lhhunghimself
commented
1 year ago Save the workflow first and then run. You are running from a symlink which is locked after you ran it for some reason. If you make a copy first, this is no longer a problem.
Hong
On Fri, Apr 21, 2023 at 9:11 PM karenangella @.***> wrote:
I was running the base jupyter notebook widget on AWS ec2 m5.xlarge. It opens the jupyter notebook windows just fine and I stopped the widget from running. But when I tried to save the workflow that contains the jupyter notebook, it gives me this errors:
Exception: shutil.Error: [('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', "[Errno 2] No such file or directory: '/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")] Module: shutil:365 Widget Scheme: /tmp/ows-h1fzkkx1.ows.xml Version: 3.14.0.dev0+Unknown Environment: Python 3.6.9 on Linux 6.1.23-36.46.amzn2023.x86_64 #1 https://github.com/BioDepot/BioDepot-workflow-builder/pull/1 SMP PREEMPT_DYNAMIC Mon Apr 10 22:43:13 UTC 2023 x86_64 Installed Packages: AnyQt==0.2.0, Bottleneck==1.3.6, CommonMark==0.7.5, Jupyter==0.0.0, Miscellaneous==0.0.0, Orange3==3.14.0.dev0+unknown, RNA-seq==0.0.0, Scripting==0.0.0, SecretStorage==2.3.1, User==0.0.0, Utilities==0.0.0, asn1crypto==0.24.0, beautifulsoup4==4.11.2, certifi==2022.12.7, chardet==5.0.0, charset-normalizer==2.0.12, cryptography==2.1.4, docker==5.0.3, docutils==0.18.1, future==0.18.3, idna==2.6, importlib-metadata==4.8.3, joblib==1.1.1, jsonpickle==2.2.0, keyring==10.6.0, keyrings.alt==3.0, numpy==1.19.5, pip==20.0.1, pycrypto==2.6.1, pygobject==3.26.1, pyqtgraph==0.11.1, pysam==0.20.0, pyxdg==0.25, requests==2.27.1, scikit-learn==0.24.2, scipy==1.5.4, serverfiles==0.3.1, setuptools==59.6.0, six==1.11.0, soupsieve==2.3.2.post1, threadpoolctl==3.1.0, typing-extensions==4.1.1, urllib3==1.26.14, websocket-client==1.3.1, wheel==0.37.1, xlrd==2.0.1, zipp==3.6.0 Machine ID: 2485377892354 Stack Trace: Traceback (most recent call last): File "/orange3/Orange/canvas/application/canvasmain.py", line 1608, in save_scheme_as iconFile=self.saveWorkflowSettings["icon"], File "/coreutils/workflowTools.py", line 325, in exportWorkflow shutil.copytree(widgetPath, uniquePath) File "/usr/lib/python3.6/shutil.py", line 365, in copytree raise Error(errors) shutil.Error: [('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', "[Errno 2] No such file or directory: '/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")]
Local Variables: OrderedDict([('copy_function', <function copy2 at 0x7f9b3c6d0bf8>), ('dst', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base'), ('dstname', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/jupyter_base.states'), ('errors',
[('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock',
'/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '[Errno 2] No such file or directory: '
"'/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")]), ('ignore', None), ('ignore_dangling_symlinks', False), ('ignored_names', set()), ('name', 'jupyter_base.states'), ('names', ['Dockerfiles', 'icon', 'jupyter_base.attrs', 'jupyter_base.json', 'jupyter_base.py', 'jupyter_base.states']), ('src', '/widgets/Jupyter/jupyter_base'), ('srcname', '/widgets/Jupyter/jupyter_base/jupyter_base.states'), ('symlinks', False)])
[image: Screen Shot 2023-04-21 at 8 58 12 PM] https://user-images.githubusercontent.com/55929761/233761624-916b532d-801e-4524-aeee-202c03966393.png
— Reply to this email directly, view it on GitHub https://github.com/BioDepot/BioDepot-workflow-builder/issues/59, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPY22KLFQGUKII6HLRFDITXCNK7FANCNFSM6AAAAAAXHSGH3I . You are receiving this because you are subscribed to this thread.Message ID: @.***>
I was running the base jupyter notebook widget on AWS ec2 m5.xlarge. It opens the jupyter notebook windows just fine and I stopped the widget from running. But when I tried to save the workflow that contains the jupyter notebook, it gives me this errors:
Exception: shutil.Error: [('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', "[Errno 2] No such file or directory: '/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")] Module: shutil:365 Widget Scheme: /tmp/ows-h1fzkkx1.ows.xml Version: 3.14.0.dev0+Unknown Environment: Python 3.6.9 on Linux 6.1.23-36.46.amzn2023.x86_64 #1 SMP PREEMPT_DYNAMIC Mon Apr 10 22:43:13 UTC 2023 x86_64 Installed Packages: AnyQt==0.2.0, Bottleneck==1.3.6, CommonMark==0.7.5, Jupyter==0.0.0, Miscellaneous==0.0.0, Orange3==3.14.0.dev0+unknown, RNA-seq==0.0.0, Scripting==0.0.0, SecretStorage==2.3.1, User==0.0.0, Utilities==0.0.0, asn1crypto==0.24.0, beautifulsoup4==4.11.2, certifi==2022.12.7, chardet==5.0.0, charset-normalizer==2.0.12, cryptography==2.1.4, docker==5.0.3, docutils==0.18.1, future==0.18.3, idna==2.6, importlib-metadata==4.8.3, joblib==1.1.1, jsonpickle==2.2.0, keyring==10.6.0, keyrings.alt==3.0, numpy==1.19.5, pip==20.0.1, pycrypto==2.6.1, pygobject==3.26.1, pyqtgraph==0.11.1, pysam==0.20.0, pyxdg==0.25, requests==2.27.1, scikit-learn==0.24.2, scipy==1.5.4, serverfiles==0.3.1, setuptools==59.6.0, six==1.11.0, soupsieve==2.3.2.post1, threadpoolctl==3.1.0, typing-extensions==4.1.1, urllib3==1.26.14, websocket-client==1.3.1, wheel==0.37.1, xlrd==2.0.1, zipp==3.6.0 Machine ID: 2485377892354 Stack Trace: Traceback (most recent call last): File "/orange3/Orange/canvas/application/canvasmain.py", line 1608, in save_scheme_as iconFile=self.saveWorkflowSettings["icon"], File "/coreutils/workflowTools.py", line 325, in exportWorkflow shutil.copytree(widgetPath, uniquePath) File "/usr/lib/python3.6/shutil.py", line 365, in copytree raise Error(errors) shutil.Error: [('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', "[Errno 2] No such file or directory: '/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")]
Local Variables: OrderedDict([('copy_function', <function copy2 at 0x7f9b3c6d0bf8>), ('dst', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base'), ('dstname', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/jupyter_base.states'), ('errors', [('/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '/tmp/tmp21bp4vc0/widgets/seurat/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock', '[Errno 2] No such file or directory: ' "'/widgets/Jupyter/jupyter_base/Dockerfiles/.mozilla/firefox/6v20d6ix.default-release/lock'")]), ('ignore', None), ('ignore_dangling_symlinks', False), ('ignored_names', set()), ('name', 'jupyter_base.states'), ('names', ['Dockerfiles', 'icon', 'jupyter_base.attrs', 'jupyter_base.json', 'jupyter_base.py', 'jupyter_base.states']), ('src', '/widgets/Jupyter/jupyter_base'), ('srcname', '/widgets/Jupyter/jupyter_base/jupyter_base.states'), ('symlinks', False)])