Initial commit

.env

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+username=[email protected]
+submission_name = 'TristanF_Submission_1'
+password = "CWFKDLx33xwdnKtQRs"
+project_id = "syn41016074"
+SYNAPSE_AUTH_TOKEN ="eyJ0eXAiOiJKV1QiLCJraWQiOiJXN05OOldMSlQ6SjVSSzpMN1RMOlQ3TDc6M1ZYNjpKRU9VOjY0NFI6VTNJWDo1S1oyOjdaQ0s6RlBUSCIsImFsZyI6IlJTMjU2In0.eyJhY2Nlc3MiOnsic2NvcGUiOlsidmlldyIsImRvd25sb2FkIiwibW9kaWZ5Il0sIm9pZGNfY2xhaW1zIjp7fX0sInRva2VuX3R5cGUiOiJQRVJTT05BTF9BQ0NFU1NfVE9LRU4iLCJpc3MiOiJodHRwczovL3JlcG8tcHJvZC00MjYtMS5wcm9kLnNhZ2ViYXNlLm9yZy9hdXRoL3YxIiwiYXVkIjoiMCIsIm5iZiI6MTY2NjI2ODk0NSwiaWF0IjoxNjY2MjY4OTQ1LCJqdGkiOiIyMTU4Iiwic3ViIjoiMzQwMTIyMyJ9.Dv861iWmvJPbz85hrr0Tt67HixicgJG7gun5hrhhRsFabkR4auFRJuUSBaosuZqnQFzJcuLaAhbf-ZSIglss-TUcupRdM0zZQj8oDVvdLc0soUYznxttiUb5oigH0WsTmZT9Pab-Hqx8veEvKzIzKfxc_Xnlfqtxrq3Fg3xGGM-5TPxhgFTWycMmWtGci0wfuv1O0_LpsOlB7X5EKKOc6nEW3ijfrJXVIZjjDAgr1IVhusZIBY2pSTexXZW3RPW_tkAPl6tL8q7Vdhyb4p6hPopgp7A-4G-bqtAbudNihmd14PHBmtAXinCIOSBB8fMMUlhSWGmCvS5bA_c_A8dqyg"
+root_folder = "/home/tristan/Desktop/DreamHF"

.gitattributes

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+.env export-ignore

.gitignore

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+*.csv
+*.odt
+*.sif
+.Rproj.user
+R_baseline/
+TODO.md
+config.py
+*.zip
+*.mp4
+References/

Makefile

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+init:
+	pip install -r requirements.txt
+
+test:
+	nosetests tests

README.md

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+# Template-Python-Singularity
+## A template to build executable Singularity images in Python projects
+
+### Objective
+
+This repo contains a template to create a Python app that will run in an executable Singularity image. A Singularity containers can typically be used in data science projects to provide transparency and support of reproducibility.
+
+### Content
+
+* `singularity/`: singularity container
+  * singularity_test
+* `utils/` : utility scripts (to make submissions, etc)
+
+* `src/`: models
+* `data/` : input data
+* `output/` : where code output is stored
+
+### Instruction to build the singularity container from the recipe.txt
+
+To create an executable singularity container (which contains the code in /src), run :
+
+```bash
+./utils/build_container.sh
+```
+
+This will create a container container.sif in /singularity.
+To test the executable singularity container, run :
+
+```bash
+./utils/test_container.sh
+```
+
+This will output the results in singularity/test_singularity/output.
+
+### Instructions to run the model
+
+The singularity container container.sif is executable, you can reproduce the results by running:
+
+```bash
+singularity run ./singularity/container.sif <Argument for input path>
+```
+
+Note: `<Argument for input path> ` is optional, default is ./
+
+
+Note that container.sif should be in the same folder as /training and /test.
+The prediction scores on test dataset are saved in `./output/scores.csv`.
+### Instructions to run a custom model in the same environment
+
+To run a model locally on synthetic data in the container environement, activate the singularity container in Terminal using:
+
+```bash
+singularity shell ./singularity/container.sif
+```
+
+This will allow you to have an environment (`Singularity>`) to run the model without installing any additional package.
+In order to run the model, run the following command :
+
+```bash
+Singularity> python3 src/model.py <Argument for input path>
+```
+
+For example, on my computer, when my cwd is the DreamHF folder, I run :
+
+```bash
+Singularity> python3 src/model.py ./
+```
+
+This command can also be used to run the singularity without accessing the singularity shell:
+
+```bash
+singularity exec container.sif python3 src/model.py <Argument for input path>
+```
+
+
+### License
+
+This software is distributed under the GNU GENERAL PUBLIC LICENSE. Please refer to the file LICENCE.txt included for details.

requirements.txt

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+numpy==1.21.5
+pandas==1.3.5
+python-dotenv==0.21.0
+scikit_learn==1.0.2
+scikit_survival==0.17.2
+scipy==1.7.3
+synapseclient==2.7.0

singularity/recipe.txt

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+Bootstrap: docker
+FROM: python:latest
+
+%labels
+  Version v1.0
+
+%help
+  Singularity image for DreamChallenge
+
+%setup
+	mkdir -p ${SINGULARITY_ROOTFS}/src
+
+%files   
+    	./src/* /src
+
+%post
+## Install the required python packages
+	pip install numpy==1.21.5
+	pip install pandas==1.3.5
+	pip install scikit_survival==0.17.2
+	pip install scipy==1.7.3 
+	pip install python-dotenv==0.21.0 
+	pip install synapseclient==2.7.0
+
+%runscript
+	if [ $# -ne 1 ]; then
+		echo "No input directory provided, default is ./"
+		STR=$(pwd)
+		python3 ${SINGULARITY_ROOTFS}/src/model.py "${STR}"
+	else
+		python3 ${SINGULARITY_ROOTFS}/src/model.py $1
+	fi
+
+# Update apt-get
+#RUN apt-get update \
+#	&& apt-get install -y --no-install-recommends apt-utils \
+#	&& apt-get install -y --no-install-recommends \
+#	 \
+#	&& apt-get clean \
+#	&& rm -rf /var/lib/apt/lists/*

singularity/test_singularity/README.md

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+# Heart Failure Prediction : Microbiome
+## FINRISK DREAM Challenge 2022
+
+Author : Tristan Fauvel
+
+### This folder contains the necessary tools to test the execution of the submitted singularity container.

utils/.env -sample

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+username = "my_username"
+submission_name = "my_submission_name"
+password = "azerty123"
+project_id = "syn1234"
+SYNAPSE_AUTH_TOKEN ="TOKEN"
+root_folder = "/home/tristan/Desktop/DreamHF/"

utils/build_container.sh

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+#! /bin/bash
+echo "Building the singularity container ./singularity/container.sif from ./singularity/recipe.txt"
+sudo singularity build --force ./singularity/container.sif ./singularity/recipe.txt
+echo "Copying ./singularity/container.sif to ./singularity/test_singularity"
+cp ./singularity/container.sif ./singularity/test_singularity

utils/test_container.sh

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+#! /bin/bash
+echo "Run container.sif, check outputs in ./singularity/test_singularity/output"
+singularity run ./singularity/test_singularity/container.sif ./singularity/test_singularity
+read -p "Proceed to the second test? " -n 1 -r
+echo    # (optional) move to a new line
+if [[ $REPLY =~ ^[Yy]$ ]]
+then
+    singularity run ./singularity/test_singularity/container.sif  
+fi
+
+
+
+
+