# inpainting challenge
Please follow us on [Twitter](https://twitter.com/BraTS_inpaint) and take a look at the [challenge website](https://www.synapse.org/#!Synapse:syn53708249/wiki/626323).
# Announcements
**1.**: The challenge data is released with a soft launch. Soon the website will go online.
** 2: [link](https://www.synapse.org/Synapse:syn53708249/discussion/threadId=10976&replyId=33678)**
** 3: [link](https://www.synapse.org/Synapse:syn53708249/discussion/threadId=10976&replyId=33728)**
# Questions and Answers
tba
Created by Florian Kofler neuronflow Dear inpainting challenge participants,
We have now invited the first author of each team as a reviewer for BraTS 2024 on Microsoft CMT.
Please accept the invitation as soon as possible. We will then assign three short papers to be reviewed to each team.
The papers will be published in the LNCS proceedings of the inpainting challenge.
Please reach out to us now if you have not received an invitation yet.
Feel free to distribute the paper reviews within your team. Please let us know if we should invite another email address to CMT.
The deadline for the reviews is October 2nd.
Please let us know if you have questions or face any issues.
Thanks for your support!
Happy inpainting and best regards,
Florian on behalf of the inpainting challenge team Dear Participants,
I hope this message finds you well. First, let me apologize for the extended silence. We've faced some delays due to the joyful news of Verena?s baby arriving, which has understandably affected our schedule.
That said, we are pleased to finally share some overdue updates on the inpainting challenge:
We have received multiple submissions, and we are currently processing them. However, the extended inference times required by cutting-edge diffusion models have slowed down our ability to compute the metrics for the test set. As a result, it?s uncertain whether we will finalize the rankings in time for the MICCAI conference.
Nonetheless, we will host a challenge workshop during MICCAI to create a platform for discussion. We kindly ask all teams who submitted an ML cube to prepare a 3-minute video presentation explaining their inpainting method. While in-person presentations will be possible for those attending MICCAI, we still request video submissions so they can be made publicly available for those unable to attend the workshop.
Papers and Publications: In the coming days, you will be asked to review each other's papers via Microsoft CMT. All accepted submissions will be included in the LNCS proceedings. Additionally, there will be a special issue covering both the 2023 and 2024 inpainting challenges, and successful participants will be invited to submit extended versions of their work. More details on this will follow soon.
Thank you for your understanding and continued participation.
Best regards,
Florian Thank you so much @vchung ! @lulululu ,
Yes, I have been monitoring the queues for your submission and can confirm that both submissions 9748006 and 9748067 are in the system as ACCEPTED. :-) Dear @vchung ,
for some reason, it still did not work submitting as an individual using the account @lulululu .
I now found another workaround: I created a second account using a different email address and joined team SMINT (new account is @smint_member , also a certified user) and uploaded the docker and tarball using this account. This way it was even possible the upload it as team "SMINT".
Could you confirm that there is a valid submission from team SMINT, containing a docker image and a tarball? The ID should be 9748067.
If this is the case, could you please re-accept submission ID 9748006 from team melide? And also confirm this?
Thank you! @lulululu ,
Oh right! It got passed me that you are also part of team melide already. In that case, let me temporarily invalidate submission ID 9748006 (team melide's submission) so that you can submit as team SMINT. Then, I will re-accept submission ID 9748006 after you have confirmed that your inpainting submission is in.
Dear @vchung , it's me again, I'm sorry... when I now try to submit as an individual, I receive the error "Submitter may not submit as an individual when having submitted as part of a Team."
Is there any other way I can submit? Dear @vchung , thanks a lot and sorry again for the inconvenience! @lulululu ,
Thank you for explaining the situation! At this point, the best way to move forward would be to submit as an individual rather than a team to the Docker and config queues. I will make a note that submissions by you (lulululu) are actually for team SMINT. Dear @neuronflow & @vchung
We made a tiny chaos when registering for the challenges:
As we participate in two challenges (Missing MRI Challenge and Inpainting Challenge), we created two teams (we now realize that this was not good), and also submitted two separate short papers using the different team names.
@irdeirfp is the team leader of team "melide" (Missing MRI Challenge) & I'm the team leader of team SMINT (Inpainting Challenge), we both are in both teams. Since team "melide" already submitted the missing mri docker image & tarball, I cannot select team "SMINT" anymore to submit the inpainting docker image & tarball (it shows the contributors have conflicting submissions, therefore, I cannot select any contributor and without that I cannot proceed, as it shows that I did not select a contributor). I also cannot use team "melide", it is not shown on the list, only "SMINT" is shown. And leaving team "melide" did not help. Is there a way to solve this problem?
I'm really sorry for the inconvenience.
@kechen0207 ,
Thanks for the notice. The hash error may be due to a version mismatch of medperf. Specifically, checksums have updated from 40 characters to 64 since last year. Good to hear that the old checksum still works though!
And yes, a status of `MLCUBE_DOCKER_FOUND` indicates that your MLCube config file and Docker image has successfully been linked together by the submission system. @vchung
Still got the error for the hash code
"? Demo dataset synapse:syn52276405: Hash mismatch. Expected 981c97f4bf2b39543d62e2815f71cb2edcab67be97631a938bd72f23a27ae54c, found 83cb59a06de73f2b9d08270372a243aa90ff9072."
However, when I use the hash code for 2023 ("83cb59a06de73f2b9d08270372a243aa90ff9072"), it works.
Also, my MLCube submission status shows "MLCUBE_DOCKER_FOUND". Does it mean the submission is successful? @kechen0207 ,
Thanks for the notice! The Submission Dashboard has been updated accordingly.
Additionally, you should've received an email with a notification about your MLCube config file; if you did not receive it, it may have been sent to your Spam folder.
Hope this helps Dear Organizers,
I have submitted the MLCube as a team. How do I know if my submission is valid or not? This year's submission dashboard shows no information about that.
No worries; thank you for reporting here, and sorry for the inconvenience. Dear Organizers,
Currently the CMT portal does not show an option to submit a paper for the Local Inpainting Challenge (see attached image). Will this be updated?
*EDIT: was resolved in another thread, thank you :) Dear @vchung, thanks a lot, sorry for the confusion. @lulululu and team,
Thanks for reaching out! I'm looking at your team submissions (9746116, 9746125) and I see the following validation error:
```text
Submission must be a tarball or zipped archive containing at least one NIfTI file.
```
The email you received should've contained this error as well, and not the TOIL logs (what you have attached), since this is for the workflow, not submission. I apologize for the confusion in the error messages.
As for the root of the problem, I downloaded one of your submissions manually and found that the submitted prediction is not a zipfile. I checked via both the terminal and through Python:
**Terminal**
```text
$ unzip -l sampling_results_395k_validation_adapted_new.zip
Archive: sampling_results_395k_validation_adapted_new.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
```
**Python**
```python
>>> import zipfile
>>> zipfile.is_zipfile("sampling_results_395k_validation_adapted_new.zip")
False
```
Hope this helps! @vchung , could you have a look at this one, please?
https://www.synapse.org/Synapse:syn53708249/discussion/threadId=10976&replyId=32588 @ShadowTwin41
The evaluation/README.md didn't explicitly specify requirements up to now due to the implicit assumption the other notebooks were run previously.
This was fixed now as well as the image size description. Thanks for pointing it out!
Dear Inpainting Team,,
thank you for organizing this challenge!
We just saw that the inpainting evaluation queue is available now, however, we received an "invalid submission" error. As far as we understand the logs, the error is not due to our file - could you take a look at this? Please find the logs below.
Thank you in advance!
STDERR: 2024-07-11T07:51:22.031763627Z c25f3757b1d6 2024-07-11 07:51:22,031 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/validation-phase.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/validation-phase.cwl'
STDERR: 2024-07-11T07:51:27.675669816Z c25f3757b1d6 2024-07-11 07:51:27,675 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2024-07-11T07:51:27.675694461Z brats2023-main/wf-inpainting/validation-phase.cwl:59:9: Source 'filepath' of type ["null", "File"]
STDERR: 2024-07-11T07:51:27.675697494Z may be incompatible
STDERR: 2024-07-11T07:51:27.675699669Z brats2023-main/wf-inpainting/validation-phase.cwl:93:9: with sink 'input_file' of type "File"
STDERR: 2024-07-11T07:51:27.675702204Z brats2023-main/wf-inpainting/validation-phase.cwl:59:9: Source 'filepath' of type ["null", "File"]
STDERR: 2024-07-11T07:51:27.675704372Z may be incompatible
STDERR: 2024-07-11T07:51:27.675706402Z brats2023-main/wf-inpainting/validation-phase.cwl:171:9: with sink 'input_file' of type "File"
STDERR: 2024-07-11T07:51:27.946208519Z c25f3757b1d6 2024-07-11 07:51:27,945 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2024-07-11T07:51:28.448400316Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmp60wd0psr/worker_log.txt
STDERR: 2024-07-11T07:51:28.638969734Z c25f3757b1d6 2024-07-11 07:51:28,638 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2024-07-11T07:51:28.639564908Z c25f3757b1d6 2024-07-11 07:51:28,639 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_set_permissions.cwl/instance-g8a4m_4a with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:51:28.639644192Z c25f3757b1d6 2024-07-11 07:51:28,639 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-hgbj_5nu with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:51:28.639704046Z c25f3757b1d6 2024-07-11 07:51:28,639 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-x4dppq0o with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:51:28.639778250Z c25f3757b1d6 2024-07-11 07:51:28,639 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_get_submission.cwl/instance-907u8ilx with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:51:29.126668849Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpv3ydjdnw/worker_log.txt
STDERR: 2024-07-11T07:51:29.126690648Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpgcv98jvp/worker_log.txt
STDERR: 2024-07-11T07:51:29.137338193Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpv_p1ga47/worker_log.txt
STDERR: 2024-07-11T07:51:29.137359629Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpn_ghg8eu/worker_log.txt
STDERR: 2024-07-11T07:51:32.278482458Z c25f3757b1d6 2024-07-11 07:51:32,277 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_set_permissions.cwl/instance-g8a4m_4a
STDERR: 2024-07-11T07:51:32.866470599Z c25f3757b1d6 2024-07-11 07:51:32,866 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-hgbj_5nu
STDERR: 2024-07-11T07:52:00.435219036Z c25f3757b1d6 2024-07-11 07:52:00,434 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_get_submission.cwl/instance-907u8ilx
STDERR: 2024-07-11T07:52:00.435831216Z c25f3757b1d6 2024-07-11 07:52:00,435 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/steps/validate.cwl' /app/validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9e5cdc0f-4e75-483e-ba69-378c5823b6da_brats2023-main_wf-inpainting_steps_validate.cwl/instance-ewrf12xl with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:52:00.513180264Z c25f3757b1d6 2024-07-11 07:52:00,512 Thread-48 WARNING toil.statsAndLogging: Got message from job at time 07-11-2024 07:52:00: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-vxo0wx75/cleanup/file-x0ask5sg/stream used 109.22% (1.1 GB [1173884928B] used, 1.0 GB [1074741824B] requested) at the end of its run.
STDERR: 2024-07-11T07:52:00.945180084Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpffqmg_45/worker_log.txt
STDERR: 2024-07-11T07:52:13.402501562Z c25f3757b1d6 2024-07-11 07:52:13,402 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/steps/validate.cwl' /app/validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9e5cdc0f-4e75-483e-ba69-378c5823b6da_brats2023-main_wf-inpainting_steps_validate.cwl/instance-ewrf12xl
STDERR: 2024-07-11T07:52:13.403142023Z c25f3757b1d6 2024-07-11 07:52:13,402 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-spss1bap with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:52:13.403229010Z c25f3757b1d6 2024-07-11 07:52:13,403 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_validate_email.cwl/instance-93l6a3nn with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:52:13.531336282Z c25f3757b1d6 2024-07-11 07:52:13,530 Thread-48 WARNING toil.statsAndLogging: Got message from job at time 07-11-2024 07:52:13: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-vxo0wx75/cleanup/file-iy4wtbkv/stream used 109.63% (1.1 GB [1178234880B] used, 1.0 GB [1074741824B] requested) at the end of its run.
STDERR: 2024-07-11T07:52:13.895502966Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpxo_wi01x/worker_log.txt
STDERR: 2024-07-11T07:52:13.904633040Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpcaqsuxl2/worker_log.txt
STDERR: 2024-07-11T07:52:18.041335886Z c25f3757b1d6 2024-07-11 07:52:18,041 Thread-48 WARNING toil.statsAndLogging: Got message from job at time 07-11-2024 07:52:18: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-vxo0wx75/cleanup/file-ofmvj5ti/stream used 219.89% (2.2 GB [2363260928B] used, 1.0 GB [1074741824B] requested) at the end of its run.
STDERR: 2024-07-11T07:52:18.391269476Z c25f3757b1d6 2024-07-11 07:52:18,390 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-x4dppq0o
STDERR: 2024-07-11T07:52:36.962410645Z c25f3757b1d6 2024-07-11 07:52:36,962 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-spss1bap
STDERR: 2024-07-11T07:52:37.527324634Z c25f3757b1d6 2024-07-11 07:52:37,527 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_validate_email.cwl/instance-93l6a3nn
STDERR: 2024-07-11T07:52:37.527810456Z c25f3757b1d6 2024-07-11 07:52:37,527 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2024-07-11T07:52:37.570046517Z c25f3757b1d6 2024-07-11 07:52:37,569 Thread-48 WARNING toil.statsAndLogging: Got message from job at time 07-11-2024 07:52:37: Job used more disk than requested. Consider modifying the user script to avoid the chance of failure due to incorrectly requested resources. Job files/for-job/kind-CWLWorkflow/instance-vxo0wx75/cleanup/file-uyhzgu55/stream used 109.22% (1.1 GB [1173884928B] used, 1.0 GB [1074741824B] requested) at the end of its run.
STDERR: 2024-07-11T07:52:38.015507314Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpj295ctpu/worker_log.txt
STDERR: 2024-07-11T07:52:38.227594574Z c25f3757b1d6 2024-07-11 07:52:38,227 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc
STDERR: 2024-07-11T07:52:38.227988619Z c25f3757b1d6 2024-07-11 07:52:38,227 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc
STDERR: 2024-07-11T07:52:38.228149836Z c25f3757b1d6 2024-07-11 07:52:38,228 MainThread WARNING toil.leader: Log from job kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc follows:
STDERR: 2024-07-11T07:52:38.228160260Z =========>
STDERR: 2024-07-11T07:52:38.228163969Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2024-07-11T07:52:38.228166987Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2024-07-11T07:52:38.228170440Z Failed to evaluate expression:
STDERR: 2024-07-11T07:52:38.228173588Z Expression evaluation error:
STDERR: 2024-07-11T07:52:38.228176510Z Expecting value: line 1 column 1 (char 0)
STDERR: 2024-07-11T07:52:38.228179633Z script was:
STDERR: 2024-07-11T07:52:38.228182476Z 01 "use strict";
STDERR: 2024-07-11T07:52:38.228185732Z 02 var inputs = {
STDERR: 2024-07-11T07:52:38.228188826Z 03 "status": "INVALID",
STDERR: 2024-07-11T07:52:38.228192038Z 04 "previous_annotation_finished": true,
STDERR: 2024-07-11T07:52:38.228195886Z 05 "previous_email_finished": true
STDERR: 2024-07-11T07:52:38.228199654Z 06 };
STDERR: 2024-07-11T07:52:38.228202611Z 07 var self = null;
STDERR: 2024-07-11T07:52:38.228205767Z 08 var runtime = {
STDERR: 2024-07-11T07:52:38.228208622Z 09 "cores": 1,
STDERR: 2024-07-11T07:52:38.228224436Z 10 "ram": 100.0,
STDERR: 2024-07-11T07:52:38.228227698Z 11 "tmpdirSize": 1024,
STDERR: 2024-07-11T07:52:38.228231034Z 12 "outdirSize": 0.95367431640625,
STDERR: 2024-07-11T07:52:38.228234462Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/tmpqfktyzsq",
STDERR: 2024-07-11T07:52:38.228238266Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpj295ctpu/52127062-0ce5-43df-99b9-d6ef9a37ce95/tax4aw30i/tmp-out2oitipvk"
STDERR: 2024-07-11T07:52:38.228242111Z 15 };
STDERR: 2024-07-11T07:52:38.228245345Z 16 (function(){
STDERR: 2024-07-11T07:52:38.228248502Z 17 if(inputs.status == "INVALID"){
STDERR: 2024-07-11T07:52:38.228251747Z 18 throw 'invalid submission';
STDERR: 2024-07-11T07:52:38.228254878Z 19 } else {
STDERR: 2024-07-11T07:52:38.228257931Z 20 return {finished: true};
STDERR: 2024-07-11T07:52:38.228261036Z 21 }
STDERR: 2024-07-11T07:52:38.228263950Z 22 })()
STDERR: 2024-07-11T07:52:38.228266702Z stdout was: ''
STDERR: 2024-07-11T07:52:38.228269645Z stderr was: 'invalid submission'
STDERR: 2024-07-11T07:52:38.228272647Z
STDERR: 2024-07-11T07:52:38.228275366Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2024-07-11T07:52:38.228278348Z Expression evaluation error:
STDERR: 2024-07-11T07:52:38.228281071Z Expecting value: line 1 column 1 (char 0)
STDERR: 2024-07-11T07:52:38.228283949Z script was:
STDERR: 2024-07-11T07:52:38.228287008Z 01 "use strict";
STDERR: 2024-07-11T07:52:38.228290036Z 02 var inputs = {
STDERR: 2024-07-11T07:52:38.228292857Z 03 "status": "INVALID",
STDERR: 2024-07-11T07:52:38.228296128Z 04 "previous_annotation_finished": true,
STDERR: 2024-07-11T07:52:38.228299522Z 05 "previous_email_finished": true
STDERR: 2024-07-11T07:52:38.228302858Z 06 };
STDERR: 2024-07-11T07:52:38.228306385Z 07 var self = null;
STDERR: 2024-07-11T07:52:38.228309381Z 08 var runtime = {
STDERR: 2024-07-11T07:52:38.228312271Z 09 "cores": 1,
STDERR: 2024-07-11T07:52:38.228315382Z 10 "ram": 100.0,
STDERR: 2024-07-11T07:52:38.228318360Z 11 "tmpdirSize": 1024,
STDERR: 2024-07-11T07:52:38.228321759Z 12 "outdirSize": 0.95367431640625,
STDERR: 2024-07-11T07:52:38.228324960Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/tmpqfktyzsq",
STDERR: 2024-07-11T07:52:38.228328940Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpj295ctpu/52127062-0ce5-43df-99b9-d6ef9a37ce95/tax4aw30i/tmp-out2oitipvk"
STDERR: 2024-07-11T07:52:38.228337407Z 15 };
STDERR: 2024-07-11T07:52:38.228340296Z 16 (function(){
STDERR: 2024-07-11T07:52:38.228343142Z 17 if(inputs.status == "INVALID"){
STDERR: 2024-07-11T07:52:38.228346074Z 18 throw 'invalid submission';
STDERR: 2024-07-11T07:52:38.228349121Z 19 } else {
STDERR: 2024-07-11T07:52:38.228351998Z 20 return {finished: true};
STDERR: 2024-07-11T07:52:38.228355082Z 21 }
STDERR: 2024-07-11T07:52:38.228357961Z 22 })()
STDERR: 2024-07-11T07:52:38.228361311Z stdout was: ''
STDERR: 2024-07-11T07:52:38.228364385Z stderr was: 'invalid submission'
STDERR: 2024-07-11T07:52:38.228367625Z
STDERR: 2024-07-11T07:52:38.228370765Z Traceback (most recent call last):
STDERR: 2024-07-11T07:52:38.228373940Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2024-07-11T07:52:38.228377284Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2024-07-11T07:52:38.228380431Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2024-07-11T07:52:38.228383273Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2024-07-11T07:52:38.228386442Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2024-07-11T07:52:38.228389644Z return self.run(fileStore)
STDERR: 2024-07-11T07:52:38.228392882Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2024-07-11T07:52:38.228403548Z raise cwltool.errors.WorkflowException(status)
STDERR: 2024-07-11T07:52:38.228406526Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2024-07-11T07:52:38.228409633Z ERROR:toil.worker:Exiting the worker because of a failed job on host c25f3757b1d6
STDERR: 2024-07-11T07:52:38.228413092Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc to 0
STDERR: 2024-07-11T07:52:38.228417722Z <=========
STDERR: 2024-07-11T07:52:38.228668911Z c25f3757b1d6 2024-07-11 07:52:38,228 MainThread WARNING toil.leader: Job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc is completely failed
STDERR: 2024-07-11T07:52:50.090522879Z c25f3757b1d6 2024-07-11 07:52:50,090 MainThread INFO toil.leader: Finished toil run with 8 failed jobs.
STDERR: 2024-07-11T07:52:50.090578893Z c25f3757b1d6 2024-07-11 07:52:50,090 MainThread INFO toil.leader: Failed jobs at end of the run: 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-x4dppq0o 'CWLWorkflow' kind-CWLWorkflow/instance-vxo0wx75 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-hgbj_5nu 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_validate_email.cwl/instance-93l6a3nn 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/steps/validate.cwl' /app/validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9e5cdc0f-4e75-483e-ba69-378c5823b6da_brats2023-main_wf-inpainting_steps_validate.cwl/instance-ewrf12xl 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-spss1bap 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_get_submission.cwl/instance-907u8ilx
STDERR: 2024-07-11T07:52:50.103769661Z Traceback (most recent call last):
STDERR: 2024-07-11T07:52:50.103786509Z File "/usr/local/bin/toil-cwl-runner", line 8, in
STDERR: 2024-07-11T07:52:50.103789913Z sys.exit(main())
STDERR: 2024-07-11T07:52:50.103791967Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 1691, in main
STDERR: 2024-07-11T07:52:50.103794543Z outobj = toil.start(wf1)
STDERR: 2024-07-11T07:52:50.103796713Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 829, in start
STDERR: 2024-07-11T07:52:50.103798738Z return self._runMainLoop(rootJobGraph)
STDERR: 2024-07-11T07:52:50.103800961Z File "/usr/local/lib/python3.8/site-packages/toil/common.py", line 1115, in _runMainLoop
STDERR: 2024-07-11T07:52:50.103803078Z return Leader(config=self.config,
STDERR: 2024-07-11T07:52:50.103805038Z File "/usr/local/lib/python3.8/site-packages/toil/leader.py", line 269, in run
STDERR: 2024-07-11T07:52:50.103807140Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore)
STDERR: 2024-07-11T07:52:50.103811314Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/tmps2xs9y1g' contains 8 failed jobs: 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-x4dppq0o, 'CWLWorkflow' kind-CWLWorkflow/instance-vxo0wx75, 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-hgbj_5nu, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_validate_email.cwl/instance-93l6a3nn, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/brats2023-main/wf-inpainting/steps/validate.cwl' /app/validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_9e5cdc0f-4e75-483e-ba69-378c5823b6da_brats2023-main_wf-inpainting_steps_validate.cwl/instance-ewrf12xl, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_annotate_submission.cwl/instance-spss1bap, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc, 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_get_submission.cwl/instance-907u8ilx
STDERR: 2024-07-11T07:52:50.103828646Z Log from job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc follows:
STDERR: 2024-07-11T07:52:50.103832858Z =========>
STDERR: 2024-07-11T07:52:50.103834902Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2024-07-11T07:52:50.103836967Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2024-07-11T07:52:50.103839009Z Failed to evaluate expression:
STDERR: 2024-07-11T07:52:50.103840943Z Expression evaluation error:
STDERR: 2024-07-11T07:52:50.103842858Z Expecting value: line 1 column 1 (char 0)
STDERR: 2024-07-11T07:52:50.103844842Z script was:
STDERR: 2024-07-11T07:52:50.103846710Z 01 "use strict";
STDERR: 2024-07-11T07:52:50.103848790Z 02 var inputs = {
STDERR: 2024-07-11T07:52:50.103850713Z 03 "status": "INVALID",
STDERR: 2024-07-11T07:52:50.103853575Z 04 "previous_annotation_finished": true,
STDERR: 2024-07-11T07:52:50.103856755Z 05 "previous_email_finished": true
STDERR: 2024-07-11T07:52:50.103858835Z 06 };
STDERR: 2024-07-11T07:52:50.103860649Z 07 var self = null;
STDERR: 2024-07-11T07:52:50.103862540Z 08 var runtime = {
STDERR: 2024-07-11T07:52:50.103864376Z 09 "cores": 1,
STDERR: 2024-07-11T07:52:50.103866458Z 10 "ram": 100.0,
STDERR: 2024-07-11T07:52:50.103868431Z 11 "tmpdirSize": 1024,
STDERR: 2024-07-11T07:52:50.103870428Z 12 "outdirSize": 0.95367431640625,
STDERR: 2024-07-11T07:52:50.103872423Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/tmpqfktyzsq",
STDERR: 2024-07-11T07:52:50.103877671Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpj295ctpu/52127062-0ce5-43df-99b9-d6ef9a37ce95/tax4aw30i/tmp-out2oitipvk"
STDERR: 2024-07-11T07:52:50.103880092Z 15 };
STDERR: 2024-07-11T07:52:50.103881896Z 16 (function(){
STDERR: 2024-07-11T07:52:50.103883870Z 17 if(inputs.status == "INVALID"){
STDERR: 2024-07-11T07:52:50.103886260Z 18 throw 'invalid submission';
STDERR: 2024-07-11T07:52:50.103888253Z 19 } else {
STDERR: 2024-07-11T07:52:50.103890353Z 20 return {finished: true};
STDERR: 2024-07-11T07:52:50.103892293Z 21 }
STDERR: 2024-07-11T07:52:50.103894095Z 22 })()
STDERR: 2024-07-11T07:52:50.103895931Z stdout was: ''
STDERR: 2024-07-11T07:52:50.103897973Z stderr was: 'invalid submission'
STDERR: 2024-07-11T07:52:50.103901204Z
STDERR: 2024-07-11T07:52:50.103904514Z WARNING:cwltool:Failed to evaluate expression:
STDERR: 2024-07-11T07:52:50.103908127Z Expression evaluation error:
STDERR: 2024-07-11T07:52:50.103911147Z Expecting value: line 1 column 1 (char 0)
STDERR: 2024-07-11T07:52:50.103913144Z script was:
STDERR: 2024-07-11T07:52:50.103914978Z 01 "use strict";
STDERR: 2024-07-11T07:52:50.103916872Z 02 var inputs = {
STDERR: 2024-07-11T07:52:50.103918835Z 03 "status": "INVALID",
STDERR: 2024-07-11T07:52:50.103920764Z 04 "previous_annotation_finished": true,
STDERR: 2024-07-11T07:52:50.103922839Z 05 "previous_email_finished": true
STDERR: 2024-07-11T07:52:50.103924904Z 06 };
STDERR: 2024-07-11T07:52:50.103926806Z 07 var self = null;
STDERR: 2024-07-11T07:52:50.103928719Z 08 var runtime = {
STDERR: 2024-07-11T07:52:50.103930564Z 09 "cores": 1,
STDERR: 2024-07-11T07:52:50.103932455Z 10 "ram": 100.0,
STDERR: 2024-07-11T07:52:50.103934334Z 11 "tmpdirSize": 1024,
STDERR: 2024-07-11T07:52:50.103936307Z 12 "outdirSize": 0.95367431640625,
STDERR: 2024-07-11T07:52:50.103938560Z 13 "tmpdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/tmpqfktyzsq",
STDERR: 2024-07-11T07:52:50.103940779Z 14 "outdir": "/var/lib/docker/volumes/workflow_orchestrator_shared/_data/9e5cdc0f-4e75-483e-ba69-378c5823b6da/node-f5eb706f-56d1-40b9-a49d-c106bceaf89f-1cc402dd0e11d5ae18db04a6de87223d/tmpj295ctpu/52127062-0ce5-43df-99b9-d6ef9a37ce95/tax4aw30i/tmp-out2oitipvk"
STDERR: 2024-07-11T07:52:50.103943117Z 15 };
STDERR: 2024-07-11T07:52:50.103945055Z 16 (function(){
STDERR: 2024-07-11T07:52:50.103946988Z 17 if(inputs.status == "INVALID"){
STDERR: 2024-07-11T07:52:50.103948918Z 18 throw 'invalid submission';
STDERR: 2024-07-11T07:52:50.103950783Z 19 } else {
STDERR: 2024-07-11T07:52:50.103955724Z 20 return {finished: true};
STDERR: 2024-07-11T07:52:50.103957860Z 21 }
STDERR: 2024-07-11T07:52:50.103959789Z 22 })()
STDERR: 2024-07-11T07:52:50.103961747Z stdout was: ''
STDERR: 2024-07-11T07:52:50.103963683Z stderr was: 'invalid submission'
STDERR: 2024-07-11T07:52:50.103965559Z
STDERR: 2024-07-11T07:52:50.103967358Z Traceback (most recent call last):
STDERR: 2024-07-11T07:52:50.103969256Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2024-07-11T07:52:50.103971292Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2024-07-11T07:52:50.103973420Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2024-07-11T07:52:50.103975462Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2024-07-11T07:52:50.103977883Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2024-07-11T07:52:50.103981055Z return self.run(fileStore)
STDERR: 2024-07-11T07:52:50.103984491Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 937, in run
STDERR: 2024-07-11T07:52:50.103988148Z raise cwltool.errors.WorkflowException(status)
STDERR: 2024-07-11T07:52:50.103990384Z cwltool.errors.WorkflowException: permanentFail
STDERR: 2024-07-11T07:52:50.103992248Z ERROR:toil.worker:Exiting the worker because of a failed job on host c25f3757b1d6
STDERR: 2024-07-11T07:52:50.103994638Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v4.0/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc with ID kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v4.0_cwl_check_status.cwl/instance-bcqiktmc to 0
STDERR: 2024-07-11T07:52:50.103997186Z <========= I didn't know that I had to install it.
Where is that explained? So that I don't ask any more of these questions.
Also, in the evaluation notebook, it says: "Also note that your output files have to be **full size images** with dimension 250x250x144.", but aren't the images 240x240x155?
Thank you! did you install the requirements first?
In particular:
`pip install inpainting` Dear all,
I was trying to use the evaluation notebook (https://github.com/BraTS-inpainting/2024_challenge/blob/main/evaluation/evaluation.ipynb) however I cannot find the following import:
```
from inpainting.challenge_metrics_2023 import generate_metrics
```
where can I find it?
Thank you in advance! @vchung do we have an ETA for the validation phase? Thank you! Dear organisers,
I'm sorry to bother you, but is there a specific date for the start of validation?
Thank you in advance! @neuronflow,
Thank you very much for your answer! Thank you for your question @ShadowTwin41 . Your model should only inpaint healthy tissue, the task of the challenge is to synthesize a healthy version of a tumor brain. Happy inpainting! Dear organisers,
First of all, I would like to thank you for preparing this challenging task!
I have a question regarding the performance evaluation of the reconstructions. In your paper "https://arxiv.org/pdf/2305.08992" in Figure 3 you say "The algorithms are supposed to inpaint both the masked tumor as well as the masked healthy area.". However, the performance will only be tested in random healthy regions of the validation as testing set, as you say in section 2.4 "Since ground truth data is only available for the masked regions with healthy tissue, the evaluation will be restricted to these.".
My question is, should our models also be able to inpaint tumours, or to always inpain healthy tissue?
Thank you for your time!
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