def gettoid(self):
adict = self.mapped
idlist = []
for i in adict:
temp = adict[i] #each mapped record is a list
idlist += temp
#for v in temp:
# idlist+=[v]
idlist = cmn.unify(idlist)
return idlist
def detail_goserver(r_dict, d_dict, fromdb, todb, alist):
try: #the normal way
record = Entrez.read(Entrez.elink(dbfrom=fromdb, db=todb, id=alist))
r_dict, d_dict = detail_map_dict(r_dict, d_dict, record)
del record
#print 'I am normal!\n'
except:
#first try do it one by one
for aa in alist:
try:
print('try it one by one, here I am in %s .\n' % aa)
record = Entrez.read(
Entrez.elink(dbfrom=fromdb, db=todb, id=aa))
r_dict, d_dict = detail_map_dict(r_dict, d_dict, record)
del record
#print 'I succeed at my first trial!\n'
except:
#if one still fail, try sometimes
print('I need try more times on %s .\n' % aa)
flag = False
count = 0 #times trying
while (flag == False and count < 3):
count += 1
print('trying my %s times...\n' % count)
try:
time.sleep(2) #interval between times
record = Entrez.read(
Entrez.elink(dbfrom=fromdb, db=todb, id=aa))
r_dict, d_dict = detail_map_dict(
r_dict, d_dict, record)
del record
flag = True
#print 'yes, I have done it!\n'
except:
flag = False
#well, the server doesn't like me...
if flag == False:
print('something wrong with this id: %s\n' % aa)
for key in r_dict:
r_dict[key] = cmn.unify(r_dict[key])
return r_dict, d_dict
def old_goserver(r_dict,
fromdb,
todb,
alist,
linkname=None,
recr=False,
recording=False,
times=0):
try: #the normal way
#if True:
if recording:
if recr == False: #not in recursive loop
r_dict, alist = local_fetch(r_dict, alist,
"%s_%s" % (fromdb, todb))
if alist != []:
record = visit_Entrez(fromdb=fromdb,
todb=todb,
alist=alist,
linkname=linkname)
#print record
r_dict = map_dict(fromdb, todb, r_dict, record, recording=recording)
del record
#print 'I am normal!\n'
#else:
except:
#first try do it one by one
#for aa in alist:
if len(alist) == 1:
aa = alist[0]
#try:
# print 'try it one by one, here I am in %s .\n' % aa
# record=Entrez.read(Entrez.elink(dbfrom=fromdb,db=todb,id=aa))
# r_dict=map_dict(fromdb,todb,r_dict,record,exclusion)
# del record
#print 'I succeed at my first trial!\n'
#except:
#if one still fail, try sometimes
if True:
print('I need try more times on %s .\n' % aa)
flag = False
count = 0 #times trying
while (flag == False and count < 3):
count += 1
print('trying my %s times...\n' % count)
try:
time.sleep(3) #interval between times
record = visit_Entrez(fromdb=fromdb,
todb=todb,
alist=alist,
linkname=linkname)
r_dict = map_dict(fromdb,
todb,
r_dict,
record,
recording=recording)
del record
flag = True
#print 'yes, I have done it!\n'
except:
flag = False
#well, the server doesn't like me...
if flag == False:
print('something wrong with this id: %s\n' % aa)
elif times < 3:
#if the length is not one yet, divide and do again
#only go into recursion for 3 loop
times += 1
try:
midpoint = len(alist) / 2
aalist = alist[:midpoint]
ablist = alist[midpoint:]
r_dict = goserver(r_dict,
fromdb,
todb,
aalist,
linkname=linkname,
recr=True,
recording=recording,
times=times)
r_dict = goserver(r_dict,
fromdb,
todb,
ablist,
linkname=linkname,
recr=True,
recording=recording,
times=times)
except RuntimeError as theError:
if theError == "maximum recursion depth exceeded":
for item in alist:
r_dict = goserver(r_dict,
fromdb,
todb, [item],
linkname=linkname,
recr=True,
recording=recording)
else: #more than 3 times
for item in alist:
r_dict = goserver(r_dict,
fromdb,
todb, [item],
linkname=linkname,
recr=True,
recording=recording,
times=4)
for key in r_dict:
r_dict[key] = cmn.unify(r_dict[key])
return r_dict