after_merge stringlengths 28 79.6k | before_merge stringlengths 20 79.6k | url stringlengths 38 71 | full_traceback stringlengths 43 922k | traceback_type stringclasses 555
values |
|---|---|---|---|---|
def _configure_node_from_config(self, config):
"""
Startup elements in the node as specified in the provided node configuration.
"""
self.log.info("Configuring node from local configuration ...")
# get contoller configuration subpart
controller = config.get("controller", {})
# start Manhol... | def _configure_node_from_config(self, config):
"""
Startup elements in the node as specified in the provided node configuration.
"""
self.log.info("Configuring node from local configuration ...")
# get contoller configuration subpart
controller = config.get("controller", {})
# start Manhol... | https://github.com/crossbario/crossbar/issues/1179 | 2017-09-05T14:52:34+0200 [Controller 15960] Starting 2 workers ...
2017-09-05T14:52:34+0200 [Controller 15960] Router worker "worker-001" starting ..
2017-09-05T14:52:34+0200 [Router 15969] Started Router worker "worker-001" [crossbar.worker.router.RouterWorkerSession / CPython-EPollReactor]
2017-09-05T14:52:34+... | builtins.AssertionError |
def stop_component(self, component_id, details=None):
"""
Stop a component currently running within this container.
:param component_id: The ID of the component to stop.
:type component_id: int
:param details: Caller details.
:type details: instance of :class:`autobahn.wamp.types.CallDetails`
... | def stop_component(self, component_id, details=None):
"""
Stop a component currently running within this container.
:param component_id: The ID of the component to stop.
:type component_id: int
:param details: Caller details.
:type details: instance of :class:`autobahn.wamp.types.CallDetails`
... | https://github.com/crossbario/crossbar/issues/1179 | 2017-09-05T14:52:34+0200 [Controller 15960] Starting 2 workers ...
2017-09-05T14:52:34+0200 [Controller 15960] Router worker "worker-001" starting ..
2017-09-05T14:52:34+0200 [Router 15969] Started Router worker "worker-001" [crossbar.worker.router.RouterWorkerSession / CPython-EPollReactor]
2017-09-05T14:52:34+... | builtins.AssertionError |
def authorize(self, session, uri, action, options):
"""
Authorize a session connected under this role to perform the given
action on the given URI.
:param session: The WAMP session that requests the action.
:type session: Instance of :class:`autobahn.wamp.protocol.ApplicationSession`
:param uri... | def authorize(self, session, uri, action, options):
"""
Authorize a session connected under this role to perform the given
action on the given URI.
:param session: The WAMP session that requests the action.
:type session: Instance of :class:`autobahn.wamp.protocol.ApplicationSession`
:param uri... | https://github.com/crossbario/crossbar/issues/1437 | 2018-11-11T20:19:23+0100 [Router 9015] Unhandled error in Deferred:
2018-11-11T20:19:23+0100 [Router 9015]
Traceback (most recent call last):
File ".../lib/python3.7/site-packages/crossbar/router/router.py", line 278, in process
self._dealer.processCall(session, msg)
File ".../lib/python3.7/site-packages/cr... | autobahn.wamp.exception.SerializationError |
def start_router_transport(self, id, config, details=None):
"""
Start a transport on this router worker.
:param id: The ID of the transport to start.
:type id: str
:param config: The transport configuration.
:type config: dict
"""
self.log.debug("{name}.start_router_transport", name=sel... | def start_router_transport(self, id, config, details=None):
"""
Start a transport on this router worker.
:param id: The ID of the transport to start.
:type id: str
:param config: The transport configuration.
:type config: dict
"""
self.log.debug("{name}.start_router_transport", name=sel... | https://github.com/crossbario/crossbar/issues/1080 | 2017-05-15T17:29:32+0000 [Router 1609] KeyError: 'endpoint': Traceback (most recent call last):
File "/home/ubuntu/crossbar-pypy2-1/site-packages/autobahn/twisted/websocket.py", line 162, in _onMessage
self.onMessage(payload, isBinary)
File "/home/ubuntu/crossbar-pypy2-1/site-packages/autobahn/wamp/websocket.py",... | exceptions.KeyError |
def _create_web_factory(self, config, is_secure):
options = config.get("options", {})
# create Twisted Web root resource
if "/" in config["paths"]:
root_config = config["paths"]["/"]
root = self._create_resource(root_config, nested=False)
else:
root = Resource404(self._templates... | def _create_web_factory(self, config):
options = config.get("options", {})
# create Twisted Web root resource
if "/" in config["paths"]:
root_config = config["paths"]["/"]
root = self._create_resource(root_config, nested=False)
else:
root = Resource404(self._templates, b"")
... | https://github.com/crossbario/crossbar/issues/1080 | 2017-05-15T17:29:32+0000 [Router 1609] KeyError: 'endpoint': Traceback (most recent call last):
File "/home/ubuntu/crossbar-pypy2-1/site-packages/autobahn/twisted/websocket.py", line 162, in _onMessage
self.onMessage(payload, isBinary)
File "/home/ubuntu/crossbar-pypy2-1/site-packages/autobahn/wamp/websocket.py",... | exceptions.KeyError |
def detach(self, session):
"""
Implements :func:`crossbar.router.interfaces.IDealer.detach`
"""
if session in self._session_to_registrations:
# send out Errors for any in-flight calls we have
outstanding = self._callee_to_invocations.get(session, [])
for invoke in outstanding:
... | def detach(self, session):
"""
Implements :func:`crossbar.router.interfaces.IDealer.detach`
"""
if session in self._session_to_registrations:
# send out Errors for any in-flight calls we have
outstanding = self._callee_to_invocations.get(session, [])
for invoke in outstanding:
... | https://github.com/crossbario/crossbar/issues/980 | 3/2/2017 8:26:29 PM2017-03-02T20:26:29+0000 [Router 13] Unhandled error in Deferred:
3/2/2017 8:26:29 PM2017-03-02T20:26:29+0000 [Router 13]
3/2/2017 8:26:29 PMTraceback (most recent call last):
3/2/2017 8:26:29 PM File "/usr/local/lib/python3.6/site-packages/crossbar/router/router.py", line 192, in pr... | PMbuiltins.AttributeError |
def onClose(self, wasClean):
"""
Implements :func:`autobahn.wamp.interfaces.ITransportHandler.onClose`
"""
self._transport = None
if self._session_id:
# fire callback and close the transport
try:
self.onLeave(types.CloseDetails())
except Exception:
se... | def onClose(self, wasClean):
"""
Implements :func:`autobahn.wamp.interfaces.ITransportHandler.onClose`
"""
self._transport = None
if self._session_id:
# fire callback and close the transport
try:
self.onLeave(types.CloseDetails())
except Exception:
se... | https://github.com/crossbario/crossbar/issues/980 | 3/2/2017 8:26:29 PM2017-03-02T20:26:29+0000 [Router 13] Unhandled error in Deferred:
3/2/2017 8:26:29 PM2017-03-02T20:26:29+0000 [Router 13]
3/2/2017 8:26:29 PMTraceback (most recent call last):
3/2/2017 8:26:29 PM File "/usr/local/lib/python3.6/site-packages/crossbar/router/router.py", line 192, in pr... | PMbuiltins.AttributeError |
def make_stderr_observer(
levels=(LogLevel.warn, LogLevel.error, LogLevel.critical),
show_source=False,
format="standard",
colour=False,
_file=None,
_categories=None,
):
"""
Create an observer which prints logs to L{sys.stderr}.
"""
if _file is None:
_file = sys.__stderr_... | def make_stderr_observer(
levels=(LogLevel.warn, LogLevel.error, LogLevel.critical),
show_source=False,
format="standard",
colour=False,
_file=None,
_categories=None,
):
"""
Create an observer which prints logs to L{sys.stderr}.
"""
if _file is None:
_file = sys.__stderr_... | https://github.com/crossbario/crossbar/issues/702 | Unhandled Error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/twisted/web/http.py", line 1439, in dataReceived
finishCallback(data[contentLength:])
File "/usr/local/lib/python2.7/dist-packages/twisted/web/http.py", line 1704, in _finishRequestBody
self.allContentReceived()
File "/usr/l... | exceptions.AttributeError |
def StandardErrorObserver(event):
if event["log_level"] not in levels:
return
if event.get("log_system", "-") == "-":
logSystem = "{:<10} {:>6}".format("Controller", os.getpid())
else:
logSystem = event["log_system"]
if show_source and event.get("log_namespace") is not None:
... | def StandardErrorObserver(event):
if event["log_level"] not in levels:
return
if event.get("log_system", "-") == "-":
logSystem = "{:<10} {:>6}".format("Controller", os.getpid())
else:
logSystem = event["log_system"]
if show_source and event.get("log_namespace") is not None:
... | https://github.com/crossbario/crossbar/issues/702 | Unhandled Error
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/twisted/web/http.py", line 1439, in dataReceived
finishCallback(data[contentLength:])
File "/usr/local/lib/python2.7/dist-packages/twisted/web/http.py", line 1704, in _finishRequestBody
self.allContentReceived()
File "/usr/l... | exceptions.AttributeError |
def create_native_worker_client_factory(router_session_factory, on_ready, on_exit):
"""
Create a transport factory for talking to native workers.
The node controller talks WAMP-WebSocket-over-STDIO with spawned (native) workers.
The node controller runs a client transport factory, and the native worke... | def create_native_worker_client_factory(router_session_factory, on_ready, on_exit):
"""
Create a transport factory for talking to native workers.
The node controller talks WAMP-WebSocket-over-STDIO with spawned (native) workers.
The node controller runs a client transport factory, and the native worke... | https://github.com/crossbario/crossbar/issues/305 | $ crossbar init
$ crossbar start
2015-04-14 19:05:22+0000 [Controller 8740] Log opened.
2015-04-14 19:05:22+0000 [Controller 8740] ==================== Crossbar.io ====================
2015-04-14 19:05:22+0000 [Controller 8740] Crossbar.io 0.10.4 starting
2015-04-14 19:05:22+0000 [Controller 8740] Running on C... | ApplicationError |
def wrapcloseterm(self, widget):
"""A child terminal has closed, so this container must die"""
dbg("Paned::wrapcloseterm: Called on %s" % widget)
if self.closeterm(widget):
# At this point we only have one child, which is the surviving term
sibling = self.children[0]
first_term_sibl... | def wrapcloseterm(self, widget):
"""A child terminal has closed, so this container must die"""
dbg("Paned::wrapcloseterm: Called on %s" % widget)
if self.closeterm(widget):
# At this point we only have one child, which is the surviving term
sibling = self.children[0]
first_term_sibl... | https://github.com/gnome-terminator/terminator/issues/68 | Truncated backtrace:
paned.py:311:wrapcloseterm:AttributeError: 'NoneType' object has no attribute 'grab_focus'
Traceback (most recent call last):
File "/usr/lib/python3.8/site-packages/terminatorlib/paned.py", line 311, in wrapcloseterm
Terminator().find_terminal_by_uuid(sibling.get_toplevel().last_active_term.urn).g... | AttributeError |
def get_default_cwd():
"""Determine a reasonable default cwd"""
try:
cwd = os.getcwd()
except (FileNotFoundError, OSError):
err("unable to set current working directory, does not exist")
cwd = "/"
return cwd
| def get_default_cwd():
"""Determine a reasonable default cwd"""
cwd = os.getcwd()
if not os.path.exists(cwd) or not os.path.isdir(cwd):
try:
cwd = pwd.getpwuid(os.getuid())[5]
except KeyError:
cwd = "/"
return cwd
| https://github.com/gnome-terminator/terminator/issues/58 | Traceback (most recent call last):
File "/usr/local/bin/terminator", line 87, in <module>
dbus_service = ipc.DBusService()
File "/usr/local/lib/python3.7/dist-packages/terminatorlib/ipc.py", line 42, in __init__
self.prepare_attributes()
File "/usr/local/lib/python3.7/dist-packages/terminatorlib/ipc.py", line 56, in pr... | FileNotFoundError |
def __init__(self):
"""Class initialiser"""
GObject.GObject.__init__(self)
self.terminator = Terminator()
self.terminator.register_terminal(self)
# FIXME: Surely these should happen in Terminator::register_terminal()?
self.connect("enumerate", self.terminator.do_enumerate)
self.connect("fo... | def __init__(self):
"""Class initialiser"""
GObject.GObject.__init__(self)
self.terminator = Terminator()
self.terminator.register_terminal(self)
# FIXME: Surely these should happen in Terminator::register_terminal()?
self.connect("enumerate", self.terminator.do_enumerate)
self.connect("fo... | https://github.com/gnome-terminator/terminator/issues/10 | $ terminator
Traceback (most recent call last):
File "/usr/bin/terminator", line 122, in <module>
TERMINATOR.create_layout(OPTIONS.layout)
File "/usr/share/terminator/terminatorlib/terminator.py", line 311, in create_layout
window, terminal = self.new_window()
File "/usr/share/terminator/terminatorlib/terminator.py", l... | AttributeError |
def _add_regex(self, name, re):
if REGEX_MODERN:
reg = Vte.Regex.new_for_match(re, len(re), self.regex_flags)
self.matches[name] = self.vte.match_add_regex(reg, 0)
else:
reg = GLib.Regex.new(re, self.regex_flags, 0)
self.matches[name] = self.vte.match_add_gregex(reg, 0)
self.... | def _add_regex(self, name, re):
reg = Vte.Regex.new_for_match(re, len(re), self.regex_flags)
self.matches[name] = self.vte.match_add_regex(reg, 0)
self.vte.match_set_cursor_name(self.matches[name], "pointer")
| https://github.com/gnome-terminator/terminator/issues/10 | $ terminator
Traceback (most recent call last):
File "/usr/bin/terminator", line 122, in <module>
TERMINATOR.create_layout(OPTIONS.layout)
File "/usr/share/terminator/terminatorlib/terminator.py", line 311, in create_layout
window, terminal = self.new_window()
File "/usr/share/terminator/terminatorlib/terminator.py", l... | AttributeError |
def can_init():
"""This function returns True iff stderr is a TTY and we are not inside a
REPL. Iff this function returns `True`, a call to :meth:`init` will let
``pwnlib`` manage the terminal.
"""
if sys.platform == "win32":
return False
if not sys.stdout.isatty():
return Fal... | def can_init():
"""This function returns True iff stderr is a TTY and we are not inside a
REPL. Iff this function returns `True`, a call to :meth:`init` will let
``pwnlib`` manage the terminal.
"""
if sys.platform == "win32":
return False
if not sys.stdout.isatty():
return Fal... | https://github.com/Gallopsled/pwntools/issues/826 | In 1: from pwn import *
Out 1:
---------------------------------------------------------------------------
error Traceback (most recent call last)
<ipython-input-1-d810d1e70089> in <module>()
----> 1 from pwn import *
/usr/local/lib/python2.7/dist-packages/pwn/__init__.py in <module... | ImportError |
def init():
global cache
# Detect running under Jupyter
try:
if get_ipython().__class__.__name__ == "ZMQInteractiveShell":
os.environ["PWNLIB_NOTERM"] = "1"
os.environ["JUPYTER_DETECTED"] = "yes"
except NameError:
pass
if "PWNLIB_NOTERM" not in os.environ:
... | def init():
global cache
if "PWNLIB_NOTERM" not in os.environ:
# Fix for BPython
try:
curses.setupterm()
except curses.error as e:
import traceback
print(
"Warning:",
"".join(traceback.format_exception_only(e.__class__... | https://github.com/Gallopsled/pwntools/issues/826 | In 1: from pwn import *
Out 1:
---------------------------------------------------------------------------
error Traceback (most recent call last)
<ipython-input-1-d810d1e70089> in <module>()
----> 1 from pwn import *
/usr/local/lib/python2.7/dist-packages/pwn/__init__.py in <module... | ImportError |
def __init__(
self, parent, process=None, tty=False, wd=None, env=None, raw=True, *args, **kwargs
):
super(ssh_channel, self).__init__(*args, **kwargs)
# keep the parent from being garbage collected in some cases
self.parent = parent
self.returncode = None
self.host = parent.host
self.tty ... | def __init__(
self, parent, process=None, tty=False, wd=None, env=None, raw=True, *args, **kwargs
):
super(ssh_channel, self).__init__(*args, **kwargs)
# keep the parent from being garbage collected in some cases
self.parent = parent
self.returncode = None
self.host = parent.host
self.tty ... | https://github.com/Gallopsled/pwntools/issues/1468 | [+] Downloading '/proc/sys/kernel/core_pattern': Found '/proc/sys/kernel/core_pattern' in ssh cache
[+] Downloading '/proc/sys/kernel/core_uses_pid': Found '/proc/sys/kernel/core_uses_pid' in ssh cache
[DEBUG] core_pattern: b'|/usr/share/apport/apport %p %s %c %d %P %E'
[DEBUG] core_uses_pid: False
[DEBUG] Not a proces... | TypeError |
def process(
self,
argv=None,
executable=None,
tty=True,
cwd=None,
env=None,
timeout=Timeout.default,
run=True,
stdin=0,
stdout=1,
stderr=2,
preexec_fn=None,
preexec_args=(),
raw=True,
aslr=None,
setuid=None,
shell=False,
):
r"""
Executes a pro... | def process(
self,
argv=None,
executable=None,
tty=True,
cwd=None,
env=None,
timeout=Timeout.default,
run=True,
stdin=0,
stdout=1,
stderr=2,
preexec_fn=None,
preexec_args=(),
raw=True,
aslr=None,
setuid=None,
shell=False,
):
r"""
Executes a pro... | https://github.com/Gallopsled/pwntools/issues/1468 | [+] Downloading '/proc/sys/kernel/core_pattern': Found '/proc/sys/kernel/core_pattern' in ssh cache
[+] Downloading '/proc/sys/kernel/core_uses_pid': Found '/proc/sys/kernel/core_uses_pid' in ssh cache
[DEBUG] core_pattern: b'|/usr/share/apport/apport %p %s %c %d %P %E'
[DEBUG] core_uses_pid: False
[DEBUG] Not a proces... | TypeError |
def _peekkey_ss3(offset):
global _cbuf
if len(_cbuf) <= offset:
return Key(kc.TYPE_UNICODE, "O", kc.MOD_ALT)
cmd = _cbuf[offset]
if cmd < 0x40 or cmd >= 0x80:
return
_cbuf = _cbuf[offset:]
if chr(cmd) in _csi_ss3s:
return Key(*_csi_ss3s[chr(cmd)])
if chr(cmd) in _cs... | def _peekkey_ss3(offset):
global _cbuf
if len(_cbuf) <= offset:
return Key(kc.TYPE_UNICODE, "O", kc.MOD_ALT)
cmd = _cbuf[offset]
if cmd < 0x40 or cmd >= 0x80:
return
_cbuf = _cbuf[numb:] # XXX: numb is not defined
if chr(cmd) in _csi_ss3s:
return Key(*_csi_ss3s[chr(cmd)... | https://github.com/Gallopsled/pwntools/issues/974 | Traceback (most recent call last):
File "foo.py", line 907, in <module>
inp = sys.stdin.readline().strip().decode('utf-8')
File "/lib/python2.7/site-packages/pwnlib/term/readline.py", line 412, in readline
return readline(size)
File "/lib/python2.7/site-packages/pwnlib/term/readline.py", line 376, in readline
keymap.ha... | NameError |
def __getattr__(self, desc):
try:
ds = desc.replace("gray", "bright_black").split("_")
init = ""
while ds:
d = ds[0]
try:
init += self._attributes[d]
ds.pop(0)
except KeyError:
break
def c():
... | def __getattr__(self, desc):
ds = desc.replace("gray", "bright_black").split("_")
init = ""
while ds:
d = ds[0]
try:
init += self._attributes[d]
ds.pop(0)
except KeyError:
break
def c():
bright = 0
c = ds.pop(0)
if c ==... | https://github.com/Gallopsled/pwntools/issues/342 | import pwnlib
pwnlib.term.text.__lol__
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "pwnlib/term/text.py", line 99, in __getattr__
init += self._fg_color(c())
File "pwnlib/term/text.py", line 93, in c
return self._colors[c] + bright
KeyError: '' | KeyError |
def __init__(
self,
transforms,
bbox_params=None,
keymap=None,
update_pad_shape=False,
skip_img_without_anno=False,
):
if Compose is None:
raise RuntimeError("albumentations is not installed")
# Args will be modified later, copying it will be safer
transforms = copy.deepcopy... | def __init__(
self,
transforms,
bbox_params=None,
keymap=None,
update_pad_shape=False,
skip_img_without_anno=False,
):
if Compose is None:
raise RuntimeError("albumentations is not installed")
self.transforms = transforms
self.filter_lost_elements = False
self.update_pad... | https://github.com/open-mmlab/mmdetection/issues/4599 | Original Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/torch/utils/data/_utils/worker.py", line 178, in _worker_loop
data = fetcher.fetch(index)
File "/usr/local/lib/python3.6/dist-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possib... | ValueError |
def show_result(
self,
img,
result,
score_thr=0.3,
bbox_color="green",
text_color="green",
thickness=1,
font_scale=0.5,
win_name="",
show=False,
wait_time=0,
out_file=None,
):
"""Draw `result` over `img`.
Args:
img (str or Tensor): The image to be display... | def show_result(
self,
img,
result,
score_thr=0.3,
bbox_color="green",
text_color="green",
thickness=1,
font_scale=0.5,
win_name="",
show=False,
wait_time=0,
out_file=None,
):
"""Draw `result` over `img`.
Args:
img (str or Tensor): The image to be display... | https://github.com/open-mmlab/mmdetection/issues/2734 | Traceback (most recent call last):
File "demo/image_demo.py", line 26, in <module>
main()
File "demo/image_demo.py", line 22, in main
show_result_pyplot(model, args.img, result, score_thr=args.score_thr)
File "/root/mmdetection-master/mmdet/apis/inference.py", line 146, in show_result_pyplot
img = model.show_result(img... | IndexError |
def show_result(self, data, result, **kwargs):
if self.with_mask:
ms_bbox_result, ms_segm_result = result
if isinstance(ms_bbox_result, dict):
result = (ms_bbox_result["ensemble"], ms_segm_result["ensemble"])
else:
if isinstance(result, dict):
result = result["ens... | def show_result(self, data, result, **kwargs):
if self.with_mask:
ms_bbox_result, ms_segm_result = result
if isinstance(ms_bbox_result, dict):
result = (ms_bbox_result["ensemble"], ms_segm_result["ensemble"])
else:
if isinstance(result, dict):
result = result["ens... | https://github.com/open-mmlab/mmdetection/issues/2734 | Traceback (most recent call last):
File "demo/image_demo.py", line 26, in <module>
main()
File "demo/image_demo.py", line 22, in main
show_result_pyplot(model, args.img, result, score_thr=args.score_thr)
File "/root/mmdetection-master/mmdet/apis/inference.py", line 146, in show_result_pyplot
img = model.show_result(img... | IndexError |
def printf(self, format, *args):
"""
Inspired from numba/cgutils.py
Calls printf().
Argument `format` is expected to be a Python string.
Values to be printed are listed in `args`.
Note: There is no checking to ensure there is correct number of values
in `args` and there type matches the de... | def printf(self, format, *args):
"""
Inspired from numba/cgutils.py
Calls printf().
Argument `format` is expected to be a Python string.
Values to be printed are listed in `args`.
Note: There is no checking to ensure there is correct number of values
in `args` and there type matches the de... | https://github.com/cea-sec/miasm/issues/630 | TEST/ANALYSIS dse.py llvm
ERROR dse.py llvm
Traceback (most recent call last):
File "dse.py", line 157, in <module>
test(jit_engine)()
File "dse.py", line 61, in __call__
self.run()
File "dse.py", line 67, in run
self.myjit.continue_run()
File "/usr/local/lib/python2.7/dist-packages/miasm2/jitter/jitload.py", line 369,... | KeyError |
def parse_reports(self):
"""Find Picard OxoGMetrics reports and parse their data"""
# Set up vars
self.picard_OxoGMetrics_data = dict()
# Go through logs and find Metrics
for f in self.find_log_files("picard/oxogmetrics", filehandles=True):
# We use lists to make sure that we don't overwri... | def parse_reports(self):
"""Find Picard OxoGMetrics reports and parse their data"""
# Set up vars
self.picard_OxoGMetrics_data = dict()
# Go through logs and find Metrics
for f in self.find_log_files("picard/oxogmetrics", filehandles=True):
# We use lists to make sure that we don't overwri... | https://github.com/ewels/MultiQC/issues/1265 | $ multiqc -f abcd_CL1005827_L01_R1-indexcov.ped -o OUT
[INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : work/qc/abcd_CL1005827_L01_R1/coverage/indexcov/abcd_CL1005827_L01_R1-indexcov.ped
[INFO ] bcbio : Found 0 repor... | AttributeError |
def plot(data, pconfig=None):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Don't just use {} ... | def plot(data, pconfig=None):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Don't just use {} ... | https://github.com/ewels/MultiQC/issues/1265 | $ multiqc -f abcd_CL1005827_L01_R1-indexcov.ped -o OUT
[INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : work/qc/abcd_CL1005827_L01_R1/coverage/indexcov/abcd_CL1005827_L01_R1-indexcov.ped
[INFO ] bcbio : Found 0 repor... | AttributeError |
def plot(data, pconfig=None):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Don't just use {} ... | def plot(data, pconfig=None):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Don't just use {} ... | https://github.com/ewels/MultiQC/issues/1265 | $ multiqc -f abcd_CL1005827_L01_R1-indexcov.ped -o OUT
[INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : work/qc/abcd_CL1005827_L01_R1/coverage/indexcov/abcd_CL1005827_L01_R1-indexcov.ped
[INFO ] bcbio : Found 0 repor... | AttributeError |
def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="Kraken",
anchor="kraken",
href="https://ccb.jhu.edu/software/kraken/",
info="is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of ... | def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="Kraken",
anchor="kraken",
href="https://ccb.jhu.edu/software/kraken/",
info="is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of ... | https://github.com/ewels/MultiQC/issues/1276 | Module kraken raised an exception: Traceback (most recent call last):
File "/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/multiqc.py", line 569, in run
output = mod()
File "//multiqc/1.9/lib/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/modules/kraken/kraken.py", line 60, in __init__
self.sum_sample_co... | ZeroDivisionError |
def sum_sample_counts(self):
"""Sum counts across all samples for kraken data"""
# Sum the percentages for each taxa across all samples
# Allows us to pick top-5 for each rank
# Use percentages instead of counts so that deeply-sequences samples
# are not unfairly over-represented
for s_name, da... | def sum_sample_counts(self):
"""Sum counts across all samples for kraken data"""
# Sum the percentages for each taxa across all samples
# Allows us to pick top-5 for each rank
# Use percentages instead of counts so that deeply-sequences samples
# are not unfairly over-represented
for s_name, da... | https://github.com/ewels/MultiQC/issues/1276 | Module kraken raised an exception: Traceback (most recent call last):
File "/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/multiqc.py", line 569, in run
output = mod()
File "//multiqc/1.9/lib/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/modules/kraken/kraken.py", line 60, in __init__
self.sum_sample_co... | ZeroDivisionError |
def general_stats_cols(self):
"""Add a couple of columns to the General Statistics table"""
# Get top taxa in most specific taxa rank that we have
top_five = []
top_rank_code = None
top_rank_name = None
for rank_code, rank_name in self.t_ranks.items():
try:
sorted_pct = sort... | def general_stats_cols(self):
"""Add a couple of columns to the General Statistics table"""
# Get top taxa in most specific taxa rank that we have
top_five = []
top_rank_code = None
top_rank_name = None
for rank_code, rank_name in self.t_ranks.items():
try:
sorted_pct = sort... | https://github.com/ewels/MultiQC/issues/1276 | Module kraken raised an exception: Traceback (most recent call last):
File "/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/multiqc.py", line 569, in run
output = mod()
File "//multiqc/1.9/lib/python3.7/site-packages/multiqc-1.9-py3.7.egg/multiqc/modules/kraken/kraken.py", line 60, in __init__
self.sum_sample_co... | ZeroDivisionError |
def custom_module_classes():
"""
MultiQC Custom Content class. This module does a lot of different
things depending on the input and is as flexible as possible.
NB: THIS IS TOTALLY DIFFERENT TO ALL OTHER MODULES
"""
# Dict to hold parsed data. Each key should contain a custom data type
# e... | def custom_module_classes():
"""
MultiQC Custom Content class. This module does a lot of different
things depending on the input and is as flexible as possible.
NB: THIS IS TOTALLY DIFFERENT TO ALL OTHER MODULES
"""
# Dict to hold parsed data. Each key should contain a custom data type
# e... | https://github.com/ewels/MultiQC/issues/1221 | Traceback (most recent call last):
File "/home/noronhaa/.local/lib/python3.8/site-packages/numpy/core/__init__.py", line 24, in <module>
from . import multiarray
File "/home/noronhaa/.local/lib/python3.8/site-packages/numpy/core/multiarray.py", line 14, in <module>
from . import overrides
File "/home/noronhaa/.local/li... | ImportError |
def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | https://github.com/ewels/MultiQC/issues/1217 | [INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /mnt/home/juriski/projects/scratch/MiSeq_run_200529/results/kaiju1/taxa/genus
[INFO ] kaiju : Found 1 reports
[ERROR ] multiqc : Oops! The 'kaiju' MultiQC mod... | AttributeError |
def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | https://github.com/ewels/MultiQC/issues/1217 | [INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /mnt/home/juriski/projects/scratch/MiSeq_run_200529/results/kaiju1/taxa/genus
[INFO ] kaiju : Found 1 reports
[ERROR ] multiqc : Oops! The 'kaiju' MultiQC mod... | AttributeError |
def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | def kaiju_stats_table(self):
"""Take the parsed stats from the Kaiju reports and add them to the
basic stats table at the top of the report"""
headers = {}
general_data = {}
taxo_ranks = self.kaiju_data.keys()
# print only phylum rank in general table.
if len(taxo_ranks) >= 1 and "phylum" i... | https://github.com/ewels/MultiQC/issues/1217 | [INFO ] multiqc : This is MultiQC v1.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /mnt/home/juriski/projects/scratch/MiSeq_run_200529/results/kaiju1/taxa/genus
[INFO ] kaiju : Found 1 reports
[ERROR ] multiqc : Oops! The 'kaiju' MultiQC mod... | AttributeError |
def parse_qorts(self, f):
s_names = None
for l in f["f"]:
s = l.split("\t")
if s_names is None:
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s[1:]]
if len(s_names) <= 2 and s_names[0].endswith("COUNT"):
if f["fn"] == "QC.summary.txt":
... | def parse_qorts(self, f):
s_names = None
for l in f["f"]:
s = l.split("\t")
if s_names is None:
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s[1:]]
if len(s_names) <= 2 and s_names[0].endswith("COUNT"):
if f["fn"] == "QC.summary.txt":
... | https://github.com/ewels/MultiQC/issues/1153 | Traceback (most recent call last):
File "/Users/Ernesto/opt/miniconda3/lib/python3.7/site-packages/multiqc/multiqc.py", line 546, in run
output = mod()
File "/Users/Ernesto/opt/miniconda3/lib/python3.7/site-packages/multiqc/modules/qorts/qorts.py", line 29, in __init__
self.parse_qorts(f)
File "/Users/Ernesto/opt/minic... | ValueError |
def fastqc_general_stats(self):
"""Add some single-number stats to the basic statistics
table at the top of the report"""
# Prep the data
data = dict()
for s_name in self.fastqc_data:
bs = self.fastqc_data[s_name]["basic_statistics"]
try:
# FastQC reports with 0 reads wi... | def fastqc_general_stats(self):
"""Add some single-number stats to the basic statistics
table at the top of the report"""
# Prep the data
data = dict()
for s_name in self.fastqc_data:
bs = self.fastqc_data[s_name]["basic_statistics"]
data[s_name] = {
"percent_gc": bs["%G... | https://github.com/ewels/MultiQC/issues/1129 | [INFO ] multiqc : This is MultiQC v1.8
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /home/bioinf/gbs_data/sample3/log
[INFO ] trimmomatic : Found 179 logs
[INFO ] fastqc : Found 368 reports
[ERROR ] multiqc : Oops! The 'fastqc' MultiQC m... | KeyError |
def gc_content_plot(self):
"""Create the HTML for the FastQC GC content plot"""
data = dict()
data_norm = dict()
for s_name in self.fastqc_data:
try:
data[s_name] = {
d["gc_content"]: d["count"]
for d in self.fastqc_data[s_name]["per_sequence_gc_conte... | def gc_content_plot(self):
"""Create the HTML for the FastQC GC content plot"""
data = dict()
data_norm = dict()
for s_name in self.fastqc_data:
try:
data[s_name] = {
d["gc_content"]: d["count"]
for d in self.fastqc_data[s_name]["per_sequence_gc_conte... | https://github.com/ewels/MultiQC/issues/1129 | [INFO ] multiqc : This is MultiQC v1.8
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /home/bioinf/gbs_data/sample3/log
[INFO ] trimmomatic : Found 179 logs
[INFO ] fastqc : Found 368 reports
[ERROR ] multiqc : Oops! The 'fastqc' MultiQC m... | KeyError |
def custom_module_classes():
"""
MultiQC Custom Content class. This module does a lot of different
things depending on the input and is as flexible as possible.
NB: THIS IS TOTALLY DIFFERENT TO ALL OTHER MODULES
"""
# Dict to hold parsed data. Each key should contain a custom data type
# e... | def custom_module_classes():
"""
MultiQC Custom Content class. This module does a lot of different
things depending on the input and is as flexible as possible.
NB: THIS IS TOTALLY DIFFERENT TO ALL OTHER MODULES
"""
# Dict to hold parsed data. Each key should contain a custom data type
# e... | https://github.com/ewels/MultiQC/issues/1071 | [INFO ] multiqc : This is MultiQC v1.8
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching : /home/sande/Dropbox/Studie/PhD/snakemake-workflows/some_data.out
[ERROR ] multiqc : Oops! The 'custom_content' MultiQC module broke...
Please copy the following traceback... | ValueError |
def write_data_file(data, fn, sort_cols=False, data_format=None):
"""Write a data file to the report directory. Will not do anything
if config.data_dir is not set.
:param: data - a 2D dict, first key sample name (row header),
second key field (column header).
:param: fn - Desired filename. D... | def write_data_file(data, fn, sort_cols=False, data_format=None):
"""Write a data file to the report directory. Will not do anything
if config.data_dir is not set.
:param: data - a 2D dict, first key sample name (row header),
second key field (column header).
:param: fn - Desired filename. D... | https://github.com/ewels/MultiQC/issues/1091 | Module custom_content raised an exception: Traceback (most recent call last):
File "/usr/lib/python3.6/site-packages/multiqc-1.8.dev0-py3.6.egg/EGG-INFO/scripts/multiqc", line 440, in multiqc
output = mod()
File "/usr/lib/python3.6/site-packages/multiqc-1.8.dev0-py3.6.egg/multiqc/modules/custom_content/custom_content.p... | TypeError |
def run(
analysis_dir,
dirs=False,
dirs_depth=None,
no_clean_sname=False,
title=None,
report_comment=None,
template=None,
module_tag=(),
module=(),
exclude=(),
outdir=None,
ignore=(),
ignore_samples=(),
sample_names=None,
sample_filters=None,
file_list=Fal... | def run(
analysis_dir,
dirs=False,
dirs_depth=None,
no_clean_sname=False,
title=None,
report_comment=None,
template=None,
module_tag=(),
module=(),
exclude=(),
outdir=None,
ignore=(),
ignore_samples=(),
sample_names=None,
sample_filters=None,
file_list=Fal... | https://github.com/ewels/MultiQC/issues/806 | [2018-07-26 14:06:51,065] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
[2018-07-26 14:06:51,132] multiqc [DEBUG ] No samples found: clusterflow
[2018-07-26 14:06:51,135] multiqc [DEBUG ] No samples... | OSError |
def move_tmp_log(logger):
"""Move the temporary log file to the MultiQC data directory
if it exists."""
try:
# https://stackoverflow.com/questions/15435652/python-does-not-release-filehandles-to-logfile
logging.shutdown()
shutil.copy(log_tmp_fn, os.path.join(config.data_dir, "multiq... | def move_tmp_log(logger):
"""Move the temporary log file to the MultiQC data directory
if it exists."""
try:
# https://stackoverflow.com/questions/15435652/python-does-not-release-filehandles-to-logfile
logging.shutdown()
shutil.move(log_tmp_fn, os.path.join(config.data_dir, "multiq... | https://github.com/ewels/MultiQC/issues/806 | [2018-07-26 14:06:51,065] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports
[2018-07-26 14:06:51,132] multiqc [DEBUG ] No samples found: clusterflow
[2018-07-26 14:06:51,135] multiqc [DEBUG ] No samples... | OSError |
def parse_plotProfile(self):
"""Find plotProfile output"""
self.deeptools_plotProfile = dict()
for f in self.find_log_files("deeptools/plotProfile", filehandles=False):
parsed_data, bin_labels, converted_bin_labels = self.parsePlotProfileData(f)
for k, v in parsed_data.items():
i... | def parse_plotProfile(self):
"""Find plotProfile output"""
self.deeptools_plotProfile = dict()
for f in self.find_log_files("deeptools/plotProfile", filehandles=False):
parsed_data, bin_labels, converted_bin_labels = self.parsePlotProfileData(f)
for k, v in parsed_data.items():
i... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parseBamPEFDistributionFile(self, f):
d = dict()
lastsample = []
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if cols[0] == "#bamPEFragmentSize":
continue
elif cols[0] == "Size":
continue
else:
s_name = self.clean_s... | def parseBamPEFDistributionFile(self, f):
d = dict()
lastsample = []
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if cols[0] == "#bamPEFragmentSize":
continue
elif cols[0] == "Size":
continue
else:
s_name = self.clean_s... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parseBamPEFile(self, f):
d = {}
headers = None
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if headers is None:
headers = cols
else:
s_name = None
for idx, h in enumerate(headers):
if idx == 0:
... | def parseBamPEFile(self, f):
d = {}
headers = None
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if headers is None:
headers = cols
else:
s_name = None
for idx, h in enumerate(headers):
if idx == 0:
... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parseEstimateReadFilteringFile(self, f):
d = {}
firstLine = True
for line in f["f"].splitlines():
if firstLine:
firstLine = False
continue
cols = line.strip().split("\t")
if len(cols) != 12:
# This is not really the output from estimateReadFil... | def parseEstimateReadFilteringFile(self, f):
d = {}
firstLine = True
for line in f["f"].splitlines():
if firstLine:
firstLine = False
continue
cols = line.strip().split("\t")
if len(cols) != 12:
# This is not really the output from estimateReadFil... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parsePlotEnrichment(self, f):
d = {}
firstLine = True
for line in f["f"].splitlines():
if firstLine:
firstLine = False
continue
cols = line.strip().split("\t")
if len(cols) != 5:
log.warning(
"{} was initially flagged as the ou... | def parsePlotEnrichment(self, f):
d = {}
firstLine = True
for line in f["f"].splitlines():
if firstLine:
firstLine = False
continue
cols = line.strip().split("\t")
if len(cols) != 5:
log.warning(
"{} was initially flagged as the ou... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parsePlotFingerprintOutRawCounts(self, f):
d = dict()
samples = []
firstLine = True
for line in f["f"].splitlines():
cols = line.strip().split("\t")
if cols[0] == "#plotFingerprint --outRawCounts":
continue
if firstLine:
for c in cols:
... | def parsePlotFingerprintOutRawCounts(self, f):
d = dict()
samples = []
firstLine = True
for line in f["f"].splitlines():
cols = line.strip().split("\t")
if cols[0] == "#plotFingerprint --outRawCounts":
continue
if firstLine:
for c in cols:
... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parsePlotPCAData(self, f):
d = dict()
samples = []
for line in f["f"].splitlines():
cols = line.strip().split("\t")
if cols[0] == "#plotPCA --outFileNameData":
continue
elif cols[0] == "Component":
for c in cols[1 : (len(cols) - 1)]:
c = st... | def parsePlotPCAData(self, f):
d = dict()
samples = []
for line in f["f"].splitlines():
cols = line.strip().split("\t")
if cols[0] == "#plotPCA --outFileNameData":
continue
elif cols[0] == "Component":
for c in cols[1 : (len(cols) - 1)]:
c = st... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parsePlotProfileData(self, f):
d = dict()
bin_labels = []
bins = []
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if cols[0] == "bin labels":
for col in cols[2 : len(cols)]:
if col not in list(filter(None, bin_labels)):
... | def parsePlotProfileData(self, f):
d = dict()
bin_labels = []
bins = []
for line in f["f"].splitlines():
cols = line.rstrip().split("\t")
if cols[0] == "bin labels":
for col in cols[2 : len(cols)]:
if col not in list(filter(None, bin_labels)):
... | https://github.com/ewels/MultiQC/issues/1011 | Module deeptools raised an exception: Traceback (most recent call last):
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
output = mod()
File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __in... | ValueError |
def parse_logs(self, file_type, root, s_name, fn, f, **kw):
log.debug("Parsing %s/%s", root, fn)
if not file_type in file_types:
log.error("Unknown output type '%s'. Error in config?", file_type)
return False
log_descr = file_types[file_type]
if "not_implemented" in log_descr:
lo... | def parse_logs(self, file_type, root, s_name, fn, f, **kw):
log.debug("Parsing %s/%s", root, fn)
if not file_type in file_types:
log.error("Unknown output type '%s'. Error in config?", file_type)
return False
log_descr = file_types[file_type]
if "not_implemented" in log_descr:
lo... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def plot_aqhist(samples, file_type, **plot_args):
"""Create line graph plot of histogram data for BBMap 'aqhist' output.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample][... | def plot_aqhist(samples, file_type, **plot_args):
"""Create line graph plot of histogram data for BBMap 'aqhist' output.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample][... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def plot_basic_hist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'file_type'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]... | def plot_basic_hist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'file_type'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def plot_covhist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'covhist'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["dat... | def plot_covhist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'covhist'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["dat... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def plot_ihist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'ihist'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["data"][... | def plot_ihist(samples, file_type, **plot_args):
"""Create line graph plot for basic histogram data for 'ihist'.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["data"][... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def plot_qhist(samples, file_type, **plot_args):
"""Create line graph plot of histogram data for BBMap 'qhist' output.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["d... | def plot_qhist(samples, file_type, **plot_args):
"""Create line graph plot of histogram data for BBMap 'qhist' output.
The 'samples' parameter could be from the bbmap mod_data dictionary:
samples = bbmap.MultiqcModule.mod_data[file_type]
"""
sumy = sum(
[
int(samples[sample]["d... | https://github.com/ewels/MultiQC/issues/952 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'qc/'
Searching 252 files.. [####################################] 100%
[INFO ] preseq : Found 24 reports
[INFO ] rseqc : Found 12 read_distribution reports
[... | UnboundLocalError |
def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="Peddy",
anchor="peddy",
href="https://github.com/brentp/peddy",
info="calculates genotype :: pedigree correspondence checks, ancestry checks and sex checks using VCF files.",
)
... | def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="Peddy",
anchor="peddy",
href="https://github.com/brentp/peddy",
info="calculates genotype :: pedigree correspondence checks, ancestry checks and sex checks using VCF files.",
)
... | https://github.com/ewels/MultiQC/issues/1024 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination... | KeyError |
def parse_peddy_csv(self, f, pattern):
"""Parse csv output from peddy"""
parsed_data = dict()
headers = None
s_name_idx = None
for l in f["f"].splitlines():
s = l.split(",")
if headers is None:
headers = s
try:
s_name_idx = [headers.index("samp... | def parse_peddy_csv(self, f, pattern):
"""Parse csv output from peddy"""
parsed_data = dict()
headers = None
s_name_idx = None
for l in f["f"].splitlines():
s = l.split(",")
if headers is None:
headers = s
try:
s_name_idx = [headers.index("samp... | https://github.com/ewels/MultiQC/issues/1024 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination... | KeyError |
def peddy_pca_plot(self):
ancestry_colors = {
"SAS": "rgb(68,1,81,1)",
"EAS": "rgb(59,81,139,1)",
"AMR": "rgb(33,144,141,1)",
"AFR": "rgb(92,200,99,1)",
"EUR": "rgb(253,231,37,1)",
}
background_ancestry_colors = {
"SAS": "rgb(68,1,81,0.1)",
"EAS": "rgb... | def peddy_pca_plot(self):
ancestry_colors = {
"SAS": "rgb(68,1,81,1)",
"EAS": "rgb(59,81,139,1)",
"AMR": "rgb(33,144,141,1)",
"AFR": "rgb(92,200,99,1)",
"EUR": "rgb(253,231,37,1)",
}
background_ancestry_colors = {
"SAS": "rgb(68,1,81,0.1)",
"EAS": "rgb... | https://github.com/ewels/MultiQC/issues/1024 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination... | KeyError |
def peddy_het_check_plot(self):
"""plot the het_check scatter plot"""
# empty dictionary to add sample names, and dictionary of values
data = {}
# for each sample, and list in self.peddy_data
for s_name, d in self.peddy_data.items():
# check the sample contains the required columns
... | def peddy_het_check_plot(self):
"""plot the het_check scatter plot"""
# empty dictionary to add sample names, and dictionary of values
data = {}
# for each sample, and list in self.peddy_data
for s_name, d in self.peddy_data.items():
# check the sample contains the required columns
... | https://github.com/ewels/MultiQC/issues/1024 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination... | KeyError |
def peddy_sex_check_plot(self):
data = {}
sex_index = {"female": 0, "male": 1, "unknown": 2}
for s_name, d in self.peddy_data.items():
if "sex_het_ratio" in d and "ped_sex_sex_check" in d:
data[s_name] = {
"x": sex_index.get(d["ped_sex_sex_check"], 2),
"y... | def peddy_sex_check_plot(self):
data = {}
sex_index = {"female": 0, "male": 1, "unknown": 2}
for s_name, d in self.peddy_data.items():
if "sex_het_ratio" in d and "ped_sex_sex_check" in d:
data[s_name] = {
"x": sex_index.get(d["ped_sex_sex_check"], 2),
"y... | https://github.com/ewels/MultiQC/issues/1024 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/multiqc/report/metrics/target_info.yaml'
[INFO ] multiqc : Searching '/home/ubuntu/naumenko/sample_b2/work/qc/ts_bcbio/contamination... | KeyError |
def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="QUAST",
anchor="quast",
href="http://quast.bioinf.spbau.ru/",
info="is a quality assessment tool for genome assemblies, written by "
"the Center for Algorithmic Biotechnology.",
... | def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="QUAST",
anchor="quast",
href="http://quast.bioinf.spbau.ru/",
info="is a quality assessment tool for genome assemblies, written by "
"the Center for Algorithmic Biotechnology.",
... | https://github.com/ewels/MultiQC/issues/954 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Prepending directory to sample names
[INFO ] multiqc : Searching 'outputs'
[INFO ] multiqc : Only using modules quast
[INFO ] quast : Found 16 reports
[ERROR ] ... | ValueError |
def parse_quast_log(self, f):
lines = f["f"].splitlines()
# Pull out the sample names from the first row
s_names = lines[0].split("\t")
# Prepend directory name(s) to sample names as configured
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s_names]
for s_name in s_names[1:]:
... | def parse_quast_log(self, f):
lines = f["f"].splitlines()
# Pull out the sample names from the first row
s_names = lines[0].split("\t")
# Prepend directory name(s) to sample names as configured
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s_names]
for s_name in s_names[1:]:
... | https://github.com/ewels/MultiQC/issues/954 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Prepending directory to sample names
[INFO ] multiqc : Searching 'outputs'
[INFO ] multiqc : Only using modules quast
[INFO ] quast : Found 16 reports
[ERROR ] ... | ValueError |
def quast_contigs_barplot(self):
"""Make a bar plot showing the number and length of contigs for each assembly"""
# Prep the data
data = dict()
categories = []
for s_name, d in self.quast_data.items():
nums_by_t = dict()
for k, v in d.items():
m = re.match(r"# contigs \(... | def quast_contigs_barplot(self):
"""Make a bar plot showing the number and length of contigs for each assembly"""
# Prep the data
data = dict()
categories = []
for s_name, d in self.quast_data.items():
nums_by_t = dict()
for k, v in d.items():
m = re.match("# contigs \(>... | https://github.com/ewels/MultiQC/issues/954 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Prepending directory to sample names
[INFO ] multiqc : Searching 'outputs'
[INFO ] multiqc : Only using modules quast
[INFO ] quast : Found 16 reports
[ERROR ] ... | ValueError |
def quast_predicted_genes_barplot(self, partial=False):
"""
Make a bar plot showing the number and length of predicted genes
for each assembly
"""
# Prep the data
# extract the ranges given to quast with "--gene-thresholds"
# keys look like:
# `# predicted genes (>= 300 bp)`
# `... | def quast_predicted_genes_barplot(self):
"""
Make a bar plot showing the number and length of predicted genes
for each assembly
"""
# Prep the data
# extract the ranges given to quast with "--gene-thresholds"
prefix = "# predicted genes (>= "
suffix = " bp)"
all_thresholds = sorted(... | https://github.com/ewels/MultiQC/issues/954 | [INFO ] multiqc : This is MultiQC v1.7
[INFO ] multiqc : Template : default
[INFO ] multiqc : Prepending directory to sample names
[INFO ] multiqc : Searching 'outputs'
[INFO ] multiqc : Only using modules quast
[INFO ] quast : Found 16 reports
[ERROR ] ... | ValueError |
def parse_file_as_json(self, myfile):
try:
content = json.loads(myfile["f"])
except ValueError:
log.warn("Could not parse file as json: {}".format(myfile["fn"]))
return
runId = content["RunId"]
if runId not in self.bcl2fastq_data:
self.bcl2fastq_data[runId] = dict()
r... | def parse_file_as_json(self, myfile):
try:
content = json.loads(myfile["f"])
except ValueError:
log.warn("Could not parse file as json: {}".format(myfile["fn"]))
return
runId = content["RunId"]
if runId not in self.bcl2fastq_data:
self.bcl2fastq_data[runId] = dict()
r... | https://github.com/ewels/MultiQC/issues/907 | [ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
If possible, please include a log file that triggers the error - the last file found was:
NB500904_0187/fastq/stats/Stats.json
==========================... | KeyError |
def parse_fastp_log(self, f):
"""Parse the JSON output from fastp and save the summary statistics"""
try:
parsed_json = json.load(f["f"])
except:
log.warn("Could not parse fastp JSON: '{}'".format(f["fn"]))
return None
# Fetch a sample name from the command
s_name = f["s_nam... | def parse_fastp_log(self, f):
"""Parse the JSON output from fastp and save the summary statistics"""
try:
parsed_json = json.load(f["f"])
except:
log.warn("Could not parse fastp JSON: '{}'".format(f["fn"]))
return None
# Fetch a sample name from the command
s_name = f["s_nam... | https://github.com/ewels/MultiQC/issues/845 | lucas-maciel@lucasmaciel-Inspiron-7472:~/QC_fastq/fastp$ multiqc .
[INFO ] multiqc : This is MultiQC v1.7.dev0
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
[ERROR ] multiqc : Oops! The 'fastp' MultiQC module broke...
Please copy the following traceback a... | ZeroDivisionError |
def parse_samtools_idxstats(self):
"""Find Samtools idxstats logs and parse their data"""
self.samtools_idxstats = dict()
for f in self.find_log_files("samtools/idxstats"):
parsed_data = parse_single_report(f["f"])
if len(parsed_data) > 0:
if f["s_name"] in self.samtools_idxstat... | def parse_samtools_idxstats(self):
"""Find Samtools idxstats logs and parse their data"""
self.samtools_idxstats = dict()
for f in self.find_log_files("samtools/idxstats"):
parsed_data = parse_single_report(f["f"])
if len(parsed_data) > 0:
if f["s_name"] in self.samtools_idxstat... | https://github.com/ewels/MultiQC/issues/680 | #original
multiqc --force ./
[INFO ] multiqc : This is MultiQC v1.0
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching './'
[INFO ] snpeff : Found 28 reports
[WARNING] bargraph : Tried to make bar plot, but had no data
[INFO ] picard : Found 13... | ZeroDivisionError |
def split_data_by_lane_and_sample(self):
for runId in self.bcl2fastq_data.keys():
for lane in self.bcl2fastq_data[runId].keys():
uniqLaneName = self.prepend_runid(runId, lane)
self.bcl2fastq_bylane[uniqLaneName] = {
"total": self.bcl2fastq_data[runId][lane]["total"],
... | def split_data_by_lane_and_sample(self):
for runId in self.bcl2fastq_data.keys():
for lane in self.bcl2fastq_data[runId].keys():
uniqLaneName = self.prepend_runid(runId, lane)
self.bcl2fastq_bylane[uniqLaneName] = {
"total": self.bcl2fastq_data[runId][lane]["total"],
... | https://github.com/ewels/MultiQC/issues/731 | multiqc --outdir x .
[INFO ] multiqc : This is MultiQC v1.5
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 770 files.. [####################################] 100%
[ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the ... | ZeroDivisionError |
def add_general_stats(self):
data = {}
for key in self.bcl2fastq_bysample.keys():
try:
perfectPercent = float(
100.0
* self.bcl2fastq_bysample[key]["perfectIndex"]
/ self.bcl2fastq_bysample[key]["total"]
)
except ZeroDivisio... | def add_general_stats(self):
data = {
key: {
"yieldQ30": self.bcl2fastq_bysample[key]["yieldQ30"],
"total": self.bcl2fastq_bysample[key]["total"],
"perfectPercent": "{0:.1f}".format(
float(
100.0
* self.bcl2fastq_bys... | https://github.com/ewels/MultiQC/issues/731 | multiqc --outdir x .
[INFO ] multiqc : This is MultiQC v1.5
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 770 files.. [####################################] 100%
[ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the ... | ZeroDivisionError |
def quast_contigs_barplot(self):
"""Make a bar plot showing the number and length of contigs for each assembly"""
# Prep the data
data = dict()
categories = []
for s_name, d in self.quast_data.items():
nums_by_t = dict()
for k, v in d.items():
m = re.match("# contigs \(>... | def quast_contigs_barplot(self):
"""Make a bar plot showing the number and length of contigs for each assembly"""
# Prep the data
data = dict()
categories = []
for s_name, d in self.quast_data.items():
nums_by_t = dict()
for k, v in d.items():
m = re.match("# contigs \(>... | https://github.com/ewels/MultiQC/issues/719 | [INFO ] multiqc : This is MultiQC v1.5
============================================================
Module quast raised an exception: Traceback (most recent call last):
File "/home/kevin/anaconda3/envs/assembly-env/bin/multiqc", line 442, in multiqc
output = mod()
File "/home/kevin/anaconda3/envs/assembly-env... | TypeError |
def parse_tag_info(self, f):
"""Parse HOMER tagdirectory taginfo.txt file to extract statistics in the first 11 lines."""
# General Stats Table
tag_info = dict()
for l in f["f"]:
s = l.split("=")
if len(s) > 1:
if s[0].strip() == "genome":
ss = s[1].split("\t"... | def parse_tag_info(self, f):
"""Parse HOMER tagdirectory taginfo.txt file to extract statistics in the first 11 lines."""
# General Stats Table
tag_info = dict()
counter = 0
for l in f["f"]:
if counter == 1:
s = l.split("\t")
tag_info["UniqPositions"] = float(s[1].str... | https://github.com/ewels/MultiQC/issues/666 | szha0069@biomate1:~/test_seq_files/analysis/tags$ multiqc .
[WARNING] multiqc : MultiQC Version v1.4 now available!
[INFO ] multiqc : This is MultiQC v1.3
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 33 files.. [################################... | IndexError |
def parse_tag_info_chrs(self, f, convChr=True):
"""Parse HOMER tagdirectory taginfo.txt file to extract chromosome coverage."""
parsed_data_total = OrderedDict()
parsed_data_uniq = OrderedDict()
remove = ["hap", "random", "chrUn", "cmd", "EBV", "GL", "NT_"]
for l in f["f"]:
s = l.split("\t")... | def parse_tag_info_chrs(self, f, convChr=True):
"""Parse HOMER tagdirectory taginfo.txt file to extract chromosome coverage."""
parsed_data_total = dict()
parsed_data_uniq = dict()
remove = ["hap", "random", "chrUn", "cmd", "EBV", "GL", "NT_"]
## skip first 11 lines
counter = 0
for l in f["f... | https://github.com/ewels/MultiQC/issues/666 | szha0069@biomate1:~/test_seq_files/analysis/tags$ multiqc .
[WARNING] multiqc : MultiQC Version v1.4 now available!
[INFO ] multiqc : This is MultiQC v1.3
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 33 files.. [################################... | IndexError |
def parse_qorts(self, f):
s_names = None
for l in f["f"]:
s = l.split("\t")
if s_names is None:
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s[1:]]
if len(s_names) <= 2 and s_names[0] == "COUNT":
if f["fn"] == "QC.summary.txt":
... | def parse_qorts(self, f):
s_names = None
for l in f["f"]:
s = l.split("\t")
if s_names is None:
s_names = [self.clean_s_name(s_name, f["root"]) for s_name in s[1:]]
if len(s_names) == 1 and s_names[0] == "COUNT":
s_names = [f["s_name"]]
for s_n... | https://github.com/ewels/MultiQC/issues/639 | multiqc input/pipeline5a-exemplar6 -o multiqc-pipeline5a-exemplar6
[INFO ] multiqc : This is MultiQC v1.3
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching 'input/pipeline5a-exemplar6'
Searching 662 files.. [####################################] 100%
[ERROR ] m... | ValueError |
def parse_reports(self):
"""Find Picard InsertSizeMetrics reports and parse their data"""
# Set up vars
self.picard_insertSize_data = dict()
self.picard_insertSize_histogram = dict()
self.picard_insertSize_samplestats = dict()
# Go through logs and find Metrics
for f in self.find_log_files... | def parse_reports(self):
"""Find Picard InsertSizeMetrics reports and parse their data"""
# Set up vars
self.picard_insertSize_data = dict()
self.picard_insertSize_histogram = dict()
self.picard_insertSize_samplestats = dict()
# Go through logs and find Metrics
for f in self.find_log_files... | https://github.com/ewels/MultiQC/issues/630 | [ERROR ] multiqc : Oops! The 'picard' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
(if possible, include a log file that triggers the error)
============================================================
Module picard raised an exception: Tr... | TypeError |
def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="bcl2fastq",
anchor="bcl2fastq",
href="https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html",
info="can be used to both demultiplex data and conv... | def __init__(self):
# Initialise the parent object
super(MultiqcModule, self).__init__(
name="bcl2fastq",
anchor="bcl2fastq",
href="https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html",
info="can be used to both demultiplex data and conv... | https://github.com/ewels/MultiQC/issues/595 | [ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
(if possible, include a log file that triggers the error)
============================================================
Module bcl2fastq raised an excepti... | KeyError |
def parse_file_as_json(self, myfile):
try:
content = json.loads(myfile["f"])
except ValueError:
log.warn("Could not parse file as json: {}".format(myfile["fn"]))
return
runId = content["RunId"]
if not runId in self.bcl2fastq_data:
self.bcl2fastq_data[runId] = dict()
r... | def parse_file_as_json(self, myfile):
try:
content = json.loads(myfile["f"])
except ValueError:
log.warn("Could not parse file as json: {}".format(myfile["fn"]))
return
runId = content["RunId"]
if not runId in self.bcl2fastq_data:
self.bcl2fastq_data[runId] = dict()
r... | https://github.com/ewels/MultiQC/issues/595 | [ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
(if possible, include a log file that triggers the error)
============================================================
Module bcl2fastq raised an excepti... | KeyError |
def split_data_by_lane_and_sample(self):
for runId in self.bcl2fastq_data.keys():
for lane in self.bcl2fastq_data[runId].keys():
uniqLaneName = self.prepend_runid(runId, lane)
self.bcl2fastq_bylane[uniqLaneName] = {
"total": self.bcl2fastq_data[runId][lane]["total"],
... | def split_data_by_lane_and_sample(self):
for runId in self.bcl2fastq_data.keys():
for lane in self.bcl2fastq_data[runId].keys():
uniqLaneName = self.prepend_runid(runId, lane)
self.bcl2fastq_bylane[uniqLaneName] = {
"total": self.bcl2fastq_data[runId][lane]["total"],
... | https://github.com/ewels/MultiQC/issues/595 | [ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
(if possible, include a log file that triggers the error)
============================================================
Module bcl2fastq raised an excepti... | KeyError |
def fqscreen_simple_plot(self):
"""Makes a simple bar plot with summed alignment counts for
each species, stacked."""
# First, sum the different types of alignment counts
data = OrderedDict()
cats = OrderedDict()
for s_name in self.fq_screen_data:
data[s_name] = OrderedDict()
su... | def fqscreen_simple_plot(self):
"""Makes a simple bar plot with summed alignment counts for
each species, stacked."""
# First, sum the different types of alignment counts
data = OrderedDict()
cats = OrderedDict()
for s_name in self.fq_screen_data:
data[s_name] = OrderedDict()
su... | https://github.com/ewels/MultiQC/issues/537 | Module fastq_screen raised an exception: Traceback (most recent call last):
File "/home/es249628/bin/mypyenv-py3/bin/multiqc", line 364, in multiqc
output = mod()
File "/home/es249628/bin/mypyenv-py3/lib/python3.4/site-packages/multiqc/modules/fastq_screen/fastq_screen.py", line 55, in __init__
self.add_section( plot =... | KeyError |
def __init__(self, data, headers=None, pconfig=None):
"""Prepare data for use in a table or plot"""
if headers is None:
headers = []
if pconfig is None:
pconfig = {}
# Given one dataset - turn it into a list
if type(data) is not list:
data = [data]
if type(headers) is no... | def __init__(self, data, headers=None, pconfig=None):
"""Prepare data for use in a table or plot"""
if headers is None:
headers = []
if pconfig is None:
pconfig = {}
# Given one dataset - turn it into a list
if type(data) is not list:
data = [data]
if type(headers) is no... | https://github.com/ewels/MultiQC/issues/521 | [INFO ] multiqc : This is MultiQC v1.2.dev0 (e86ba77)
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 3 files.. [####################################] 100%
Traceback (most recent call last):
File "/tank/home/s216121/miniconda3/bin/multiqc", line 6, in <m... | TypeError |
def write_data_file(data, fn, sort_cols=False, data_format=None):
"""Write a data file to the report directory. Will not do anything
if config.data_dir is not set.
:param: data - a 2D dict, first key sample name (row header),
second key field (column header).
:param: fn - Desired filename. D... | def write_data_file(data, fn, sort_cols=False, data_format=None):
"""Write a data file to the report directory. Will not do anything
if config.data_dir is not set.
:param: data - a 2D dict, first key sample name (row header),
second key field (column header).
:param: fn - Desired filename. D... | https://github.com/ewels/MultiQC/issues/519 | [INFO ] multiqc : This is MultiQC v1.2.dev0 (e86ba77)
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
Searching 3 files.. [####################################] 100%
[ERROR ] multiqc : Oops! The 'bcl2fastq' MultiQC module broke...
Please copy the followin... | TypeError |
def parse_htseq_report(self, f):
"""Parse the HTSeq Count log file."""
keys = [
"__no_feature",
"__ambiguous",
"__too_low_aQual",
"__not_aligned",
"__alignment_not_unique",
]
parsed_data = dict()
assigned_counts = 0
for l in f["f"]:
s = l.split("\t... | def parse_htseq_report(self, f):
"""Parse the HTSeq Count log file."""
keys = [
"__no_feature",
"__ambiguous",
"__too_low_aQual",
"__not_aligned",
"__alignment_not_unique",
]
parsed_data = dict()
assigned_counts = 0
for l in f["f"]:
s = l.split("\t... | https://github.com/ewels/MultiQC/issues/391 | [INFO ] multiqc : This is MultiQC v1.0.dev0
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '/home/mlotshwa/RNA_Seq_TB_project/Run2'
[ERROR ] multiqc : Oops! The 'htseq' MultiQC module broke...
Please copy the following traceback and report it at https://github... | IndexError |
def plot(data, pconfig={}):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Given one dataset -... | def plot(data, pconfig={}):
"""Plot a line graph with X,Y data.
:param data: 2D dict, first keys as sample names, then x:y data pairs
:param pconfig: optional dict with config key:value pairs. See CONTRIBUTING.md
:return: HTML and JS, ready to be inserted into the page
"""
# Given one dataset -... | https://github.com/ewels/MultiQC/issues/392 | [INFO ] multiqc : This is MultiQC v0.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
[ERROR ] multiqc : Oops! The 'qualimap' MultiQC module broke...
Please copy the following traceback and report it at https://github.com/ewels/MultiQC/issues
(if possible,... | IndexError |
def get_stack(self, name_or_stack_id):
all_stacks = dict(self.deleted_stacks, **self.stacks)
if name_or_stack_id in all_stacks:
# Lookup by stack id - deleted stacks incldued
return all_stacks[name_or_stack_id]
else:
# Lookup by stack name - undeleted stacks only
for stack in... | def get_stack(self, name_or_stack_id):
all_stacks = dict(self.deleted_stacks, **self.stacks)
if name_or_stack_id in all_stacks:
# Lookup by stack id - deleted stacks incldued
return all_stacks[name_or_stack_id]
else:
# Lookup by stack name - undeleted stacks only
for stack in... | https://github.com/spulec/moto/issues/3558 | Traceback (most recent call last):
File "/home/user/git/modamod/inspiring-murdock/.venv/bin/inv", line 33, in <module>
sys.exit(load_entry_point('invoke==1.4.1', 'console_scripts', 'inv')())
File "/home/user/git/modamod/inspiring-murdock/.venv/lib/python3.8/site-packages/invoke-1.4.1-py3.8.egg/invoke/program.py", line ... | jinja2.exceptions.UndefinedError |
def list_stack_resources(self, stack_name_or_id):
stack = self.get_stack(stack_name_or_id)
return stack.stack_resources
| def list_stack_resources(self, stack_name_or_id):
stack = self.get_stack(stack_name_or_id)
if stack is None:
return None
return stack.stack_resources
| https://github.com/spulec/moto/issues/3558 | Traceback (most recent call last):
File "/home/user/git/modamod/inspiring-murdock/.venv/bin/inv", line 33, in <module>
sys.exit(load_entry_point('invoke==1.4.1', 'console_scripts', 'inv')())
File "/home/user/git/modamod/inspiring-murdock/.venv/lib/python3.8/site-packages/invoke-1.4.1-py3.8.egg/invoke/program.py", line ... | jinja2.exceptions.UndefinedError |
def describe_stack_resource(self):
stack_name = self._get_param("StackName")
stack = self.cloudformation_backend.get_stack(stack_name)
logical_resource_id = self._get_param("LogicalResourceId")
for stack_resource in stack.stack_resources:
if stack_resource.logical_resource_id == logical_resourc... | def describe_stack_resource(self):
stack_name = self._get_param("StackName")
stack = self.cloudformation_backend.get_stack(stack_name)
logical_resource_id = self._get_param("LogicalResourceId")
for stack_resource in stack.stack_resources:
if stack_resource.logical_resource_id == logical_resourc... | https://github.com/spulec/moto/issues/3558 | Traceback (most recent call last):
File "/home/user/git/modamod/inspiring-murdock/.venv/bin/inv", line 33, in <module>
sys.exit(load_entry_point('invoke==1.4.1', 'console_scripts', 'inv')())
File "/home/user/git/modamod/inspiring-murdock/.venv/lib/python3.8/site-packages/invoke-1.4.1-py3.8.egg/invoke/program.py", line ... | jinja2.exceptions.UndefinedError |
def list_stack_resources(self):
stack_name_or_id = self._get_param("StackName")
resources = self.cloudformation_backend.list_stack_resources(stack_name_or_id)
template = self.response_template(LIST_STACKS_RESOURCES_RESPONSE)
return template.render(resources=resources)
| def list_stack_resources(self):
stack_name_or_id = self._get_param("StackName")
resources = self.cloudformation_backend.list_stack_resources(stack_name_or_id)
if resources is None:
raise ValidationError(stack_name_or_id)
template = self.response_template(LIST_STACKS_RESOURCES_RESPONSE)
ret... | https://github.com/spulec/moto/issues/3558 | Traceback (most recent call last):
File "/home/user/git/modamod/inspiring-murdock/.venv/bin/inv", line 33, in <module>
sys.exit(load_entry_point('invoke==1.4.1', 'console_scripts', 'inv')())
File "/home/user/git/modamod/inspiring-murdock/.venv/lib/python3.8/site-packages/invoke-1.4.1-py3.8.egg/invoke/program.py", line ... | jinja2.exceptions.UndefinedError |
def run(self):
"""
Run the container.
Logic is as follows:
Generate container info (eventually from task definition)
Start container
Loop whilst not asked to stop and the container is running.
Get all logs from container between the last time I checked and now.
Convert logs into cloud... | def run(self):
"""
Run the container.
Logic is as follows:
Generate container info (eventually from task definition)
Start container
Loop whilst not asked to stop and the container is running.
Get all logs from container between the last time I checked and now.
Convert logs into cloud... | https://github.com/spulec/moto/issues/3475 | ======================================================================
FAIL: test_batch.test_submit_job
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/travis/virtualenv/python3.7.6/lib/python3.7/site-packages/nose/case.py", line 198, in runTest
self... | AssertionError |
def describe_log_groups(self, limit, log_group_name_prefix, next_token):
if log_group_name_prefix is None:
log_group_name_prefix = ""
groups = [
group.to_describe_dict()
for name, group in self.groups.items()
if name.startswith(log_group_name_prefix)
]
groups = sorted(gr... | def describe_log_groups(self, limit, log_group_name_prefix, next_token):
if log_group_name_prefix is None:
log_group_name_prefix = ""
if next_token is None:
next_token = 0
groups = [
group.to_describe_dict()
for name, group in self.groups.items()
if name.startswith(l... | https://github.com/spulec/moto/issues/3395 | Traceback (most recent call last):
File "foo.py", line 13, in <module>
client.describe_log_groups(nextToken=result['nextToken'])
File "/home/ubuntu/.venvs/moto-test-case/lib/python3.8/site-packages/botocore/client.py", line 357, in _api_call
return self._make_api_call(operation_name, kwargs)
File "/home/ubuntu/.venvs/m... | botocore.exceptions.ParamValidationError |
def describe_log_groups(self):
log_group_name_prefix = self._get_param("logGroupNamePrefix")
next_token = self._get_param("nextToken")
limit = self._get_param("limit", 50)
assert limit <= 50
groups, next_token = self.logs_backend.describe_log_groups(
limit, log_group_name_prefix, next_token
... | def describe_log_groups(self):
log_group_name_prefix = self._get_param("logGroupNamePrefix")
next_token = self._get_param("nextToken")
limit = self._get_param("limit", 50)
assert limit <= 50
groups, next_token = self.logs_backend.describe_log_groups(
limit, log_group_name_prefix, next_token
... | https://github.com/spulec/moto/issues/3395 | Traceback (most recent call last):
File "foo.py", line 13, in <module>
client.describe_log_groups(nextToken=result['nextToken'])
File "/home/ubuntu/.venvs/moto-test-case/lib/python3.8/site-packages/botocore/client.py", line 357, in _api_call
return self._make_api_call(operation_name, kwargs)
File "/home/ubuntu/.venvs/m... | botocore.exceptions.ParamValidationError |
def create_subnet(
self,
vpc_id,
cidr_block,
availability_zone=None,
availability_zone_id=None,
context=None,
tags=[],
):
subnet_id = random_subnet_id()
vpc = self.get_vpc(
vpc_id
) # Validate VPC exists and the supplied CIDR block is a subnet of the VPC's
vpc_cidr_b... | def create_subnet(
self,
vpc_id,
cidr_block,
availability_zone=None,
availability_zone_id=None,
context=None,
tags=[],
):
subnet_id = random_subnet_id()
vpc = self.get_vpc(
vpc_id
) # Validate VPC exists and the supplied CIDR block is a subnet of the VPC's
vpc_cidr_b... | https://github.com/spulec/moto/issues/3385 | {'Subnet': {'AvailabilityZone': 'us-west-2a', 'AvailabilityZoneId': 'usw2-az2', 'AvailableIpAddressCount': 251, 'CidrBlock': '10.0.0.0/24', 'DefaultForAz': False, 'MapPublicIpOnLaunch': False, 'State': 'pending', 'SubnetId': 'subnet-89f4d757', 'VpcId': 'vpc-5c9431df', 'OwnerId': '111122223333', 'AssignIpv6AddressOnCrea... | botocore.exceptions.ClientError |
def __init__(
self,
name,
value,
storage="STANDARD",
etag=None,
is_versioned=False,
version_id=0,
max_buffer_size=DEFAULT_KEY_BUFFER_SIZE,
multipart=None,
):
self.name = name
self.last_modified = datetime.datetime.utcnow()
self.acl = get_canned_acl("private")
self.web... | def __init__(
self,
name,
value,
storage="STANDARD",
etag=None,
is_versioned=False,
version_id=0,
max_buffer_size=DEFAULT_KEY_BUFFER_SIZE,
multipart=None,
):
self.name = name
self.last_modified = datetime.datetime.utcnow()
self.acl = get_canned_acl("private")
self.web... | https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def value(self, new_value):
self._value_buffer.seek(0)
self._value_buffer.truncate()
# Hack for working around moto's own unit tests; this probably won't
# actually get hit in normal use.
if isinstance(new_value, six.text_type):
new_value = new_value.encode(DEFAULT_TEXT_ENCODING)
self._... | def value(self, new_value):
self._value_buffer.seek(0)
self._value_buffer.truncate()
# Hack for working around moto's own unit tests; this probably won't
# actually get hit in normal use.
if isinstance(new_value, six.text_type):
new_value = new_value.encode(DEFAULT_TEXT_ENCODING)
self._... | https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def append_to_value(self, value):
self.contentsize += len(value)
self._value_buffer.seek(0, os.SEEK_END)
self._value_buffer.write(value)
self.last_modified = datetime.datetime.utcnow()
self._etag = None # must recalculate etag
if self._is_versioned:
self._version_id = str(uuid.uuid4())... | def append_to_value(self, value):
self._value_buffer.seek(0, os.SEEK_END)
self._value_buffer.write(value)
self.last_modified = datetime.datetime.utcnow()
self._etag = None # must recalculate etag
if self._is_versioned:
self._version_id = str(uuid.uuid4())
else:
self._version_id... | https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def size(self):
return self.contentsize
| def size(self):
self._value_buffer.seek(0, os.SEEK_END)
return self._value_buffer.tell()
| https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def __getstate__(self):
state = self.__dict__.copy()
state["value"] = self.value
del state["_value_buffer"]
del state["lock"]
return state
| def __getstate__(self):
state = self.__dict__.copy()
state["value"] = self.value
del state["_value_buffer"]
return state
| https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def __setstate__(self, state):
self.__dict__.update({k: v for k, v in six.iteritems(state) if k != "value"})
self._value_buffer = tempfile.SpooledTemporaryFile(max_size=self._max_buffer_size)
self.value = state["value"]
self.lock = threading.Lock()
| def __setstate__(self, state):
self.__dict__.update({k: v for k, v in six.iteritems(state) if k != "value"})
self._value_buffer = tempfile.SpooledTemporaryFile(max_size=self._max_buffer_size)
self.value = state["value"]
| https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def complete(self, body):
decode_hex = codecs.getdecoder("hex_codec")
total = bytearray()
md5s = bytearray()
last = None
count = 0
for pn, etag in body:
part = self.parts.get(pn)
part_etag = None
if part is not None:
part_etag = part.etag.replace('"', "")
... | def complete(self, body):
decode_hex = codecs.getdecoder("hex_codec")
total = bytearray()
md5s = bytearray()
last = None
count = 0
for pn, etag in body:
part = self.parts.get(pn)
part_etag = None
if part is not None:
part_etag = part.etag.replace('"', "")
... | https://github.com/spulec/moto/issues/2789 | Traceback (most recent call last):
File "/Users/myuser/projects/project/web/pdf_file_downloader.py", line 16, in download
self.s3.download_file(self.bucket_name, self.file_name, self.local_path())
File "/Users/myuser/Library/Caches/pypoetry/virtualenvs/project-X5XCMv3p-py3.6/lib/python3.6/site-packages/boto3/s3/inject.... | botocore.exceptions.ClientError |
def __init__(self, name, job_def, job_queue, log_backend, container_overrides):
"""
Docker Job
:param name: Job Name
:param job_def: Job definition
:type: job_def: JobDefinition
:param job_queue: Job Queue
:param log_backend: Log backend
:type log_backend: moto.logs.models.LogsBackend
... | def __init__(self, name, job_def, job_queue, log_backend, container_overrides):
"""
Docker Job
:param name: Job Name
:param job_def: Job definition
:type: job_def: JobDefinition
:param job_queue: Job Queue
:param log_backend: Log backend
:type log_backend: moto.logs.models.LogsBackend
... | https://github.com/spulec/moto/issues/2777 | 2020-02-28 23:16:27 - werkzeug - INFO - 127.0.0.1 - - [28/Feb/2020 23:16:27] "POST /v1/describejobs HTTP/1.1" 500 -
2020-02-28 23:16:27 - werkzeug - ERROR - Error on request:
Traceback (most recent call last):
File "/builds/dazza-codes/python-notes/.venv/lib/python3.6/site-packages/werkzeug/serving.py", ... | AttributeError |
def describe(self):
result = {
"jobDefinition": self.job_definition.arn,
"jobId": self.job_id,
"jobName": self.job_name,
"jobQueue": self.job_queue.arn,
"status": self.job_state,
"dependsOn": [],
}
if result["status"] not in ["SUBMITTED", "PENDING", "RUNNABLE"... | def describe(self):
result = {
"jobDefinition": self.job_definition.arn,
"jobId": self.job_id,
"jobName": self.job_name,
"jobQueue": self.job_queue.arn,
"startedAt": datetime2int(self.job_started_at),
"status": self.job_state,
"dependsOn": [],
}
if sel... | https://github.com/spulec/moto/issues/2777 | 2020-02-28 23:16:27 - werkzeug - INFO - 127.0.0.1 - - [28/Feb/2020 23:16:27] "POST /v1/describejobs HTTP/1.1" 500 -
2020-02-28 23:16:27 - werkzeug - ERROR - Error on request:
Traceback (most recent call last):
File "/builds/dazza-codes/python-notes/.venv/lib/python3.6/site-packages/werkzeug/serving.py", ... | AttributeError |
def run(self):
"""
Run the container.
Logic is as follows:
Generate container info (eventually from task definition)
Start container
Loop whilst not asked to stop and the container is running.
Get all logs from container between the last time I checked and now.
Convert logs into cloud... | def run(self):
"""
Run the container.
Logic is as follows:
Generate container info (eventually from task definition)
Start container
Loop whilst not asked to stop and the container is running.
Get all logs from container between the last time I checked and now.
Convert logs into cloud... | https://github.com/spulec/moto/issues/2777 | 2020-02-28 23:16:27 - werkzeug - INFO - 127.0.0.1 - - [28/Feb/2020 23:16:27] "POST /v1/describejobs HTTP/1.1" 500 -
2020-02-28 23:16:27 - werkzeug - ERROR - Error on request:
Traceback (most recent call last):
File "/builds/dazza-codes/python-notes/.venv/lib/python3.6/site-packages/werkzeug/serving.py", ... | AttributeError |
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