diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/datasets.py | 371 | ||||
| -rw-r--r-- | gn3/computations/traits.py | 56 |
2 files changed, 0 insertions, 427 deletions
diff --git a/gn3/computations/datasets.py b/gn3/computations/datasets.py deleted file mode 100644 index b69583e..0000000 --- a/gn3/computations/datasets.py +++ /dev/null @@ -1,371 +0,0 @@ -"""module contains the code all related to datasets""" -import json -from math import ceil -from collections import defaultdict - -from typing import Optional -from typing import List - -from dataclasses import dataclass -from MySQLdb import escape_string # type: ignore - -import requests -from gn3.settings import GN2_BASE_URL - - -def retrieve_trait_sample_data(dataset, - trait_name: str, - database, - group_species_id=None) -> List: - """given the dataset id and trait_name fetch the\ - sample_name,value from the dataset""" - - # should pass the db as arg all do a setup - - (dataset_name, dataset_id, dataset_type) = (dataset.get("name"), dataset.get( - "id"), dataset.get("type")) - - dataset_query = get_query_for_dataset_sample(dataset_type) - results = [] - sample_query_values = { - "Publish": (trait_name, dataset_id), - "Geno": (group_species_id, trait_name, dataset_name), - "ProbeSet": (trait_name, dataset_name) - } - - if dataset_query: - formatted_query = dataset_query % sample_query_values[dataset_type] - - results = fetch_from_db_sample_data(formatted_query, database) - - return results - - -def fetch_from_db_sample_data(formatted_query: str, database_instance) -> List: - """this is the function that does the actual fetching of\ - results from the database""" - try: - cursor = database_instance.cursor() - cursor.execute(formatted_query) - results = cursor.fetchall() - - except Exception as error: - raise error - - cursor.close() - - return results - - -def get_query_for_dataset_sample(dataset_type) -> Optional[str]: - """this functions contains querys for\ - getting sample data from the db depending in - dataset""" - dataset_query = {} - - pheno_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 - """ - geno_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 - """ - - probeset_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 - """ - - dataset_query["Publish"] = pheno_query - dataset_query["Geno"] = geno_query - dataset_query["ProbeSet"] = probeset_query - - return dataset_query.get(dataset_type) - - -@dataclass -class Dataset: - """class for creating datasets""" - name: Optional[str] = None - dataset_type: Optional[str] = None - dataset_id: int = -1 - - -def create_mrna_tissue_dataset(dataset_name, dataset_type): - """an mrna assay is a quantitative assessment(assay) associated\ - with an mrna trait.This used to be called probeset,but that term\ - only referes specifically to the afffymetrix platform and is\ - far too speficified""" - - return Dataset(name=dataset_name, dataset_type=dataset_type) - - -def dataset_type_getter(dataset_name, redis_instance=None) -> Optional[str]: - """given the dataset name fetch the type\ - of the dataset this in turn enables fetching\ - the creation of the correct object could utilize\ - redis for the case""" - - results = redis_instance.get(dataset_name, None) - - if results: - return results - - return fetch_dataset_type_from_gn2_api(dataset_name) - - -def fetch_dataset_type_from_gn2_api(dataset_name): - """this function is only called when the\ - the redis is empty and does have the specificied\ - dataset_type""" - # should only run once - - dataset_structure = {} - - map_dataset_to_new_type = { - "Phenotypes": "Publish", - "Genotypes": "Geno", - "MrnaTypes": "ProbeSet" - } - - data = json.loads(requests.get( - GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content) - _name = dataset_name - 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]: - # assumes the first is dataset_short_name - short_dataset_name = next( - item for item in dataset if item != "None" and item is not None) - - dataset_structure[short_dataset_name] = map_dataset_to_new_type.get( - dataset_type, "MrnaTypes") - return dataset_structure - - -def dataset_creator_store(dataset_type): - """function contains key value pairs for\ - the function need to be called to create\ - each dataset_type""" - - dataset_obj = { - "ProbeSet": create_mrna_tissue_dataset - } - - return dataset_obj[dataset_type] - - -def create_dataset(dataset_type=None, dataset_name: str = None): - """function for creating new dataset temp not implemented""" - if dataset_type is None: - dataset_type = dataset_type_getter(dataset_name) - - dataset_creator = dataset_creator_store(dataset_type) - results = dataset_creator( - dataset_name=dataset_name, dataset_type=dataset_type) - return results - - -def fetch_dataset_sample_id(samplelist: List, database, species: str) -> dict: - """fetch the strain ids from the db only if\ - it is in the samplelist""" - # xtodo create an in clause for samplelist - - strain_query = """ - SELECT Strain.Name, Strain.Id FROM Strain, Species - WHERE Strain.Name IN {} - and Strain.SpeciesId=Species.Id - and Species.name = '{}' - """ - - database_cursor = database.cursor() - database_cursor.execute(strain_query.format(samplelist, species)) - - results = database_cursor.fetchall() - - return dict(results) - - -def divide_into_chunks(the_list, number_chunks): - """Divides a list into approximately number_chunks - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3) - [[1, 2, 7], [3, 22, 8], [5, 22, 333]]""" - - length = len(the_list) - if length == 0: - return [[]] - - if length <= number_chunks: - number_chunks = length - chunk_size = int(ceil(length/number_chunks)) - chunks = [] - - for counter in range(0, length, chunk_size): - chunks.append(the_list[counter:counter+chunk_size]) - return chunks - - -def escape(string_): - """function escape sql value""" - return escape_string(string_).decode('utf8') - - -def mescape(*items) -> List: - """multiple escape for query values""" - - return [escape_string(str(item)).decode('utf8') for item in items] - - -def get_traits_data(sample_ids, database_instance, dataset_name, dataset_type): - """function to fetch trait data""" - # 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 - - _trait_data = defaultdict(list) - chunk_size = 61 - number_chunks = int(ceil(len(sample_ids) / chunk_size)) - for sample_ids_step in divide_into_chunks(sample_ids, number_chunks): - if dataset_type == "Publish": - full_dataset_type = "Phenotype" - else: - full_dataset_type = dataset_type - temp = ['T%s.value' % item for item in sample_ids_step] - - if dataset_type == "Publish": - query = "SELECT {}XRef.Id,".format(escape(dataset_type)) - - else: - query = "SELECT {}.Name,".format(escape(full_dataset_type)) - - query += ', '.join(temp) - query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(full_dataset_type, - dataset_type, - dataset_type)) - for item in sample_ids_step: - - query += """ - left join {}Data as T{} on T{}.Id = {}XRef.DataId - and T{}.StrainId={}\n - """.format(*mescape(dataset_type, item, - item, dataset_type, item, item)) - - if dataset_type == "Publish": - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - and {}.Id = {}XRef.{}Id - order by {}.Id - """.format(*mescape(dataset_type, dataset_type, - dataset_type, dataset_type, - dataset_name, full_dataset_type, - dataset_type, dataset_type, - full_dataset_type)) - - else: - query += """ - WHERE {}XRef.{}FreezeId = {}Freeze.Id - and {}Freeze.Name = '{}' - and {}.Id = {}XRef.{}Id - order by {}.Id - """.format(*mescape(dataset_type, dataset_type, - dataset_type, dataset_type, - dataset_name, dataset_type, - dataset_type, dataset_type, - full_dataset_type)) - - # print(query) - - _results = fetch_from_db_sample_data(query, database_instance) - - return [] - - -def get_probeset_trait_data(strain_ids: List, conn, dataset_name) -> dict: - """function for getting trait data\ - for probeset data type similar to\ - get trait data only difference is that\ - it uses sub queries""" - - trait_data: dict = {} - - trait_id_name = {} - - traits_query = """ - SELECT ProbeSetXRef.DataId,ProbeSet.Name FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id - and ProbeSetFreeze.Name = '{}' - and ProbeSet.Id = ProbeSetXRef.ProbeSetId - order by ProbeSet.Id - """.format(dataset_name) - - query = """ - SELECT * from ProbeSetData - where StrainID in ({}) - and id in (SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) - WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id - and ProbeSetFreeze.Name = '{}' - and ProbeSet.Id = ProbeSetXRef.ProbeSetId - order by ProbeSet.Id) - """.format(",".join(str(strain_id) for strain_id in strain_ids), dataset_name) - - with conn: - cursor = conn.cursor() - cursor.execute(query) - _results = cursor.fetchall() - cursor.execute(traits_query) - trait_id_name = dict(cursor.fetchall()) - - for trait_id, _strain_id, strain_value in _results: - trait_name = trait_id_name[trait_id] - if trait_data.get(trait_name): - trait_data[trait_name].append(strain_value) - else: - trait_data[trait_name] = [] - - trait_data[trait_name].append(strain_value) - - return trait_data diff --git a/gn3/computations/traits.py b/gn3/computations/traits.py deleted file mode 100644 index 1aa2970..0000000 --- a/gn3/computations/traits.py +++ /dev/null @@ -1,56 +0,0 @@ -"""module contains all operating related to traits""" -from gn3.computations.datasets import retrieve_trait_sample_data - - -def fetch_trait(dataset, trait_name: str, database) -> dict: - """this method creates a trait by\ - fetching required data given the\ - dataset and trait_name""" - - created_trait = { - "dataset": dataset, - "trait_name": trait_name - } - - trait_data = get_trait_sample_data(dataset, trait_name, database) - - created_trait["trait_data"] = trait_data - - return created_trait - - -def get_trait_sample_data(trait_dataset, trait_name, database) -> dict: - """first try to fetch the traits sample data from redis if that\ - try to fetch from the traits dataset redis is only used for\ - temp dataset type which is not used in this case """ - - sample_results = retrieve_trait_sample_data( - trait_dataset, trait_name, database) - - trait_data = {} - - for (name, sample_value, _variance, _numcase, _name2) in sample_results: - - trait_data[name] = sample_value - return trait_data - - -def get_trait_info_data(trait_dataset, - trait_name: str, - database_instance, - get_qtl_info: bool = False) -> dict: - """given a dataset and trait_name return a dict containing all info\ - regarding the get trait""" - - _temp_var_holder = (trait_dataset, trait_name, - database_instance, get_qtl_info) - trait_info_data = { - "description": "", - "chr": "", - "locus": "", - "mb": "", - "abbreviation": "", - "trait_display_name": "" - - } - return trait_info_data |