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- Fix bug
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@LucaCilibrasi
LucaCilibrasi committed Sep 3, 2021
1 parent 048cfc7 commit 9b9e6e4
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Showing 2 changed files with 235 additions and 102 deletions.
318 changes: 217 additions & 101 deletions backend/apis/analyze.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@
client = MongoClient(uri)
db = client.gcm_gisaid

collection_db = db.seq_2021_08_26

########################################################################################################


Expand Down Expand Up @@ -339,6 +341,7 @@ def post(self):
single_line = {'lineage': item['lineage']}
country_count = item['country_count']
country_count = country_count.replace('"', "")
country_count = country_count.replace(")\\", "")
country_count = country_count.replace("\\", "")
country_count = country_count.replace("{", "")
country_count = country_count.replace("}", "")
Expand Down Expand Up @@ -1258,106 +1261,6 @@ def get_all_accession_id():
}


def prova_mongo_db():
print("prova Mongo")
seq = db.seq
print("prova Mongo2")

# "$match": {
# # 'covv_collection_date': {
# # '$gte': "2019-01-01",
# # '$lte': "2021-07-31",
# # '$regex': "\d\d\d\d-\d\d-\d\d"
# # },
# # 'covv_location': {
# # '$regex': "Italy"
# # },

pipeline = [
{
"$match": {
'location.geo_group': {
'$eq': 'Oceania'
},
'location.country': {
'$eq': 'Australia'
},
'location.region': {
'$eq': 'Northern Territory'
},
},
},
{"$unwind": "$muts"},
{"$group":
#{"_id": "$_id",
{"_id":
{'pro': "$muts.pro",
'org': "$muts.org",
'loc': "$muts.loc",
'alt': "$muts.alt",
},
"count": {"$sum": 1}
}
},
{'$sort':
{"_id.pro": -1}
}
]
print("start")
results = seq.aggregate(pipeline, )
print("stop", len(list(results)))
# for i, x in enumerate(results):
# print("qui", x)
# if i < 1:
# print("qui", x)
# break
print("fine prova Mongo2")


def get_all_geo_mongoDB():
print("inizio request geo")
start_date = datetime.strptime("2019-01-01", '%Y-%m-%d')
results = db.seq.aggregate(
[
{
"$match": {
'collection_date': {
'$gte': start_date
},
'c_coll_date_prec': {
'$eq': 2
},
},
},
{
"$group": {"_id":
{"geo_group": "$location.geo_group",
"country": "$location.country",
"region": "$location.region",
"province": "$location.province"
},
"count": {"$sum": 1}
}
},
]
)
list_geo_dict = []
for single_item in results:
single_item_remodel = {'geo_group': single_item['_id']['geo_group'],
'country': single_item['_id']['country'],
'region': single_item['_id']['region'],
'province': single_item['_id']['province'], 'count': single_item['count']}
list_geo_dict.append(single_item_remodel)
all_geo_dict['all_geo'] = list_geo_dict
print("fine request geo")
x = datetime.today()
y = x.replace(day=x.day, hour=2, minute=0, second=0, microsecond=0) + timedelta(days=1)
delta_t = y - x
secs = delta_t.total_seconds()
t4 = Timer(secs, get_all_geo)
t4.start()


@api.route('/selectorQueryMongoDB')
class FieldList(Resource):
@api.doc('selector_query_mongo_db')
Expand Down Expand Up @@ -1462,6 +1365,29 @@ def post(self):
real_field = translate_dictionary[field_name]
if field_name == 'geo_group' or field_name == 'country' or field_name == 'region' or field_name == 'province':
real_field = 'location.' + field_name
# group_part["_id"] = {"value":
# {"$cond":
# [{"$eq": [f"${real_field}", ""]},
# None,
# {"$cond":
# [{"$eq": [f"${real_field}", None]},
# f"${real_field}",
# {"$concat": [
# {"$toUpper":
# {"$substrCP": [f"${real_field}", 0, 1]}
# },
# {
# "$substrCP": [
# f"${real_field}", 1,
# {"$subtract": [{"$strLenCP": f"${real_field}"}, 1]}
# ]
# }
# ]}
# ]
# }
# ]
# },
# }
group_part["_id"] = {"value": f"${real_field}"}
group_part["count"] = {"$sum": 1}
query_group = {"$group": group_part}
Expand All @@ -1472,7 +1398,7 @@ def post(self):
query.append(query_sort)
# print("query", query)

results = db.seq.aggregate(query)
results = collection_db.aggregate(query)

list_dict = []
for single_item in list(results):
Expand All @@ -1488,6 +1414,196 @@ def post(self):
return list_dict


def get_all_geo_mongoDB():
print("inizio request geo")
start_date = datetime.strptime("2019-01-01", '%Y-%m-%d')
query = [
{
"$match": {
'collection_date': {
'$gte': start_date
},
'c_coll_date_prec': {
'$eq': 2
},
},
},
{
"$group": {"_id":
{
'geo_group': '$location.geo_group',
'country': '$location.country',
'region': '$location.region',
'province': '$location.province',
},
"count": {"$sum": 1}
}
},
]

# {"geo_group":
# {"$cond":
# [{"$eq": ["$location.geo_group", ""]},
# None,
# {"$cond":
# [{"$eq": ["$location.geo_group", None]},
# "$location.geo_group",
# {"$concat": [
# {"$toUpper":
# {"$substrCP": ["$location.geo_group", 0, 1]}
# },
# {
# "$substrCP": [
# "$location.geo_group", 1,
# {"$subtract": [{"$strLenCP": "$location.geo_group"}, 1]}
# ]
# }
# ]}
# ]
# }
# ]
# },
# "country":
# {"$cond":
# [{"$eq": ["$location.country", ""]},
# None,
# {"$cond":
# [{"$eq": ["$location.country", None]},
# "$location.country",
# {"$concat": [
# {"$toUpper":
# {"$substrCP": ["$location.country", 0, 1]}
# },
# {
# "$substrCP": [
# "$location.country", 1,
# {"$subtract": [{"$strLenCP": "$location.country"}, 1]}
# ]
# }
# ]}
# ]
# }
# ]
# },
# "region":
# {"$cond":
# [{"$eq": ["$location.region", ""]},
# None,
# {"$cond":
# [{"$eq": ["$location.region", None]},
# "$location.region",
# {"$concat": [
# {"$toUpper":
# {"$substrCP": ["$location.region", 0, 1]}
# },
# {
# "$substrCP": [
# "$location.region", 1,
# {"$subtract": [{"$strLenCP": "$location.region"}, 1]}
# ]
# }
# ]}
# ]
# }
# ]
# },
# "province":
# {"$cond":
# [{"$eq": ["$location.province", ""]},
# None,
# {"$cond":
# [{"$eq": ["$location.province", None]},
# "$location.province",
# {"$concat": [
# {"$toUpper":
# {"$substrCP": ["$location.province", 0, 1]}
# },
# {
# "$substrCP": [
# "$location.province", 1,
# {"$subtract": [{"$strLenCP": "$location.province"}, 1]}
# ]
# }
# ]}
# ]
# }
# ]
# },

results = collection_db.aggregate(query)
list_geo_dict = []
for single_item in results:
single_item_remodel = {'geo_group': single_item['_id']['geo_group'],
'country': single_item['_id']['country'],
'region': single_item['_id']['region'],
'province': single_item['_id']['province'], 'count': single_item['count']}
list_geo_dict.append(single_item_remodel)
all_geo_dict['all_geo'] = list_geo_dict
print("fine request geo")
x = datetime.today()
y = x.replace(day=x.day, hour=2, minute=0, second=0, microsecond=0) + timedelta(days=1)
delta_t = y - x
secs = delta_t.total_seconds()
t4 = Timer(secs, get_all_geo)
t4.start()


def prova_mongo_db():
print("prova Mongo")
seq = collection_db
print("prova Mongo2")

# "$match": {
# # 'covv_collection_date': {
# # '$gte': "2019-01-01",
# # '$lte': "2021-07-31",
# # '$regex': "\d\d\d\d-\d\d-\d\d"
# # },
# # 'covv_location': {
# # '$regex': "Italy"
# # },

pipeline = [
{
"$match": {
'location.geo_group': {
'$eq': 'Oceania'
},
'location.country': {
'$eq': 'Australia'
},
'location.region': {
'$eq': 'Northern Territory'
},
},
},
{"$unwind": "$muts"},
{"$group":
#{"_id": "$_id",
{"_id":
{'pro': "$muts.pro",
'org': "$muts.org",
'loc': "$muts.loc",
'alt': "$muts.alt",
},
"count": {"$sum": 1}
}
},
{'$sort':
{"_id.pro": -1}
}
]
print("start")
results = seq.aggregate(pipeline, )
print("stop", len(list(results)))
# for i, x in enumerate(results):
# print("qui", x)
# if i < 1:
# print("qui", x)
# break
print("fine prova Mongo2")


def prova_mongo_2():
print("qui2")

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