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HelloWorld Failed #365

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athanell opened this issue Jan 19, 2021 · 2 comments · Fixed by #367
Closed

HelloWorld Failed #365

athanell opened this issue Jan 19, 2021 · 2 comments · Fixed by #367

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@athanell
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Hello,
After running the following

conda activate InnerEye

export PYTHONPATH=`pwd`

python InnerEye/ML/runner.py --model=HelloWorld

I got the errors listed below:

s/2021-01-19T151718Z_HelloWorld
2021-01-19T15:17:18Z INFO     Logs folder: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/logs
2021-01-19T15:17:18Z INFO     Creating the adjusted output folder structure.
2021-01-19T15:17:18Z INFO     Running outside of AzureML.
2021-01-19T15:17:18Z INFO     All results will be written to a subfolder of the project root folder.
2021-01-19T15:17:18Z INFO     Run outputs folder: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld
2021-01-19T15:17:18Z INFO     Logs folder: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/logs
2021-01-19T15:17:18Z INFO     extra_code_directory is unset
Setting logging level to 20
Setting up logging with level 20 to file /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/logs/stdout.txt
2021-01-19T15:17:20Z INFO     Generating new fontManager, this may take some time...
2021-01-19T15:17:23Z INFO     Setting multiprocessing start method to 'fork'
2021-01-19T15:17:23Z INFO     Model training will use the local dataset provided in /home/athanell/projects/InnerEye-DeepLearning/Tests/ML/test_data
2021-01-19T15:17:23Z INFO     
Arguments:
        __center_size_param_value: None
        __dataset_data_frame_param_value: None
        __inference_stride_size_param_value: None
        __largest_connected_component_foreground_classes_param_value: None
        __min_l_rate_param_value: 0
        __model_category_param_value: ModelCategory.Segmentation
        __model_name_param_value: HelloWorld
        __overrides_param_value: None
        __use_gpu_param_value: False
        _architecture_param_value: UNet3D
        _azure_dataset_id_param_value: hello_world
        _class_weights_param_value: [0.02, 0.49, 0.49]
        _colours_param_value: [(130, 183, 14), (238, 127, 26)]
        _comparison_blob_storage_paths_param_value: None
        _crop_size_param_value: (64, 64, 64)
        _datasets_for_inference: None
        _datasets_for_training: None
        _epochs_to_test_param_value: None
        _feature_channels_param_value: [4]
        _file_system_config_param_value: <DeepLearningFileSystemConfig DeepLearningFileSystemConfig00010>
        _fill_holes_param_value: [True, True]
        _ground_truth_ids_display_names_param_value: ['region', 'region_1']
        _ground_truth_ids_param_value: ['region', 'region_1']
        _image_channels_param_value: ['channel1', 'channel2']
        _instance__params : {}
        _l_rate_multi_step_milestones_param_value: None
        _level_param_value: 50
        _local_dataset_param_value: /home/athanell/projects/InnerEye-DeepLearning/Tests/ML/test_data
        _local_weights_path_param_value: None
        _mask_id_param_value: mask
        _multiprocessing_start_method_param_value: MultiprocessingStartMethod.fork
        _name_param_value : HelloWorld00008
        _norm_method_param_value: PhotometricNormalizationMethod.CtWindow
        _num_dataload_workers_param_value: 0
        _num_epochs_param_value: 2
        _param_watchers   : {}
        _save_start_epoch_param_value: 1
        _save_step_epochs_param_value: 1
        _slice_exclusion_rules_param_value: []
        _start_epoch_param_value: 0
        _summed_probability_rules_param_value: []
        _tail_param_value : None
        _test_crop_size_param_value: (64, 64, 64)
        _test_diff_epochs_param_value: 1
        _test_start_epoch_param_value: 2
        _test_step_epochs_param_value: 1
        _train_batch_size_param_value: 2
        _use_mixed_precision_param_value: True
        _window_param_value: 200
        initialized       : True
        param             : <param.parameterized.Parameters object at 0x7fb5fac6b978>

2021-01-19T15:17:23Z INFO     
2021-01-19T15:17:23Z INFO     **** STARTING: Model training **********************************************************************
2021-01-19T15:17:23Z INFO     
2021-01-19T15:17:23Z INFO     Train: 3, Test: 1, and Val: 2. Total subjects: 6
2021-01-19T15:17:23Z INFO     
2021-01-19T15:17:23Z INFO     **** STARTING: Visualizing the effect of sampling random crops for training ************************
2021-01-19T15:17:23Z INFO     
2021-01-19T15:17:23Z INFO     Processing dataset (name=None)
2021-01-19T15:17:23Z INFO     Processing sample: 1
2021-01-19T15:17:26Z INFO     
2021-01-19T15:17:26Z INFO     **** FINISHED: Visualizing the effect of sampling random crops for training after 2.34 seconds *****
2021-01-19T15:17:26Z INFO     
2021-01-19T15:17:26Z INFO     Starting to read and parse the datasets.
2021-01-19T15:17:26Z INFO     Processing dataset (name=None)
2021-01-19T15:17:26Z INFO     Processing dataset (name=None)
2021-01-19T15:17:26Z INFO     Creating the data loader for the training set.
2021-01-19T15:17:26Z INFO     Creating the data loader for the validation set.
2021-01-19T15:17:26Z INFO     Finished creating the data loaders.
2021-01-19T15:17:26Z INFO     Writing model summary to: logs/model_summaries/model_log001.txt
Attempted to log scalar metric LoggingColumns.NumTrainableParameters:
506139
2021-01-19T15:17:27Z INFO     Making no adjustments to the model because no GPU was found.
2021-01-19T15:17:28Z INFO     Models are saved at /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/checkpoints
2021-01-19T15:17:28Z INFO     Starting training
2021-01-19T15:17:28Z INFO     Starting epoch 1
2021-01-19T15:17:28Z INFO     Loaded the first minibatch of training data in 0.10 sec.
2021-01-19T15:17:34Z INFO     Epoch 1 training took 6.03 sec, of which waiting for next minibatch took 0.14 sec total. 2 minibatches in total.
2021-01-19T15:17:34Z INFO     Loaded the first minibatch of validation data in 0.08 sec.
2021-01-19T15:17:35Z INFO     Epoch 1 validation took 1.37 sec, of which waiting for next minibatch took 0.08 sec total. 1 minibatches in total.
2021-01-19T15:17:35Z INFO     Saved model checkpoint for epoch 1 to /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/checkpoints/1_checkpoint.pth.tar
2021-01-19T15:17:35Z INFO     Starting epoch 2
2021-01-19T15:17:35Z INFO     Loaded the first minibatch of training data in 0.08 sec.
2021-01-19T15:17:40Z INFO     Epoch 2 training took 4.73 sec, of which waiting for next minibatch took 0.12 sec total. 2 minibatches in total.
2021-01-19T15:17:41Z INFO     Loaded the first minibatch of validation data in 0.08 sec.
2021-01-19T15:17:42Z INFO     Epoch 2 validation took 1.31 sec, of which waiting for next minibatch took 0.08 sec total. 1 minibatches in total.
2021-01-19T15:17:42Z INFO     Saved model checkpoint for epoch 2 to /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/checkpoints/2_checkpoint.pth.tar
2021-01-19T15:17:42Z INFO     Finished training
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     **** FINISHED: Model training after 18.38 seconds **************************************************
2021-01-19T15:17:42Z INFO     
Attempted to log scalar metric Train epochs:
2
2021-01-19T15:17:42Z INFO     Using checkpoints from current run for epoch 2.
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     **** STARTING: Registering default model ***********************************************************
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     Could not load the run context. Logging offline
2021-01-19T15:17:42Z WARNING  Unable to retrieve AzureML workspace. Was the Azure setup completed?
2021-01-19T15:17:42Z INFO     No model was registered in AzureML.
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     **** FINISHED: Registering default model after 0.00 seconds ****************************************
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     **** STARTING: Running default model on test set ***************************************************
2021-01-19T15:17:42Z INFO     
2021-01-19T15:17:42Z INFO     Using checkpoints from current run for epoch 2.
2021-01-19T15:17:42Z INFO     Train: 3, Test: 1, and Val: 2. Total subjects: 6
2021-01-19T15:17:42Z INFO     Results directory: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/epoch_002/Test
2021-01-19T15:17:42Z INFO     Starting evaluation of model HelloWorld on epoch 2 Test set
2021-01-19T15:17:42Z INFO     Processing dataset (name=None)
2021-01-19T15:17:42Z INFO     Processing dataset (name=None)
2021-01-19T15:17:42Z INFO     Processing dataset (name=None)
2021-01-19T15:17:42Z INFO     Loading checkpoint /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/checkpoints/2_checkpoint.pth.tar
2021-01-19T15:17:42Z INFO     Loaded model from checkpoint (epoch: 2)
2021-01-19T15:17:42Z INFO     Writing model summary to: logs/model_summaries/model_log001.txt
Setting up logging with level 20 to file logs/model_summaries/model_log001.txt
2021-01-19T15:17:42Z INFO     Making no adjustments to the model because no GPU was found.
2021-01-19T15:17:43Z INFO     Predicting for image 1 of 1...
2021-01-19T15:17:43Z INFO     Inference pipeline (0), Predicting patient: 6
2021-01-19T15:17:58Z INFO     Evaluating predictions for patient 6
2021-01-19T15:18:00Z INFO     Finished evaluation of model HelloWorld on epoch 2 Test set
2021-01-19T15:18:00Z INFO     Epoch:   2 | Mean Dice: 0.222681
2021-01-19T15:18:00Z INFO     
2021-01-19T15:18:00Z INFO     **** FINISHED: Running default model on test set after 18.55 seconds *******************************
2021-01-19T15:18:00Z INFO     
2021-01-19T15:18:00Z INFO     
2021-01-19T15:18:00Z INFO     **** STARTING: Running default model on val set ****************************************************
2021-01-19T15:18:00Z INFO     
2021-01-19T15:18:00Z INFO     Using checkpoints from current run for epoch 2.
2021-01-19T15:18:00Z INFO     Train: 3, Test: 1, and Val: 2. Total subjects: 6
2021-01-19T15:18:00Z INFO     Results directory: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/epoch_002/Val
2021-01-19T15:18:00Z INFO     Starting evaluation of model HelloWorld on epoch 2 Val set
2021-01-19T15:18:00Z INFO     Processing dataset (name=None)
2021-01-19T15:18:00Z INFO     Processing dataset (name=None)
2021-01-19T15:18:00Z INFO     Processing dataset (name=None)
2021-01-19T15:18:00Z INFO     Loading checkpoint /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/checkpoints/2_checkpoint.pth.tar
2021-01-19T15:18:00Z INFO     Loaded model from checkpoint (epoch: 2)
2021-01-19T15:18:00Z INFO     Writing model summary to: logs/model_summaries/model_log002.txt
Setting up logging with level 20 to file logs/model_summaries/model_log002.txt
2021-01-19T15:18:01Z INFO     Making no adjustments to the model because no GPU was found.
2021-01-19T15:18:02Z INFO     Predicting for image 1 of 2...
2021-01-19T15:18:02Z INFO     Inference pipeline (0), Predicting patient: 4
2021-01-19T15:18:08Z INFO     Predicting for image 2 of 2...
2021-01-19T15:18:08Z INFO     Inference pipeline (0), Predicting patient: 5
2021-01-19T15:18:13Z INFO     Evaluating predictions for patient 4
2021-01-19T15:18:13Z INFO     Evaluating predictions for patient 5
2021-01-19T15:18:17Z INFO     Finished evaluation of model HelloWorld on epoch 2 Val set
2021-01-19T15:18:17Z INFO     Epoch:   2 | Mean Dice: 0.222681
2021-01-19T15:18:17Z INFO     
2021-01-19T15:18:17Z INFO     **** FINISHED: Running default model on val set after 16.34 seconds ********************************
2021-01-19T15:18:17Z INFO     
2021-01-19T15:18:17Z WARNING  Couldn't register model in offline mode
2021-01-19T15:18:17Z INFO     Saving report in html
Writing report to /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/report.ipynb
2021-01-19T15:18:17Z INFO     Input Notebook:  /home/athanell/projects/InnerEye-DeepLearning/InnerEye/ML/reports/segmentation_report.ipynb
2021-01-19T15:18:17Z INFO     Output Notebook: /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/report.ipynb
2021-01-19T15:18:17Z INFO     Generating grammar tables from /home/athanell/anaconda3/envs/InnerEye/lib/python3.7/site-packages/blib2to3/Grammar.txt
2021-01-19T15:18:17Z INFO     Writing grammar tables to /home/athanell/.cache/black/20.8b1/Grammar3.7.3.final.0.pickle
2021-01-19T15:18:17Z INFO     Writing failed: [Errno 2] No such file or directory: '/home/athanell/.cache/black/20.8b1/tmpxo8ehk_0'
2021-01-19T15:18:17Z INFO     Generating grammar tables from /home/athanell/anaconda3/envs/InnerEye/lib/python3.7/site-packages/blib2to3/PatternGrammar.txt
2021-01-19T15:18:17Z INFO     Writing grammar tables to /home/athanell/.cache/black/20.8b1/PatternGrammar3.7.3.final.0.pickle
2021-01-19T15:18:17Z INFO     Writing failed: [Errno 2] No such file or directory: '/home/athanell/.cache/black/20.8b1/tmp90_9zx5u'
2021-01-19T15:18:17Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': None,
 'id': 'impossible-palace',
 'metadata': {'papermill': {'duration': None,
                            'end_time': None,
                            'exception': None,
                            'start_time': None,
                            'status': 'pending'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:17Z INFO     Executing notebook with kernel: python3
2021-01-19T15:18:17Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': None,
 'id': 'impossible-palace',
 'metadata': {'papermill': {'duration': None,
                            'end_time': None,
                            'exception': None,
                            'start_time': None,
                            'status': 'pending'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:17Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': None,
 'id': 'impossible-palace',
 'metadata': {'papermill': {'duration': None,
                            'end_time': None,
                            'exception': None,
                            'start_time': None,
                            'status': 'pending'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:17Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': None,
 'id': 'impossible-palace',
 'metadata': {'papermill': {'duration': None,
                            'end_time': None,
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'running'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:17Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:18Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:18Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:18Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:18Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:18Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:19Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:20Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:20Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
Running conversion to HTML for /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/report.ipynb
2021-01-19T15:18:20Z ERROR    Notebook JSON is invalid: Additional properties are not allowed ('id' was unexpected)

Failed validating 'additionalProperties' in code_cell:

On instance['cells'][1]:
{'cell_type': 'code',
 'execution_count': 2,
 'id': 'impossible-palace',
 'metadata': {'execution': {'iopub.execute_input': '2021-01-19T15:18:17.995154Z',
                            'iopub.status.busy': '2021-01-19T15:18:17.994497Z',
                            'iopub.status.idle': '2021-01-19T15:18:17.996900Z',
                            'shell.execute_reply': '2021-01-19T15:18:17.997312Z'},
              'papermill': {'duration': 0.009306,
                            'end_time': '2021-01-19T15:18:17.997422',
                            'exception': False,
                            'start_time': '2021-01-19T15:18:17.988116',
                            'status': 'completed'},
              'tags': ['injected-parameters']},
 'outputs': ['...0 outputs...'],
 'source': '# Parameters\n'
           'innereye_path = "/home/athanell/projects/InnerEye-D...'}
2021-01-19T15:18:20Z INFO     Writing 631250 bytes to /home/athanell/projects/InnerEye-DeepLearning/outputs/2021-01-19T151718Z_HelloWorld/report.html
(InnerEye) athanell@InnerEyeVm:~/projects/InnerEye-DeepLearning$

The OS version is:

(InnerEye) athanell@InnerEyeVm:~/projects/InnerEye-DeepLearning$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.5 LTS
Release:        18.04
Codename:       bionic

The anaconda version is

athanell@InnerEyeVm:~/projects/InnerEye-DeepLearning$ conda list anaconda$
# packages in environment at /home/athanell/anaconda3:
#
# Name                    Version                   Build  Channel
anaconda                  2020.11                  py38_0

The python version is:

(InnerEye) athanell@InnerEyeVm:~/projects/InnerEye-DeepLearning$ python --version
Python 3.7.3
@Shruthi42 Shruthi42 mentioned this issue Jan 20, 2021
Merged
ant0nsc pushed a commit that referenced this issue Jan 20, 2021
@Shruthi42
Update notebook formats to 4.5 (#367)
db4d261 
With the accepted JEP to add cell IDs to the notebook format, notebooks now have a unique cell ID associated with each cell.

Fixes #365
@Shruthi42
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@athanell, thanks for reporting this. This is now fixed in the latest code by #367.

@athanell
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@Shruthi42 , thank you for resolving this issue so fast.

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Update notebook formats to 4.5 microsoft/InnerEye-DeepLearning
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@Shruthi42 @athanell