - # some code should be added added here - - 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) - - 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))) - - 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)) - - trait_info = g.db.execute(query).fetchone() - else: # Temp type - query = """SELECT %s FROM %s WHERE Name = %s""" - - 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 - trait.description_display = "" - 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() - - if not trait.year.isdigit(): - trait.pubmed_text = "N/A" - else: - trait.pubmed_text = trait.year - - # moved to config - - PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract" - - if trait.pubmed_id: - trait.pubmed_link = 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) - - 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) - - 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) - - 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) - - 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 diff --git a/gn3/base/webqtlCaseData.py b/gn3/base/webqtlCaseData.py deleted file mode 100644 index 8395af8..0000000 --- a/gn3/base/webqtlCaseData.py +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. -# -# This program is free software: you can redistribute it and/or modify it -# under the terms of the GNU Affero General Public License -# as published by the Free Software Foundation, either version 3 of the -# License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the GNU Affero General Public License for more details. -# -# This program is available from Source Forge: at GeneNetwork Project -# (sourceforge.net/projects/genenetwork/). -# -# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) -# at rwilliams@uthsc.edu and xzhou15@uthsc.edu -# -# This module is used by GeneNetwork project (www.genenetwork.org) -# -# Created by GeneNetwork Core Team 2010/08/10 - - -# uncomment below - -# from utility.logger import getLogger -# logger = getLogger(__name__) - -# import utility.tools - -# utility.tools.show_settings() -# pylint: disable-all - -class webqtlCaseData: - """one case data in one trait""" - - def __init__(self, name, value=None, variance=None, num_cases=None, name2=None): - self.name = name - self.name2 = name2 # Other name (for traits like BXD65a) - self.value = value # Trait Value - self.variance = variance # Trait Variance - self.num_cases = num_cases # Number of individuals/cases - self.extra_attributes = None - self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word) - self.outlier = None # Not set to True/False until later - - def __repr__(self): - case_data_string = "<webqtlCaseData> " - if self.value is not None: - case_data_string += "value=%2.3f" % self.value - if self.variance is not None: - case_data_string += " variance=%2.3f" % self.variance - if self.num_cases: - case_data_string += " ndata=%s" % self.num_cases - if self.name: - case_data_string += " name=%s" % self.name - if self.name2: - case_data_string += " name2=%s" % self.name2 - return case_data_string - - @property - def class_outlier(self): - """Template helper""" - if self.outlier: - return "outlier" - return "" - - @property - def display_value(self): - if self.value is not None: - return "%2.3f" % self.value - return "x" - - @property - def display_variance(self): - if self.variance is not None: - return "%2.3f" % self.variance - return "x" - - @property - def display_num_cases(self): - if self.num_cases is not None: - return "%s" % self.num_cases - return "x"
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