[BUG] ERROR: Failed to fetch MAP manifest.

[jpcenteno80]

Describe the bug
Above error displayed when trying to run packaged app.

Steps/Code to reproduce bug

# Inside monai-deploy-app-sdk/examples/apps/
monai-deploy package ./simple_imaging_app -t simple_app:latest

# output:
Building MONAI Application Package... Done
[2021-10-08 11:04:07,763] [INFO] (app_packager) - Successfully built simple_app:latest

monai-deploy run simple_app:latest input output # where input has brain_mr_input.jpg and output is an empty directory

# output:
Checking dependencies...
--> Verifying if "docker" is installed...

--> Verifying if "simple_app:latest" is available...

Checking for MAP "simple_app:latest" locally
"simple_app:latest" found.

Reading MONAI App Package manifest...
 > export '/var/run/monai/export/' detected
fatal: Access to the path '/var/run/monai/export/config/pkg.json' is denied.
ERROR: Failed to fetch MAP manifest.
Execution Aborted

Expected behavior
App should run.

Environment details (please complete the following information)

• OS/Platform: Ubuntu 18
• Python Version: 3.9.7
• Method of MONAI Deploy App SDK install: pip install monai-deploy-app-sdk
• SDK Version: 0.1.0

Additional context
This is an AWS instance where I created my own user. App was packaged under my user.

[gigony]

Hi @jpcenteno80 !

Thanks for the report!

The issue was reproducible and the fix is available by #168.
Could you please confirm if the issue is fixed by the following patch package?

pip install -i https://test.pypi.org/simple/ monai-deploy-app-sdk==0.0.165

Thanks!

[jpcenteno80]

Thank you, the issue was fixed.

On a separate note, I'm still learning how to package apps with the proper requirements. I am using the following directive:

@md.env(pip_packages=['monai==0.7.0', 'numpy>=1.20.1', 'SimpleITK>=2.0.2'])

The app I am building is very similar to the simple_imaging_app from your examples. First I built it without monai==0.7.0 and it gave me an error when I tried to run the app (did not find a monai package). Then I added the monai requirement and the packaged app worked. Where I was a bit confused, is why it did not throw an error about monai-deploy-app-sdk not being in the requirements. I guess it is just picking that up for "free" since I am packaging it using monai-deploy. I just thought that monai alone would also be picked up "automatically", without need to specify it in the requirements.

Thanks for the patch!

[gigony]

Thanks @jpcenteno80 for the feedback!

monai-deploy-app-sdk package and its dependent pip packages are copied/added by default when monai-deploy package command is used.

monai-deploy-app-sdk/monai/deploy/packager/util.py

Lines 155 to 158 in 41eddc4

	# Copy monai-app-sdk module to temp directory (under 'monai-deploy-app-sdk' folder)
	monai_app_sdk_path = os.path.join(dist_module_path("monai-deploy-app-sdk"), "monai", "deploy")
	target_monai_app_sdk_path = os.path.join(temp_dir, "monai-deploy-app-sdk")
	shutil.copytree(monai_app_sdk_path, target_monai_app_sdk_path)

monai-deploy-app-sdk/monai/deploy/packager/util.py

Lines 165 to 167 in 41eddc4

	# Append required packages for SDK to pip_packages
	monai_app_sdk_requires = dist_requires("monai-deploy-app-sdk")
	pip_packages.extend(monai_app_sdk_requires)

monai-deploy-app-sdk/monai/deploy/packager/templates.py

Line 47 in 20bb941

COPY --chown=monai:monai ./monai-deploy-app-sdk /home/monai/.local/lib/python3.8/site-packages/monai/deploy/

monai-deploy-app-sdk is a general-purpose deploy framework on the healthcare domain (such as genomics/biochemistry workflows) so it doesn't depend on monai package (MONAI Core) and it needs to be manually specified if your application uses monai package.

We have a plan to support automatic inferring pip packages used in the application in the future.

• [FEA] Support inferring pip packages used in the application when packaging the app #170

Could you please share the error message when monai library is not specified in @md.env decorator?

Was your application using monai library?
If not, it is a bug and I have a fix for that below.

• Make InMemImageReader work even when monai is not used/available #169

Please let us know.

Thank you for trying out MONAI Deploy App SDK and giving us the valuable feedback!

[jpcenteno80]

Thanks for the additional information.

Back to the error when monai is not specified in the @md.env decorator:
The app I created does not use monai directly, it relies on the operators already implemented in monai-deploy-app-sdk plus an additional operator created by me. Imports for both app.py and my own nrrd_converter_operator.py are below:

# app.py
from monai.deploy.core import Application
from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
from monai.deploy.operators.dicom_series_selector_operator import DICOMSeriesSelectorOperator
from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator
from nrrd_converter_operator import NRRDConverterOperator

# nrrd_converter_operator.py
import hashlib, os
import numpy as np, SimpleITK as sitk

import monai.deploy.core as md
from monai.deploy.core import DataPath, ExecutionContext, Image, InputContext, IOType, Operator, OutputContext
from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
from monai.deploy.operators.dicom_series_to_volume_operator import DICOMSeriesToVolumeOperator

The error I was getting before adding monai to the @md.env decorator is the following:

Checking dependencies...
--> Verifying if "docker" is installed...

--> Verifying if "dicom_to_nrrd_op:latest" is available...

Checking for MAP "dicom_to_nrrd_op:latest" locally
"dicom_to_nrrd_op:latest" found.

Reading MONAI App Package manifest...
Traceback (most recent call last):
  File "/opt/monai/app/app.py", line 2, in <module>
    from monai.deploy.operators.dicom_data_loader_operator import DICOMDataLoaderOperator
  File "/home/monai/.local/lib/python3.8/site-packages/monai/deploy/operators/__init__.py", line 29, in <module>
    from .monai_seg_inference_operator import MonaiSegInferenceOperator
  File "/home/monai/.local/lib/python3.8/site-packages/monai/deploy/operators/monai_seg_inference_operator.py", line 237, in <module>
    class InMemImageReader(ImageReader):
  File "/home/monai/.local/lib/python3.8/site-packages/monai/deploy/utils/importutil.py", line 258, in __getattr__
    raise self._exception
  File "/home/monai/.local/lib/python3.8/site-packages/monai/deploy/utils/importutil.py", line 217, in optional_import
    pkg = __import__(module)  # top level module
monai.deploy.utils.importutil.OptionalImportError: from monai.data import ImageReader (No module named 'monai.data').

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

And an additional comment regarding image sizes... I noticed in the documentation that future support for smaller base images is in the pipeline, so that is great. This small app I created is ~15 gigs, using the default nvidia pytorch image:

nvcr.io/nvidia/pytorch   21.07-py3                 7beec3ff8d35        2 months ago        15GB

I tried to build it with a smaller base image, but it throws an error:

monai-deploy package src/dicom_series_to_nrrd_app -t dicom_to_nrrd_op:latest -b nvcr.io/nvidia/cuda:11.4.1-base-ubuntu18.04 

# error
Building MONAI Application Package... -The command '/bin/sh -c pip install --no-cache-dir --upgrade -r /tmp/requirements.txt' returned a non-zero code: 1

Also noticed in the documentation that images from nvcr.io are supported, so that is why I tried the command above.

# from the docs
The current implementation (as of 0.1.0) of the Packager ONLY supports CUDA and Pytorch images from nvcr.io as base images for the MAP. There are efforts in progress to add support for smaller images from dockerhub.

Thanks again for the help!