- Optimize import

DEIB-GECO · Sep 10, 2021 · 22b5f17 · 22b5f17
1 parent f90d823
commit 22b5f17
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diff --git a/backend/apis/__init__.py b/backend/apis/__init__.py
@@ -1,10 +1,10 @@
 from flask import Blueprint
 from flask_restplus import Api
 
-from .ufl import api as ufl
-from .private import api as private
 from .analyze import api as analyze
 from .downloadLineagesInfo import api as downloadLineagesInfo
+from .private import api as private
+from .ufl import api as ufl
 
 enable_doc = True
 

diff --git a/backend/apis/analyze.py b/backend/apis/analyze.py
@@ -1,25 +1,22 @@
 from __future__ import print_function
 
+import copy
 import http
 import json
-import pandas as pd
-import copy
-
-import statsmodels.stats.multitest as sms
-from scipy.stats import binom, chi2_contingency
-from flask_restplus import Namespace, Resource
-
 from datetime import datetime, timedelta
 from threading import Timer
 
+import pandas as pd
+import statsmodels.stats.multitest as sms
+from flask_restplus import Namespace, Resource
 from pymongo import MongoClient
+from scipy.stats import chi2_contingency
 
 from .downloadLineagesInfo import dict_lineage_mutation
 
 api = Namespace('analyze', description='analyze')
 
 uri = "mongodb://localhost:23456/gcm_gisaid"
-# uri = "mongodb://localhost:23457/gcm_gisaid"
 client = MongoClient(uri)
 db = client.gcm_gisaid
 
@@ -2584,15 +2581,17 @@ def post(self):
                 if key == 'minDate':
                     start_date = datetime.strptime(f"{query_background[key]}", '%Y-%m-%d')
                     where_part_background_overlapping['collection_date']['$gte'] = start_date
-                    if where_part_target_overlapping['collection_date']['$gte'] < start_date\
-                            < where_part_target_overlapping['collection_date']['$lte']:
-                        where_part_target_overlapping['collection_date']['$gte'] = start_date
+                    if "$lte" in where_part_target_overlapping['collection_date']:
+                        if where_part_target_overlapping['collection_date']['$gte'] < start_date\
+                                < where_part_target_overlapping['collection_date']['$lte']:
+                            where_part_target_overlapping['collection_date']['$gte'] = start_date
                 elif key == 'maxDate':
                     stop_date = datetime.strptime(f"{query_background[key]}", '%Y-%m-%d')
                     where_part_background_overlapping['collection_date']['$lte'] = stop_date
-                    if where_part_target_overlapping['collection_date']['$gte'] < stop_date \
-                            < where_part_target_overlapping['collection_date']['$lte']:
-                        where_part_target_overlapping['collection_date']['$lte'] = stop_date
+                    if "$lte" in where_part_target_overlapping['collection_date']:
+                        if where_part_target_overlapping['collection_date']['$gte'] < stop_date \
+                                < where_part_target_overlapping['collection_date']['$lte']:
+                            where_part_target_overlapping['collection_date']['$lte'] = stop_date
 
                 elif key == 'toExclude':
                     for fieldToExclude in query_background[key]:

diff --git a/backend/apis/analyze_file.py b/backend/apis/analyze_file.py
@@ -1,35 +1,18 @@
 from __future__ import print_function
+
+import collections
 # %config Completer.use_jedi = False
 import datetime
-import os
-import re
-
-import requests
-import io
 import http.client
+import io
+import itertools
 import json
-
-import pandas as pd
 from collections import defaultdict
-from Bio import SeqIO
 from io import StringIO
-from Bio import Align, Seq, pairwise2
-from Bio.Data import CodonTable
-import numpy as np
-import itertools
-import collections
-import logomaker
-import tqdm
-import psycopg2
-import matplotlib.pyplot as plt
-
-from ipywidgets import interact, interactive, fixed, interact_manual
-import ipywidgets as widgets
-from IPython.core.display import HTML
 
+import pandas as pd
 from flask_restplus import Namespace, Resource
 
-
 api = Namespace('analyze_file', description='analyze_file')
 
 

diff --git a/backend/apis/analyze_file_example.py b/backend/apis/analyze_file_example.py
@@ -1,31 +1,12 @@
 from __future__ import print_function
-# %config Completer.use_jedi = False
 
-import requests
 import io
-import http.client
-import json
-
-import pandas as pd
 from collections import defaultdict
-from Bio import SeqIO
-from io import StringIO
-from Bio import Align, Seq, pairwise2
-from Bio.Data import CodonTable
-import numpy as np
-import itertools
-import collections
-import logomaker
-import tqdm
-import psycopg2
-import matplotlib.pyplot as plt
-
-from ipywidgets import interact, interactive, fixed, interact_manual
-import ipywidgets as widgets
-from IPython.core.display import HTML
 
 from flask_restplus import Namespace, Resource
 
+# %config Completer.use_jedi = False
+
 
 api = Namespace('analyze_file_example', description='analyze_file_example')
 

diff --git a/backend/apis/downloadLineagesInfo.py b/backend/apis/downloadLineagesInfo.py
@@ -1,12 +1,10 @@
 import json
-
-import requests
-import lxml.html
-import pandas as pd
-
 from datetime import datetime, timedelta
 from threading import Timer
 
+import lxml.html
+import pandas as pd
+import requests
 from flask_restplus import Namespace
 
 api = Namespace('downloadLineagesInfo', description='downloadLineagesInfo')

diff --git a/backend/apis/private.py b/backend/apis/private.py
@@ -1,35 +1,23 @@
 from __future__ import print_function
+
+import collections
 # %config Completer.use_jedi = False
 import datetime
-import os
-import re
-
-import requests
-import io
 import http.client
+import io
+import itertools
 import json
+import os
+from collections import defaultdict
+from io import StringIO
 
 import pandas as pd
-from collections import defaultdict
+import tqdm
 from Bio import SeqIO
-from io import StringIO
-from Bio import Align, Seq, pairwise2
+from Bio import pairwise2
 from Bio.Data import CodonTable
-import numpy as np
-import itertools
-import collections
-import logomaker
-import tqdm
-import psycopg2
-import matplotlib.pyplot as plt
-
-from ipywidgets import interact, interactive, fixed, interact_manual
-import ipywidgets as widgets
-from IPython.core.display import HTML
-
 from flask_restplus import Namespace, Resource
 
-
 api = Namespace('private', description='private')
 
 

diff --git a/backend/apis/ufl.py b/backend/apis/ufl.py
@@ -1,12 +1,9 @@
+import http.client
 import json
-import urllib
 
 import requests
-import http.client
-
 from flask_restplus import Namespace, Resource
 
-
 api = Namespace('ufl', description='ufl')
 
 http.client._MAXLINE = 655360

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/certifi/__init__.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/certifi/__init__.py
@@ -1,3 +1 @@
-from .core import contents, where
-
 __version__ = "2020.11.08"
diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/__init__.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/__init__.py
@@ -16,9 +16,7 @@
 ######################### END LICENSE BLOCK #########################
 
 
-from .compat import PY2, PY3
 from .universaldetector import UniversalDetector
-from .version import __version__, VERSION
 
 
 def detect(byte_str):

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/big5prober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/big5prober.py
@@ -25,9 +25,9 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import Big5DistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import BIG5_SM_MODEL
 
 

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/chardistribution.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/chardistribution.py
@@ -25,14 +25,14 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .euctwfreq import (EUCTW_CHAR_TO_FREQ_ORDER, EUCTW_TABLE_SIZE,
-                        EUCTW_TYPICAL_DISTRIBUTION_RATIO)
+from .big5freq import (BIG5_CHAR_TO_FREQ_ORDER, BIG5_TABLE_SIZE,
+                       BIG5_TYPICAL_DISTRIBUTION_RATIO)
 from .euckrfreq import (EUCKR_CHAR_TO_FREQ_ORDER, EUCKR_TABLE_SIZE,
                         EUCKR_TYPICAL_DISTRIBUTION_RATIO)
+from .euctwfreq import (EUCTW_CHAR_TO_FREQ_ORDER, EUCTW_TABLE_SIZE,
+                        EUCTW_TYPICAL_DISTRIBUTION_RATIO)
 from .gb2312freq import (GB2312_CHAR_TO_FREQ_ORDER, GB2312_TABLE_SIZE,
                          GB2312_TYPICAL_DISTRIBUTION_RATIO)
-from .big5freq import (BIG5_CHAR_TO_FREQ_ORDER, BIG5_TABLE_SIZE,
-                       BIG5_TYPICAL_DISTRIBUTION_RATIO)
 from .jisfreq import (JIS_CHAR_TO_FREQ_ORDER, JIS_TABLE_SIZE,
                       JIS_TYPICAL_DISTRIBUTION_RATIO)
 

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/charsetgroupprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/charsetgroupprober.py
@@ -25,8 +25,8 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .enums import ProbingState
 from .charsetprober import CharSetProber
+from .enums import ProbingState
 
 
 class CharSetGroupProber(CharSetProber):

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/eucjpprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/eucjpprober.py
@@ -25,11 +25,11 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .enums import ProbingState, MachineState
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import EUCJPDistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .enums import ProbingState, MachineState
 from .jpcntx import EUCJPContextAnalysis
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import EUCJP_SM_MODEL
 
 

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/euckrprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/euckrprober.py
@@ -25,9 +25,9 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import EUCKRDistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import EUCKR_SM_MODEL
 
 

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/euctwprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/euctwprober.py
@@ -25,11 +25,12 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import EUCTWDistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import EUCTW_SM_MODEL
 
+
 class EUCTWProber(MultiByteCharSetProber):
     def __init__(self):
         super(EUCTWProber, self).__init__()

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/gb2312prober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/gb2312prober.py
@@ -25,11 +25,12 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import GB2312DistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import GB2312_SM_MODEL
 
+
 class GB2312Prober(MultiByteCharSetProber):
     def __init__(self):
         super(GB2312Prober, self).__init__()

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/mbcsgroupprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/mbcsgroupprober.py
@@ -27,15 +27,15 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
+from .big5prober import Big5Prober
 from .charsetgroupprober import CharSetGroupProber
-from .utf8prober import UTF8Prober
-from .sjisprober import SJISProber
+from .cp949prober import CP949Prober
 from .eucjpprober import EUCJPProber
-from .gb2312prober import GB2312Prober
 from .euckrprober import EUCKRProber
-from .cp949prober import CP949Prober
-from .big5prober import Big5Prober
 from .euctwprober import EUCTWProber
+from .gb2312prober import GB2312Prober
+from .sjisprober import SJISProber
+from .utf8prober import UTF8Prober
 
 
 class MBCSGroupProber(CharSetGroupProber):

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/sbcsgroupprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/sbcsgroupprober.py
@@ -27,17 +27,17 @@
 ######################### END LICENSE BLOCK #########################
 
 from .charsetgroupprober import CharSetGroupProber
-from .sbcharsetprober import SingleByteCharSetProber
+from .hebrewprober import HebrewProber
+from .langbulgarianmodel import Latin5BulgarianModel, Win1251BulgarianModel
 from .langcyrillicmodel import (Win1251CyrillicModel, Koi8rModel,
                                 Latin5CyrillicModel, MacCyrillicModel,
                                 Ibm866Model, Ibm855Model)
 from .langgreekmodel import Latin7GreekModel, Win1253GreekModel
-from .langbulgarianmodel import Latin5BulgarianModel, Win1251BulgarianModel
+from .langhebrewmodel import Win1255HebrewModel
 # from .langhungarianmodel import Latin2HungarianModel, Win1250HungarianModel
 from .langthaimodel import TIS620ThaiModel
-from .langhebrewmodel import Win1255HebrewModel
-from .hebrewprober import HebrewProber
 from .langturkishmodel import Latin5TurkishModel
+from .sbcharsetprober import SingleByteCharSetProber
 
 
 class SBCSGroupProber(CharSetGroupProber):

diff --git a/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/sjisprober.py b/backend/venv/lib/python3.9/site-packages/pip/_vendor/chardet/sjisprober.py
@@ -25,12 +25,12 @@
 # 02110-1301  USA
 ######################### END LICENSE BLOCK #########################
 
-from .mbcharsetprober import MultiByteCharSetProber
-from .codingstatemachine import CodingStateMachine
 from .chardistribution import SJISDistributionAnalysis
+from .codingstatemachine import CodingStateMachine
+from .enums import ProbingState, MachineState
 from .jpcntx import SJISContextAnalysis
+from .mbcharsetprober import MultiByteCharSetProber
 from .mbcssm import SJIS_SM_MODEL
-from .enums import ProbingState, MachineState
 
 
 class SJISProber(MultiByteCharSetProber):
Original file line number	Diff line number	Diff line change
		@@ -1,3 +1 @@
		from .core import contents, where

		__version__ = "2020.11.08"