def test_GO_relation_5():
bp = GO.GO_category({
'id': ['GO:0008150'],
'name': ['biological_process'],
'def': ['']
})
mp = GO.GO_category({
'id': ['GO:0008152'],
'name': ['metabolic process'],
'def': ['']
})
cp = GO.GO_category({
'id': ['GO:0009987'],
'name': ['cellular process'],
'def': ['']
})
m = GO.GO_category({
'id': ['GO:0032259'],
'name': ['methylation'],
'def': ['']
})
is_a = GO.GO_relation({
'id': ['is_a'],
'name': ['is_a'],
'is_transitive': [True]
})
is_a.add_pair(mp, bp)
is_a.add_pair(cp, bp)
is_a.add_pair(m, mp)
is_a.add_pair(bp, m) # Introduce a cycle for testing.
is_a_copy = is_a.copy()
assert is_a == is_a_copy
def run(self):
self.connect()
self.login()
time.sleep(1)
line = ''
while not self._terminate:
for char in self._sock.recv(1024):
if char not in '\r\n':
line += char
continue
if char == '\r': continue
if char == '\n':
if self._irc_debug: print '[-s2c-] %s'%line
prefix = ''
command = ''
arguments = ''
if line[0] == ':':
line = line[1:]
i = line.find(' ')
prefix = GO.unicod(line[0:i])
line = line[i+1:]
i = line.find(' ')
command = 'on_%s'%line[0:i]
arguments = GO.unicod(line[i+1:])
if command in dir(self): Thread(target=getattr(self, command), args=(prefix, arguments)).start()
line = ''
def test_GO_relation_1():
relation = GO.GO_relation({'id': ['rel'], 'name': ['relation']})
assert relation.id == 'rel'
assert relation.name == 'relation'
assert relation.is_transitive == False
assert relation.others == {}
assert str(relation) == '<rel>'
def test_GO_relation_4():
bp = GO.GO_category({
'id': ['GO:0008150'],
'name': ['biological_process'],
'def': ['']
})
mp = GO.GO_category({
'id': ['GO:0008152'],
'name': ['metabolic process'],
'def': ['']
})
cp = GO.GO_category({
'id': ['GO:0009987'],
'name': ['cellular process'],
'def': ['']
})
m = GO.GO_category({
'id': ['GO:0032259'],
'name': ['methylation'],
'def': ['']
})
is_a = GO.GO_relation({
'id': ['is_a'],
'name': ['is_a'],
'is_transitive': [True]
})
is_a.add_pair(mp, bp)
is_a.add_pair(cp, bp)
is_a.add_pair(m, mp)
is_a.add_pair(m, bp) # Because the relation is transitive.
assert (cp, bp) in is_a
assert (m, bp) in is_a
assert (m, mp) in is_a
assert (mp, bp) in is_a
assert not (bp, cp) in is_a
assert not (bp, m) in is_a
assert not (bp, mp) in is_a
assert not (cp, m) in is_a
assert not (cp, mp) in is_a
assert not (m, cp) in is_a
assert not (mp, cp) in is_a
assert not (mp, m) in is_a
assert is_a[bp] == set()
assert is_a[cp] == {bp}
assert is_a[m] == {bp, mp}
assert is_a[mp] == {bp}
assert sorted(is_a) == [(mp, bp), (cp, bp), (m, bp), (m, mp)]
def putcmd(self, cmd):
if self._connected:
cmd = GO.utf8(cmd)
self._mutex.acquire()
if self._irc_debug: print '[-c2s-] %s'%cmd
self._sock.sendall(cmd)
self._sock.sendall('\r\n')
self._mutex.release()
def test_GO_category_1():
category = GO.GO_category({
'id': ['42'],
'name': ['fortytwo'],
'def': ['answer']
})
assert category.id == '42'
assert category.name == 'fortytwo'
assert category.defination == 'answer'
assert category.others == {}
assert str(category) == '42 (fortytwo)'
def test_GO_1():
go = GO.GO('go.obo')
assert 'is_a' in go.relations
assert 'ends_during' in go.relations
assert 'happens_during' in go.relations
assert 'has_part' in go.relations
assert 'negatively_regulates' in go.relations
assert 'never_in_taxon' in go.relations
assert 'occurs_in' in go.relations
assert 'part_of' in go.relations
assert 'positively_regulates' in go.relations
assert 'regulates' in go.relations
assert 'starts_during' in go.relations
def seekGOTerms(keywords, output_file = None):
'''
keywords: A list of words to search for.
'''
ret = {} # Key: GO ID, Value: Term
for gid in go.go_terms.keys():
gx = GO.GOTerm()
gx = go.getGOTermOf(gid)
desc = gx.getGOName()
for k in keywords:
k = k.upper()
if desc.upper().find(k) >= 0:
ret[gid] = desc
print gid, desc
break
f=None
if output_file is not None:
f=open(output_file, 'w')
for gid in ret.keys():
s = '\t'+gid+'\t# '+ret[gid]
if f is not None:
f.write(s+'\n')
else:
print s
if f is not None:
f.close()
#keywords = ['transcription', 'translation', 'transcribed' ]
#keywords = ['cell cycle', 'division' ]
#keywords = [ 'cytoskeleton' ]
#keywords = [ 'metabolism' ]
#keywords = ['Protein folding', 'chaperone', 'heat shock' ]
#keywords = ['proteolysis', 'proteasom', 'ubiquitin' ]
#keywords = [ 'splicing', 'spliceosom' ]
#keywords = [ 'transport', 'localiz' ]
#keywords = [ 'oxidoreduct' ]
#output_file = 'r:/tmp.txt'
if len(sys.argv) == 4:
global go
go_file = sys.argv[1]
keyword = sys.argv[2].replace('"', '')
keywords = [keyword]
output_file = sys.argv[3]
go = GO.GO(obo_file = go_file)
seekGOTerms(keywords, output_file)
print 'DONE'
else:
displayHelp()
def history(self, cmd):
(ok, date) = self._check_for_date(''.join(cmd.arguments()))
if ok:
exists = False
for chan_message in GO.storage.get_channel_log(cmd.channel().name(), date):
cmd.reply(u'%s [%s] %s: %s'%(cmd.channel().name(), chan_message[0].strftime('%H:%M:%S'), GO.unicod(chan_message[1]), GO.unicod(chan_message[2])))
exists = True
if not exists:
cmd.reply(u'За данную дату сообщения на канале %s отсутствуют'%cmd.channel().name())
else:
cmd.reply_error(date)
def wiki(self, cmd):
(ok, kw) = self._check_for_string('%20'.join(cmd.arguments()))
if ok:
downloaded = urllib2.urlopen('http://ru.wikipedia.org/w/api.php?format=xml&action=opensearch&search=%s'%GO.utf8(kw))
dom = parseString(downloaded.read())
downloaded.close()
root = dom.getElementsByTagName('SearchSuggestion')[0].getElementsByTagName('Section')[0]
cnt = root.getElementsByTagName('Item').length
if cnt == 0:
cmd.reply(u'Нет такого в википедии')
elif cnt > 1:
for a in root.getElementsByTagName('Item'):
if a.getElementsByTagName('Text')[0].firstChild.data.strip() == u' '.join(cmd.arguments()):
cmd.reply(u'%s (%s)'%(a.getElementsByTagName('Description')[0].firstChild.data.strip(), a.getElementsByTagName('Url')[0].firstChild.data.strip()))
cmd.reply(u'Варианты: %s'%u', '.join([a.getElementsByTagName('Text')[0].firstChild.data.strip() for a in root.getElementsByTagName('Item')]))
elif cnt == 1:
i = root.getElementsByTagName('Item')[0]
cmd.reply(u'%s (%s)'%(i.getElementsByTagName('Description')[0].firstChild.data.strip(), i.getElementsByTagName('Url')[0].firstChild.data.strip()))
else:
cmd.reply_error(kw)
def sync_forums_data(self):
#self.download_part_of_all()
GO.bot.send_channel_log(u'RSDN. Синхронизация. Запуск.')
msgcount = { True: 0, False: 0 }
mdrcount = { True: 0, False: 0 }
ratcount = { True: 0, False: 0 }
sync_iteration = 0
while True:
msgcnt = 0
ratcnt = 0
mdrcnt = 0
sync_iteration += 1
GO.bot.send_channel_log(u'RSDN. Синхронизация. Итерация: %d.'%sync_iteration)
GO.bot.send_channel_log(u'RSDN. Синхронизация. Будет загружено отсутствующих сообщений: %d'%(self.max_broken_per_sync_iteration if len(self._missed_rsdn_messages_mids) > self.max_broken_per_sync_iteration else len(self._missed_rsdn_messages_mids)))
newData = self.sync_new_data()
GO.bot.send_channel_log(u'RSDN. Синхронизация. Сообщения загружены. В итерацию не попало %d отсутствующих сообщений'%len(self._missed_rsdn_messages_mids))
if newData == None:
break
if len(newData['newMessages']):
GO.bot.send_channel_log(u'RSDN. Синхронизация. Обработка сообщений.')
for message in newData['newMessages'][0]:
msgcount[GO.storage.update_rsdn_messages(message)] += 1
fid = message['forumId']
if fid and self.date_is_today(message['messageDate']):
forum_name = self.forums[fid]['sname']
text = u'`%s`. Автор: %s'%(
message['subject'],
message['userNick'],
)
urls = u' | '.join([
u'#%s'%forum_name,
self.get_forum_url_by_id(fid),
self.get_message_url_by_id(message['messageId']),
self.get_member_url_by_id(message['userId'])
])
GO.bot.send_rsdn_notification(u'В форуме `%s` новое сообщение: %s'%(
self.forums[fid]['name'],
text
))
GO.bot.send_rsdn_notification(urls)
if message['parentId'] == 0:
GO.bot.send_channel_notification(forum_name, u'Новый топик %s'%text)
GO.bot.send_channel_notification(forum_name, urls)
else:
parent_msg = GO.storage.get_rsdn_message(message['parentId'])
if parent_msg != None:
GO.bot.send_user_notification(parent_msg[2], u'В форуме `%s` ответ на сообщение `%s`: %s'%(
self.forums[fid]['name'],
GO.unicod(parent_msg[4]),
text
))
GO.bot.send_user_notification(parent_msg[2], urls)
#self.mineMissedInMessages(newData['newMessages'][0])
if len(newData['newRating']):
GO.bot.send_channel_log(u'RSDN. Синхронизация. Обработка рейтинга.')
for rating in newData['newRating'][0]:
ratcount[GO.storage.update_rsdn_rating(rating)] += 1
if self.date_is_today(rating['rateDate']):
target_msg = GO.storage.get_rsdn_message(rating['messageId'])
if target_msg == None:
self.get_rsdn_topic(rating['messageId'])
target_msg = GO.storage.get_rsdn_message(rating['messageId'])
from_user = GO.storage.get_rsdn_member(rating['userId'])
if from_user == None:
self.get_rsdn_member(rating['userId'])
from_user = GO.storage.get_rsdn_member(rating['userId'])
rate = rating['rate']
r = ''
if rate > 0: r = u'%d'%(rating['userRating']*rate)
elif rate == 0: r = u'-1'
elif rate == -2: r = u':)'
elif rate == -4: r = u'+1'
text = u'Оценка %s сообщению `%s` от пользователя %s'%(
r,
GO.unicod(target_msg[4]) if target_msg != None else u'--нет-в-бд--',
GO.unicod(from_user[1]) if target_msg != None else u'--нет-в-бд--'
)
urls = u' | '.join([
self.get_message_url_by_id(rating['messageId']),
self.get_member_url_by_id(rating['userId'])
])
GO.bot.send_rsdn_notification(text)
GO.bot.send_rsdn_notification(urls)
if target_msg != None:
GO.bot.send_user_notification(target_msg[2], u'В форуме `%s` ответ на сообщение `%s`: %s'%(
self.forums[fid]['name'],
GO.unicod(target_msg[4]),
text
))
GO.bot.send_user_notification(target_msg[2], urls)
#self.mineMissedInMessages(newData['newRating'][0])
if len(newData['newModerate']):
GO.bot.send_channel_log(u'RSDN. Синхронизация. Обработка модерирования.')
for moderate in newData['newModerate'][0]:
mdrcount[GO.storage.update_rsdn_moderate(moderate)] += 1
#self.mineMissedInMessages(newData['newModerate'][0])
GO.bot.send_channel_log(u'RSDN. Синхронизация. Получение списка отсутствующих сообщений.')
for mid in GO.storage.get_broken_messages(list(self.forums.keys())):
if mid not in self._missed_rsdn_messages_mids:
self._missed_rsdn_messages_mids.append(mid)
#print len(newData['newRating']), len(newData['newModerate']), len(newData['newMessages']), len(self._missed_rsdn_messages_mids)
if len(newData['newRating']) == 0 and len(newData['newModerate']) == 0 and len(newData['newMessages']) == 0 and len(self._missed_rsdn_messages_mids) < self.min_broken_per_sync_iteration:
break
GO.bot.send_channel_log(u'RSDN. Синхронизация. Собщения: принято %d, из них новых %d, обновлено %d.'%(msgcount[True]+msgcount[False], msgcount[False], msgcount[True]))
GO.bot.send_channel_log(u'RSDN. Синхронизация. Оценки: принято %d, из них новых %d, обновлено %d.'%(ratcount[True]+ratcount[False], ratcount[False], ratcount[True]))
GO.bot.send_channel_log(u'RSDN. Синхронизация. Модерирование: принято %d, из них новых %d, обновлено %d.'%(mdrcount[True]+mdrcount[False], mdrcount[False], mdrcount[True]))
newUsers = self.sync_new_users()
if newUsers != None:
usrcount = { True: 0, False: 0 }
for newUsersBit in newUsers:
for user in newUsersBit['users'][0]:
usrcount[GO.storage.update_rsdn_members(user)] += 1
GO.bot.send_rsdn_notification(u'Новый пользователь `%s`, `%s`, `%s`: %s'%(
user['userName'],
user['userNick'],
user['realName'],
self.get_member_url_by_id(user['userId'])
))
GO.bot.send_channel_log(u'RSDN. Синхронизация. Новые пользователи: принято %d, из них новых %d, обновлено %d.'%(usrcount[True]+usrcount[False], usrcount[False], usrcount[True]))
if len(self._missed_rsdn_members_uids):
users = self.load_members_by_ids(self._missed_rsdn_members_uids)
self._missed_rsdn_members_uids = []
if users:
usrcount = { True: 0, False: 0 }
for user in users['users'][0]:
usrcount[GO.storage.update_rsdn_members(user)] += 1
GO.bot.send_channel_log(u'RSDN. Синхронизация. Пропущенные пользователи: принято %d, из них новых %d, обновлено %d.'%(usrcount[True]+usrcount[False], usrcount[False], usrcount[True]))
GO.bot.send_channel_log(u'RSDN. Синхронизация. Закончено.')
def test__pop_single_value_2():
with pytest.raises(KeyError):
GO._pop_single_value('42', {})
def test__pop_single_value_1():
attributes = {'42': ['answer'], 'foo': ['bar']}
answer = GO._pop_single_value('42', attributes)
assert answer == 'answer'
assert attributes == {'foo': ['bar']}
def test_GO_2():
go = GO.GO('go.obo')
assert len((go.relations['is_a'], [go.categories['GO:0000022']])) == 2
def test__pop_single_value_5():
with pytest.raises(TypeError):
GO._pop_single_value('42', None)
def test__pop_single_value_4():
with pytest.raises(ValueError):
GO._pop_single_value('42', {'42': []})
