def parse_counts(biom_file, tree_file=None):
counts = []
table = biom.load_table(biom_file)
if tree_file:
tree = ParsedTree(
tree_file,
'newick',
taxon_name_re,
lineage_prefixes=['k__', 'p__', 'c__', 'o__', 'f__', 'g__', 's__'])
tree.set_index_clades(contains=['A', 'T', 'G', 'C'])
for obs_id, samp_id in table.nonzero():
lineage = parse_lineage(table, obs_id)
if not lineage and tree:
lineage = parse_lineage(table,
obs_id,
parsed_tree=tree,
index_only=True)
seq_var = parse_sequencing_variant(obs_id)
count = table.get_value_by_ids(obs_id, samp_id)
counts.append(
Count(samp_id=samp_id,
obs_id=obs_id,
count=count,
seq_var=seq_var,
lineage=lineage))
return counts
def get(self):
self.echo('home.html', {
'title': "首页",
'topic_objs': Commomkvdb.get_topic_by_keys('recent-topic-home'),
'site_counts': Count.get_site_counts(),
'newest_node': Node.get_newest(),
'recent_node': Node.get_recent_node(),
'hot_node': Node.get_hot_node(),
#'recent_topic_objs': Commomkvdb.get_comment_topic_by_keys('recent-topic-home'),
'comment_topic_objs': Commomkvdb.get_comment_topic_by_keys('recent-comment-topic-home'),
}, layout='_layout.html')
def get(self):
self.echo(
'home.html',
{
'title':
"首页",
'topic_objs':
Commomkvdb.get_topic_by_keys('recent-topic-home'),
'site_counts':
Count.get_site_counts(),
'newest_node':
Node.get_newest(),
'recent_node':
Node.get_recent_node(),
'hot_node':
Node.get_hot_node(),
#'recent_topic_objs': Commomkvdb.get_comment_topic_by_keys('recent-topic-home'),
'comment_topic_objs':
Commomkvdb.get_comment_topic_by_keys(
'recent-comment-topic-home'),
},
layout='_layout.html')
with session_scope() as session_2:
for exp_id, experiment in experiments.items():
for subject in experiment.subjects:
for sample in subject.samples:
for prep in sample.preparations:
for workflow in prep.workflows:
try:
workflow.count_dict
except AttributeError:
continue
for count in workflow.count_dict[sample.orig_sample_id]:
fact = Count(experiment=experiment,
subject=subject,
sample=sample,
sample_site=sample.sampling_site,
sample_time=sample.sampling_time,
preparation=prep,
workflow=workflow,
lineage=count.lineage,
seq_variant=count.seq_var,
count=count.count)
session_2.add(fact)
end = time.time()
print("Main loop took: ", end-start)
def parser(session):
"""Parse individual prep and BIOM files when parsing a study.
Note: This method will produce duplicates of sample, subject, and
processing data each time a BIOM file is inserted. It also unfortunately
duplicates count data (for each processing in the prep data file). This
def post(self, nodeid='1'):
n_obj = Node.get_by_key('n-' + str(nodeid))
if not n_obj:
self.set_status(404)
self.write('404')
return
errors = []
author = str(self.get_cookie('username', ''))
title = self.get_argument('title', '')
content = self.get_argument('content', '')
t_obj = TOPIC_DICT.copy()
if title and content:
if len(title) <= TITLE_MAX_S and len(content) <= CONTENT_MAX_S:
int_time = int(time())
#check spam
u_topic_time = kv.get('u_topic_time:' + author)
if u_topic_time:
tlist = u_topic_time.split(',')
if len(tlist) == MEMBER_RECENT_TOPIC and (
int_time - int(tlist[-1])) < 3600:
self.write(
u'403:不要发帖太频繁了 <a href="/newpost/%s">请返回</a>' %
nodeid)
return
#check repeat
content = textilize(content)
#content = safe_encode(content)
con_md5 = md5(content.encode('utf-8')).hexdigest()
if mc.get('c_' + con_md5):
self.write(u'403:请勿灌水 <a href="/newpost/%s">请返回</a>' %
nodeid)
return
else:
mc.set('c_' + con_md5, '1', 36000)
t_obj['title'] = title
t_obj['nodeid'] = str(nodeid)
t_obj['nodename'] = n_obj['name']
t_obj['author'] = author
t_obj['add'] = int_time
t_obj['content'] = content
if n_obj['count']:
topic_id = int(n_obj['count']) + 1
else:
topic_id = 1
if Topic.add(topic_id, t_obj):
topic_key = 't-%s-%s' % (str(nodeid), str(topic_id))
#node count +1
n_obj['count'] = str(topic_id)
Commomkvdb.save('n-' + str(nodeid), n_obj)
#member recent +key
#Member.add_key_rencent_topic(author, topic_key)
rt_obj = kv.get('topic-' + author)
if rt_obj:
olist = rt_obj.split(',')
if topic_key not in olist:
olist.insert(0, topic_key)
rt_obj = ','.join(olist[:MEMBER_RECENT_TOPIC])
kv.set('topic-' + author, rt_obj)
else:
rt_obj = topic_key
kv.set('topic-' + author, topic_key)
#recent in home +key
Commomkvdb.add_key_rencent_topic('recent-topic-home',
topic_key)
#all topic counter +1
Count.key_incr('all-topic-num')
#hot node
tqueue = TaskQueue('default')
tqueue.add(
Task('/task/hotnode/%s/%s' %
('n-' + str(nodeid), str(topic_id)),
delay=5))
#notifications
mentions = findall_mentions(t_obj['content'], author)
if mentions:
tqueue.add(
Task('/task/mentions/' + topic_key,
'member=' + ','.join(mentions),
delay=8))
#set for check spam
#u_topic_time = kv.get('u_topic_time:'+author)
if u_topic_time:
tlist = u_topic_time.split(',')
if str(int_time) not in tlist:
tlist.insert(0, str(int_time))
u_topic_time = ','.join(
tlist[:MEMBER_RECENT_TOPIC])
kv.set('u_topic_time:' + author, u_topic_time)
else:
u_topic_time = str(int_time)
kv.set('u_topic_time:' + author, u_topic_time)
##set new sr_code
cur_user = self.cur_user()
code_list = [cur_user['code'], u_topic_time]
u_comment_time = kv.get('u_comment_time:' + author)
if u_comment_time:
code_list.append(u_comment_time)
self.set_cookie('usercode',
md5(''.join(code_list)).hexdigest(),
path="/",
expires_days=365)
#del cache
clear_cache_multi([
'get_topic_by_keys:recent-topic-home',
'get_topic_by_keys:topic-' + author,
'get_comment_topic_by_keys:recent-topic-home',
'get_comment_topic_by_keys:recent-comment-topic-home',
'cur_user:'******'/' + topic_key)
return
else:
errors.append("服务器出现错误，请稍后再试")
else:
t_obj['title'] = title
t_obj['content'] = content
errors.append(u"注意标题和内容的最大字数:%s %d" %
(len(title), len(content)))
else:
errors.append("标题和内容必填")
self.echo('newpost.html', {
'title': "发新帖子",
'errors': errors,
'n_obj': n_obj,
't_obj': t_obj,
},
layout='_layout.html')
def post(self, nodeid, topicid):
author = str(self.get_cookie('username', ''))
content = self.get_argument('content', '')
if author and content and len(content) <= COMMENT_MAX_S:
int_time = int(time())
#check spam
u_comment_time = kv.get('u_comment_time:' + author)
if u_comment_time:
tlist = u_comment_time.split(',')
if len(tlist) == MEMBER_RECENT_TOPIC and (
int_time - int(tlist[-1])) < 3600:
self.write(u'403:不要回复太频繁了 <a href="/t-%s-%s">请返回</a>' %
(nodeid, topicid))
return
#check repeat
content = textilize(content)
#content = safe_encode(content)
con_md5 = md5(content.encode('utf-8')).hexdigest()
if mc.get('c_' + con_md5):
self.write(u'403:请勿灌水 <a href="/t-%s-%s">请返回</a>' %
(nodeid, topicid))
return
else:
mc.set('c_' + con_md5, '1', 36000)
##
t_key = 't-%s-%s' % (str(nodeid), str(topicid))
t_obj = Topic.get_by_key(t_key)
if t_obj['cnum']:
id_num = int(t_obj['cnum']) + 1
else:
id_num = 1
c_key = 't-%s-%s-%d' % (str(nodeid), str(topicid), id_num)
c_obj = COMMENT_DICT.copy()
c_obj['author'] = author
c_obj['add'] = int_time
c_obj['content'] = content
if Commomkvdb.save(c_key, c_obj):
#topic commont count +1
t_obj['cnum'] = id_num
t_obj['reply'] = author
t_obj['edit'] = int_time
Commomkvdb.save(t_key, t_obj)
#member recent +key
#Member.add_key_rencent_comment_topic(author, t_key)
rt_obj = kv.get('comment-topic-' + author)
if rt_obj:
olist = rt_obj.split(',')
if t_key in olist:
olist.remove(t_key)
olist.insert(0, t_key)
kv.set('comment-topic-' + author,
','.join(olist[:MEMBER_RECENT_TOPIC]))
else:
kv.set('comment-topic-' + author, t_key)
#recent comment in home +key
Commomkvdb.add_key_rencent_topic('recent-comment-topic-home',
t_key)
#all comment counter +1
Count.key_incr('all-comment-num')
#notifications
if t_obj['author'] != author:
mentions = findall_mentions(
c_obj['content'] + ' @%s ' % t_obj['author'], author)
else:
mentions = findall_mentions(c_obj['content'], author)
if mentions:
tqueue = TaskQueue('default')
tqueue.add(
Task('/task/mentions/' + t_key,
'member=' + ','.join(mentions),
delay=5))
#set for check spam
#u_comment_time = kv.get('u_comment_time:'+author)
if u_comment_time:
tlist = u_comment_time.split(',')
if str(int_time) not in tlist:
tlist.insert(0, str(int_time))
u_comment_time = ','.join(tlist[:MEMBER_RECENT_TOPIC])
kv.set('u_comment_time:' + author, u_comment_time)
else:
u_comment_time = str(int_time)
kv.set('u_comment_time:' + author, u_comment_time)
##set new sr_code
cur_user = self.cur_user()
code_list = [cur_user['code']]
u_topic_time = kv.get('u_topic_time:' + author)
if u_topic_time:
code_list.append(u_topic_time)
if u_comment_time:
code_list.append(u_comment_time)
self.set_cookie('usercode',
md5(''.join(code_list)).hexdigest(),
path="/",
expires_days=365)
#del cache
cachekeys = [
'get_topic_by_keys:recent-comment-topic-home',
'get_topic_by_keys:comment-topic-' + author,
'get_comment_topic_by_keys:recent-topic-home',
'get_comment_topic_by_keys:recent-comment-topic-home',
'cur_user:'******'recent-topic-home')
if tks and t_key in tks.split(','):
cachekeys.append('get_topic_by_keys:recent-topic-home')
if id_num < EACH_PAGE_COMMENT_NUM:
cachekeys.append('get_comments:%s:1' % t_key)
else:
cachekeys.append('get_comments:%s:%d' % (t_key, [
i for i in range(1, id_num, EACH_PAGE_COMMENT_NUM)
][-1]))
clear_cache_multi(cachekeys)
self.redirect('/' + t_key)
return
else:
self.set_status(403)
self.write('错误: 403 (请返回填写内容 或 内容太长了)')
def post(self, nodeid='1'):
n_obj = Node.get_by_key('n-'+str(nodeid))
if not n_obj:
self.set_status(404)
self.write('404')
return
errors = []
author = str(self.get_cookie('username',''))
title = self.get_argument('title','')
content = self.get_argument('content','')
t_obj = TOPIC_DICT.copy()
if title and content:
if len(title)<=TITLE_MAX_S and len(content)<=CONTENT_MAX_S:
int_time = int(time())
#check spam
u_topic_time = kv.get('u_topic_time:'+author)
if u_topic_time:
tlist = u_topic_time.split(',')
if len(tlist)== MEMBER_RECENT_TOPIC and (int_time-int(tlist[-1])) < 3600:
self.write(u'403:不要发帖太频繁了 <a href="/newpost/%s">请返回</a>' % nodeid)
return
#check repeat
content = textilize(content)
#content = safe_encode(content)
con_md5 = md5(content.encode('utf-8')).hexdigest()
if mc.get('c_'+con_md5):
self.write(u'403:请勿灌水 <a href="/newpost/%s">请返回</a>' % nodeid)
return
else:
mc.set('c_'+con_md5, '1', 36000)
t_obj['title'] = title
t_obj['nodeid'] = str(nodeid)
t_obj['nodename'] = n_obj['name']
t_obj['author'] = author
t_obj['add'] = int_time
t_obj['content'] = content
if n_obj['count']:
topic_id = int(n_obj['count']) + 1
else:
topic_id = 1
if Topic.add(topic_id, t_obj):
topic_key = 't-%s-%s' % (str(nodeid), str(topic_id))
#node count +1
n_obj['count'] = str(topic_id)
Commomkvdb.save('n-'+str(nodeid), n_obj)
#member recent +key
#Member.add_key_rencent_topic(author, topic_key)
rt_obj = kv.get('topic-'+author)
if rt_obj:
olist = rt_obj.split(',')
if topic_key not in olist:
olist.insert(0, topic_key)
rt_obj = ','.join(olist[:MEMBER_RECENT_TOPIC])
kv.set('topic-'+author, rt_obj)
else:
rt_obj = topic_key
kv.set('topic-'+author, topic_key)
#recent in home +key
Commomkvdb.add_key_rencent_topic('recent-topic-home', topic_key)
#all topic counter +1
Count.key_incr('all-topic-num')
#hot node
tqueue = TaskQueue('default')
tqueue.add(Task('/task/hotnode/%s/%s' % ('n-'+str(nodeid), str(topic_id)), delay=5))
#notifications
mentions = findall_mentions(t_obj['content'], author)
if mentions:
tqueue.add(Task('/task/mentions/'+topic_key, 'member='+','.join(mentions), delay=8))
#set for check spam
#u_topic_time = kv.get('u_topic_time:'+author)
if u_topic_time:
tlist = u_topic_time.split(',')
if str(int_time) not in tlist:
tlist.insert(0, str(int_time))
u_topic_time = ','.join(tlist[:MEMBER_RECENT_TOPIC])
kv.set('u_topic_time:'+author, u_topic_time)
else:
u_topic_time = str(int_time)
kv.set('u_topic_time:'+author, u_topic_time)
##set new sr_code
cur_user = self.cur_user()
code_list = [cur_user['code'],u_topic_time]
u_comment_time = kv.get('u_comment_time:'+author)
if u_comment_time:
code_list.append(u_comment_time)
self.set_cookie('usercode', md5(''.join(code_list)).hexdigest(), path="/", expires_days = 365 )
#del cache
clear_cache_multi(['get_topic_by_keys:recent-topic-home','get_topic_by_keys:topic-' + author, 'get_comment_topic_by_keys:recent-topic-home', 'get_comment_topic_by_keys:recent-comment-topic-home','cur_user:'******'/'+topic_key)
return
else:
errors.append("服务器出现错误，请稍后再试")
else:
t_obj['title'] = title
t_obj['content'] = content
errors.append(u"注意标题和内容的最大字数:%s %d" % (len(title), len(content)))
else:
errors.append("标题和内容必填")
self.echo('newpost.html', {
'title': "发新帖子",
'errors':errors,
'n_obj': n_obj,
't_obj': t_obj,
}, layout='_layout.html')
def post(self, nodeid, topicid):
author = str(self.get_cookie('username',''))
content = self.get_argument('content','')
if author and content and len(content)<=COMMENT_MAX_S:
int_time = int(time())
#check spam
u_comment_time = kv.get('u_comment_time:'+author)
if u_comment_time:
tlist = u_comment_time.split(',')
if len(tlist)== MEMBER_RECENT_TOPIC and (int_time-int(tlist[-1])) < 3600:
self.write(u'403:不要回复太频繁了 <a href="/t-%s-%s">请返回</a>' % (nodeid, topicid))
return
#check repeat
content = textilize(content)
#content = safe_encode(content)
con_md5 = md5(content.encode('utf-8')).hexdigest()
if mc.get('c_'+con_md5):
self.write(u'403:请勿灌水 <a href="/t-%s-%s">请返回</a>' % (nodeid, topicid))
return
else:
mc.set('c_'+con_md5, '1', 36000)
##
t_key = 't-%s-%s' % (str(nodeid), str(topicid))
t_obj = Topic.get_by_key(t_key)
if t_obj['cnum']:
id_num = int(t_obj['cnum']) + 1
else:
id_num = 1
c_key = 't-%s-%s-%d' % (str(nodeid), str(topicid), id_num)
c_obj = COMMENT_DICT.copy()
c_obj['author'] = author
c_obj['add'] = int_time
c_obj['content'] = content
if Commomkvdb.save(c_key, c_obj):
#topic commont count +1
t_obj['cnum'] = id_num
t_obj['reply'] = author
t_obj['edit'] = int_time
Commomkvdb.save(t_key, t_obj)
#member recent +key
#Member.add_key_rencent_comment_topic(author, t_key)
rt_obj = kv.get('comment-topic-'+author)
if rt_obj:
olist = rt_obj.split(',')
if t_key in olist:
olist.remove(t_key)
olist.insert(0, t_key)
kv.set('comment-topic-'+author, ','.join(olist[:MEMBER_RECENT_TOPIC]))
else:
kv.set('comment-topic-'+author, t_key)
#recent comment in home +key
Commomkvdb.add_key_rencent_topic('recent-comment-topic-home', t_key)
#all comment counter +1
Count.key_incr('all-comment-num')
#notifications
if t_obj['author'] != author:
mentions = findall_mentions(c_obj['content']+' @%s '%t_obj['author'], author)
else:
mentions = findall_mentions(c_obj['content'], author)
if mentions:
tqueue = TaskQueue('default')
tqueue.add(Task('/task/mentions/'+t_key, 'member='+','.join(mentions), delay=5))
#set for check spam
#u_comment_time = kv.get('u_comment_time:'+author)
if u_comment_time:
tlist = u_comment_time.split(',')
if str(int_time) not in tlist:
tlist.insert(0, str(int_time))
u_comment_time = ','.join(tlist[:MEMBER_RECENT_TOPIC])
kv.set('u_comment_time:'+author, u_comment_time)
else:
u_comment_time = str(int_time)
kv.set('u_comment_time:'+author, u_comment_time)
##set new sr_code
cur_user = self.cur_user()
code_list = [cur_user['code']]
u_topic_time = kv.get('u_topic_time:'+author)
if u_topic_time:
code_list.append(u_topic_time)
if u_comment_time:
code_list.append(u_comment_time)
self.set_cookie('usercode', md5(''.join(code_list)).hexdigest(), path="/", expires_days = 365 )
#del cache
cachekeys = ['get_topic_by_keys:recent-comment-topic-home', 'get_topic_by_keys:comment-topic-'+author, 'get_comment_topic_by_keys:recent-topic-home', 'get_comment_topic_by_keys:recent-comment-topic-home','cur_user:'******'recent-topic-home')
if tks and t_key in tks.split(','):
cachekeys.append('get_topic_by_keys:recent-topic-home')
if id_num<EACH_PAGE_COMMENT_NUM:
cachekeys.append('get_comments:%s:1' % t_key)
else:
cachekeys.append('get_comments:%s:%d' % (t_key, [i for i in range(1,id_num,EACH_PAGE_COMMENT_NUM)][-1]))
clear_cache_multi(cachekeys)
self.redirect('/'+t_key)
return
else:
self.set_status(403)
self.write('错误: 403 (请返回填写内容 或 内容太长了)')