tcompa
commented
10 months ago Example 02 fails with this traceback
<nav class="bg-light border-bottom"><div class="container d-flex flex-wrap"><ul class="nav me-auto"><li class="nav-item"><a href="http://localhost:5173/" class="nav-link">Home</a></li> <li class="nav-item"><a href="http://localhost:5173/projects" class="nav-link">Projects</a></li> <li class="nav-item"><a href="http://localhost:5173/tasks" class="nav-link">Tasks</a></li></ul> <ul class="nav"><span class="navbar-text">admin@fractal.xy</span> <li class="nav-item"><a href="http://localhost:5173/auth/logout" class="nav-link">Logout</a></li></ul></div></nav> <div class="container p-4"><div class="d-flex justify-content-between align-items-center"><nav aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item" aria-current="page"><a href="http://localhost:5173/projects">Projects</a></li> <li class="breadcrumb-item" aria-current="page"><a href="http://localhost:5173/projects/2">proj-cardio-2x2-zenodo-subset-1</a></li> <li class="breadcrumb-item active" aria-current="page">Jobs</li></ol></nav> <div></div></div> <div class="container"><div class="d-flex justify-content-between align-items-center my-3"><h1>Project's Jobs</h1></div> <div class="d-flex justify-content-end align-items-center my-3"><div></div></div></div></div> <div id="jobUpdatesError"></div>
Id ⇅ | Start ⇅ | End ⇅ | Workflow ⇅ | Input dataset ⇅ | Output dataset ⇅ | Status ⇅ | Options
-- | -- | -- | -- | -- | -- | -- | --
<div class="modal show" id="workflowJobLogsModal" tabindex="-1" style="display: block;" aria-modal="true" role="dialog"><div class="modal-dialog modal-fullscreen"><div class="modal-content"><div class="modal-header"><h1 class="h5 modal-title">Workflow Job logs</h1> </div></div></div></div><div class="modal-body bg-tertiary text-secondary"><div id="workflowJobLogsError"></div> <pre>TASK ERROR:Task id: 16 (Napari workflows wrapper), e.workflow_task_order=9
TRACEBACK:
2023-10-13 09:24:47,505; INFO; START napari_workflows_wrapper task
WARNING: Could not load OpenGL library.
2023-10-13 09:24:47,617; WARNING; Could not load OpenGL library.
/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_tools_menu/__init__.py:10: UserWarning: Importing QT failed; now introducing dummy definitions of QMenu class and register_function decorator.
warnings.warn("Importing QT failed; now introducing dummy definitions of QMenu class and register_function decorator.")
/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_tools_menu/__init__.py:221: UserWarning: Error in monkey patching napari. Please let @haesleinleinhuepf know at
https://github.com/haesleinhuepf/napari-tools-menu/issues
warnings.warn("Error in monkey patching napari. Please let @haesleinleinhuepf know at\nhttps://github.com/haesleinhuepf/napari-tools-menu/issues")
Traceback (most recent call last):
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/napari_workflows_wrapper.py", line 655, in <module>
run_fractal_task(
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
metadata_update = task_function(**pars)
^^^^^^^^^^^^^^^^^^^^^
File "pydantic/decorator.py", line 40, in pydantic.decorator.validate_arguments.validate.wrapper_function
from contextlib import _GeneratorContextManager
File "pydantic/decorator.py", line 134, in pydantic.decorator.ValidatedFunction.call
File "pydantic/decorator.py", line 206, in pydantic.decorator.ValidatedFunction.execute
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/napari_workflows_wrapper.py", line 141, in napari_workflows_wrapper
wf: napari_workflows.Worfklow = load_workflow(workflow_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_workflows/_io_yaml_v1.py", line 36, in load_workflow
return unsafe_load(stream)
^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/__init__.py", line 145, in unsafe_load
return load(stream, UnsafeLoader)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/__init__.py", line 81, in load
return loader.get_single_data()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 51, in get_single_data
return self.construct_document(node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 60, in construct_document
for dummy in generator:
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 413, in construct_yaml_map
value = self.construct_mapping(node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 218, in construct_mapping
return super().construct_mapping(node, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 143, in construct_mapping
value = self.construct_object(value_node, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 100, in construct_object
data = constructor(self, node)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 523, in construct_python_tuple
return tuple(self.construct_sequence(node))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 129, in construct_sequence
return [self.construct_object(child, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 129, in <listcomp>
return [self.construct_object(child, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 102, in construct_object
data = constructor(self, tag_suffix, node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 570, in construct_python_name
return self.find_python_name(suffix, node.start_mark)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 719, in find_python_name
return super(UnsafeConstructor, self).find_python_name(name, mark, unsafe=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 551, in find_python_name
__import__(module_name)
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_segment_blobs_and_things_with_membranes/__init__.py", line 23, in <module>
from napari_time_slicer import time_slicer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_time_slicer/__init__.py", line 4, in <module>
from ._function import napari_experimental_provide_function
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_time_slicer/_function.py", line 7, in <module>
from napari.layers import Image, Labels, Layer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/__init__.py", line 9, in <module>
from napari.layers.base import Layer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/base/__init__.py", line 1, in <module>
from napari.layers.base._base_constants import ActionType
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/base/_base_constants.py", line 4, in <module>
from napari.utils.misc import StringEnum
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/__init__.py", line 2, in <module>
from napari.utils.colormaps import Colormap
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/__init__.py", line 2, in <module>
from napari.utils.colormaps.colormap import Colormap
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/colormap.py", line 7, in <module>
from napari.utils.color import ColorArray
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/color.py", line 7, in <module>
from napari.utils.colormaps.standardize_color import transform_color
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/standardize_color.py", line 27, in <module>
from vispy.color import ColorArray, get_color_dict, get_color_names
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/color/__init__.py", line 12, in <module>
from .colormap import (Colormap, BaseColormap, # noqa
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/color/colormap.py", line 14, in <module>
import vispy.gloo
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/__init__.py", line 47, in <module>
from . import gl # noqa
^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/gl/__init__.py", line 230, in <module>
from . import es2 as default_backend # noqa
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/gl/es2.py", line 48, in <module>
raise OSError('GL ES 2.0 library not found')
OSError: GL ES 2.0 library not found
</pre></div>[Home](http://localhost:5173/)
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[proj-cardio-2x2-zenodo-subset-1](http://localhost:5173/projects/2)
Jobs
Project's Jobs
Id ⇅ Start ⇅ End ⇅ Workflow ⇅ Input dataset ⇅ Output dataset ⇅ Status ⇅ Options
2 13/10/2023, 11:20:36 13/10/2023, 11:24:48 Workflow cardio-2x2-zenodo-subset-1 input-ds-cardio-2x2-zenodo-subset-1 output-ds-cardio-2x2-zenodo-subset-1 failed
Workflow Job logs
TASK ERROR:Task id: 16 (Napari workflows wrapper), e.workflow_task_order=9
TRACEBACK:
2023-10-13 09:24:47,505; INFO; START napari_workflows_wrapper task
WARNING: Could not load OpenGL library.
2023-10-13 09:24:47,617; WARNING; Could not load OpenGL library.
/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_tools_menu/__init__.py:10: UserWarning: Importing QT failed; now introducing dummy definitions of QMenu class and register_function decorator.
warnings.warn("Importing QT failed; now introducing dummy definitions of QMenu class and register_function decorator.")
/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_tools_menu/__init__.py:221: UserWarning: Error in monkey patching napari. Please let @haesleinleinhuepf know at
https://github.com/haesleinhuepf/napari-tools-menu/issues
warnings.warn("Error in monkey patching napari. Please let @haesleinleinhuepf know at\nhttps://github.com/haesleinhuepf/napari-tools-menu/issues")
Traceback (most recent call last):
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/napari_workflows_wrapper.py", line 655, in <module>
run_fractal_task(
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
metadata_update = task_function(**pars)
^^^^^^^^^^^^^^^^^^^^^
File "pydantic/decorator.py", line 40, in pydantic.decorator.validate_arguments.validate.wrapper_function
from contextlib import _GeneratorContextManager
File "pydantic/decorator.py", line 134, in pydantic.decorator.ValidatedFunction.call
File "pydantic/decorator.py", line 206, in pydantic.decorator.ValidatedFunction.execute
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/fractal_tasks_core/tasks/napari_workflows_wrapper.py", line 141, in napari_workflows_wrapper
wf: napari_workflows.Worfklow = load_workflow(workflow_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_workflows/_io_yaml_v1.py", line 36, in load_workflow
return unsafe_load(stream)
^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/__init__.py", line 145, in unsafe_load
return load(stream, UnsafeLoader)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/__init__.py", line 81, in load
return loader.get_single_data()
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 51, in get_single_data
return self.construct_document(node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 60, in construct_document
for dummy in generator:
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 413, in construct_yaml_map
value = self.construct_mapping(node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 218, in construct_mapping
return super().construct_mapping(node, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 143, in construct_mapping
value = self.construct_object(value_node, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 100, in construct_object
data = constructor(self, node)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 523, in construct_python_tuple
return tuple(self.construct_sequence(node))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 129, in construct_sequence
return [self.construct_object(child, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 129, in <listcomp>
return [self.construct_object(child, deep=deep)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 102, in construct_object
data = constructor(self, tag_suffix, node)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 570, in construct_python_name
return self.find_python_name(suffix, node.start_mark)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 719, in find_python_name
return super(UnsafeConstructor, self).find_python_name(name, mark, unsafe=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/yaml/constructor.py", line 551, in find_python_name
__import__(module_name)
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_segment_blobs_and_things_with_membranes/__init__.py", line 23, in <module>
from napari_time_slicer import time_slicer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_time_slicer/__init__.py", line 4, in <module>
from ._function import napari_experimental_provide_function
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari_time_slicer/_function.py", line 7, in <module>
from napari.layers import Image, Labels, Layer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/__init__.py", line 9, in <module>
from napari.layers.base import Layer
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/base/__init__.py", line 1, in <module>
from napari.layers.base._base_constants import ActionType
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/layers/base/_base_constants.py", line 4, in <module>
from napari.utils.misc import StringEnum
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/__init__.py", line 2, in <module>
from napari.utils.colormaps import Colormap
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/__init__.py", line 2, in <module>
from napari.utils.colormaps.colormap import Colormap
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/colormap.py", line 7, in <module>
from napari.utils.color import ColorArray
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/color.py", line 7, in <module>
from napari.utils.colormaps.standardize_color import transform_color
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/napari/utils/colormaps/standardize_color.py", line 27, in <module>
from vispy.color import ColorArray, get_color_dict, get_color_names
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/color/__init__.py", line 12, in <module>
from .colormap import (Colormap, BaseColormap, # noqa
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/color/colormap.py", line 14, in <module>
import vispy.gloo
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/__init__.py", line 47, in <module>
from . import gl # noqa
^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/gl/__init__.py", line 230, in <module>
from . import es2 as default_backend # noqa
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/fractal_share/tasks/.fractal/fractal_tasks_core0.12.2/venv/lib/python3.11/site-packages/vispy/gloo/gl/es2.py", line 48, in <module>
raise OSError('GL ES 2.0 library not found')
OSError: GL ES 2.0 library not foundI'll now explore whether this is related to fractal-containers or it also happens locally.
closes #23