Comments (8)
@mocsharp
@MMelQin
Yes v0.6 is there a work around till bug is fixed.
from monai-deploy.
mdl-wm | 2023-10-31 09:18:13.2528|20001|ERROR|Monai.Deploy.Storage.MinIO.MinIoStorageService|MessageId=860e66da-f16b-4ceb-8db5-580a43ec03ee, ApplicationId=4c9072a1-35f5-4d85-847d-dafca22244a8, CorrelationId=15d68444-fa6e-4c17-8fa8-e4318ca0ead7, RecievedTime=10/31/2023 09:18:13 System.Collections.Generic.Dictionary2[System.String,System.Object] System.Collections.Generic.Dictionary
2[System.String,System.Object] System.Collections.Generic.Dictionary2[System.String,System.Object]|File '1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/10edc066-56bc-43cf-8cf2-47291ebf3dfc/env_MONAI_OUTPUTPATH' could not be found in 'monaideploy'. mdl-wm | 2023-10-31 09:18:13.2567|700000|DEBUG|Monai.Deploy.WorkflowManager.WorkfowExecuter.Services.WorkflowExecuterService|MessageId=860e66da-f16b-4ceb-8db5-580a43ec03ee, ApplicationId=4c9072a1-35f5-4d85-847d-dafca22244a8, CorrelationId=15d68444-fa6e-4c17-8fa8-e4318ca0ead7, RecievedTime=10/31/2023 09:18:13 System.Collections.Generic.Dictionary
2[System.String,System.Object] System.Collections.Generic.Dictionary2[System.String,System.Object] System.Collections.Generic.Dictionary
2[System.String,System.Object]|Artifact Passed data Artifact {"name":"env_MONAI_OUTPUTPATH","value":"1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/10edc066-56bc-43cf-8cf2-47291ebf3dfc/env_MONAI_OUTPUTPATH","mandatory":true}, Path 1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/10edc066-56bc-43cf-8cf2-47291ebf3dfc/env_MONAI_OUTPUTPATH, ArtifactType Post-Task Output Artifact, Exists False
mdl-wm | 2023-10-31 09:18:13.2601|700004|DEBUG|Monai.Deploy.WorkflowManager.WorkfowExecuter.Services.WorkflowExecuterService|MessageId=860e66da-f16b-4ceb-8db5-580a43ec03ee, ApplicationId=4c9072a1-35f5-4d85-847d-dafca22244a8, CorrelationId=15d68444-fa6e-4c17-8fa8-e4318ca0ead7, RecievedTime=10/31/2023 09:18:13 System.Collections.Generic.Dictionary2[System.String,System.Object] System.Collections.Generic.Dictionary
2[System.String,System.Object] System.Collections.Generic.Dictionary2[System.String,System.Object]|Mandatory output artefacts for task liver are missing. mdl-wm | 2023-10-31 09:18:13.2622|200015|INFO|Monai.Deploy.WorkflowManager.WorkfowExecuter.Services.WorkflowExecuterService|MessageId=860e66da-f16b-4ceb-8db5-580a43ec03ee, ApplicationId=4c9072a1-35f5-4d85-847d-dafca22244a8, CorrelationId=15d68444-fa6e-4c17-8fa8-e4318ca0ead7, RecievedTime=10/31/2023 09:18:13 System.Collections.Generic.Dictionary
2[System.String,System.Object] System.Collections.Generic.Dictionary2[System.String,System.Object] System.Collections.Generic.Dictionary
2[System.String,System.Object]|TaskFailed, Task {"execution_id":"10edc066-56bc-43cf-8cf2-47291ebf3dfc","workflow_instance_id":"6df274a9-49ab-4847-b1dc-69a8154a6612","task_type":"docker","task_start_time":"2023-10-31T09:18:03.181Z","task_end_time":null,"execution_stats":{"IdentityKey":"8c2ed70e1b0acac04df8f916cd995ec8c13d9486294cf5eacf37e4a28346777e","workflowId":"6df274a9-49ab-4847-b1dc-69a8154a6612","duration":"1793.7903","startedAt":"2023-10-31T09:18:08","finishedAt":"2023-10-31T09:18:10"},"task_plugin_arguments":{"container_image":"sameershanbhogue/my_app-x64-workstation-dgpu-linux-amd64:1.0","server_url":"unix:///var/run/docker.sock","entrypoint":"/bin/bash,-c","command":"python3 -u /opt/monai/app/app.py","task_timeout_minutes":"30","temp_storage_container_path":"/var/lib/monai/","env_MONAI_INPUTPATH":"/var/monai/input/","env_MONAI_OUTPUTPATH":"/var/monai/output/","env_MONAI_MODELPATH":"/opt/monai/models/","env_MONAI_WORKDIR":"/var/monai/"},"task_id":"liver","previous_task_id":"router","status":2,"reason":0,"input_artifacts":{"env_MONAI_INPUTPATH":"1918d483-8609-4c64-b622-6413f43f9abb/dcm"},"output_artifacts":{},"output_directory":"1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/10edc066-56bc-43cf-8cf2-47291ebf3dfc","result":{"JobIdentity":"8c2ed70e1b0acac04df8f916cd995ec8c13d9486294cf5eacf37e4a28346777e"},"next_timeout":"2023-10-31T10:18:03.181Z","timeout_interval":60.0,"acknowledged_task_errors":null}, workflowInstance {"Version":"1.0.0","id":"6df274a9-49ab-4847-b1dc-69a8154a6612","ae_title":"MONAI-DEPLOY","workflow_name":"ai-liver-seg","workflow_id":"abdf887f-126d-4de6-bbb9-3e58a3ba81a8","payload_id":"1918d483-8609-4c64-b622-6413f43f9abb","start_time":"2023-10-31T09:18:02.967Z","status":0,"bucket_id":"monaideploy","input_metadata":{},"tasks":[{"execution_id":"8833f1c4-81c7-43d5-90b5-62a8a065aa15","workflow_instance_id":"6df274a9-49ab-4847-b1dc-69a8154a6612","task_type":"router","task_start_time":"2023-10-31T09:18:02.969Z","task_end_time":"2023-10-31T09:18:03.3Z","execution_stats":{},"task_plugin_arguments":{"workflow_name":"ai-liver-seg"},"task_id":"router","previous_task_id":"","status":3,"reason":0,"input_artifacts":{},"output_artifacts":{},"output_directory":"1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/8833f1c4-81c7-43d5-90b5-62a8a065aa15","result":{},"next_timeout":"2023-10-31T10:18:02.969Z","timeout_interval":60.0,"acknowledged_task_errors":null},{"execution_id":"10edc066-56bc-43cf-8cf2-47291ebf3dfc","workflow_instance_id":"6df274a9-49ab-4847-b1dc-69a8154a6612","task_type":"docker","task_start_time":"2023-10-31T09:18:03.181Z","task_end_time":null,"execution_stats":{"IdentityKey":"8c2ed70e1b0acac04df8f916cd995ec8c13d9486294cf5eacf37e4a28346777e","workflowId":"6df274a9-49ab-4847-b1dc-69a8154a6612","duration":"1793.7903","startedAt":"2023-10-31T09:18:08","finishedAt":"2023-10-31T09:18:10"},"task_plugin_arguments":{"container_image":"sameershanbhogue/my_app-x64-workstation-dgpu-linux-amd64:1.0","server_url":"unix:///var/run/docker.sock","entrypoint":"/bin/bash,-c","command":"python3 -u /opt/monai/app/app.py","task_timeout_minutes":"30","temp_storage_container_path":"/var/lib/monai/","env_MONAI_INPUTPATH":"/var/monai/input/","env_MONAI_OUTPUTPATH":"/var/monai/output/","env_MONAI_MODELPATH":"/opt/monai/models/","env_MONAI_WORKDIR":"/var/monai/"},"task_id":"liver","previous_task_id":"router","status":2,"reason":0,"input_artifacts":{"env_MONAI_INPUTPATH":"1918d483-8609-4c64-b622-6413f43f9abb/dcm"},"output_artifacts":{},"output_directory":"1918d483-8609-4c64-b622-6413f43f9abb/workflows/6df274a9-49ab-4847-b1dc-69a8154a6612/10edc066-56bc-43cf-8cf2-47291ebf3dfc","result":{"JobIdentity":"8c2ed70e1b0acac04df8f916cd995ec8c13d9486294cf5eacf37e4a28346777e"},"next_timeout":"2023-10-31T10:18:03.181Z","timeout_interval":60.0,"acknowledged_task_errors":null}],"acknowledged_workflow_errors":null}, patientDetails {"patient_id":"C3N-00198","patient_name":"C3N-00198","patient_sex":"M","patient_dob":null,"patient_age":"055Y","patient_hospital_id":null}, correlationId 15d68444-fa6e-4c17-8fa8-e4318ca0ead7, taskStatus Failed
Is this error related to the bug
from monai-deploy.
@SameerShanbhogue did you build your app using MONAI Deploy App SDK 0.5 or 0.6? If 0.6, then it is likely to be related. Thanks.
from monai-deploy.
@SameerShanbhogue did you build your app using MONAI Deploy App SDK 0.5 or 0.6? If 0.6, then it is likely to be related. Thanks.
The log entry has the telltale sign that @SameerShanbhogue indeed built and tested the MAP with App SDK v0.6.
'''
"task_plugin_arguments":{"container_image":"sameershanbhogue/my_app-x64-workstation-dgpu-linux-amd64:1.0","server_url":"unix:///var/run/docker.sock","entrypoint":"/bin/bash,-c","command":"python3 -u /opt/monai/app/app.py","
'''
from monai-deploy.
I have a fix coming soon!
from monai-deploy.
@SameerShanbhogue Please try https://github.com/Project-MONAI/monai-deploy/releases/tag/monai-deploy-express-v0.5.0 and let me know if that works for you! Thanks!
from monai-deploy.
@mocsharp @MMelQin Yes v0.6 is there a work around till bug is fixed.
As @mocsharp mentioned, the fix is known, and pull request already reviewed and merged. Please try MD Express v0.5.0 as mentioned above.
As for workaround with earlier version of MD Express, there is no good ones if the MAP (App SDK v0.6) is built with no-root user, because the Task Manager (and the Docker plugin), when run in container as root, will dynamically create a folder on the host FS to use as the output folder for the MAP container, and the dynamically created folder would not have "Write" permission for other users.
If you build the MAP with container user be root, then it would work. However, the Packager in v0.6 has a little issue where it does not fall back if GUID 0 in the container already exists, and would fail; this issue has also been addressed, but to be released in v1.0.
from monai-deploy.
MD Express v0.5.0 with Liver Tumor 2.0 workflow definition works !!
from monai-deploy.
Related Issues (20)
- DICOM data upload
- e2e test scenarios: KeyError: 'nifti_affine_transform' in liver_seg HOT 1
- Workflow Request Message change request HOT 2
- Rebuild of Monai Deploy Express HOT 5
- MONAI Deploy Express Workflow Manager http://localhost:5001/ gives HTTP ERROR 404 HOT 8
- Workflow won't trigger/complete on Linux server(with no GPU) HOT 13
- Minio Storage Service error HOT 3
- MD Express: Issues with .env and docker-compose file
- MD Express - Hello World - No dicom list printed with curl - MAPs not getting launched HOT 3
- HL7 support HOT 6
- Deploying MONAI in Azure HOT 6
- Remove deployed workflow definition from MONAI Deploy Workflow Manager HOT 3
- Automated functional e2e test
- MD Express – Hello World example – no file list output HOT 8
- MD Express error when starting from within a docker HOT 5
- MD Express dicom seg is flipped when displayed on OHIF viewer HOT 7
- MD Express Request a way to debug track jobs HOT 2
- MD Express: Request a way to clean up data from incoming requests HOT 2
- MDExpress: Orthanc Configurations HOT 7
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from monai-deploy.