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Update example apps' test data path, patch hsdk in local env, and ensure correct MD SDK is used in dev env #516

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Merged
MMelQin merged 5 commits into from
Jan 17, 2025
Merged

Update example apps' test data path, patch hsdk in local env, and ensure correct MD SDK is used in dev env #516

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c60696a
Add post intall action to patch holoscan package, v2.7 and 2.8
MMelQin Jan 15, 2025
b6fbb45
Update fixed turorials
MMelQin Jan 16, 2025
abf9699
Updated the setup post install action, local sdk version, and noteboo…
MMelQin Jan 17, 2025
aaa4581
Updated the doc too
MMelQin Jan 17, 2025
f8089f6
Fix linting error
MMelQin Jan 17, 2025
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7 changes: 3 additions & 4 deletions docs/source/getting_started/tutorials/mednist_app.md
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Expand Up @@ -56,6 +56,8 @@ jupyter-lab

## Executing from Shell

**_Note:_** Data files are now access controlled. Please first request permission to access the [shared folder on Google Drive](https://drive.google.com/drive/folders/1EONJsrwbGsS30td0hs8zl4WKjihew1Z3?usp=sharing). Please download zip file, `mednist_classifier_data.zip` in the `medmist_classifier_app` folder, to the same folder as the notebook example.

```bash
# Clone the github project (the latest version of the main branch only)
git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git
Expand All @@ -67,11 +69,8 @@ pip install monai-deploy-app-sdk

# Download/Extract mednist_classifier_data.zip from https://drive.google.com/file/d/1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E/view?usp=sharing

# Download mednist_classifier_data.zip
pip install gdown
gdown https://drive.google.com/uc?id=1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E

# After downloading mednist_classifier_data.zip from the web browser or using gdown
# After having downloaded mednist_classifier_data.zip from the web browser or using gdown
unzip -o mednist_classifier_data.zip

# Install necessary packages required by the app
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7 changes: 3 additions & 4 deletions docs/source/getting_started/tutorials/monai_bundle_app.md
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Expand Up @@ -46,6 +46,8 @@ jupyter-lab

## Executing from Shell

**_Note:_** Data files are now access controlled. Please first request permission to access the [shared folder on Google Drive](https://drive.google.com/drive/folders/1EONJsrwbGsS30td0hs8zl4WKjihew1Z3?usp=sharing). Please download zip file, `mednist_classifieai_spleen_seg_bundle_data.zip` in the `ai_spleen_seg_app` folder, to the same folder as the notebook example.

```bash
# Clone the github project (the latest version of main branch only)
git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git
Expand All @@ -57,10 +59,7 @@ pip install --upgrade monai-deploy-app-sdk

# Download/Extract ai_spleen_bundle_data zip file from https://drive.google.com/file/d/1cJq0iQh_yzYIxVElSlVa141aEmHZADJh/view?usp=sharing

# Download the zip file containing both the model and test data
pip install gdown
gdown https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ

# Download the zip file containing both the model and test data.
# After downloading it using gdown, unzip the zip file saved by gdown and
# copy the model file into a folder structure that is required by CLI Packager
rm -rf dcm
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7 changes: 3 additions & 4 deletions docs/source/getting_started/tutorials/multi_model_app.md
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Expand Up @@ -34,6 +34,8 @@ jupyter-lab

## Executing from Shell

**_Note:_** Data files are now access controlled. Please first request permission to access the [shared folder on Google Drive](https://drive.google.com/drive/folders/1EONJsrwbGsS30td0hs8zl4WKjihew1Z3?usp=sharing). Please download zip file, `ai_multi_model_bundle_data.zip` in the `ai_multi_ai_app` folder, to the same folder as the notebook example.

```bash
# Clone the github project (the latest version of main branch only)
git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git
Expand All @@ -43,10 +45,7 @@ cd monai-deploy-app-sdk
# Install monai-deploy-app-sdk package
pip install --upgrade monai-deploy-app-sdk

# Download the zip file containing both the model and test data
pip install gdown
gdown https://drive.google.com/uc?id=1llJ4NGNTjY187RLX4MtlmHYhfGxBNWmd

# Download the zip file containing both the model and test data.
# After downloading it using gdown, unzip the zip file saved by gdown
rm -rf dcm && rm -rf multi_models
unzip -o ai_multi_model_bundle_data.zip
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11 changes: 4 additions & 7 deletions docs/source/getting_started/tutorials/segmentation_app.md
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Expand Up @@ -33,7 +33,9 @@ jupyter-lab
```

## Executing from Shell
Please note that this part of the example uses the latest application source code on Github, as well as the corresponding test data.

**_Note:_** Data files are now access controlled. Please first request permission to access the [shared folder on Google Drive](https://drive.google.com/drive/folders/1EONJsrwbGsS30td0hs8zl4WKjihew1Z3?usp=sharing). Please download zip file, `ai_spleen_seg_bundle_data.zip` in the `ai_spleen_seg_app` folder, to the same folder as the notebook example.

```bash
# Clone the github project (the latest version of main branch only)
git clone --branch main --depth 1 https://github.com/Project-MONAI/monai-deploy-app-sdk.git
Expand All @@ -43,12 +45,7 @@ cd monai-deploy-app-sdk
# Install monai-deploy-app-sdk package
pip install --upgrade monai-deploy-app-sdk

# Download/Extract ai_spleen_bundle_data zip file from https://drive.google.com/file/d/1cJq0iQh_yzYIxVElSlVa141aEmHZADJh/view?usp=sharing

# Download the zip file containing both the model and test data
pip install gdown
gdown https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ

# Download the zip file containing both the model and test data.
# After downloading it using gdown, unzip the zip file saved by gdown and
# copy the model file into a folder structure that is required by CLI Packager
rm -rf dcm
Expand Down
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