def get(cls, cli, sp=None, port_id=None):
ret = VNXSPPortList(cli)
if sp is not None:
ret = filter(lambda p: p.sp == sp, ret)
if port_id is not None:
ret = filter(lambda p: p.port_id == port_id, ret)
if sp is not None and port_id is not None and len(ret) == 1:
ret = ret[0]
return ret
def get(cls, cli, sp=None, port_id=None):
ret = VNXSPPortList(cli)
if sp is not None:
ret = filter(lambda p: p.sp == sp, ret)
if port_id is not None:
ret = filter(lambda p: p.port_id == port_id, ret)
if sp is not None and port_id is not None and len(ret) == 1:
ret = ret[0]
return ret
def get(cls, cli, sp=None, port_id=None, vport_id=None):
if sp is not None and port_id is not None and vport_id is not None:
ret = VNXConnectionPort(sp, port_id, vport_id, cli)
else:
ret = VNXConnectionPortList(cli)
if sp is not None:
ret = filter(lambda p: p.sp == sp, ret)
if port_id is not None:
ret = filter(lambda p: p.port_id == port_id, ret)
if port_id is not None:
ret = filter(lambda p: p.virtual_port_id == vport_id, ret)
return ret
def do_run(self, left, right, arg, scope):
if 'index' in self.optargs and self.optargs['index'] != 'id':
index_func, is_multi = self.find_index_func_for_scope(
self.optargs['index'], arg)
if isinstance(index_func, RFunc):
map_fn = lambda d: index_func.run([d], scope)
else:
map_fn = index_func
result = []
left = list(left)
if is_multi:
seen_ids = set([])
for elem in left:
indexed = map_fn(elem)
if not isinstance(indexed, (tuple, list)):
indexed = [indexed]
indexed = set(indexed)
for match_item in right:
if match_item in indexed:
if elem['id'] not in seen_ids:
seen_ids.add(elem['id'])
result.append(elem)
break
else:
for elem in left:
if map_fn(elem) in right:
result.append(elem)
return result
else:
return filter(util.match_attr_multi('id', right), left)
def do_run(self, left, right, arg, scope):
if 'index' in self.optargs and self.optargs['index'] != 'id':
index_func, is_multi = self.find_index_func_for_scope(
self.optargs['index'],
arg
)
if isinstance(index_func, RFunc):
map_fn = lambda d: index_func.run([d], scope)
else:
map_fn = index_func
result = []
left = list(left)
if is_multi:
seen_ids = set([])
for elem in left:
indexed = map_fn(elem)
if not isinstance(indexed, (tuple, list)):
indexed = [indexed]
indexed = set(indexed)
for match_item in right:
if match_item in indexed:
if elem['id'] not in seen_ids:
seen_ids.add(elem['id'])
result.append(elem)
break
else:
for elem in left:
if map_fn(elem) in right:
result.append(elem)
return result
else:
return filter(util.match_attr_multi('id', right), left)
def get(cls, cli, sp=None, port_id=None, vport_id=None):
if sp is not None and port_id is not None and vport_id is not None:
ret = VNXConnectionPort(sp, port_id, vport_id, cli)
else:
ret = VNXConnectionPortList(cli)
if sp is not None:
ret = filter(lambda p: p.sp == sp, ret)
if port_id is not None:
ret = filter(lambda p: p.port_id == port_id, ret)
if port_id is not None:
ret = filter(lambda p: p.virtual_port_id == vport_id,
ret)
return ret
def test_get_seqs_by_ctg(self):
iids_by_ctg = [[1, 2, 4], [1, 2], [3, 5], [4], [6], [2, 4]]
get_seq = lambda i: 'ACGT' if i in [2, 4] else 'A'*i
reds = [make_mock_red(i, i, get_seq(i), 'D'*len(get_seq(i)))
for i in range(1, len(iids_by_ctg)+ 1)]
fastq_records = [make_seq_record(get_seq(i)) for i in range(1, len(iids_by_ctg)+1)]
saved_records = fastq_records[:]
random.shuffle(fastq_records)
result = filter(bool, map(tuple, a2f.get_seqs_by_ctg(fastq_records, reds, iids_by_ctg)))
getters_by_ctg = map(lambda A: itemgetter(*[i - 1 for i in A]), iids_by_ctg)
raw_expected = [get(saved_records) for get in getters_by_ctg]
expected = filter(bool, map(lambda a: (a,) if type(a) is not tuple else a, raw_expected))
# Bio.Seq objects can't be compared directly need to get __dict__ attribute
dicter = lambda tup: [obj.seq.tostring() for obj in tup]
self.assertEquals(map(dicter, expected), map(dicter, result))
pass
def has_snap(self):
""" This method won't count the snaps in "destroying" state!
:return: false if no snaps or all snaps are destroying.
"""
return len(
filter(lambda s: s.state != SnapStateEnum.DESTROYING,
self.snapshots)) > 0
def to_int_arr(inputs):
if inputs is not None:
if isinstance(inputs, six.string_types):
inputs = re.split(',| ', inputs)
ints = map(to_int, inputs)
ret = list(filter(partial(is_not, None), ints))
else:
ret = []
return ret
def to_int_arr(inputs):
if inputs is not None:
if isinstance(inputs, six.string_types):
inputs = re.split(',| ', inputs)
ints = map(to_int, inputs)
ret = list(filter(partial(is_not, None), ints))
else:
ret = []
return ret
def _get_member(self, index):
def filter_by_sp_name(member):
sp = VNXSPEnum.from_str(member.name)
return sp == index
result = filter(filter_by_sp_name, self.list)
ret = None
if len(result) > 0:
ret = result[0]
return ret
def get_candidate_sequences(self, under_index):
'''
:param int under_index: the current position in the matrix which is under-covered.
Candidates have not been used already, overlap the current index, and are not "orphan" or "anomalous" reads.
orphaned/anomalous reads don't get spotted by default mpileup command. see https://github.com/VDBWRAIR/ngs_mapper/issues/112
'''
#TODO: have this only look backwards until reach under-covered index
start = max(under_index - self.max_seq_length, 0)
sub_matrix = self.seq_matrix[start:under_index+1]
'''flatten the matrix'''
prev_seqs = [seq for row in sub_matrix for seq in row]
return filter(lambda seq: seq.overlap >= under_index and self.allow(seq) and not seq.picked, prev_seqs)
def get_startup(cls, node):
"""
Generate the appropriate command-line based on node interfaces.
"""
cmd = cls.startup[0]
netifs = filter(lambda x: not getattr(x, "control", False),
node.netifs())
if len(netifs) > 0:
interfacenames = map(lambda x: x.name, netifs)
cmd += " -i "
cmd += " -i ".join(interfacenames)
return (cmd, )
def get_candidate_sequences(self, under_index):
'''
:param int under_index: the current position in the matrix which is under-covered.
Candidates have not been used already, overlap the current index, and are not "orphan" or "anomalous" reads.
orphaned/anomalous reads don't get spotted by default mpileup command. see https://github.com/VDBWRAIR/ngs_mapper/issues/112
'''
#TODO: have this only look backwards until reach under-covered index
start = max(under_index - self.max_seq_length, 0)
sub_matrix = self.seq_matrix[start:under_index + 1]
'''flatten the matrix'''
prev_seqs = [seq for row in sub_matrix for seq in row]
return filter(
lambda seq: seq.overlap >= under_index and self.allow(seq) and
not seq.picked, prev_seqs)
def test_noniterators_produce_lists(self):
l = range(10)
self.assertTrue(isinstance(l, list))
l2 = zip(l, list('ABCDE')*2)
self.assertTrue(isinstance(l2, list))
double = lambda x: x*2
l3 = map(double, l)
self.assertTrue(isinstance(l3, list))
is_odd = lambda x: x % 2 == 1
l4 = filter(is_odd, range(10))
self.assertEqual(l4, [1, 3, 5, 7, 9])
self.assertTrue(isinstance(l4, list))
def _get_correct_checkpoint(root, checkpoint):
ckptPath = root.joinpath("checkpoints")
if ckptPath.is_dir():
if checkpoint != 'latest':
allCheckPoints = filter(lambda x: x.name == checkpoint,
ckptPath.iterdir())
relevant_checkpoint = None if len(
allCheckPoints) == 0 else allCheckPoints[0]
else:
allCheckPoints = list(ckptPath.iterdir())
relevant_checkpoint = None if len(allCheckPoints) == 0 else sorted(
allCheckPoints, key=lambda x: int(x.name), reverse=True)[0]
return relevant_checkpoint
else:
raise IOError("Checkpoint path does not exist!!")
def get_seqs_by_ctg(fastq_records, reds, iids_by_ctg):
'''
Transforms the fastq records and reds into pandas.DataFrame objects and joins them on the sequence string column.
Then, this DataFrame is sliced according to ``iids_by_ctg`` and returned. The result is a 2D list of SeqRecord objects
organized by the contigs they mapped to.
:param list fastq_records: a collection of Bio.SeqRecord objects
:param list reds: a collection of amos.RED objects
:param list iids_by_ctg: a 2D list of iids (organized by contig)
:return A 2D list of bio.SeqRecord objects organized by the contig they map to.
'''
fastq_df = bio_records_as_df(fastq_records)
reds_df = amos_reds_as_df(collection=reds)
fastq_df, reds_df = fastq_df.set_index('seq'), reds_df.set_index('seq')
assert reds_df.shape == fastq_df.shape, "should have the same number of columns (seqs, seq_obj/iid) and rows (fastq reads / AMOS REDs."
reds_with_seqs_df = join_non_unique_dataframes(reds_df, fastq_df)
dfs_by_ctg = extract_dfs_by_iids(reds_with_seqs_df, iids_by_ctg)
seqs_by_ctg = [df['seq_obj'] for df in dfs_by_ctg]
assert not filter(series_contains_nan, seqs_by_ctg), "NaN value found in resulting dataframe, something went wrong."
return seqs_by_ctg
def get_seqs_by_ctg(fastq_records, reds, iids_by_ctg):
'''
Transforms the fastq records and reds into pandas.DataFrame objects and joins them on the sequence string column.
Then, this DataFrame is sliced according to ``iids_by_ctg`` and returned. The result is a 2D list of SeqRecord objects
organized by the contigs they mapped to.
:param list fastq_records: a collection of Bio.SeqRecord objects
:param list reds: a collection of amos.RED objects
:param list iids_by_ctg: a 2D list of iids (organized by contig)
:return A 2D list of bio.SeqRecord objects organized by the contig they map to.
'''
fastq_df = bio_records_as_df(fastq_records)
reds_df = amos_reds_as_df(collection=reds)
fastq_df, reds_df = fastq_df.set_index('seq'), reds_df.set_index('seq')
assert reds_df.shape == fastq_df.shape, "should have the same number of columns (seqs, seq_obj/iid) and rows (fastq reads / AMOS REDs."
reds_with_seqs_df = join_non_unique_dataframes(reds_df, fastq_df)
dfs_by_ctg = extract_dfs_by_iids(reds_with_seqs_df, iids_by_ctg)
seqs_by_ctg = [df['seq_obj'] for df in dfs_by_ctg]
assert not filter(
series_contains_nan, seqs_by_ctg
), "NaN value found in resulting dataframe, something went wrong."
return seqs_by_ctg
def get_startup(cls, node):
"""
Generate the appropriate command-line based on node interfaces.
"""
cmd = cls.startup[0]
cmd += " -l /var/log/nrlnhdp.log"
cmd += " -rpipe %s_nhdp" % node.name
servicenames = map(lambda x: x.name, node.services)
if "SMF" in servicenames:
cmd += " -flooding ecds"
cmd += " -smfClient %s_smf" % node.name
netifs = filter(lambda x: not getattr(x, "control", False),
node.netifs())
if len(netifs) > 0:
interfacenames = map(lambda x: x.name, netifs)
cmd += " -i "
cmd += " -i ".join(interfacenames)
return (cmd, )
def generate_config(cls, node, filename):
"""
Generate a startup script for SMF. Because nrlsmf does not
daemonize, it can cause problems in some situations when launched
directly using vcmd.
"""
cfg = "#!/bin/sh\n"
cfg += "# auto-generated by nrl.py:NrlSmf.generateconfig()\n"
comments = ""
cmd = "nrlsmf instance %s_smf" % node.name
servicenames = map(lambda x: x.name, node.services)
netifs = filter(lambda x: not getattr(x, "control", False),
node.netifs())
if len(netifs) == 0:
return ""
if "arouted" in servicenames:
comments += "# arouted service is enabled\n"
cmd += " tap %s_tap" % (node.name, )
cmd += " unicast %s" % cls.firstipv4prefix(node, 24)
cmd += " push lo,%s resequence on" % netifs[0].name
if len(netifs) > 0:
if "NHDP" in servicenames:
comments += "# NHDP service is enabled\n"
cmd += " ecds "
elif "OLSR" in servicenames:
comments += "# OLSR service is enabled\n"
cmd += " smpr "
else:
cmd += " cf "
interfacenames = map(lambda x: x.name, netifs)
cmd += ",".join(interfacenames)
cmd += " hash MD5"
cmd += " log /var/log/nrlsmf.log"
cfg += comments + cmd + " < /dev/null > /dev/null 2>&1 &\n\n"
return cfg
def saveGissue():
token = vim.eval("g:github_access_token")
if not token:
print("github-issues.vim: In order to save an issue or add a comment, you need to define a GitHub token. See: https://github.com/jaxbot/github-issues.vim#configuration")
return
parens = getFilenameParens()
number = parens[2]
encoding = "utf-8" # TODO: Get this from vim
issue = {
'title': '',
'body': '',
'assignees': '',
'labels': '',
'milestone': ''
}
commentmode = 0
comment = ""
for line in vim.current.buffer:
if commentmode == 1:
if line == "## Add a comment":
commentmode = 2
continue
if commentmode == 2:
if line != "":
commentmode = 3
comment += line + "\n"
continue
if commentmode == 3:
comment += line + "\n"
continue
if line == "## Comments":
commentmode = 1
continue
if len(line.split("## Reported By:")) > 1:
continue
title = line.split("## Title:")
if len(title) > 1:
issue['title'] = title[1].strip().split(" (" + number + ")")[0]
continue
state = line.split("## State:")
if len(state) > 1:
if state[1].strip().lower() == "closed":
issue['state'] = "closed"
else:
issue['state'] = "open"
continue
milestone = line.split("## Milestone:")
if len(milestone) > 1:
milestones = getMilestoneList(parens[0] + "/" + parens[1], "")
milestone = milestone[1].strip()
for mstone in milestones:
if mstone["title"] == milestone:
issue['milestone'] = str(mstone["number"])
break
continue
labels = line.split("## Labels:")
if len(labels) > 1:
issue['labels'] = labels[1].lstrip().split(', ')
continue
assignees = line.split("## Assignees:")
if len(assignees) > 1:
issue['assignees'] = assignees[1].lstrip().split(' ')
continue
if line == SHOW_COMMITS or line == SHOW_FILES_CHANGED or "## Branch Name:" in line:
continue
if issue['body'] != '':
issue['body'] += '\n'
issue['body'] += line
# remove blank entries
issue['labels'] = filter(bool, issue['labels'])
if number == "new":
if issue['assignees'] == '':
del issue['assignees']
if issue['milestone'] == '':
del issue['milestone']
if issue['body'] == '':
del issue['body']
data = ""
try:
repourl = getUpstreamRepoURI()
url = ghUrl("/issues", repourl)
data = json.dumps(issue).encode(encoding)
request = urllib2.Request(url, data)
data = json.loads(urllib2.urlopen(request, timeout=2).read())
parens[2] = str(data['number'])
vim.current.buffer.name = "gissues/" + \
parens[0] + "/" + parens[1] + "/" + parens[2]
except urllib2.HTTPError as e:
if "code" in e and e.code == 410 or e.code == 404:
print(
"github-issues.vim: Error creating issue. Do you have a github_access_token defined?")
else:
print("github-issues.vim: Unknown HTTP error:")
print(e)
print(data)
print(url)
print(issue)
else:
repourl = vim.eval("b:ghissue_repourl")
url = ghUrl("/issues/" + number, repourl)
data = json.dumps(issue).encode(encoding)
# TODO: Fix POST data should be bytes.
request = urllib2.Request(url, data)
request.get_method = lambda: 'PATCH'
try:
urllib2.urlopen(request, timeout=2)
except urllib2.HTTPError as e:
if "code" in e and e.code == 410 or e.code == 404:
print("Could not update the issue as it does not belong to you!")
if commentmode == 3:
try:
url = ghUrl("/issues/" + parens[2] + "/comments", repourl)
data = json.dumps({'body': comment}).encode(encoding)
request = urllib2.Request(url, data)
urllib2.urlopen(request, timeout=2)
except urllib2.HTTPError as e:
if "code" in e and e.code == 410 or e.code == 404:
print(
"Could not post comment. Do you have a github_access_token defined?")
if commentmode == 3 or number == "new":
showIssue()
# mark it as "saved"
vim.command("setlocal nomodified")
def do_run(self, sequence, filt_fn, arg, scope):
return filter(filt_fn, sequence)
def do_run(self, sequence, filter_fn, arg, scope):
return len(filter(filter_fn, list(sequence)))
def do_run(self, sequence, to_match, arg, scope):
return filter(util.match_attrs(to_match), sequence)
def do_run(self, sequence, filt_fn, arg, scope):
return filter(filt_fn, sequence)
def do_run(self, sequence, to_match, arg, scope):
return filter(util.match_attrs(to_match), sequence)
def do_run(self, sequence, filter_fn, arg, scope):
return len(filter(filter_fn, list(sequence)))