def glycan_to_biosynthesis_enzymes(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("usecases_group_one", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = get_mongo_query("glycan_to_biosynthesis_enzymes", query_obj)
#return mongo_query
collection = "c_glycan"
cache_collection = "c_cache"
search_type = "glycan_to_biosynthesis_enzymes"
record_type = "protein"
record_list = []
prj_obj = {"enzyme": 1}
obj = dbh[collection].find_one(mongo_query, prj_obj)
seen = {}
if obj != None:
for o in obj["enzyme"]:
if o["uniprot_canonical_ac"] not in seen:
seen[o["uniprot_canonical_ac"]] = True
tax_id = o["tax_id"]
if query_obj["tax_id"] == 0:
record_list.append(o["uniprot_canonical_ac"])
elif tax_id == query_obj["tax_id"]:
record_list.append(o["uniprot_canonical_ac"])
query_obj["organism"] = {
"id": query_obj["tax_id"],
"name": config_obj["taxid2name"][str(query_obj["tax_id"])]
}
query_obj.pop("tax_id")
res_obj = {}
ts_format = "%Y-%m-%d %H:%M:%S %Z%z"
ts = datetime.datetime.now(pytz.timezone('US/Eastern')).strftime(ts_format)
cache_coll = "c_cache"
list_id = ""
if len(record_list) != 0:
hash_obj = hashlib.md5(record_type + "_" + json.dumps(query_obj))
list_id = hash_obj.hexdigest()
cache_info = {
"query": query_obj,
"ts": ts,
"record_type": record_type,
"search_type": search_type
}
util.cache_record_list(dbh, list_id, record_list, cache_info,
cache_coll, config_obj)
res_obj = {"list_id": list_id}
return res_obj
def auth_userid(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("auth_userid", {}, config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_userid"
res_obj = {}
i = 0
while True:
user_id = util.get_random_string(32).lower()
user_obj = {"userid": user_id}
if dbh[collection].find(user_obj).count() == 0:
ts = datetime.datetime.now(
pytz.timezone('US/Eastern')).strftime('%Y-%m-%d %H:%M:%S %Z%z')
user_obj["created_ts"] = ts
result = dbh[collection].insert_one(user_obj)
return {"user": user_id}
if i > 100000:
return {"error_list": [{"error_code": "userid-generator-failed"}]}
i += 1
def disease_to_glycosyltransferases(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query(
"disease_to_glycosyltransferases_direct", query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_protein"
results = []
mongo_query = usecases_apilib.get_mongo_query(
"disease_to_glycosyltransferases", query_obj)
results_dict = {}
i = 0
collection = "c_protein"
main_id = "uniprot_canonical_ac"
for obj_one in dbh[collection].find(mongo_query):
canon = obj_one[main_id]
i += 1
if i > config_obj["max_results_count"]["protein"]:
break
results_dict[canon] = obj_one
res_obj = get_results_batch(results_dict, query_obj, config_obj)
return res_obj
def commonquery_search_protein(query_obj, config_obj, result_type):
collection = "c_protein"
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
query_obj = clean_protein_query(dbh, query_obj, config_obj)
error_list = errorlib.get_errors_in_query("commonquery_search_protein",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = get_protein_mongo_query(query_obj)
res_obj = {}
seen = {}
prj_obj = {"uniprot_canonical_ac": 1, "glycosylation": 1}
for obj in dbh[collection].find(mongo_query, prj_obj):
if result_type in ["protein_list", "count_list"]:
canon = obj["uniprot_canonical_ac"]
res_obj[canon] = get_protein_list_record(obj)
elif result_type == "glycan_list":
if "glycosylation" in obj:
for xobj in obj["glycosylation"]:
glytoucan_ac = xobj["glytoucan_ac"]
o = dbh["c_glycan"].find_one(
{"glytoucan_ac": glytoucan_ac})
if o != None and glytoucan_ac not in seen:
res_obj[glytoucan_ac] = get_glycan_list_record(o)
seen[glytoucan_ac] = True
return res_obj
def protein_to_glycosequons(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("usecases_group_seven",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
#mongo_query = {"uniprot_canonical_ac":query_obj["uniprot_canonical_ac"]}
mongo_query = {
"$or": [{
"uniprot_canonical_ac": {
'$eq': query_obj["uniprot_canonical_ac"]
}
}, {
"uniprot_ac": {
'$eq': query_obj["uniprot_canonical_ac"]
}
}]
}
#return mongo_query
collection = "c_protein"
cache_collection = "c_cache"
obj = dbh[collection].find_one(mongo_query)
tmp_list = obj["site_annotation"] if obj != None else []
results = []
for o in tmp_list:
if o["annotation"] == "n_glycosylation_sequon":
results.append(o)
res_obj = {}
if len(results) == 0:
res_obj = {"list_id": ""}
else:
ts = datetime.datetime.now(
pytz.timezone('US/Eastern')).strftime('%Y-%m-%d %H:%M:%S %Z%z')
hash_obj = hashlib.md5(json.dumps(query_obj))
list_id = hash_obj.hexdigest()
search_results_obj = {}
search_results_obj["list_id"] = list_id
cache_info = {
"query": query_obj,
"ts": ts,
"record_type": "glycosequon",
"search_type": "protein_to_glycosequons"
}
search_results_obj["cache_info"] = cache_info
search_results_obj["results"] = results
result = dbh[cache_collection].delete_many({"list_id": list_id})
result = dbh[cache_collection].insert_one(search_results_obj)
res_obj["list_id"] = list_id
return res_obj
def gene(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("gene_search_direct", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = protein_apilib.get_mongo_query(query_obj)
#return mongo_query
collection = "c_protein"
main_id = "uniprot_canonical_ac"
results_dict = {}
i = 0
for obj in dbh[collection].find(mongo_query):
i += 1
if i > config_obj["max_results_count"]["protein"]:
break
if main_id not in obj:
continue
results_dict[obj[main_id]] = obj
res_obj = get_results_batch(results_dict, query_obj, config_obj)
return res_obj
def auth_userinfo(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("auth_userinfo", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
res_obj = auth_tokenstatus({"token": query_obj["token"]}, config_obj)
user_info = dbh["c_users"].find_one({'email': res_obj["email"].lower()})
if "access" not in user_info:
return {"error_list": [{"error_code": "no-write-access"}]}
if user_info["access"] != "write":
return {"error_list": [{"error_code": "no-write-access"}]}
res_obj = dbh["c_users"].find_one({'email': query_obj["email"].lower()})
res_obj.pop("_id")
res_obj.pop("password")
return res_obj
def biosynthesis_enzyme_to_glycans(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query(
"biosynthesis_enzyme_to_glycans_direct", query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_glycan"
results = []
mongo_query = usecases_apilib.get_mongo_query(
"biosynthesis_enzyme_to_glycans", query_obj)
results_dict = {}
i = 0
collection = "c_glycan"
main_id = "glytoucan_ac"
for obj_two in dbh[collection].find(mongo_query):
if main_id not in obj_two:
continue
glytoucan_ac = obj_two[main_id]
if i > config_obj["max_results_count"]["glycan"]:
break
results_dict[glytoucan_ac] = obj_two
res_obj = get_results_batch(results_dict, query_obj, config_obj)
return res_obj
def auth_register(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("auth_register", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_users"
query_obj["email"] = query_obj["email"].lower()
query_obj["password"] = bcrypt.hashpw(
query_obj["password"].encode('utf-8'), bcrypt.gensalt())
query_obj["status"] = 0
query_obj["access"] = "readonly"
query_obj["role"] = ""
res_obj = {}
if dbh[collection].find({"email": query_obj["email"]}).count() != 0:
res_obj = {"error_list": [{"error_code": "email-already-regisgered"}]}
else:
res = dbh[collection].insert_one(query_obj)
res_obj = {"type": "success"}
return res_obj
def protein_alignment(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("protein_alignment", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_cluster"
mongo_query = {"uniprot_canonical_ac": query_obj["uniprot_canonical_ac"]}
obj = dbh[collection].find_one(mongo_query)
selected_cls_id = ""
for cls_id in obj["clusterlist"]:
if cls_id.find(query_obj["cluster_type"]) != -1:
selected_cls_id = cls_id
break
if selected_cls_id == "":
return {"error_list": [{"error_code": "non-existent-cluster-type"}]}
#check for post-access error, error_list should be empty upto this line
post_error_list = []
if selected_cls_id == "":
post_error_list.append({"error_code": "non-existent-record"})
return {"error_list": post_error_list}
collection = "c_alignment"
mongo_query = {"cls_id": selected_cls_id}
#return mongo_query
obj = dbh[collection].find_one(mongo_query)
if obj == None:
post_error_list.append({"error_code": "non-existent-record"})
return {"error_list": post_error_list}
#If the object has a property that is not in the specs, remove it
util.clean_obj(obj, config_obj["removelist"]["c_alignment"], "c_alignment")
#make canoncal sequence first in the list
new_list_one = []
new_list_two = []
for o in obj["sequences"]:
if o["uniprot_ac"] == query_obj["uniprot_canonical_ac"]:
new_list_one.append(o)
else:
new_list_two.append(o)
obj["sequences"] = new_list_one + new_list_two
new_obj = obj
return obj
def home_init(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("pages_home_init",{}, config_obj)
if error_list != []:
return {"error_list":error_list}
ts = datetime.datetime.now(pytz.timezone('US/Eastern')).strftime('%Y-%m-%d %H:%M:%S %Z%z')
res_obj = {"version":[], "statistics":[]}
for doc in dbh["c_version"].find({}):
doc.pop("_id")
res_obj["version"].append(doc)
path_obj = config_obj[config_obj["server"]]["pathinfo"]
species_obj = {}
in_file = path_obj["datareleasespath"]
in_file += "data/v-%s/misc/species_info.csv" % (config_obj["datarelease"])
libgly.load_species_info(species_obj, in_file)
tax_id_list = []
for k in species_obj:
obj = species_obj[k]
if obj["is_reference"] == "yes":
tax_id_list.append(str(obj["tax_id"]))
for doc in dbh["c_stat"].find({}):
for tax_id in sorted(doc["oldstat"]):
if tax_id not in tax_id_list:
tax_id_list.append(tax_id)
for doc in dbh["c_stat"].find({}):
doc.pop("_id")
for tax_id in list(set(tax_id_list)):
res_obj["statistics"].append(doc["oldstat"][tax_id])
#uncomment this when the frontend is ready to consume new stat format
#res_obj["statistics"] = doc["newstat"]
res_obj["events"] = []
doc_list = dbh["c_event"].find({"visibility":"visible"}).sort('createdts', pymongo.DESCENDING)
for doc in doc_list:
doc["id"] = str(doc["_id"])
doc.pop("_id")
for k in ["createdts", "updatedts"]:
if k not in doc:
continue
doc[k] = doc[k].strftime('%Y-%m-%d %H:%M:%S %Z%z')
res_obj["events"].append(doc)
return res_obj
def verlist(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
out_obj = []
for coll in dbh.collection_names():
if coll.find("c_bco_v-") != -1:
rel = coll[8:]
out_obj.append(rel)
return out_obj
def categorized_typeahead(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("categorized_typeahead",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_protein"
mongo_query = {}
if query_obj["field"] == "go_term":
mongo_query = {
"go_annotation.categories.go_terms.name": {
'$regex': query_obj["value"],
'$options': 'i'
}
}
hit_dict = {}
seen = {}
total = 0
limit_one = query_obj["total_limit"]
limit_two = query_obj["categorywise_limit"]
prj_obj = {"go_annotation": 1}
for obj in dbh[collection].find(mongo_query, prj_obj):
for cat_obj in obj["go_annotation"]["categories"]:
cat = cat_obj["name"]
for term_obj in cat_obj["go_terms"]:
term = term_obj["name"]
if term.lower().find(query_obj["value"].lower()) != -1:
if cat not in hit_dict:
hit_dict[cat] = []
seen[cat] = {}
if term not in seen[cat] and len(
hit_dict[cat]) < limit_two:
o = {"label": term, "category": cat}
hit_dict[cat].append(o)
seen[cat][term] = True
total += 1
if total >= limit_one:
break
res_obj = []
for cat in hit_dict:
for o in hit_dict[cat]:
res_obj.append(o)
return res_obj
def site_detail(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("site_detail", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_protein"
canon, start_pos, end_pos = query_obj["site_id"].split(".")
mongo_query = {"uniprot_canonical_ac": canon}
if canon.find("-") == -1:
mongo_query = {"uniprot_ac": canon}
canon_doc = dbh[collection].find_one(mongo_query)
collection = "c_site"
mongo_query = {"id": query_obj["site_id"]}
site_doc = dbh[collection].find_one(mongo_query)
if site_doc == None:
canon = canon_doc["uniprot_canonical_ac"]
mongo_query = {"id": "%s.%s.%s" % (canon, start_pos, end_pos)}
site_doc = dbh[collection].find_one(mongo_query)
#check for post-access error, error_list should be empty upto this line
post_error_list = []
if site_doc == None:
post_error_list.append({"error_code": "non-existent-record"})
return {"error_list": post_error_list}
url = config_obj["urltemplate"]["uniprot"] % (
canon_doc["uniprot_canonical_ac"])
site_doc["uniprot_id"] = canon_doc[
"uniprot_id"] if "uniprot_id" in canon_doc else ""
site_doc["uniprot"] = {
"uniprot_canonical_ac": canon_doc["uniprot_canonical_ac"],
"uniprot_id": canon_doc["uniprot_id"],
"url": url,
"length": canon_doc["sequence"]["length"]
}
for k in [
"uniprot", "sequence", "mass", "protein_names", "gene",
"gene_names", "species", "refseq"
]:
if k in canon_doc and k not in site_doc:
site_doc[k] = canon_doc[k]
return site_doc
def site_search_init(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
collection = "c_searchinit"
doc = dbh[collection].find_one({})
res_obj = doc["site"]
return res_obj
def glycan_detail(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("glycan_detail", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_glycan"
q = {"record_id": {'$eq': query_obj["glytoucan_ac"].upper()}}
history_obj = dbh["c_idtrack"].find_one(q)
mongo_query = {"glytoucan_ac": {'$eq': query_obj["glytoucan_ac"].upper()}}
obj = dbh[collection].find_one(mongo_query)
#check for post-access error, error_list should be empty upto this line
post_error_list = []
if obj == None:
post_error_list.append({"error_code": "non-existent-record"})
res_obj = {"error_list": post_error_list}
if history_obj != None:
res_obj["reason"] = history_obj["history"]
return res_obj
url = config_obj["urltemplate"]["glytoucan"] % (obj["glytoucan_ac"])
obj["glytoucan"] = {
"glytoucan_ac": obj["glytoucan_ac"],
"glytoucan_url": url
}
obj["history"] = history_obj["history"] if history_obj != None else []
#Remove 0 count residues
tmp_list = []
for o in obj["composition"]:
if o["count"] > 0:
tmp_list.append(o)
obj["composition"] = tmp_list
util.clean_obj(obj, config_obj["removelist"]["c_glycan"], "c_glycan")
if "enzyme" in obj:
for o in obj["enzyme"]:
if "gene_url" in o:
o["gene_link"] = o["gene_url"]
return util.order_obj(obj, config_obj["objectorder"]["glycan"])
def disease_to_glycosyltransferases(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("usecases_group_six", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = get_mongo_query("disease_to_glycosyltransferases", query_obj)
#return mongo_query
collection = "c_protein"
cache_collection = "c_cache"
search_type = "disease_to_glycosyltransferases"
record_type = "protein"
record_list = []
for obj in dbh[collection].find(mongo_query,
config_obj["projectedfields"][collection]):
record_list.append(obj["uniprot_canonical_ac"])
query_obj["organism"] = {
"id": query_obj["tax_id"],
"name": config_obj["taxid2name"][str(query_obj["tax_id"])]
}
query_obj.pop("tax_id")
res_obj = {}
ts_format = "%Y-%m-%d %H:%M:%S %Z%z"
ts = datetime.datetime.now(pytz.timezone('US/Eastern')).strftime(ts_format)
cache_coll = "c_cache"
list_id = ""
if len(record_list) != 0:
hash_obj = hashlib.md5(record_type + "_" + json.dumps(query_obj))
list_id = hash_obj.hexdigest()
cache_info = {
"query": query_obj,
"ts": ts,
"record_type": record_type,
"search_type": search_type
}
util.cache_record_list(dbh, list_id, record_list, cache_info,
cache_coll, config_obj)
res_obj = {"list_id": list_id}
return res_obj
def auth_login(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("auth_login", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_users"
query_obj["email"] = query_obj["email"].lower()
login_user = dbh[collection].find_one({'email': query_obj["email"]})
res_obj = {}
if login_user:
stored_password = login_user['password'].encode('utf-8')
submitted_password = query_obj['password'].encode('utf-8')
if login_user["status"] == 0:
res_obj = {"error_list": [{"error_code": "inactive-account"}]}
elif bcrypt.hashpw(submitted_password,
stored_password) == stored_password:
token = make_hash_string() + make_hash_string()
ts = datetime.datetime.now()
session_obj = {
"email": query_obj["email"],
"token": token,
"createdts": ts
}
res = dbh["c_session"].insert_one(session_obj)
res_obj = {"type": "success", "token": token}
else:
res_obj = {
"error_list": [{
"error_code":
"invalid-email/password-combination"
}]
}
else:
res_obj = {
"error_list": [{
"error_code": "invalid-email/password-combination"
}]
}
return res_obj
def glycan_search_init(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
error_list = errorlib.get_errors_in_query("glycan_searchinit", {},
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_searchinit"
res_obj = dbh[collection].find_one({})
return res_obj["glycan"]
def protein_search(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("protein_search", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = get_mongo_query(query_obj)
#return mongo_query
#path_obj = config_obj[config_obj["server"]]["htmlpath"]
#blast_db = path_obj["datareleasespath"] + "data/v-%s/blastdb/canonicalsequences"
#blast_db = blast_db % (config_obj["datarelease"])
#cmd = "%s -db %s -query %s -evalue %s -outfmt %s"
#cmd = cmd % (path_obj["blastp"], blast_db,"tmp/q.fasta", 0.1, 7)
collection = "c_protein"
record_list = []
record_type = "protein"
prj_obj = {"uniprot_canonical_ac": 1}
for obj in dbh[collection].find(mongo_query, prj_obj):
record_list.append(obj["uniprot_canonical_ac"])
ts_format = "%Y-%m-%d %H:%M:%S %Z%z"
ts = datetime.datetime.now(pytz.timezone('US/Eastern')).strftime(ts_format)
cache_coll = "c_cache"
list_id = ""
if len(record_list) != 0:
hash_obj = hashlib.md5(record_type + "_" + json.dumps(query_obj))
list_id = hash_obj.hexdigest()
cache_info = {
"query": query_obj,
"ts": ts,
"record_type": record_type,
"search_type": "search"
}
util.cache_record_list(dbh, list_id, record_list, cache_info,
cache_coll, config_obj)
res_obj = {"list_id": list_id}
return res_obj
def event_delete(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
#Collect errors
error_list = errorlib.get_errors_in_query("event_delete", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
res_obj = auth_apilib.auth_tokenstatus({"token": query_obj["token"]},
config_obj)
#check validity of token
if "error_list" in res_obj:
return res_obj
if "status" not in res_obj:
return {"error_list": [{"error_code": "invalid-token"}]}
if res_obj["status"] != 1:
return {"error_list": [{"error_code": "invalid-token"}]}
#check write-access
user_info = dbh["c_users"].find_one({'email': res_obj["email"].lower()})
if "access" not in user_info:
return {"error_list": [{"error_code": "no-write-access"}]}
if user_info["access"] != "write":
return {"error_list": [{"error_code": "no-write-access"}]}
res_obj = {}
try:
q_obj = {"_id": ObjectId(query_obj["id"])}
doc = dbh["c_event"].find_one(q_obj)
if doc == None:
res_obj = {"error_list": [{"error_code": "record-not-found"}]}
else:
update_obj = {"visibility": "hidden"}
res = dbh["c_event"].update_one(q_obj, {'$set': update_obj},
upsert=True)
res_obj = {"type": "success"}
except Exception as e:
res_obj = {"error_list": [{"error_code": str(e)}]}
return res_obj
def auth_userupdate(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
#Collect errors
error_list = errorlib.get_errors_in_query("auth_userupdate", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
res_obj = auth_tokenstatus({"token": query_obj["token"]}, config_obj)
if "error_list" in res_obj:
return res_obj
if "status" not in res_obj:
return {"error_list": [{"error_code": "invalid-token"}]}
if res_obj["status"] != 1:
return {"error_list": [{"error_code": "invalid-token"}]}
try:
user_info = dbh["c_users"].find_one(
{'email': res_obj["email"].lower()})
q_obj = {"email": query_obj["email"]}
update_obj = {}
if "access" not in query_obj and "role" not in query_obj and "password" in query_obj and res_obj[
"email"].lower() == query_obj["email"]:
update_obj["password"] = bcrypt.hashpw(
query_obj["password"].encode('utf-8'), bcrypt.gensalt())
else:
if "role" not in user_info:
return {"error_list": [{"error_code": "no-admin-role"}]}
if user_info["role"] != "admin":
return {"error_list": [{"error_code": "no-admin-role"}]}
for k in query_obj:
if k == "password":
update_obj[k] = bcrypt.hashpw(query_obj[k].encode('utf-8'),
bcrypt.gensalt())
elif k not in ["token", "email"]:
update_obj[k] = query_obj[k]
res = dbh["c_users"].update_one(q_obj, {'$set': update_obj},
upsert=True)
return {"type": "success"}
except Exception as e:
return {"error_list": [{"error_code": str(e)}]}
def bcolist(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
out_obj = {}
for doc in dbh["c_bco"].find({}):
if "bco_id" in doc:
bco_id = doc["bco_id"]
if "io_domain" in doc:
if "output_subdomain" in doc["io_domain"]:
if doc["io_domain"]["output_subdomain"] != []:
file_name = doc["io_domain"]["output_subdomain"][0][
"uri"]["filename"]
out_obj[bco_id] = file_name
return out_obj
def protein(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#glycan.attached is not implemented in c_protein jsons yet
if "glycan" in query_obj:
if "relation" in query_obj["glycan"]:
if query_obj["glycan"]["relation"] not in [
"attached", "binding", "any"
]:
return {
"error_list": [{
"error_code": "invalid-parameter-value",
"field": "glycan.relation"
}]
}
#Collect errors
error_list = errorlib.get_errors_in_query("protein_search_direct",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = protein_apilib.get_mongo_query(query_obj)
#return mongo_query
collection = "c_protein"
main_id = "uniprot_canonical_ac"
results_dict = {}
i = 0
for obj in dbh[collection].find(mongo_query):
i += 1
if i > config_obj["max_results_count"]["protein"]:
break
if main_id not in obj:
continue
results_dict[obj[main_id]] = obj
res_obj = get_results_batch(results_dict, query_obj, config_obj)
return res_obj
def event_addnew(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("event_addnew", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
res_obj = auth_apilib.auth_tokenstatus({"token": query_obj["token"]},
config_obj)
#check validity of token
if "error_list" in res_obj:
return res_obj
if "status" not in res_obj:
return {"error_list": [{"error_code": "invalid-token"}]}
if res_obj["status"] != 1:
return {"error_list": [{"error_code": "invalid-token"}]}
#check write-access
user_info = dbh["c_users"].find_one({'email': res_obj["email"].lower()})
if "access" not in user_info:
return {"error_list": [{"error_code": "no-write-access"}]}
if user_info["access"] != "write":
return {"error_list": [{"error_code": "no-write-access"}]}
res_obj = {}
try:
query_obj.pop("token")
query_obj["createdts"] = datetime.datetime.now()
query_obj["updatedts"] = query_obj["createdts"]
res = dbh["c_event"].insert_one(query_obj)
res_obj = {"type": "success"}
except Exception as e:
res_obj = {"error_list": [{"error_code": str(e)}]}
return res_obj
def search_init(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("usecases_search_init", {},
config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_searchinit"
res_obj = dbh[collection].find_one({})
if res_obj == None or "usecases" not in res_obj:
return {"error_list": [{"error_code": "non-existent-search-init"}]}
return res_obj["usecases"]
def messagelist(config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
out_obj = []
import pymongo
#q_obj = { "creation_time": { "$exists": True} }
q_obj = {}
for doc in dbh["c_message"].find(q_obj).sort('creation_time',
pymongo.DESCENDING):
doc.pop("_id")
for k in ["creation_time", "update_time", "ts"]:
if k not in doc:
continue
doc[k] = doc[k].strftime('%Y-%m-%d %H:%M:%S %Z%z')
out_obj.append(doc)
return out_obj
def protein_search_simple(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("protein_search_simple",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
mongo_query = get_simple_mongo_query(query_obj)
#print mongo_query
collection = "c_protein"
record_list = []
record_type = "protein"
prj_obj = {"uniprot_canonical_ac": 1}
for obj in dbh[collection].find(mongo_query, prj_obj):
record_list.append(obj["uniprot_canonical_ac"])
ts_format = "%Y-%m-%d %H:%M:%S %Z%z"
ts = datetime.datetime.now(pytz.timezone('US/Eastern')).strftime(ts_format)
cache_coll = "c_cache"
list_id = ""
if len(record_list) != 0:
hash_obj = hashlib.md5(record_type + "_" + json.dumps(query_obj))
list_id = hash_obj.hexdigest()
cache_info = {
"query": query_obj,
"ts": ts,
"record_type": record_type,
"search_type": "search_simple"
}
util.cache_record_list(dbh, list_id, record_list, cache_info,
cache_coll, config_obj)
res_obj = {"list_id": list_id}
return res_obj
def auth_contactlist(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
path_obj = config_obj[config_obj["server"]]["pathinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
#Collect errors
error_list = errorlib.get_errors_in_query("auth_contactlist", query_obj,
config_obj)
if error_list != []:
return {"error_list": error_list}
res_obj = auth_tokenstatus({"token": query_obj["token"]}, config_obj)
if "error_list" in res_obj:
return res_obj
if "status" not in res_obj:
return {"error_list": [{"error_code": "invalid-token"}]}
if res_obj["status"] != 1:
return {"error_list": [{"error_code": "invalid-token"}]}
import pymongo
doc_list = []
try:
q_obj = {} if query_obj["visibility"] == "all" else {
"visibility": query_obj["visibility"]
}
doc_list = dbh["c_message"].find(q_obj).sort('creation_time',
pymongo.DESCENDING)
except Exception as e:
return {"error_list": [{"error_code": str(e)}]}
out_obj = []
for doc in doc_list:
doc["id"] = str(doc["_id"])
doc.pop("_id")
for k in ["creation_time", "update_time", "ts"]:
if k not in doc:
continue
doc[k] = doc[k].strftime('%Y-%m-%d %H:%M:%S %Z%z')
out_obj.append(doc)
return out_obj
def protein_to_homologs(query_obj, config_obj):
db_obj = config_obj[config_obj["server"]]["dbinfo"]
dbh, error_obj = util.connect_to_mongodb(db_obj) #connect to mongodb
if error_obj != {}:
return error_obj
#Collect errors
error_list = errorlib.get_errors_in_query("protein_to_homologs_direct",
query_obj, config_obj)
if error_list != []:
return {"error_list": error_list}
collection = "c_protein"
results = []
mongo_query = {
"$or": [{
"uniprot_canonical_ac": {
'$eq': query_obj["uniprot_canonical_ac"]
}
}, {
"uniprot_ac": {
'$eq': query_obj["uniprot_canonical_ac"]
}
}]
}
results_dict = {}
i = 0
collection = "c_protein"
main_id = "uniprot_canonical_ac"
for obj_one in dbh[collection].find(mongo_query):
for o in obj_one["orthologs"]:
canon = o[main_id]
obj_two = dbh[collection].find_one({"uniprot_canonical_ac": canon})
i += 1
if i > config_obj["max_results_count"]["protein"]:
break
results_dict[canon] = obj_two
res_obj = get_results_batch(results_dict, query_obj, config_obj)
return res_obj