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 __monitor(self):
to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
while self.monitor_running:
try:
if self.invocation_grabber:
self.invocation_grabber.grab_unhandled_items()
monitor_step_timer = self.app.execution_timer_factory.get_tim... | def __monitor(self):
to_monitor = self.workflow_scheduling_manager.active_workflow_schedulers
while self.monitor_running:
if self.invocation_grabber:
self.invocation_grabber.grab_unhandled_items()
monitor_step_timer = self.app.execution_timer_factory.get_timer(
"internal... | https://github.com/galaxyproject/galaxy/issues/11433 | galaxy.workflow.scheduling_manager DEBUG 2021-02-21 15:59:02,329 Workflow invocation [540513] scheduled
galaxy.workflow.scheduling_manager DEBUG 2021-02-21 15:59:03,453 Attempting to schedule workflow invocation [(53535
2,)]
galaxy.workflow.run ERROR 2021-02-21 15:59:08,637 Failed to execute scheduled workflow.
Traceba... | psycopg2.OperationalError |
def display(
self,
trans,
history_content_id,
history_id,
preview=False,
filename=None,
to_ext=None,
raw=False,
**kwd,
):
"""
GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display
Displays history content (dataset).
The query parameter 'raw' s... | def display(
self,
trans,
history_content_id,
history_id,
preview=False,
filename=None,
to_ext=None,
raw=False,
**kwd,
):
"""
GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display
Displays history content (dataset).
The query parameter 'raw' s... | https://github.com/galaxyproject/galaxy/issues/11462 | galaxy.webapps.galaxy.api.datasets ERROR 2021-02-24 13:04:42,977 [p:41176,w:3,m:0] [uWSGIWorker3Core0] Error getting display data for dataset (e6693f4d1a4d9f91) from history (e9859c1e537d1ced)
Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/api/datasets.py", line 441, in display
hda = self.hda_manage... | galaxy.exceptions.ItemAccessibilityException |
def display(api_key, url, return_formatted=True):
"""
Sends an API GET request and acts as a generic formatter for the JSON response.
"""
try:
r = get(api_key, url)
except HTTPError as e:
print(e)
print(e.read(1024)) # Only return the first 1K of errors.
sys.exit(1)
... | def display(api_key, url, return_formatted=True):
"""
Sends an API GET request and acts as a generic formatter for the JSON response.
"""
try:
r = get(api_key, url)
except HTTPError as e:
print(e)
print(e.read(1024)) # Only return the first 1K of errors.
sys.exit(1)
... | https://github.com/galaxyproject/galaxy/issues/11193 | (.venv) rivendell$ ./scripts/api/display.py [key] http://127.0.0.1:8080/api/datatypes
Collection Members
------------------
Traceback (most recent call last):
File "./scripts/api/display.py", line 10, in <module>
display(*sys.argv[1:3])
File "/home/sergey/0dev/galaxy/_galaxy/dev/scripts/api/common.py", line 96, in disp... | AttributeError |
def execute(
trans,
tool,
mapping_params,
history,
rerun_remap_job_id=None,
collection_info=None,
workflow_invocation_uuid=None,
invocation_step=None,
max_num_jobs=None,
job_callback=None,
completed_jobs=None,
workflow_resource_parameters=None,
validate_outputs=False,... | def execute(
trans,
tool,
mapping_params,
history,
rerun_remap_job_id=None,
collection_info=None,
workflow_invocation_uuid=None,
invocation_step=None,
max_num_jobs=None,
job_callback=None,
completed_jobs=None,
workflow_resource_parameters=None,
validate_outputs=False,... | https://github.com/galaxyproject/galaxy/issues/11146 | galaxy.web_stack.transport DEBUG 2021-01-15 16:38:33,341 [p:29115,w:0,m:1] [UWSGIFarmMessageTransport.dispatcher_thread] Released lock
galaxy.web_stack.transport DEBUG 2021-01-15 16:38:33,341 [p:29117,w:0,m:3] [UWSGIFarmMessageTransport.dispatcher_thread] Acquired message lock, waiting for new message
galaxy.web_stack.... | AttributeError |
def _assign_uwsgi_mule_message_handler(
self, obj, method, configured, message_callback=None, flush=True, **kwargs
):
"""Assign object to a handler by sending a setup message to the appropriate handler pool (farm), where a handler
(mule) will receive the message and assign itself.
:param obj: ... | def _assign_uwsgi_mule_message_handler(
self, obj, method, configured, message_callback=None, flush=True, **kwargs
):
"""Assign object to a handler by sending a setup message to the appropriate handler pool (farm), where a handler
(mule) will receive the message and assign itself.
:param obj: ... | https://github.com/galaxyproject/galaxy/issues/11146 | galaxy.web_stack.transport DEBUG 2021-01-15 16:38:33,341 [p:29115,w:0,m:1] [UWSGIFarmMessageTransport.dispatcher_thread] Released lock
galaxy.web_stack.transport DEBUG 2021-01-15 16:38:33,341 [p:29117,w:0,m:3] [UWSGIFarmMessageTransport.dispatcher_thread] Acquired message lock, waiting for new message
galaxy.web_stack.... | AttributeError |
def resolve(self, enabled_container_types, tool_info, **kwds):
if (
not self.docker_cli_available
or tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mulled_targets(tool_info)
resolution_cache = k... | def resolve(self, enabled_container_types, tool_info, **kwds):
if (
tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mulled_targets(tool_info)
resolution_cache = kwds.get("resolution_cache")
return do... | https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def cached_container_description(self, targets, namespace, hash_func, resolution_cache):
try:
return docker_cached_container_description(
targets, namespace, hash_func, resolution_cache
)
except subprocess.CalledProcessError:
# We should only get here if a docker binary is av... | def cached_container_description(self, targets, namespace, hash_func, resolution_cache):
return docker_cached_container_description(
targets, namespace, hash_func, resolution_cache
)
| https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def pull(self, container):
if self.docker_cli_available:
command = container.build_pull_command()
shell(command)
| def pull(self, container):
command = container.build_pull_command()
shell(command)
| https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def resolve(
self, enabled_container_types, tool_info, install=False, session=None, **kwds
):
resolution_cache = kwds.get("resolution_cache")
if (
tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mull... | def resolve(
self, enabled_container_types, tool_info, install=False, session=None, **kwds
):
resolution_cache = kwds.get("resolution_cache")
if (
tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mull... | https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def __default_containers_resolvers(self):
default_resolvers = [
ExplicitContainerResolver(self.app_info),
ExplicitSingularityContainerResolver(self.app_info),
]
if self.enable_mulled_containers:
default_resolvers.extend(
[
CachedMulledDockerContainerResolv... | def __default_containers_resolvers(self):
default_resolvers = [
ExplicitContainerResolver(self.app_info),
ExplicitSingularityContainerResolver(self.app_info),
]
if self.enable_mulled_containers:
default_resolvers.extend(
[
CachedMulledDockerContainerResolv... | https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def resolve(self, enabled_container_types, tool_info, install=False, **kwds):
if (
not self.docker_cli_available
or tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mulled_targets(tool_info)
if le... | def resolve(self, enabled_container_types, tool_info, install=False, **kwds):
if (
tool_info.requires_galaxy_python_environment
or self.container_type not in enabled_container_types
):
return None
targets = mulled_targets(tool_info)
if len(targets) == 0:
return None
... | https://github.com/galaxyproject/galaxy/issues/11125 | urllib3.connectionpool DEBUG 2021-01-13 15:26:00,421 https://quay.io:443 "GET /api/v1/repository/biocontainers/porechop HTTP/1.1" 200 4033
galaxy.tool_util.deps.containers ERROR 2021-01-13 15:26:00,499 Could not get container description for tool 'toolshed.g2.bx.psu.edu/repos/iuc/porechop/porechop/0.2.3'
Traceback (mos... | FileNotFoundError |
def record_success(self, execution_slice, job, outputs):
super().record_success(execution_slice, job, outputs)
if not self.collection_info:
for output_name, output in outputs:
self.invocation_step.add_output(output_name, output)
self.invocation_step.job = job
| def record_success(self, execution_slice, job, outputs):
super().record_success(execution_slice, job, outputs)
if not self.collection_info:
self.invocation_step.job = job
| https://github.com/galaxyproject/galaxy/issues/10966 | Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: galaxy.workflow.run ERROR 2020-12-18 11:53:28,997 Failed to schedule Workflow[id=74152,name=COVID-19: variation analysis reporting v2], problem occurred on WorkflowStep[index=25,type=tool].
Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: Traceback (most ... | KeyError |
def ensure_implicit_collections_populated(self, history, params):
if not self.collection_info:
return
history = history or self.tool.get_default_history_by_trans(self.trans)
if self.invocation_step.is_new:
self.precreate_output_collections(history, params)
for output_name, implicit_... | def ensure_implicit_collections_populated(self, history, params):
if not self.collection_info:
return
history = history or self.tool.get_default_history_by_trans(self.trans)
if self.invocation_step.is_new:
self.precreate_output_collections(history, params)
else:
collections = {}... | https://github.com/galaxyproject/galaxy/issues/10966 | Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: galaxy.workflow.run ERROR 2020-12-18 11:53:28,997 Failed to schedule Workflow[id=74152,name=COVID-19: variation analysis reporting v2], problem occurred on WorkflowStep[index=25,type=tool].
Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: Traceback (most ... | KeyError |
def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = (
invocation_step.output_value.value
)
self.outputs[step.id] = ... | def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = (
invocation_step.output_value.value
)
self.outputs[step.id] = ... | https://github.com/galaxyproject/galaxy/issues/10966 | Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: galaxy.workflow.run ERROR 2020-12-18 11:53:28,997 Failed to schedule Workflow[id=74152,name=COVID-19: variation analysis reporting v2], problem occurred on WorkflowStep[index=25,type=tool].
Dec 18 11:53:29 sn04.bi.uni-freiburg.de python[2113691]: Traceback (most ... | KeyError |
def _download(self, rel_path):
try:
log.debug(
"Pulling key '%s' into cache to %s",
rel_path,
self._get_cache_path(rel_path),
)
key = self._bucket.get_key(rel_path)
# Test if cache is large enough to hold the new file
if self.cache_size > 0... | def _download(self, rel_path):
try:
log.debug(
"Pulling key '%s' into cache to %s",
rel_path,
self._get_cache_path(rel_path),
)
key = self._bucket.get_key(rel_path)
# Test if cache is large enough to hold the new file
if self.cache_size > 0... | https://github.com/galaxyproject/galaxy/issues/10824 | galaxy.objectstore.s3 DEBUG 2020-11-30 12:41:25,364 [p:18802,w:1,m:0] [uWSGIWorker1Core1] Pulling key '000/dataset_74.dat' into cache to /mnt/volume/shared/galaxy/var/database/object_store_cache/000/dataset_74.dat
galaxy.objectstore.s3 DEBUG 2020-11-30 12:41:25,370 [p:18802,w:1,m:0] [uWSGIWorker1Core1] Parallel pulled ... | TypeError |
def preferences(self):
user = self.trans.user
return user and user.extra_preferences or defaultdict(lambda: None)
| def preferences(self):
user = self.trans.user
return user and user.extra_preferences
| https://github.com/galaxyproject/galaxy/issues/10595 | Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: Traceback (most recent call last):
Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1040, in unicodify
Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: value = str(value)
Oct 31 10:38:52 ... | KeyError |
def extra_preferences(self):
data = defaultdict(lambda: None)
extra_user_preferences = self.preferences.get("extra_user_preferences")
if extra_user_preferences:
try:
data = json.loads(extra_user_preferences)
except Exception:
pass
return data
| def extra_preferences(self):
data = {}
extra_user_preferences = self.preferences.get("extra_user_preferences")
if extra_user_preferences:
try:
data = json.loads(extra_user_preferences)
except Exception:
pass
return data
| https://github.com/galaxyproject/galaxy/issues/10595 | Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: Traceback (most recent call last):
Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: File "/opt/galaxy/server/lib/galaxy/util/__init__.py", line 1040, in unicodify
Oct 31 10:38:52 sn04.bi.uni-freiburg.de python[1936614]: value = str(value)
Oct 31 10:38:52 ... | KeyError |
def dataset_states_and_extensions_summary(self):
if not hasattr(self, "_dataset_states_and_extensions_summary"):
db_session = object_session(self)
dc = alias(DatasetCollection.table)
de = alias(DatasetCollectionElement.table)
hda = alias(HistoryDatasetAssociation.table)
data... | def dataset_states_and_extensions_summary(self):
if not hasattr(self, "_dataset_states_and_extensions_summary"):
db_session = object_session(self)
dc = alias(DatasetCollection.table)
de = alias(DatasetCollectionElement.table)
hda = alias(HistoryDatasetAssociation.table)
data... | https://github.com/galaxyproject/galaxy/issues/8390 | [pid: 63775|app: 0|req: 160/596] 127.0.0.1 () {50 vars in 1324 bytes} [Wed Jul 31 09:38:45 2019] GET /api/histories/1cd8e2f6b131e891/contents?details=3f5830403180d620&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-07-31T16%3A38%3A41.000Z&qv=False&qv=False => generated 2 byte... | Exception |
def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
... | def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
... | https://github.com/galaxyproject/galaxy/issues/8390 | [pid: 63775|app: 0|req: 160/596] 127.0.0.1 () {50 vars in 1324 bytes} [Wed Jul 31 09:38:45 2019] GET /api/histories/1cd8e2f6b131e891/contents?details=3f5830403180d620&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-07-31T16%3A38%3A41.000Z&qv=False&qv=False => generated 2 byte... | Exception |
def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = (
invocation_step.output_value.value
)
self.outputs[step.id] = ... | def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
self.outputs[step.id] = outputs
if not already_persisted:
for output_name, output_object in outputs.items():
if hasattr(output_object, "history_content_type"):
... | https://github.com/galaxyproject/galaxy/issues/8390 | [pid: 63775|app: 0|req: 160/596] 127.0.0.1 () {50 vars in 1324 bytes} [Wed Jul 31 09:38:45 2019] GET /api/histories/1cd8e2f6b131e891/contents?details=3f5830403180d620&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-07-31T16%3A38%3A41.000Z&qv=False&qv=False => generated 2 byte... | Exception |
def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
... | def replacement_for_connection(self, connection, is_data=True):
output_step_id = connection.output_step.id
if output_step_id not in self.outputs:
template = "No outputs found for step id %s, outputs are %s"
message = template % (output_step_id, self.outputs)
raise Exception(message)
... | https://github.com/galaxyproject/galaxy/issues/8390 | [pid: 63775|app: 0|req: 160/596] 127.0.0.1 () {50 vars in 1324 bytes} [Wed Jul 31 09:38:45 2019] GET /api/histories/1cd8e2f6b131e891/contents?details=3f5830403180d620&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-07-31T16%3A38%3A41.000Z&qv=False&qv=False => generated 2 byte... | Exception |
def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
if invocation_step.output_value:
outputs[invocation_step.output_value.workflow_output.output_name] = (
invocation_step.output_value.value
)
self.outputs[step.id] = ... | def set_step_outputs(self, invocation_step, outputs, already_persisted=False):
step = invocation_step.workflow_step
self.outputs[step.id] = outputs
if not already_persisted:
for output_name, output_object in outputs.items():
if hasattr(output_object, "history_content_type"):
... | https://github.com/galaxyproject/galaxy/issues/8390 | [pid: 63775|app: 0|req: 160/596] 127.0.0.1 () {50 vars in 1324 bytes} [Wed Jul 31 09:38:45 2019] GET /api/histories/1cd8e2f6b131e891/contents?details=3f5830403180d620&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-07-31T16%3A38%3A41.000Z&qv=False&qv=False => generated 2 byte... | Exception |
def extract_steps(
trans,
history=None,
job_ids=None,
dataset_ids=None,
dataset_collection_ids=None,
dataset_names=None,
dataset_collection_names=None,
):
# Ensure job_ids and dataset_ids are lists (possibly empty)
job_ids = listify(job_ids)
dataset_ids = listify(dataset_ids)
... | def extract_steps(
trans,
history=None,
job_ids=None,
dataset_ids=None,
dataset_collection_ids=None,
dataset_names=None,
dataset_collection_names=None,
):
# Ensure job_ids and dataset_ids are lists (possibly empty)
if job_ids is None:
job_ids = []
elif type(job_ids) is no... | https://github.com/galaxyproject/galaxy/issues/10452 | Oct 18 23:43:10 sn04.bi.uni-freiburg.de uwsgi[1008399]: 80.138.30.147 - - [18/Oct/2020:23:43:09 +0200] "POST /workflow/build_from_current_history HTTP/1.1" 500 - "https://usegalaxy.eu/workflow/build_from_current_history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:81.0) Gecko/20100101 Firefox/81.0"
Oct 18 23:43:10 sn04... | AttributeError |
def __cleanup_param_values(inputs, values):
"""
Remove 'Data' values from `param_values`, along with metadata cruft,
but track the associations.
"""
associations = []
# dbkey is pushed in by the framework
if "dbkey" in values:
del values["dbkey"]
root_values = values
root_inp... | def __cleanup_param_values(inputs, values):
"""
Remove 'Data' values from `param_values`, along with metadata cruft,
but track the associations.
"""
associations = []
# dbkey is pushed in by the framework
if "dbkey" in values:
del values["dbkey"]
root_values = values
root_inp... | https://github.com/galaxyproject/galaxy/issues/10452 | Oct 18 23:43:10 sn04.bi.uni-freiburg.de uwsgi[1008399]: 80.138.30.147 - - [18/Oct/2020:23:43:09 +0200] "POST /workflow/build_from_current_history HTTP/1.1" 500 - "https://usegalaxy.eu/workflow/build_from_current_history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:81.0) Gecko/20100101 Firefox/81.0"
Oct 18 23:43:10 sn04... | AttributeError |
def cleanup(prefix, inputs, values):
for key, input in inputs.items():
if isinstance(input, DataToolParameter) or isinstance(
input, DataCollectionToolParameter
):
items = values[key]
values[key] = None
# HACK: Nested associations are not yet working, ... | def cleanup(prefix, inputs, values):
for key, input in inputs.items():
if isinstance(input, DataToolParameter) or isinstance(
input, DataCollectionToolParameter
):
tmp = values[key]
values[key] = None
# HACK: Nested associations are not yet working, bu... | https://github.com/galaxyproject/galaxy/issues/10452 | Oct 18 23:43:10 sn04.bi.uni-freiburg.de uwsgi[1008399]: 80.138.30.147 - - [18/Oct/2020:23:43:09 +0200] "POST /workflow/build_from_current_history HTTP/1.1" 500 - "https://usegalaxy.eu/workflow/build_from_current_history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:81.0) Gecko/20100101 Firefox/81.0"
Oct 18 23:43:10 sn04... | AttributeError |
def precreate_dataset_collection(
self,
structure,
allow_unitialized_element=True,
completed_collection=None,
implicit_output_name=None,
):
has_structure = not structure.is_leaf and structure.children_known
if not has_structure and allow_unitialized_element:
dataset_collection = mode... | def precreate_dataset_collection(
self,
structure,
allow_unitialized_element=True,
completed_collection=None,
implicit_output_name=None,
):
has_structure = not structure.is_leaf and structure.children_known
if not has_structure and allow_unitialized_element:
dataset_collection = mode... | https://github.com/galaxyproject/galaxy/issues/10604 | Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1827028]: galaxy.jobs DEBUG 2020-11-01 14:58:58,991 (12059080) Working directory for job is: /data/dnb03/galaxy_db/job_working_directory/012/059/12059080
Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1847375]: galaxy.jobs DEBUG 2020-11-01 14:58:58,998 (12059086) Working d... | sqlalchemy.exc.IntegrityError |
def set_collection_elements(dataset_collection, type, dataset_instances):
element_index = 0
elements = []
for element in type.generate_elements(dataset_instances):
element.element_index = element_index
element.collection = dataset_collection
elements.append(element)
element_... | def set_collection_elements(dataset_collection, type, dataset_instances):
element_index = 0
elements = []
for element in type.generate_elements(dataset_instances):
element.element_index = element_index
element.collection = dataset_collection
elements.append(element)
element_... | https://github.com/galaxyproject/galaxy/issues/10604 | Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1827028]: galaxy.jobs DEBUG 2020-11-01 14:58:58,991 (12059080) Working directory for job is: /data/dnb03/galaxy_db/job_working_directory/012/059/12059080
Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1847375]: galaxy.jobs DEBUG 2020-11-01 14:58:58,998 (12059086) Working d... | sqlalchemy.exc.IntegrityError |
def prototype(self, plugin_type):
plugin_type_object = self.get(plugin_type)
if not hasattr(plugin_type_object, "prototype_elements"):
raise Exception(
"Cannot pre-determine structure for collection of type %s" % plugin_type
)
dataset_collection = model.DatasetCollection()
f... | def prototype(self, plugin_type):
plugin_type_object = self.get(plugin_type)
if not hasattr(plugin_type_object, "prototype_elements"):
raise Exception(
"Cannot pre-determine structure for collection of type %s" % plugin_type
)
dataset_collection = model.DatasetCollection()
e... | https://github.com/galaxyproject/galaxy/issues/10604 | Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1827028]: galaxy.jobs DEBUG 2020-11-01 14:58:58,991 (12059080) Working directory for job is: /data/dnb03/galaxy_db/job_working_directory/012/059/12059080
Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1847375]: galaxy.jobs DEBUG 2020-11-01 14:58:58,998 (12059086) Working d... | sqlalchemy.exc.IntegrityError |
def collect_dynamic_outputs(
job_context,
output_collections,
):
# unmapped outputs do not correspond to explicit outputs of the tool, they were inferred entirely
# from the tool provided metadata (e.g. galaxy.json).
for unnamed_output_dict in job_context.tool_provided_metadata.get_unnamed_outputs()... | def collect_dynamic_outputs(
job_context,
output_collections,
):
# unmapped outputs do not correspond to explicit outputs of the tool, they were inferred entirely
# from the tool provided metadata (e.g. galaxy.json).
for unnamed_output_dict in job_context.tool_provided_metadata.get_unnamed_outputs()... | https://github.com/galaxyproject/galaxy/issues/10604 | Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1827028]: galaxy.jobs DEBUG 2020-11-01 14:58:58,991 (12059080) Working directory for job is: /data/dnb03/galaxy_db/job_working_directory/012/059/12059080
Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1847375]: galaxy.jobs DEBUG 2020-11-01 14:58:58,998 (12059086) Working d... | sqlalchemy.exc.IntegrityError |
def populate_collection_elements(
self,
collection,
root_collection_builder,
filenames,
name=None,
metadata_source_name=None,
final_job_state="ok",
):
# TODO: allow configurable sorting.
# <sort by="lexical" /> <!-- default -->
# <sort by="reverse_lexical" />
# <sort... | def populate_collection_elements(
self,
collection,
root_collection_builder,
filenames,
name=None,
metadata_source_name=None,
final_job_state="ok",
):
# TODO: allow configurable sorting.
# <sort by="lexical" /> <!-- default -->
# <sort by="reverse_lexical" />
# <sort... | https://github.com/galaxyproject/galaxy/issues/10604 | Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1827028]: galaxy.jobs DEBUG 2020-11-01 14:58:58,991 (12059080) Working directory for job is: /data/dnb03/galaxy_db/job_working_directory/012/059/12059080
Nov 01 14:58:58 sn04.bi.uni-freiburg.de python[1847375]: galaxy.jobs DEBUG 2020-11-01 14:58:58,998 (12059086) Working d... | sqlalchemy.exc.IntegrityError |
def export_archive(
self,
trans,
id=None,
gzip=True,
include_hidden=False,
include_deleted=False,
preview=False,
):
"""Export a history to an archive."""
#
# Get history to export.
#
if id:
history = self.history_manager.get_accessible(
self.decode_id(... | def export_archive(
self,
trans,
id=None,
gzip=True,
include_hidden=False,
include_deleted=False,
preview=False,
):
"""Export a history to an archive."""
#
# Get history to export.
#
if id:
history = self.history_manager.get_accessible(
self.decode_id(... | https://github.com/galaxyproject/galaxy/issues/10040 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 170, in decorator
rval = func(self, trans, *args, **kwargs)
TypeError: sharing() missing 1 required positional argument: 'id' | TypeError |
def execute(
self,
tool,
trans,
incoming=None,
return_job=False,
set_output_hid=True,
history=None,
job_params=None,
rerun_remap_job_id=None,
execution_cache=None,
dataset_collection_elements=None,
completed_job=None,
collection_info=None,
):
"""
Executes a to... | def execute(
self,
tool,
trans,
incoming=None,
return_job=False,
set_output_hid=True,
history=None,
job_params=None,
rerun_remap_job_id=None,
execution_cache=None,
dataset_collection_elements=None,
completed_job=None,
collection_info=None,
):
"""
Executes a to... | https://github.com/galaxyproject/galaxy/issues/9241 | 2020-01-20T10:34:14.9786332Z 2020-01-20 10:34:14,974 ERROR [galaxy.tools] Exception caught while attempting tool execution:
2020-01-20T10:34:14.9787128Z Traceback (most recent call last):
2020-01-20T10:34:14.9789375Z File "/home/runner/.planemo/gx_venv_3.7_release_20.01/lib/python3.7/site-packages/sqlalchemy/engine/b... | sqlalchemy.exc.ProgrammingError |
def handle_output(name, output, hidden=None):
if output.parent:
parent_to_child_pairs.append((output.parent, name))
child_dataset_names.add(name)
if async_tool and name in incoming:
# HACK: output data has already been created as a result of the async controller
dataid = incoming... | def handle_output(name, output, hidden=None):
if output.parent:
parent_to_child_pairs.append((output.parent, name))
child_dataset_names.add(name)
# What is the following hack for? Need to document under what
# conditions can the following occur? (james@bx.psu.edu)
# HACK: the output data... | https://github.com/galaxyproject/galaxy/issues/9241 | 2020-01-20T10:34:14.9786332Z 2020-01-20 10:34:14,974 ERROR [galaxy.tools] Exception caught while attempting tool execution:
2020-01-20T10:34:14.9787128Z Traceback (most recent call last):
2020-01-20T10:34:14.9789375Z File "/home/runner/.planemo/gx_venv_3.7_release_20.01/lib/python3.7/site-packages/sqlalchemy/engine/b... | sqlalchemy.exc.ProgrammingError |
def get_shed_config_dict(self, app):
"""
Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry
in the shed_tool_conf_dict.
"""
def _is_valid_shed_config_filename(filename):
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
include... | def get_shed_config_dict(self, app, default=None):
"""
Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry
in the shed_tool_conf_dict.
"""
def _is_valid_shed_config_filename(filename):
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def guess_shed_config(self, app):
tool_ids = []
for tool in self.metadata.get("tools", []):
tool_ids.append(tool.get("guid"))
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
include_migrated_tool_conf=True
):
name = shed_tool_conf_dict["config_filename"]
for elem in... | def guess_shed_config(self, app, default=None):
tool_ids = []
for tool in self.metadata.get("tools", []):
tool_ids.append(tool.get("guid"))
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
include_migrated_tool_conf=True
):
name = shed_tool_conf_dict["config_filename"]
... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def install(self, tool_shed_url, name, owner, changeset_revision, install_options):
# Get all of the information necessary for installing the repository from the specified tool shed.
repository_revision_dict, repo_info_dicts = self.__get_install_info_from_tool_shed(
tool_shed_url, name, owner, changeset... | def install(self, tool_shed_url, name, owner, changeset_revision, install_options):
# Get all of the information necessary for installing the repository from the specified tool shed.
repository_revision_dict, repo_info_dicts = self.__get_install_info_from_tool_shed(
tool_shed_url, name, owner, changeset... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def __initiate_and_install_repositories(
self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
):
try:
has_repository_dependencies = repository_revision_dict[
"has_repository_dependencies"
]
except KeyError:
raise exceptions.InternalServerError(
... | def __initiate_and_install_repositories(
self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
):
try:
has_repository_dependencies = repository_revision_dict[
"has_repository_dependencies"
]
except KeyError:
raise exceptions.InternalServerError(
... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def install_tool_shed_repository(
self,
tool_shed_repository,
repo_info_dict,
tool_panel_section_key,
shed_tool_conf,
tool_path,
install_resolver_dependencies,
install_tool_dependencies,
reinstalling=False,
tool_panel_section_mapping={},
install_options=None,
):
self.app.... | def install_tool_shed_repository(
self,
tool_shed_repository,
repo_info_dict,
tool_panel_section_key,
shed_tool_conf,
tool_path,
install_resolver_dependencies,
install_tool_dependencies,
reinstalling=False,
tool_panel_section_mapping={},
install_options=None,
):
self.app.... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def update_tool_shed_repository(
self,
repository,
tool_shed_url,
latest_ctx_rev,
latest_changeset_revision,
install_new_dependencies=True,
install_options=None,
):
install_options = install_options or {}
original_metadata_dict = repository.metadata
original_repository_dependenci... | def update_tool_shed_repository(
self,
repository,
tool_shed_url,
latest_ctx_rev,
latest_changeset_revision,
install_new_dependencies=True,
install_options=None,
):
install_options = install_options or {}
original_metadata_dict = repository.metadata
original_repository_dependenci... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def get_repository_tools_tups(self):
"""
Return a list of tuples of the form (relative_path, guid, tool) for each tool defined
in the received tool shed repository metadata.
"""
repository_tools_tups = []
shed_conf_dict = self.tpm.get_shed_tool_conf_dict(
self.metadata_dict.get("shed_con... | def get_repository_tools_tups(self):
"""
Return a list of tuples of the form (relative_path, guid, tool) for each tool defined
in the received tool shed repository metadata.
"""
repository_tools_tups = []
shed_conf_dict = self.tpm.get_shed_tool_conf_dict(
self.metadata_dict.get("shed_con... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def set_repository(
self, repository, relative_install_dir=None, changeset_revision=None
):
self.repository = repository
# Shed related tool panel configs are only relevant to Galaxy.
if self.app.name == "galaxy":
if relative_install_dir is None and self.repository is not None:
tool_... | def set_repository(
self, repository, relative_install_dir=None, changeset_revision=None
):
self.repository = repository
# Shed related tool panel configs are only relevant to Galaxy.
if self.app.name == "galaxy":
if relative_install_dir is None and self.repository is not None:
tool_... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def __initiate_and_install_repositories(
self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
):
try:
has_repository_dependencies = repository_revision_dict[
"has_repository_dependencies"
]
except KeyError:
raise exceptions.InternalServerError(
... | def __initiate_and_install_repositories(
self, tool_shed_url, repository_revision_dict, repo_info_dicts, install_options
):
try:
has_repository_dependencies = repository_revision_dict[
"has_repository_dependencies"
]
except KeyError:
raise exceptions.InternalServerError(
... | https://github.com/galaxyproject/galaxy/issues/8952 | Nov 09 13:22:10 sn04.bi.uni-freiburg.de uwsgi[4107748]: [pid: 4124485|app: 0|req: 9911/42155] 88.66.136.83 () {84 vars in 1575 bytes} [Sat Nov 9 13:22:10 2019] POST /admin_toolshed/repository_installation_status_updates => generated 2 bytes in 23 msecs (HTTP/1.1 200) 3 headers in 96 bytes (1 switches on core 0)
Nov 09... | ParseError |
def process_bind_param(self, value, dialect):
"""Automatically truncate string values"""
if self.impl.length and value is not None:
value = unicodify(value)[0 : self.impl.length]
return value
| def process_bind_param(self, value, dialect):
"""Automatically truncate string values"""
if self.impl.length and value is not None:
value = value[0 : self.impl.length]
return value
| https://github.com/galaxyproject/galaxy/issues/8680 | galaxy.web.framework.decorators ERROR 2019-09-19 17:20:36,279 [p:47682,w:1,m:0] [uWSGIWorker1Core0] Uncaught exception in exposed API method:
Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 157, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy... | StatementError |
def _upload_dataset(self, trans, library_id, folder_id, replace_dataset=None, **kwd):
# Set up the traditional tool state/params
cntrller = "api"
tool_id = "upload1"
message = None
file_type = kwd.get("file_type")
try:
upload_common.validate_datatype_extension(
datatypes_regi... | def _upload_dataset(self, trans, library_id, folder_id, replace_dataset=None, **kwd):
# Set up the traditional tool state/params
cntrller = "api"
tool_id = "upload1"
message = None
tool = trans.app.toolbox.get_tool(tool_id)
state = tool.new_state(trans)
populate_state(trans, tool.inputs, kwd... | https://github.com/galaxyproject/galaxy/issues/8820 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/library_contents.py", line 250, in create
status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload)
Fil... | AttributeError |
def validate_and_normalize_targets(trans, payload):
"""Validate and normalize all src references in fetch targets.
- Normalize ftp_import and server_dir src entries into simple path entries
with the relevant paths resolved and permissions / configuration checked.
- Check for file:// URLs in items src... | def validate_and_normalize_targets(trans, payload):
"""Validate and normalize all src references in fetch targets.
- Normalize ftp_import and server_dir src entries into simple path entries
with the relevant paths resolved and permissions / configuration checked.
- Check for file:// URLs in items src... | https://github.com/galaxyproject/galaxy/issues/8820 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/library_contents.py", line 250, in create
status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload)
Fil... | AttributeError |
def check_src(item):
if "object_id" in item:
raise RequestParameterInvalidException(
"object_id not allowed to appear in the request."
)
validate_datatype_extension(
datatypes_registry=trans.app.datatypes_registry, ext=item.get("ext")
)
# Normalize file:// URLs into... | def check_src(item):
if "object_id" in item:
raise RequestParameterInvalidException(
"object_id not allowed to appear in the request."
)
# Normalize file:// URLs into paths.
if item["src"] == "url" and item["url"].startswith("file://"):
item["src"] = "path"
item[... | https://github.com/galaxyproject/galaxy/issues/8820 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 282, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/library_contents.py", line 250, in create
status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload)
Fil... | AttributeError |
def parse_xml(file_name, check_exists=True):
"""Returns a parsed xml tree with comments intact."""
error_message = ""
if check_exists and not os.path.exists(file_name):
return None, "File does not exist %s" % str(file_name)
with open(file_name, "r") as fobj:
try:
tree = XmlE... | def parse_xml(file_name, check_exists=True):
"""Returns a parsed xml tree with comments intact."""
error_message = ""
if check_exists and not os.path.exists(file_name):
return None, "File does not exist %s" % str(file_name)
with open(file_name, "r") as fobj:
try:
tree = XmlE... | https://github.com/galaxyproject/galaxy/issues/8641 | tool_shed.util.xml_util ERROR 2019-09-12 19:47:44,334 [p:54106,w:1,m:0] [uWSGIWorker1Core1] Exception attempting to parse GLXFOLDER/tool-data/TOOLSHED/repos/USER/REPO/REVISION/tool_data_table_conf.xml: multiple elements on top level
Traceback (most recent call last):
File "lib/tool_shed/util/xml_util.py", line 87, in p... | xml.etree.ElementTree.ParseError |
def comment(self, data):
if self.non_comment_seen:
# Cannot start XML file with comment
self.start(XmlET.Comment, {})
self.data(data)
self.end(XmlET.Comment)
| def comment(self, data):
self.start(XmlET.Comment, {})
self.data(data)
self.end(XmlET.Comment)
| https://github.com/galaxyproject/galaxy/issues/8641 | tool_shed.util.xml_util ERROR 2019-09-12 19:47:44,334 [p:54106,w:1,m:0] [uWSGIWorker1Core1] Exception attempting to parse GLXFOLDER/tool-data/TOOLSHED/repos/USER/REPO/REVISION/tool_data_table_conf.xml: multiple elements on top level
Traceback (most recent call last):
File "lib/tool_shed/util/xml_util.py", line 87, in p... | xml.etree.ElementTree.ParseError |
def install_data_managers(
self,
shed_data_manager_conf_filename,
metadata_dict,
shed_config_dict,
relative_install_dir,
repository,
repository_tools_tups,
):
rval = []
if "data_manager" in metadata_dict:
tpm = tool_panel_manager.ToolPanelManager(self.app)
repository_... | def install_data_managers(
self,
shed_data_manager_conf_filename,
metadata_dict,
shed_config_dict,
relative_install_dir,
repository,
repository_tools_tups,
):
rval = []
if "data_manager" in metadata_dict:
tpm = tool_panel_manager.ToolPanelManager(self.app)
repository_... | https://github.com/galaxyproject/galaxy/issues/8641 | tool_shed.util.xml_util ERROR 2019-09-12 19:47:44,334 [p:54106,w:1,m:0] [uWSGIWorker1Core1] Exception attempting to parse GLXFOLDER/tool-data/TOOLSHED/repos/USER/REPO/REVISION/tool_data_table_conf.xml: multiple elements on top level
Traceback (most recent call last):
File "lib/tool_shed/util/xml_util.py", line 87, in p... | xml.etree.ElementTree.ParseError |
def _xml_replace(query, targets, parent_map):
# parent_el = query.find('..') ## Something like this would be better with newer xml library
parent_el = parent_map[query]
matching_index = -1
# for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation
for index, ... | def _xml_replace(query, targets, parent_map):
# parent_el = query.find('..') ## Something like this would be better with newer xml library
parent_el = parent_map[query]
matching_index = -1
# for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation
for index, ... | https://github.com/galaxyproject/galaxy/issues/8805 | galaxy.tools.toolbox.base ERROR 2019-10-15 10:55:57,876 Failed to load potential tool /Users/scholtalbers/workspace/je-suite/src/galaxy/je-clip.xml.
Traceback (most recent call last):
File "/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpFw8KvW/galaxy-dev/lib/galaxy/tools/toolbox/base.py", line 772, in quic... | AssertionError |
def _expand_yield_statements(macro_def, expand_el):
yield_els = [
yield_el
for macro_def_el in macro_def
for yield_el in macro_def_el.findall(".//yield")
]
expand_el_children = list(expand_el)
macro_def_parent_map = dict(
(c, p) for macro_def_el in macro_def for p in mac... | def _expand_yield_statements(macro_def, expand_el):
yield_els = [
yield_el
for macro_def_el in macro_def
for yield_el in macro_def_el.findall(".//yield")
]
expand_el_children = list(expand_el)
macro_def_parent_map = dict(
(c, p) for macro_def_el in macro_def for p in mac... | https://github.com/galaxyproject/galaxy/issues/8805 | galaxy.tools.toolbox.base ERROR 2019-10-15 10:55:57,876 Failed to load potential tool /Users/scholtalbers/workspace/je-suite/src/galaxy/je-clip.xml.
Traceback (most recent call last):
File "/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpFw8KvW/galaxy-dev/lib/galaxy/tools/toolbox/base.py", line 772, in quic... | AssertionError |
def __determine_job_destination(self, params, raw_job_destination=None):
if self.job_wrapper.tool is None:
raise JobMappingException(
"Can't map job to destination, tool '%s' is unavailable"
% self.job_wrapper.get_job().tool_id
)
if raw_job_destination is None:
ra... | def __determine_job_destination(self, params, raw_job_destination=None):
if raw_job_destination is None:
raw_job_destination = self.job_wrapper.tool.get_job_destination(params)
if raw_job_destination.runner == DYNAMIC_RUNNER_NAME:
job_destination = self.__handle_dynamic_job_destination(raw_job_d... | https://github.com/galaxyproject/galaxy/issues/8141 | Traceback (most recent call last):
File "/opt/galaxy/server/lib/galaxy/jobs/handler.py", line 374, in __handle_waiting_jobs
job_state = self.__check_job_state(job)
File "/opt/galaxy/server/lib/galaxy/jobs/handler.py", line 510, in __check_job_state
state, job_destination = self.__verify_job_ready(job, job_wrapper)
File... | AttributeError |
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
"""The header file. Provides information about dimensions, identification, and processing history."""
self.add_composite_file(
"hdr", description="The Analyze75 header file.", is_binary=True
)
"""The image file. Image data, whose dat... | def __init__(self, **kwd):
Binary.__init__(self, **kwd)
"""The header file. Provides information about dimensions, identification, and processing history."""
self.add_composite_file(
"hdr", description="The Analyze75 header file.", is_binary=False
)
"""The image file. Image data, whose da... | https://github.com/galaxyproject/galaxy/issues/7412 | Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 329, in <module>
__main__()
File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 320, in __main__
metadata.append(add_composite_file(dataset, registry, ou... | UnicodeDecodeError |
def add_composite_file(dataset, registry, output_path, files_path):
datatype = None
# Find data type
if dataset.file_type is not None:
datatype = registry.get_datatype_by_extension(dataset.file_type)
def to_path(path_or_url):
is_url = path_or_url.find("://") != -1 # todo fixme
... | def add_composite_file(dataset, registry, output_path, files_path):
datatype = None
# Find data type
if dataset.file_type is not None:
try:
datatype = registry.get_datatype_by_extension(dataset.file_type)
except Exception:
print(
"Unable to instantiat... | https://github.com/galaxyproject/galaxy/issues/7412 | Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 329, in <module>
__main__()
File "/cvmfs/main.galaxyproject.org/galaxy/tools/data_source/upload.py", line 320, in __main__
metadata.append(add_composite_file(dataset, registry, ou... | UnicodeDecodeError |
def tool_shed_repositories(self):
try:
repositories = self.cache.repositories
except AttributeError:
self.rebuild()
repositories = self.cache.repositories
tool_shed_repositories = [
repo
for repo in repositories
if isinstance(repo, self.app.install_model.ToolS... | def tool_shed_repositories(self):
try:
repositories = self.cache.repositories
except AttributeError:
self.rebuild()
repositories = self.cache.repositories
if repositories and not repositories[0]._sa_instance_state._attached:
self.rebuild()
repositories = self.cache.re... | https://github.com/galaxyproject/galaxy/issues/8015 | galaxy.tools.toolbox.base ERROR 2019-05-21 18:57:13,924 [p:1,w:0,m:0] [MainThread] Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/sam_pileup/890d97772e2a/sam_pileup/sam_pileup.xml
Traceback (most recent call last):
File "/galaxy/server/lib/galaxy/tools/toolbox/base.py", line 605, in _load_tool_tag_s... | AttributeError |
def get_file_name(self):
if not self.external_filename:
assert self.object_store is not None, (
"Object Store has not been initialized for dataset %s" % self.id
)
if self.object_store.exists(self):
return self.object_store.get_filename(self)
else:
... | def get_file_name(self):
if not self.external_filename:
assert self.object_store is not None, (
"Object Store has not been initialized for dataset %s" % self.id
)
filename = self.object_store.get_filename(self)
return filename
else:
filename = self.external_fi... | https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def get_extra_files_path(self):
# Unlike get_file_name - external_extra_files_path is not backed by an
# actual database column so if SA instantiates this object - the
# attribute won't exist yet.
if not getattr(self, "external_extra_files_path", None):
if self.object_store.exists(
s... | def get_extra_files_path(self):
# Unlike get_file_name - external_extra_files_path is not backed by an
# actual database column so if SA instantiates this object - the
# attribute won't exist yet.
if not getattr(self, "external_extra_files_path", None):
return self.object_store.get_filename(
... | https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def full_delete(self):
"""Remove the file and extra files, marks deleted and purged"""
# os.unlink( self.file_name )
try:
self.object_store.delete(self)
except galaxy.exceptions.ObjectNotFound:
pass
if self.object_store.exists(
self, extra_dir=self._extra_files_rel_path, dir_... | def full_delete(self):
"""Remove the file and extra files, marks deleted and purged"""
# os.unlink( self.file_name )
self.object_store.delete(self)
if self.object_store.exists(
self, extra_dir=self._extra_files_rel_path, dir_only=True
):
self.object_store.delete(
self, en... | https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def get_filename(self, obj, **kwargs):
"""
Override `ObjectStore`'s stub.
If `object_store_check_old_style` is set to `True` in config then the
root path is checked first.
"""
if self.check_old_style:
path = self._construct_path(obj, old_style=True, **kwargs)
# For backward comp... | def get_filename(self, obj, **kwargs):
"""
Override `ObjectStore`'s stub.
If `object_store_check_old_style` is set to `True` in config then the
root path is checked first.
"""
if self.check_old_style:
path = self._construct_path(obj, old_style=True, **kwargs)
# For backward comp... | https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def collect_primary_datasets(job_context, output, input_ext):
tool = job_context.tool
job_working_directory = job_context.job_working_directory
sa_session = job_context.sa_session
# Loop through output file names, looking for generated primary
# datasets in form specified by discover dataset patter... | def collect_primary_datasets(job_context, output, input_ext):
tool = job_context.tool
job_working_directory = job_context.job_working_directory
sa_session = job_context.sa_session
# Loop through output file names, looking for generated primary
# datasets in form specified by discover dataset patter... | https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def _dataset_wrapper(self, dataset, dataset_paths, **kwargs):
wrapper_kwds = kwargs.copy()
if dataset and dataset_paths:
real_path = dataset.file_name
if real_path in dataset_paths:
wrapper_kwds["dataset_path"] = dataset_paths[real_path]
return DatasetFilenameWrapper(dataset, **w... | def _dataset_wrapper(self, dataset, dataset_paths, **kwargs):
wrapper_kwds = kwargs.copy()
if dataset:
real_path = dataset.file_name
if real_path in dataset_paths:
wrapper_kwds["dataset_path"] = dataset_paths[real_path]
return DatasetFilenameWrapper(dataset, **wrapper_kwds)
| https://github.com/galaxyproject/galaxy/issues/7368 | galaxy.workflow.run_request INFO 2019-02-13 14:22:26,638 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150481
galaxy.workflow.run_request INFO 2019-02-13 14:22:26,639 [p:336,w:1,m:0] [uWSGIWorker1Core3] Creating a step_state for step.id 150482
galaxy.workflow.run_request INFO 2019-02-13 14:22:26... | Exception |
def __main__():
input_name = sys.argv[1]
output_name = sys.argv[2]
skipped_lines = 0
first_skipped_line = 0
out = open(output_name, "w")
i = 0
for i, line in enumerate(open(input_name)):
complete_bed = False
line = line.rstrip("\r\n")
if (
line
... | def __main__():
input_name = sys.argv[1]
output_name = sys.argv[2]
skipped_lines = 0
first_skipped_line = 0
out = open(output_name, "w")
out.write("##gff-version 2\n")
out.write("##bed_to_gff_converter.py\n\n")
i = 0
for i, line in enumerate(open(input_name)):
complete_bed = ... | https://github.com/galaxyproject/galaxy/issues/7771 | Dataset Error
An error occured while running the tool toolshed.g2.bx.psu.edu/repos/iuc/cwpair2/cwpair2/1.0.0.
Tool execution generated the following messages:
Unable to parse file "/galaxy-repl/main/files/031/018/dataset_31018984.dat".
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/shed_tools/... | ValueError |
def register(
self, trans, email=None, username=None, password=None, confirm=None, subscribe=False
):
"""
Register a new user.
"""
if not trans.app.config.allow_user_creation and not trans.user_is_admin:
message = "User registration is disabled. Please contact your local Galaxy administrato... | def register(
self,
trans,
email=None,
username=None,
password=None,
confirm=None,
subscribe=False,
**kwd,
):
"""
Register a new user.
"""
if not trans.app.config.allow_user_creation and not trans.user_is_admin:
message = "User registration is disabled. Please co... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def __autoregistration(self, trans, login, password):
"""
Does the autoregistration if enabled. Returns a message
"""
autoreg = trans.app.auth_manager.check_auto_registration(trans, login, password)
user = None
if autoreg["auto_reg"]:
email = autoreg["email"]
username = autoreg["... | def __autoregistration(
self, trans, login, password, status, kwd, no_password_check=False, cntrller=None
):
"""
Does the autoregistration if enabled. Returns a message
"""
autoreg = trans.app.auth_manager.check_auto_registration(
trans, login, password, no_password_check=no_password_check
... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def __validate_login(self, trans, payload={}, **kwd):
"""Handle Galaxy Log in"""
if not payload:
payload = kwd
message = trans.check_csrf_token(payload)
if message:
return self.message_exception(trans, message)
login = payload.get("login")
password = payload.get("password")
r... | def __validate_login(self, trans, payload={}, **kwd):
"""Handle Galaxy Log in"""
if not payload:
payload = kwd
message = trans.check_csrf_token(payload)
if message:
return self.message_exception(trans, message)
login = payload.get("login")
password = payload.get("password")
r... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def resend_verification(self, trans):
"""
Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.
"""
message, status = self.resend_activation_email(trans, None, None)
if status:
return trans.show_ok_message(message)
else:
return tr... | def resend_verification(self, trans):
"""
Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead.
"""
message, status = self.resend_activation_email(trans, None, None)
if status == "done":
return trans.show_ok_message(message)
else:
... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def resend_activation_email(self, trans, email, username):
"""
Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link.
"""
if (
email is None
): # User is coming from outside registration form, load email from trans
... | def resend_activation_email(self, trans, email, username):
"""
Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link.
"""
if (
email is None
): # User is coming from outside registration form, load email from trans
... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def create(self, trans, payload={}, **kwd):
if not payload:
payload = kwd
message = trans.check_csrf_token(payload)
if message:
return self.message_exception(trans, message)
user, message = self.user_manager.register(
trans, **_filtered_registration_params_dict(payload)
)
... | def create(self, trans, payload={}, **kwd):
if not payload:
payload = kwd
message = trans.check_csrf_token(payload)
if message:
return self.message_exception(trans, message)
user, message = self.user_manager.register(trans, **payload)
if message:
return self.message_exception... | https://github.com/galaxyproject/galaxy/issues/7617 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/user.py", line 114, in login
return self.__validate_login(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/controllers/user... | AttributeError |
def send_mail(frm, to, subject, body, config, html=None):
"""
Sends an email.
:type frm: str
:param frm: from address
:type to: str
:param to: to address
:type subject: str
:param subject: Subject line
:type body: str
:param body: Body text (should be plain text)
:ty... | def send_mail(frm, to, subject, body, config, html=None):
"""
Sends an email.
:type frm: str
:param frm: from address
:type to: str
:param to: to address
:type subject: str
:param subject: Subject line
:type body: str
:param body: Body text (should be plain text)
:ty... | https://github.com/galaxyproject/galaxy/issues/7809 | Traceback (most recent call last):
File "lib/galaxy/managers/users.py", line 365, in send_activation_email
util.send_mail(frm, to, subject, body, self.app.config)
File "lib/galaxy/util/__init__.py", line 1436, in send_mail
msg = email_mime_text.MIMEText(body.encode('ascii', 'replace'))
File "/cvmfs/test.galaxyproject.o... | AttributeError |
def add_output(self, workflow_output, step, output_object):
if step.type == "parameter_input":
# TODO: these should be properly tracked.
return
if output_object.history_content_type == "dataset":
output_assoc = WorkflowInvocationOutputDatasetAssociation()
output_assoc.workflow_in... | def add_output(self, workflow_output, step, output_object):
if output_object.history_content_type == "dataset":
output_assoc = WorkflowInvocationOutputDatasetAssociation()
output_assoc.workflow_invocation = self
output_assoc.workflow_output = workflow_output
output_assoc.workflow_ste... | https://github.com/galaxyproject/galaxy/issues/7263 | galaxy.workflow.scheduling_manager DEBUG 2019-01-23 23:20:06,529 [p:6571,w:0,m:3] [WorkflowRequestMonitor.monitor_thread] Attempting to schedule workflow invocation [(808,)]
galaxy.workflow.run ERROR 2019-01-23 23:20:06,736 [p:6571,w:0,m:3] [WorkflowRequestMonitor.monitor_thread] Failed to schedule Workflow[id=879,name... | AttributeError |
def url_get(base_url, password_mgr=None, pathspec=None, params=None):
"""Make contact with the uri provided and return any contents."""
# Uses system proxy settings if they exist.
proxy = urlrequest.ProxyHandler()
if password_mgr is not None:
auth = urlrequest.HTTPDigestAuthHandler(password_mgr)... | def url_get(base_url, password_mgr=None, pathspec=None, params=None):
"""Make contact with the uri provided and return any contents."""
# Uses system proxy settings if they exist.
proxy = urlrequest.ProxyHandler()
if password_mgr is not None:
auth = urlrequest.HTTPDigestAuthHandler(password_mgr)... | https://github.com/galaxyproject/galaxy/issues/7769 | Traceback (most recent call last):
File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__
app_iter = self.application(environ, sr_checker)
File "/home/nate/work/galaxy2/.venv/lib/python3.5/site-packages/paste/recursive.py", line 85, in __call__
return self.application(environ, start_response)
File "... | TypeError |
def get_app_kwds(cls, config_section, app_name=None):
kwds = {
"config_file": None,
"config_section": config_section,
}
uwsgi_opt = uwsgi.opt
config_file = None
# check for --set galaxy_config_file=<path>, this overrides whatever config file uWSGI was loaded with (which
# may not... | def get_app_kwds(cls, config_section, app_name=None):
kwds = {
"config_file": None,
"config_section": config_section,
}
uwsgi_opt = uwsgi.opt
config_file = None
# check for --set galaxy_config_file=<path>, this overrides whatever config file uWSGI was loaded with (which
# may not... | https://github.com/galaxyproject/galaxy/issues/7714 | Traceback (most recent call last):
File "lib/galaxy/webapps/galaxy/buildapp.py", line 184, in uwsgi_app
return galaxy.web.framework.webapp.build_native_uwsgi_app(app_factory, "galaxy")
File "lib/galaxy/web/framework/webapp.py", line 965, in build_native_uwsgi_app
uwsgi_app = paste_factory({}, load_app_kwds=app_kwds)
Fi... | TypeError |
def guess_ext(fname, sniff_order, is_binary=False):
"""
Returns an extension that can be used in the datatype factory to
generate a data for the 'fname' file
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> datatypes_registry = example_datatype_registry_for_sample(... | def guess_ext(fname, sniff_order, is_binary=False):
"""
Returns an extension that can be used in the datatype factory to
generate a data for the 'fname' file
>>> from galaxy.datatypes.registry import example_datatype_registry_for_sample
>>> datatypes_registry = example_datatype_registry_for_sample(... | https://github.com/galaxyproject/galaxy/issues/6209 | Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/Users/guq/galaxy/tools/data_source/upload.py", line 323, in <module>
__main__()
File "/Users/guq/galaxy/tools/data_source/upload.py", line 316, in __main__
metadata.append(add_file(dataset, registry, output_path))
File "/Users/guq/galaxy/tools/data_s... | Exception |
def __int__(self):
return int(float(self))
| def __int__(self):
return int(str(self))
| https://github.com/galaxyproject/galaxy/issues/998 | Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 163, in prepare_job
job_wrapper.prepare()
File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 862, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_ev... | ValueError |
def execute(
self,
cmd,
persist=False,
timeout=DEFAULT_TIMEOUT,
timeout_check_interval=DEFAULT_TIMEOUT_CHECK_INTERVAL,
**kwds,
):
is_cmd_string = isinstance(cmd, six.string_types)
outf = TemporaryFile()
p = Popen(cmd, stdin=None, stdout=outf, stderr=PIPE, shell=is_cmd_string)
# p... | def execute(
self,
cmd,
persist=False,
timeout=DEFAULT_TIMEOUT,
timeout_check_interval=DEFAULT_TIMEOUT_CHECK_INTERVAL,
**kwds,
):
outf = TemporaryFile()
p = Popen(cmd, stdin=None, stdout=outf, stderr=PIPE)
# poll until timeout
for i in range(int(timeout / timeout_check_interval)... | https://github.com/galaxyproject/galaxy/issues/7269 | galaxy.jobs.runners.cli DEBUG 2019-01-25 19:13:53,789 [p:3868,w:1,m:0] [ShellRunner.work_thread-0] (5) submitting file: /opt/galaxy/database/jobs_directory/000/5/galaxy_5.s
h
galaxy.jobs.runners ERROR 2019-01-25 19:13:53,964 [p:3868,w:1,m:0] [ShellRunner.work_thread-0] (5) Unhandled exception calling queue_job
Tracebac... | OSError |
def top_level_workflow(self):
"""If this workflow is not attached to stored workflow directly,
recursively grab its parents until it is the top level workflow
which must have a stored workflow associated with it.
"""
top_level_workflow = self
if self.stored_workflow is None:
# TODO: enfo... | def top_level_workflow(self):
"""If this workflow is not attached to stored workflow directly,
recursively grab its parents until it is the top level workflow
which must have a stored workflow associated with it.
"""
top_level_workflow = self
if self.stored_workflow is None:
# TODO: enfo... | https://github.com/galaxyproject/galaxy/issues/7261 | Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 545, in update
**from_dict_kwds
File "/Users/mvandenb/src/galax... | AssertionError |
def update_permissions(self, trans, dataset_id, payload, **kwd):
"""
PUT /api/datasets/{encoded_dataset_id}/permissions
Updates permissions of a dataset.
:rtype: dict
:returns: dictionary containing new permissions
"""
if payload:
kwd.update(payload)
hda_ldda = kwd.get("hd... | def update_permissions(self, trans, dataset_id, payload, **kwd):
"""
PUT /api/datasets/{encoded_dataset_id}/permissions
Updates permissions of a dataset.
:rtype: dict
:returns: dictionary containing new permissions
"""
if payload:
kwd.update(payload)
hda_ldda = kwd.get("hd... | https://github.com/galaxyproject/galaxy/issues/7108 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/library_datasets.py", line 125, in show_roles return self._get_current_roles(trans, library_dataset)
File "lib/galaxy/webapps/gala... | AttributeError |
def _get_current_roles(self, trans, library_dataset):
"""
Find all roles currently connected to relevant permissions
on the library dataset and the underlying dataset.
:param library_dataset: the model object
:type library_dataset: LibraryDataset
:rtype: dictionary
:return... | def _get_current_roles(self, trans, library_dataset):
"""
Find all roles currently connected to relevant permissions
on the library dataset and the underlying dataset.
:param library_dataset: the model object
:type library_dataset: LibraryDataset
:rtype: dictionary
:return... | https://github.com/galaxyproject/galaxy/issues/7108 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/galaxy/api/library_datasets.py", line 125, in show_roles return self._get_current_roles(trans, library_dataset)
File "lib/galaxy/webapps/gala... | AttributeError |
def process_key(incoming_key, incoming_value, d):
key_parts = incoming_key.split("|")
if len(key_parts) == 1:
# Regular parameter
d[incoming_key] = incoming_value
elif key_parts[0].rsplit("_", 1)[-1].isdigit():
# Repeat
input_name_index = key_parts[0].rsplit("_", 1)
i... | def process_key(incoming_key, d):
key_parts = incoming_key.split("|")
if len(key_parts) == 1:
# Regular parameter
d[incoming_key] = object()
elif key_parts[0].rsplit("_", 1)[-1].isdigit():
# Repeat
input_name_index = key_parts[0].rsplit("_", 1)
input_name, index = inp... | https://github.com/galaxyproject/galaxy/issues/7048 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 418, in create
return self._create(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 476, in _cr... | AttributeError |
def expand_meta_parameters(trans, tool, incoming):
"""
Take in a dictionary of raw incoming parameters and expand to a list
of expanded incoming parameters (one set of parameters per tool
execution).
"""
to_remove = []
for key in incoming.keys():
if key.endswith("|__identifier__"):
... | def expand_meta_parameters(trans, tool, incoming):
"""
Take in a dictionary of raw incoming parameters and expand to a list
of expanded incoming parameters (one set of parameters per tool
execution).
"""
to_remove = []
for key in incoming.keys():
if key.endswith("|__identifier__"):
... | https://github.com/galaxyproject/galaxy/issues/7048 | Traceback (most recent call last):
File "lib/galaxy/web/framework/decorators.py", line 283, in decorator
rval = func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 418, in create
return self._create(trans, payload, **kwd)
File "lib/galaxy/webapps/galaxy/api/tools.py", line 476, in _cr... | AttributeError |
def get_private_user_role(self, user, auto_create=False):
role = (
self.sa_session.query(self.model.Role)
.filter(
and_(
self.model.UserRoleAssociation.table.c.user_id == user.id,
self.model.Role.table.c.id
== self.model.UserRoleAssociation... | def get_private_user_role(self, user, auto_create=False):
role = (
self.sa_session.query(self.model.Role)
.filter(
and_(
self.model.Role.table.c.name == user.email,
self.model.Role.table.c.type == self.model.Role.types.PRIVATE,
)
)
... | https://github.com/galaxyproject/galaxy/issues/6756 | galaxy.web.framework.decorators ERROR 2018-09-21 22:02:02,371 [p:10163,w:3,m:0] [uWSGIWorker3Core1] Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/work/project/w4m/galaxy4metabolomics/galaxy/lib/galaxy/web/framework/decorators.py", line 154, in decorator
rval = func(self, trans, *ar... | AttributeError |
def __init__(
self,
config_file,
tool_source,
app,
guid=None,
repository_id=None,
allow_code_files=True,
):
"""Load a tool from the config named by `config_file`"""
# Determine the full path of the directory where the tool config is
self.config_file = config_file
self.tool_di... | def __init__(
self,
config_file,
tool_source,
app,
guid=None,
repository_id=None,
allow_code_files=True,
):
"""Load a tool from the config named by `config_file`"""
# Determine the full path of the directory where the tool config is
self.config_file = config_file
self.tool_di... | https://github.com/galaxyproject/galaxy/issues/6584 | galaxy.tools.toolbox.base INFO 2018-08-09 10:57:04,513 Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpicezz6xb/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2018-08-09 10:57:04,519 Error reading tool from path: /Users/mvandenb/src/tools-iuc/tools/fastp/fastp.xml
Traceback (mo... | KeyError |
def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
"""
Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
"""
history_id = kwd.get("history_id", None)
history = None
if (
workflow_building_mode is workflow_building_modes.U... | def to_json(self, trans, kwd={}, job=None, workflow_building_mode=False):
"""
Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
"""
history_id = kwd.get("history_id", None)
history = None
if (
workflow_building_mode is workflow_building_modes.U... | https://github.com/galaxyproject/galaxy/issues/6584 | galaxy.tools.toolbox.base INFO 2018-08-09 10:57:04,513 Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpicezz6xb/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2018-08-09 10:57:04,519 Error reading tool from path: /Users/mvandenb/src/tools-iuc/tools/fastp/fastp.xml
Traceback (mo... | KeyError |
def __init__(self):
self._hash_by_tool_paths = {}
self._tools_by_path = {}
self._tool_paths_by_id = {}
self._macro_paths_by_id = {}
self._tool_ids_by_macro_paths = {}
self._mod_time_by_path = {}
self._new_tool_ids = set()
self._removed_tool_ids = set()
self._removed_tools_by_path = {... | def __init__(self):
self._hash_by_tool_paths = {}
self._tools_by_path = {}
self._tool_paths_by_id = {}
self._macro_paths_by_id = {}
self._tool_ids_by_macro_paths = {}
self._mod_time_by_path = {}
self._new_tool_ids = set()
self._removed_tool_ids = set()
| https://github.com/galaxyproject/galaxy/issues/6584 | galaxy.tools.toolbox.base INFO 2018-08-09 10:57:04,513 Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpicezz6xb/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2018-08-09 10:57:04,519 Error reading tool from path: /Users/mvandenb/src/tools-iuc/tools/fastp/fastp.xml
Traceback (mo... | KeyError |
def cleanup(self):
"""
Remove uninstalled tools from tool cache if they are not on disk anymore or if their content has changed.
Returns list of tool_ids that have been removed.
"""
removed_tool_ids = []
try:
paths_to_cleanup = {
path: tool.all_ids
for path, tool... | def cleanup(self):
"""
Remove uninstalled tools from tool cache if they are not on disk anymore or if their content has changed.
Returns list of tool_ids that have been removed.
"""
removed_tool_ids = []
try:
paths_to_cleanup = {
path: tool.all_ids
for path, tool... | https://github.com/galaxyproject/galaxy/issues/6584 | galaxy.tools.toolbox.base INFO 2018-08-09 10:57:04,513 Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpicezz6xb/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2018-08-09 10:57:04,519 Error reading tool from path: /Users/mvandenb/src/tools-iuc/tools/fastp/fastp.xml
Traceback (mo... | KeyError |
def reset_status(self):
"""
Reset tracking of new and newly disabled tools.
"""
self._new_tool_ids = set()
self._removed_tool_ids = set()
self._removed_tools_by_path = {}
| def reset_status(self):
"""Reset self._new_tool_ids and self._removed_tool_ids once
all operations that need to know about new tools have finished running."""
self._new_tool_ids = set()
self._removed_tool_ids = set()
| https://github.com/galaxyproject/galaxy/issues/6584 | galaxy.tools.toolbox.base INFO 2018-08-09 10:57:04,513 Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmpicezz6xb/tool_conf.xml
galaxy.tools.toolbox.base ERROR 2018-08-09 10:57:04,519 Error reading tool from path: /Users/mvandenb/src/tools-iuc/tools/fastp/fastp.xml
Traceback (mo... | KeyError |
def to_dict(self, view="collection", value_mapper=None, app=None):
as_dict = super(ToolOutput, self).to_dict(
view=view, value_mapper=value_mapper, app=app
)
format = self.format
if format and format != "input" and app:
edam_format = app.datatypes_registry.edam_formats.get(self.format)
... | def to_dict(self, view="collection", value_mapper=None, app=None):
as_dict = super(ToolOutput, self).to_dict(view=view, value_mapper=value_mapper)
format = self.format
if format and format != "input" and app:
edam_format = app.datatypes_registry.edam_formats.get(self.format)
as_dict["edam_fo... | https://github.com/galaxyproject/galaxy/issues/6537 | gi.tools.show_tool(tool_id, io_details = True)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/path/to/bioblend/galaxy/tools/__init__.py", line 98, in show_tool
return self._get(id=tool_id, params=params)
File "/path/to/bioblend/galaxy/client.py", line 136, in _get
status_code=r.status_cod... | bioblend.ConnectionError |
def sliced_input_collection_structure(self, input_name):
unqualified_recurse = self.tool.profile < 18.09 and "|" not in input_name
def find_collection(input_dict, input_name):
for key, value in input_dict.items():
if key == input_name:
return value
if isinstance(... | def sliced_input_collection_structure(self, input_name):
input_collection = self.example_params[input_name]
collection_type_description = self.trans.app.dataset_collections_service.collection_type_descriptions.for_collection_type(
input_collection.collection.collection_type
)
subcollection_mappi... | https://github.com/galaxyproject/galaxy/issues/6157 | 127.0.0.1 - - [16/May/2018:23:42:03 +0100] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/sickle/sickle/1.33.1/build HTTP/1.1" 200 - "http://127.0.0.1:8080/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsickle%2Fsickle%2F1.33.1&version=1.33.1&__identifer=eqdjaao7u85" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;... | KeyError |
def add_file(dataset, registry, output_path):
ext = None
compression_type = None
line_count = None
converted_path = None
stdout = None
link_data_only_str = dataset.get("link_data_only", "copy_files")
if link_data_only_str not in ["link_to_files", "copy_files"]:
raise UploadProblemExc... | def add_file(dataset, registry, output_path):
ext = None
compression_type = None
line_count = None
converted_path = None
stdout = None
link_data_only_str = dataset.get("link_data_only", "copy_files")
if link_data_only_str not in ["link_to_files", "copy_files"]:
raise UploadProblemExc... | https://github.com/galaxyproject/galaxy/issues/5915 | Fatal error: Exit code 1 ()
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/tools/data_source/upload.py", line 321, in <module>
__main__()
File "/Users/mvandenb/src/galaxy/tools/data_source/upload.py", line 314, in __main__
metadata.append(add_file(dataset, registry, output_path))
File "/Users/mvand... | AttributeError |
def copy_sample_file(app, filename, dest_path=None):
"""
Copies a sample file at `filename` to `the dest_path`
directory and strips the '.sample' extensions from `filename`.
Returns the path to the copied file (with the .sample extension).
"""
if dest_path is None:
dest_path = os.path.ab... | def copy_sample_file(app, filename, dest_path=None):
"""
Copies a sample file at `filename` to `the dest_path`
directory and strips the '.sample' extensions from `filename`.
"""
if dest_path is None:
dest_path = os.path.abspath(app.config.tool_data_path)
sample_file_name = basic_util.str... | https://github.com/galaxyproject/galaxy/issues/5648 | galaxy.tools.data WARNING 2018-03-06 20:31:23,419 [p:121,w:1,m:0] [uWSGIWorker1Core2] Cannot find index file '/export/galaxy-central/database/files/tmp-toolshed-gmfcr9qbPdD/bowtie2_indices.loc' for tool data table 'bowtie2_indexes'
galaxy.tools.data DEBUG 2018-03-06 20:31:23,419 [p:121,w:1,m:0] [uWSGIWorker1Core2] Load... | IOError |
def handle_missing_index_file(
app, tool_path, sample_files, repository_tools_tups, sample_files_copied
):
"""
Inspect each tool to see if it has any input parameters that are dynamically
generated select lists that depend on a .loc file. This method is not called
from the tool shed, but from Galax... | def handle_missing_index_file(
app, tool_path, sample_files, repository_tools_tups, sample_files_copied
):
"""
Inspect each tool to see if it has any input parameters that are dynamically
generated select lists that depend on a .loc file. This method is not called
from the tool shed, but from Galax... | https://github.com/galaxyproject/galaxy/issues/5648 | galaxy.tools.data WARNING 2018-03-06 20:31:23,419 [p:121,w:1,m:0] [uWSGIWorker1Core2] Cannot find index file '/export/galaxy-central/database/files/tmp-toolshed-gmfcr9qbPdD/bowtie2_indices.loc' for tool data table 'bowtie2_indexes'
galaxy.tools.data DEBUG 2018-03-06 20:31:23,419 [p:121,w:1,m:0] [uWSGIWorker1Core2] Load... | IOError |
def __link_file_check(self):
"""outputs_to_working_directory breaks library uploads where data is
linked. This method is a hack that solves that problem, but is
specific to the upload tool and relies on an injected job param. This
method should be removed ASAP and replaced with some properly generic
... | def __link_file_check(self):
"""outputs_to_working_directory breaks library uploads where data is
linked. This method is a hack that solves that problem, but is
specific to the upload tool and relies on an injected job param. This
method should be removed ASAP and replaced with some properly generic
... | https://github.com/galaxyproject/galaxy/issues/5424 | galaxy.jobs.handler WARNING 2018-01-31 15:36:15,704 (78691) Tool 'motifgen-fasta_1' removed from tool config, unable to recover job
galaxy.jobs DEBUG 2018-01-31 15:36:15,705 (78691) Working directory for job is: /tools/galaxy_ratschlab/database/job_working_directory/078/78691
Traceback (most recent call last):
File "/t... | AttributeError |
def _write_integrated_tool_panel_config_file(self):
"""
Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators
use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
"""
tracking_directory... | def _write_integrated_tool_panel_config_file(self):
"""
Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators
use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right.
"""
tracking_directory... | https://github.com/galaxyproject/galaxy/issues/5031 | Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "lib/galaxy/tools/toolbox/watcher.py", line 138, in ... | OSError |
def guess_shed_config(self, app, default=None):
tool_ids = []
metadata = self.metadata or {}
for tool in metadata.get("tools", []):
tool_ids.append(tool.get("guid"))
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
include_migrated_tool_conf=True
):
name = shed_tool_conf... | def guess_shed_config(self, app, default=None):
tool_ids = []
metadata = self.metadata or {}
for tool in metadata.get("tools", []):
tool_ids.append(tool.get("guid"))
for shed_tool_conf_dict in app.toolbox.dynamic_confs(
include_migrated_tool_conf=True
):
name = shed_tool_conf... | https://github.com/galaxyproject/galaxy/issues/5031 | Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "lib/galaxy/tools/toolbox/watcher.py", line 138, in ... | OSError |
def to_xml_file(self, shed_tool_data_table_config, new_elems=None, remove_elems=None):
"""
Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.
remove_elems are removed before new_elems are added.
"""
if not (new_elems or remove_elems):
log.debug(
... | def to_xml_file(self, shed_tool_data_table_config, new_elems=None, remove_elems=None):
"""
Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.
remove_elems are removed before new_elems are added.
"""
if not (new_elems or remove_elems):
log.debug(
... | https://github.com/galaxyproject/galaxy/issues/5031 | Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "lib/galaxy/tools/toolbox/watcher.py", line 138, in ... | OSError |
def pause(self, job=None, message=None):
if job is None:
job = self.get_job()
if message is None:
message = "Execution of this dataset's job is paused"
if job.state == job.states.NEW:
for dataset_assoc in job.output_datasets + job.output_library_datasets:
dataset_assoc.da... | def pause(self, job=None, message=None):
if job is None:
job = self.get_job()
if message is None:
message = "Execution of this dataset's job is paused"
if job.state == job.states.NEW:
for dataset_assoc in job.output_datasets + job.output_library_datasets:
dataset_assoc.da... | https://github.com/galaxyproject/galaxy/issues/5222 | galaxy.jobs.handler DEBUG 2017-12-15 09:04:34,777 (3332) Dispatching to slurm runner
galaxy.jobs DEBUG 2017-12-15 09:04:34,808 (3332) Persisting job destination (destination id: cluster16c40)
galaxy.jobs.runners DEBUG 2017-12-15 09:04:34,815 Job [3332] queued (37.893 ms)
galaxy.jobs.handler INFO 2017-12-15 09:04:34,822... | ValueError |
def execute(
self,
tool,
trans,
incoming={},
return_job=False,
set_output_hid=True,
history=None,
job_params=None,
rerun_remap_job_id=None,
execution_cache=None,
dataset_collection_elements=None,
):
"""
Executes a tool, creating job and tool outputs, associating them,... | def execute(
self,
tool,
trans,
incoming={},
return_job=False,
set_output_hid=True,
history=None,
job_params=None,
rerun_remap_job_id=None,
execution_cache=None,
dataset_collection_elements=None,
):
"""
Executes a tool, creating job and tool outputs, associating them,... | https://github.com/galaxyproject/galaxy/issues/5222 | galaxy.jobs.handler DEBUG 2017-12-15 09:04:34,777 (3332) Dispatching to slurm runner
galaxy.jobs DEBUG 2017-12-15 09:04:34,808 (3332) Persisting job destination (destination id: cluster16c40)
galaxy.jobs.runners DEBUG 2017-12-15 09:04:34,815 Job [3332] queued (37.893 ms)
galaxy.jobs.handler INFO 2017-12-15 09:04:34,822... | ValueError |
def shutdown(self):
self.watchers.shutdown()
self.workflow_scheduling_manager.shutdown()
self.job_manager.shutdown()
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
self.update_repository_manager.shutdown()
try:
self.control_worker.shutdown()
exc... | def shutdown(self):
self.workflow_scheduling_manager.shutdown()
self.job_manager.shutdown()
self.object_store.shutdown()
if self.heartbeat:
self.heartbeat.shutdown()
self.update_repository_manager.shutdown()
try:
self.control_worker.shutdown()
except AttributeError:
#... | https://github.com/galaxyproject/galaxy/issues/4738 | galaxy.tools.deps.installable WARNING 2017-10-03 12:25:28,961 Conda not installed and auto-installation disabled.
galaxy.tools.deps.installable WARNING 2017-10-03 12:25:29,016 Conda not installed and auto-installation disabled.
galaxy.datatypes.registry DEBUG 2017-10-03 12:25:29,034 Loaded external metadata tool: __SET... | IOError |
def create(
self,
trans,
parent,
name,
collection_type,
element_identifiers=None,
elements=None,
implicit_collection_info=None,
trusted_identifiers=None,
hide_source_items=False,
tags=None,
):
"""
PRECONDITION: security checks on ability to add to parent
occurred ... | def create(
self,
trans,
parent,
name,
collection_type,
element_identifiers=None,
elements=None,
implicit_collection_info=None,
trusted_identifiers=None,
hide_source_items=False,
tags=None,
):
"""
PRECONDITION: security checks on ability to add to parent
occurred ... | https://github.com/galaxyproject/galaxy/issues/4975 | galaxy.tools.actions INFO 2017-11-10 17:17:20,507 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3] (39.007 ms)
galaxy.tools.actions INFO 2017-11-10 17:17:20,511 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/htse... | KeyError |
def copy(self, cls=None):
if cls:
new_ta = cls()
else:
new_ta = type(self)()
new_ta.tag_id = self.tag_id
new_ta.user_tname = self.user_tname
new_ta.value = self.value
new_ta.user_value = self.user_value
return new_ta
| def copy(self):
new_ta = type(self)()
new_ta.tag_id = self.tag_id
new_ta.user_tname = self.user_tname
new_ta.value = self.value
new_ta.user_value = self.user_value
return new_ta
| https://github.com/galaxyproject/galaxy/issues/4975 | galaxy.tools.actions INFO 2017-11-10 17:17:20,507 Verified access to datasets for Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.6.1galaxy3] (39.007 ms)
galaxy.tools.actions INFO 2017-11-10 17:17:20,511 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/htse... | KeyError |
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