Merge branch 'testing' of github.com:genenetwork/genenetwork2 into feature/add_rqtl_pairscan

2 files changed, 133 insertions, 60 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8906ab69..af248659 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -20,7 +20,7 @@
 from dataclasses import dataclass
 from dataclasses import field
 from dataclasses import InitVar
-from typing import Optional, Dict
+from typing import Optional, Dict, List
 from db.call import fetchall, fetchone, fetch1
 from utility.logger import getLogger
 from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
@@ -39,6 +39,9 @@ from db import webqtlDatabaseFunction
 from base import species
 from base import webqtlConfig
 from flask import Flask, g
+from base.webqtlConfig import TMPDIR
+from urllib.parse import urlparse
+from utility.tools import SQL_URI
 import os
 import math
 import string
@@ -50,6 +53,8 @@ import requests
 import gzip
 import pickle as pickle
 import itertools
+import hashlib
+import datetime
 
 from redis import Redis
 
@@ -397,7 +402,8 @@ class DatasetGroup:
             self.parlist = [maternal, paternal]
 
     def get_study_samplelists(self):
-        study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists')
+        study_sample_file = locate_ignore_error(
+            self.name + ".json", 'study_sample_lists')
         try:
             f = open(study_sample_file)
         except:
@@ -423,8 +429,6 @@ class DatasetGroup:
         if result is not None:
             self.samplelist = json.loads(result)
         else:
-            logger.debug("Cache not hit")
-
             genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
             if genotype_fn:
                 self.samplelist = get_group_samplelists.get_samplelist(
@@ -447,7 +451,6 @@ class DatasetGroup:
         # genotype_1 is Dataset Object without parents and f1
         # genotype_2 is Dataset Object with parents and f1 (not for intercross)
 
-
         # reaper barfs on unicode filenames, so here we ensure it's a string
         if self.genofile:
             if "RData" in self.genofile:  # ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
@@ -726,7 +729,6 @@ class DataSet:
         data_results = self.chunk_dataset(query_results, len(sample_ids))
         self.samplelist = sorted_samplelist
         self.trait_data = data_results
-        
 
     def get_trait_data(self, sample_list=None):
         if sample_list:
@@ -745,66 +747,75 @@ class DataSet:
             and Species.name = '{}'
             """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
         results = dict(g.db.execute(query).fetchall())
-        sample_ids = [results[item] for item in self.samplelist]
+        sample_ids = [results.get(item)
+                      for item in self.samplelist if item is not None]
 
         # 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)
+        cached_results = fetch_cached_results(self.name, self.type)
+        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))
 
-        trait_count = len(trait_sample_data[0])
-        self.trait_data = collections.defaultdict(list)
+                results = g.db.execute(query).fetchall()
+                trait_sample_data.append([list(result) for result in results])
 
-        # 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:])
+            trait_count = len(trait_sample_data[0])
+            self.trait_data = collections.defaultdict(list)
+
+            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)):
+                    self.trait_data[trait_name] += (
+                        trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
+
+            cache_dataset_results(
+                self.name, self.type, self.trait_data)
+        else:
+
+            self.trait_data = cached_results
 
 
 class PhenotypeDataSet(DataSet):
@@ -1242,3 +1253,65 @@ def geno_mrna_confidentiality(ob):
 
     if confidential:
         return True
+
+
+def parse_db_url():
+    parsed_db = urlparse(SQL_URI)
+
+    return (parsed_db.hostname, parsed_db.username,
+            parsed_db.password, parsed_db.path[1:])
+
+
+def query_table_timestamp(dataset_type: str):
+    """function to query the update timestamp of a given dataset_type"""
+
+    # computation data and actions
+
+    fetch_db_name = parse_db_url()
+    query_update_time = f"""
+                    SELECT UPDATE_TIME FROM   information_schema.tables
+                    WHERE  TABLE_SCHEMA = '{fetch_db_name[-1]}'
+                    AND TABLE_NAME = '{dataset_type}Data'
+                """
+
+    date_time_obj = g.db.execute(query_update_time).fetchone()[0]
+    return date_time_obj.strftime("%Y-%m-%d %H:%M:%S")
+
+
+def generate_hash_file(dataset_name: str, dataset_type: 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(string_unicode)
+    return md5hash.hexdigest()
+
+
+def cache_dataset_results(dataset_name: str, dataset_type: str, query_results: List):
+    """function to cache dataset query results to file
+    input dataset_name and type query_results(already processed in default dict format)
+    """
+    # data computations actions
+    # store the file path on redis
+
+    table_timestamp = query_table_timestamp(dataset_type)
+
+
+    file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp)
+    file_path = os.path.join(TMPDIR, f"{file_name}.json")
+
+    with open(file_path, "w") as file_handler:
+        json.dump(query_results, file_handler)
+
+
+def fetch_cached_results(dataset_name: str, dataset_type: str):
+    """function to fetch the cached results"""
+
+    table_timestamp = query_table_timestamp(dataset_type)
+
+    file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp)
+    file_path = os.path.join(TMPDIR, f"{file_name}.json")
+    try:
+        with open(file_path, "r") as file_handler:
+
+            return json.load(file_handler)
+    except FileNotFoundError:
+        pass
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 96a09302..f0749858 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -7,7 +7,7 @@ from base.webqtlCaseData import webqtlCaseData
 from base.data_set import create_dataset
 from utility import hmac
 from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
+from utility.tools import GN2_BASE_URL, GN_PROXY_URL
 from utility.redis_tools import get_redis_conn, get_resource_id
 
 from utility.db_tools import escape
@@ -361,10 +361,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
+        the_url = GN_PROXY_URL + "run-action?resource={}&user={}&branch=data&action=view".format(
             resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+        the_url = GN_PROXY_URL + "run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
             resource_id, g.user_session.user_id, trait.name)
 
     try: