diff options
Diffstat (limited to 'wqflask/base/data_set.py')
| -rw-r--r-- | wqflask/base/data_set.py | 115 |
1 files changed, 61 insertions, 54 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 11ed2495..1a208050 100644 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -39,6 +39,7 @@ from db import webqtlDatabaseFunction from base import species from base import webqtlConfig from flask import Flask, g +from base.webqtlConfig import TMPDIR import os import math import string @@ -50,6 +51,7 @@ import requests import gzip import pickle as pickle import itertools +import hashlib from redis import Redis @@ -751,54 +753,64 @@ class DataSet: # 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)) + cached_results = fetch_cached_results(self.name) + # cached_results = None + if cached_results is None: + 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) + results = g.db.execute(query).fetchall() + trait_sample_data.append([list(result) for result in results]) + + cache_dataset_results( + self.name, "cached_time_stamp", trait_sample_data) + + else: + trait_sample_data = cached_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 + data_start_pos = 1 for trait_counter in range(trait_count): trait_name = trait_sample_data[0][trait_counter][0] for chunk_counter in range(int(number_chunks)): @@ -1247,39 +1259,34 @@ def generate_hash_file(dataset_name: str, dataset_timestamp: str): """given the trait_name generate a unique name for this""" string_unicode = f"{dataset_name}{dataset_timestamp}".encode() - md5hash = hashlib.md5(str2hash.encode(string_unicode)) + md5hash = hashlib.md5(string_unicode) return md5hash.hexdigest() -def cache_dataset_results(dataset_name: str, query_results: List): +def cache_dataset_results(dataset_name: str, dataset_timestamp: str, query_results: List): """function to cache dataset query results to file""" - # check if file exists clear if it does - # aslo check for the timestamp - # hash for unique name ??? are dataset name unique # data computations actions # store the file path on redis - # hash functiob - file_name = generate_hash_file(dataset_name, "dataset_timestamp") + file_name = generate_hash_file(dataset_name, dataset_timestamp) file_path = os.path.join(TMPDIR, f"{file_name}.json") - query_results = [list(results) for result in query_results] - with open(file_path, "w") as file_handler: json.dump(query_results, file_handler) def fetch_cached_results(dataset_name: str): """function to fetch the cached results""" + # store the timestamp in redis - file_name = generate_hash_file(dataset_name,) - file_path = os.path.join(TMPDIR, f"{file_path}.json") - + file_name = generate_hash_file(dataset_name, "cached_time_stamp") + file_path = os.path.join(TMPDIR, f"{file_name}.json") try: - with open(file_path) as file_handler: + with open(file_path, "r") as file_handler: data = json.load(file_handler) + # print(file_handler) # check if table has been modified return data except FileNotFoundError: |