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    "info": {
        "author": "Layne Sadler",
        "author_email": "layne.sadler@gmail.com",
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            "License :: OSI Approved :: MIT License",
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            "Programming Language :: Python :: 3"
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        "description": "---\n# GORpyter\n\n1. Python package (with pandas serialization) that wraps the R SDK of the GOR Query API.\n2. Docker image for JupyterLab (Python & R kernels) with both the Python & R SDK dependencies installed.\n\n* `gp.query()` converts the R tibble dataframe into a pandas dataframe on the fly.\n* rpy2 package is used to wrap the gorr R library functions in Python.\n* Jupyter R kernel has tidyverse (tricky install) and gorr (non-CRAN) packages installed.\n* Docker image also includes OpenJDK 1.8 in case users want to install Spark.\n\n\n##### TLDR \n```\n$ docker pull hashrocketsyntax/gorpyter:augustus\n$ docker run -it -p 8888:8888 hashrocketsyntax/gorpyter:augustus\n```\nRead the rest of the documentation for complete setup & usage.\n\n---\n\n# 1. Docker Environment\n##### LOCAL NOTEBOOK FOLDER\nCreate a folder on your local machine's desktop where you will store your notebooks. Keep the output of `pwd` handy as we will use it with the `volumes` yml key below. You can name the folder whatever you like. We'll call it 'notebooks'\n```\n$ cd ~/Desktop\n$ mkdir notebooks\n$ cd notebooks\n$ pwd\n'<PATH_TO_YOUR_NEW_FOLDER>'\n```\n\n##### DOCKER HARDWARE RESOURCES\nIn order to convert large (1M rows) R dataframes to Pandas dataframes, your Docker environment may need access to more memory. The `memory` is the most important setting below.\n\n* Stop any running containers.\n* Click on Docker icon in system tray.\n* Navigate to 'Preferences.'\n* Click the 'Resources' or 'Advanced' tab depending on your version of Docker.\n* Set the resources to the following:\n* Click 'Apply & Restart'\n\n```\nCPU:              <keep default, should already be at 4 CPU>\nMemory:           <half of what's available in 'About this Mac', 4 or 8 GB>\nSwap:             <set to maximum, 4GB>\nDisk Image Size:  <keep default>\n```\n\n##### DOCKER IMAGE & MANIFEST\nPull in this pre-built image which contains a Jupyter environment equipped with R and Python 3.7 kernels as well as the GORpyter dependencies. It's built on top of Jupyter's latest DockerHub image `jupyter/datascience-notebook:2ce7c06a61a1`. If you want to customize this image your self, see Section 3.\n```\n$ docker pull hashrocketsyntax/gorpyter:augustus\n```\nCreate a file named `docker-compose.yml` and open it with a text editor (nano or SublimeText). \n```\n$ touch docker-compose.yml\n$ nano docker-compose.yml\n```\nPaste the text below into that file. Under the `volumes` key, paste in the output of `pwd` from above.\n```\n#docker-compose.yml\nversion: \"3\"\nservices:\n  jupyter:\n    image: \"hashrocketsyntax/gorpyter:augustus\"\n    ports:\n      - \"8888:8888\"\n    volumes:\n      - <PATH_TO_YOUR_NEW_FOLDER>:/usr/local/share/man/user_notebooks\n```\nMake sure you are in the same directory as the .yml file and run it like so.\n```\n$ docker-compose up\n```\nFrom the console output, grab the URL that looks like this `http://127.0.0.1:8888/?token=<YOUR_TOKEN>` and paste it into a browser.\n\n---\n\n# 2. JupyterLab Notebooks\n##### TUTORIAL NOTEBOOKS\nThe Docker environment comes with example notebooks for both the Python and R SDK.\n\nIf you are running these notebook in the pre-built Docker environment, know that only files in the `user_notebooks` folder will be saved/ persisted. In fact, you won't be able to add/remove/copy/delete/save-changes to files outside of the `user_notebooks` directory.\n\n```\n#python_sdk_gorpyter.ipynb\n\n\npip install gorpyter --upgrade\nimport gorpyter as gp\n\n\ngp.setup()\n\"\"\"\n  CHECKLIST\n  =============================================\n\n\t\u2713 -- The version of your Jupyter Python environment is '3.7.3'.\n\t\u2713 -- The path of the Jupyter R enviroment being accessed by `rpy2` is '/opt/conda/lib/R'.\n\n\t\u2713 -- The Python dependencies of `gorpyter` are installed.\n\t\u2713 -- The `tidyverse` R library is installed in your R environment.\n\t\u2713 -- The `gorr` R library is installed in your R environment.\n\t\u2713 -- Python was able to successfully load `gorr` as a module via `rpy2`.\n\n  =============================================\n\"\"\"\n\n\napi_key = \"<YOUR_API_KEY>\"\nproject = \"<YOUR_PROJECT_NAME>\"\nconn = gp.connect(api_key, project)\n\n\ngp.query(\"<YOUR_GOR_QUERY>\", conn)\n\"\"\"\n\tnor example -- \"nor ./\"\n\tgor example -- \"gor -p chr10 #dbsnp# | TOP 100\"\n\n\tTested successfully on a 1,000,000 row result.\n\n\tDespite being run in Python, interupting the client's execution \n  of this function in `ctrl+c` manner is surprisingly still gracefully \n  intercepted by the gorr R library, and thus the server-side \n  execution of the query is simultaneously cleaned up.\n\"\"\"\n```\n##### PYTHON PACKAGE\n```\npip install gorpyter --upgrade\n```\n* `conda install` will *not* work as this package has not been published to conda-forge.\n* Latest version number can be seen here `https://pypi.org/project/gorpyter`, as compared to output of `pip show gorpyter`.\n* Installing gorpyter will also install these dependencies: rpy2>=3.0.5, tzlocal>=2.0.0, pandas>=0.25.0, numpy>=1.17.0.\n\n##### GOR QUERY LANGUAGE\n> http://docs.wuxinextcode.com/gor/basicGORqueries.html\n\n---\n\n# 3. Optional -- Customizing the Docker Image\nIn order to create your own Docker image based on `jupyter/datascience-notebook:latest`, follow these instructions.\n\nWith these files in the same directory:\n* Dockerfile\n* python_sdk.ipynb\n* r_sdk.ipynb\n\nRun `docker build -t your-image-name:your-new-tag .` from within that directory.\n\nHere are the commands contained in the Dockerfile.\n```\n#Dockerfile\nFROM jupyter/datascience-notebook:latest\nMAINTAINER layne sadler <lsadler@wuxinextcode.com>\n\n\n# ====== PRE SUDO ======\nENV JUPYTER_ENABLE_LAB=yes\n\n# If you run pip as sudo it continually prints errors.\n# Tidyverse is already installed, and installing gorpyter installs the correct versions of other Python dependencies.\nRUN pip install gorpyter\nRUN Rscript -e \"install.packages('https://cdn.nextcode.com/public/libraries/gorr_0.2.5.tar.gz', repos = NULL, type = 'source')\"\nENV R_HOME=/opt/conda/lib/R\n\n# https://refspecs.linuxfoundation.org/FHS_3.0/fhs/ch04s09.html\n# Looks like /usr/local/man is symlinking all R/W toward /usr/local/share/man instead\nCOPY python_sdk.ipynb /usr/local/share/man\nCOPY r_sdk.ipynb /usr/local/share/man\nENV NOTEBOOK_DIR=/usr/local/share/man\nWORKDIR /usr/local/share/man\n\n\n# ====== SUDO ======\nUSER root\n\n# Spark requires Java 8.\nRUN sudo apt-get update && sudo apt-get install openjdk-8-jdk -y\nENV JAVA_HOME=/usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java\n\n# If you COPY files into the same VOLUME that you mount in docker-compose.yml, then those files will disappear at runtime.\n# `user_notebooks/` is the folder that gets mapped as a VOLUME to the user's local folder during runtime.\nRUN mkdir /usr/local/share/man/user_notebooks\n```\n\n",
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