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update_whole_detail.py
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update_whole_detail.py
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# -*- coding: utf-8 -*-
# __author__ = 'liubinxu'
import os
import re
import datetime
from bson.son import SON
from bson.objectid import ObjectId
import types
import gridfs
import json
import unittest
from biocluster.api.database.base import Base, report_check
from biocluster.config import Config
import argparse
from bson import json_util
class RefUpdate(object):
def __init__(self, project_type, bind_object=None):
super(RefUpdate, self).__init__()
self.db = Config().get_mongo_client(mtype=project_type, db_version=0)[Config().get_mongo_dbname(project_type, db_version=0)]
self._project_type = project_type
def update_record_by_dict(self, collection_name, query_dict, insert_dict):
conn = self.db[collection_name]
print(query_dict)
print("***", query_dict)
if "_id" in query_dict:
query_dic = {"_id": query_dict["_id"]}
else:
query_dic = query_dict
print query_dic
print insert_dict
conn.update(query_dic, {"$set": insert_dict}, upsert=True)
def get_exp_details(self, task_id):
conn = self.db["exp"]
exp_record = conn.find_one({
"task_id": task_id,
"level": "T"
})
query_dict = {
"exp_id": exp_record["main_id"],
}
conn = self.db["exp_detail"]
results = conn.find(query_dict)
g2t = dict()
for result in results:
if "gene_id" in result:
if result["gene_id"] in g2t:
g2t[result["gene_id"]].append(result["transcript_id"])
else:
g2t[result["gene_id"]] = [result["transcript_id"]]
return g2t
def get_trans_detail(self, task_id):
conn = self.db["genes"]
gene_record = conn.find_one({
"task_id": task_id
})
query_dict = {
"genes_id": gene_record["main_id"],
"level": "T",
"category": "lncRNA"
}
print(query_dict)
conn = self.db["genes_detail"]
results = conn.find(query_dict)
t = dict()
for result in results:
t[result["transcript_id"]] = result
return t
def update(self, task_id):
g2t = self.get_exp_details(task_id)
t = self.get_trans_detail(task_id)
conn = self.db["genes"]
gene_record = conn.find_one({
"task_id": task_id
})
query_dict = {
"genes_id": gene_record["main_id"],
"level": "G"
}
# print(g2t)
# print(t)
conn = self.db["genes_detail"]
results = conn.find(query_dict)
update_list = []
old_list = []
for result in results:
gene_id = result["gene_id"]
if len(result["transcripts"]) < len(g2t[gene_id]):
tran_list2 = result["transcripts"][:]
tran_list = result["transcripts"]
tran_ids = set([x["transcript_id"] for x in tran_list])
add_trans = set(g2t[gene_id]) - tran_ids
for tran_id in add_trans:
if tran_id in t:
t_dic = t[tran_id]
tran_list.append({
"start" : t_dic["start"],
"length" : t_dic["length"],
"transcript_id" : tran_id,
"end" : t_dic["end"],
"strand" : t_dic["strand"]
})
if len(tran_list) != len(tran_list2):
update = [result["_id"], tran_list]
old_list.append([result["_id"], tran_list2])
print(update)
update_list.append(update)
with open("old.back.json", "w") as f:
f.write(json_util.dumps(old_list))
for update in update_list:
query_dict = {"_id": update[0], "genes_id": gene_record["main_id"]}
insert_dict = {"transcripts": update[1]}
conn.update(query_dict, {"$set": insert_dict}, upsert=True)
if __name__ == '__main__':
cmd_samples = '''
'''
os.environ["current_mode"]="workflow"
os.environ["NTM_PORT"]="7322"
os.environ["WFM_PORT"]="7321"
parser = argparse.ArgumentParser(description='for update by table\n ')
parser.add_argument('-p', type=str, default="ref_rna_v2", help="project type.")
parser.add_argument('-t', type=str, default=None, help='task')
parser.add_argument('-d', type=str, default=None, help='detail table')
parser.add_argument('-m', type=str, default=None, help='main_table')
args = parser.parse_args()
update_api = RefUpdate(args.p)
update_api.update(args.t)
# python ./update_by_table.py -p small_rna -c sg_annotation_query_detail -t table -q_f 'lambda x:{"query_id" : ObjectId("5c1b4504a4e1af70b4bd4543"), "transcript_id":x[0]}' -i_f 'lambda x:{"gene_name": x[1]}'