Metadata-Version: 1.1
Name: cerebralcortex-kernel
Version: 3.0.0.post13
Summary: Backend data analytics platform for MD2K software
Home-page: https://github.com/MD2Korg/CerebralCortex/
Author: MD2K.org
Author-email: dev@md2k.org
License: BSD2
Description: # CerebralCortex Kernel
        Cerebral Cortex is the big data cloud companion of mCerebrum designed to support population-scale data analysis, visualization, model development, and intervention design for mobile sensor data.
        
        You can find more information about MD2K software on our [software website](https://md2k.org/software) or the MD2K organization on our [MD2K website](https://md2k.org/).
        
        CerebralCortex Kernel is part of our [CerebralCortex cloud platform](https://github.com/MD2Korg/CerebralCortex). CerebralCortex Kernel is mainly responsible to store/retrieve mobile sensor data along with it's metadata. 
        
        **Note**:
        
        We have renamed following repositories.
        
        * CerebralCortex-Platform -> CerebralCortex
        * CerebralCortex - >  CerebralCortex-Kernel
        
        ## Documentation
        
        - [Source code documentation](https://cerebralcortex-kernel.readthedocs.io/en/3.0.1/)
        
        ## Installation
        CerebralCortex-Kernel is a part of CerebralCortex cloud platform. To test the complete cloud platform, please visit [CerebralCortex](https://github.com/MD2Korg/CerebralCortex).
        
        CerebralCortex-Kernel requires minimum [Python3.6](https://www.python.org/downloads/release/python-360/). To install CerebralCortex-Kernel as an API:
        
        ```pip3 install cerebralcortex-kernel```
        
        - Note: please use appropriate pip (e.g., pip, pip3, pip3.6 etc.) installed on your machine 
        
        
        ## Code Example
        Please have a look at [example code](https://github.com/MD2Korg/CerebralCortex-Kernel-Examples), if you want to only see an example on how to call CerebralCortex-Kernel API.
         
        ## FAQ
        **1 - Do I need whole CerebralCortex cloud platform to use CerebralCortex-Kernal?**
        
        No! If you want to use CerebralCortex-Kernel independently then you would need: 
        * Backend storage (FileSystem/HDFS and MySQL) with some data. Here is [some sample data](TODO) to play with.
        * Setup the [configurations](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/conf)
        * Use the [examples](TODO) to start exploring data
        
        **2 - I do not want tCerebralCortex-kernel (Examples)
        ================================
        
        This directory contains some of the following examples on how to
        get/save data streams and perform basic operations:
        
        -  Window stream data into 1 minute chunks
        
        Dependencies
        ------------
        
        -  `Python3.6`_
        
           -  Note: Python3.7 is not compatible with some of the requirements
           -  Make sure pip version matches Python version
        
        -  spark 2.4
        
           -  Download and extract `Spark 2.4`_
        
              -  ``cd ~/``
              -  ``wget http://apache.claz.org/spark/spark-2.4.0/spark-2.4.0-bin-hadoop2.7.tgz``
              -  ``tar -xzf spark*.tar.gz``
        
           -  Spark requires Java-8 installed
           -  Edit ``SPARK_HOME`` in
              ``CerebralCortex-Kernel-Examples/examples/basic_windowing/run.sh``
              to point to the location you extracted Spark to.
        
              -  ex: ``export SPARK_HOME=~/spark-2.4.0-bin/hadoop2.7/`` if Spark
                 was extracted to your home directory.
        
           -  ``export PYTHONPATH="${PYTHONPATH}":PATH-OF-MAIN-DIR/CerebralCortex-Kernel-Examples``
              (This is defined in
              ``CerebralCortex-Kernel-Examples/examples/basic_windowing/run.sh``)
        
        -  MySQL > 5.7
        
           -  You might have to set up a MySQL user.
        
        Installation
        ------------
        
        -  ``git clone https://github.com/MD2Korg/CerebralCortex-Kernel-Examples.git``
        
        -  ``cd CerebralCortex-Kernel-Examples``
        
        -  ``sudo pip3 install -r requirements.txt``
        
           -  Note: please use appropriate pip (e.g., pip, pip3, pip3.6 etc.)
              installed on your machine
        
        Configure CerebralCortex-Kernel
        -------------------------------
        
        -  Update MySQL settings in
           ``CerebralCortex-Kernel-Examples/conf/cerebralcortex.yml`` file, for
           example, mysql username, password etc.. Please look at the comments
           on what params shall be updated.
        
        How to run the example code?
        ----------------------------
        
        -  **Import MySQL Database:**
        
           -  ``cd CerebralCortex-Kernel-Examples/resources/db``
           -  ``mysql -u MySQL-USERNAME -pMySQL-PASSWORD < cerebralcortex.sql``
        
        -  **Run example**
        
           -  ``cd CerebralCortex-Kernel-Examples/examples/basic_windowing``
           -  ``sh run.sh``
        
        If everything works well then example code will produce similar output
        on console as below:
        
        ::
        
            +--------------------+--------------------+--------------------+
            |                user|              window|       battery_level|
            +--------------------+--------------------+--------------------+
            |00000000-afb8-476...|[2019-01-09 11:35...|[100, 100, 100, 1...|
            |00000000-afb8-476...|[2019-01-09 11:41...|[97, 97, 97, 97, ...|
            |00000000-afb8-476...|[2019-01-09 11:43...|[96, 96, 96, 96, ...|
            |00000000-afb8-476...|[2019-01-09 11:38...|[99, 99, 99, 99, ...|
            |00000000-afb8-476...|[2019-01-09 11:39...|[98, 98, 98, 98, ...|
            +--------------------+--------------------+--------------------+
            only showing top 5 rows
            
            BATTERY--org.md2k.phonesensor--PHONE-windowed-data has been stored.
        
        .. _Python3.6: https://www.python.org/downloads/release/python-360/
        .. _Spark 2.4: https://spark.apache.org/downloads.htmlo use FileSystem/HDFS as NoSQL storage. How can I change NoSQL storage backend?**
        
        CerebralCortex-Kernel follows component based structure. This makes it easier to add/remove features. 
        * Add a new class in [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/). 
        * New class must have read/write methods. Here is a sample [skeleton class](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/storage_blueprint.py) with mandatory methods required in the new class.
        * Create an object of new class in [Data-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/raw/data.py) with appropriate parameters.
        * Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in (NoSQL Storage)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml#L8] section.
        
        **3 - How can I replace MySQL with another SQL storage system?** 
        
        * Add a new class in [Data manager-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/tree/master/cerebralcortex/core/data_manager/sql). 
        * New class must implement all of the methods available in (stream_handler.py)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/stream_handler.py] class.
        * Create an object of new class in [Data-SQL](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/sql/data.py) with appropriate parameters.
        * Add appropriate configurations in [cerebralcortex.yml](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml) in (Relational Storage)[https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/conf/cerebralcortex.yml#L31] section.
        
        **4 - Where are all the backend storage related classes/methods?**    
        
        In [Data manager-Raw](https://github.com/MD2Korg/CerebralCortex-Kernel/blob/master/cerebralcortex/core/data_manager/). You can add/change any backend storage.
        
        
        ## Contributing
        Please read our [Contributing Guidelines](https://md2k.org/contributing/contributing-guidelines.html) for details on the process for submitting pull requests to us.
        
        We use the [Python PEP 8 Style Guide](https://www.python.org/dev/peps/pep-0008/).
        
        Our [Code of Conduct](https://md2k.org/contributing/code-of-conduct.html) is the [Contributor Covenant](https://www.contributor-covenant.org/).
        
        Bug reports can be submitted through [JIRA](https://md2korg.atlassian.net/secure/Dashboard.jspa).
        
        Our discussion forum can be found [here](https://discuss.md2k.org/).
        
        ## Versioning
        
        We use [Semantic Versioning](https://semver.org/) for versioning the software which is based on the following guidelines.
        
        MAJOR.MINOR.PATCH (example: 3.0.12)
        
          1. MAJOR version when incompatible API changes are made,
          2. MINOR version when functionality is added in a backwards-compatible manner, and
          3. PATCH version when backwards-compatible bug fixes are introduced.
        
        For the versions available, see [this repository's tags](https://github.com/MD2Korg/CerebralCortex/tags).
        
        ## Contributors
        
        Link to the [list of contributors](https://github.com/MD2Korg/CerebralCortex-Kernel/graphs/contributors) who participated in this project.
        
        ## License
        
        This project is licensed under the BSD 2-Clause - see the [license](https://md2k.org/software-under-the-hood/software-uth-license) file for details.
        
        ## Acknowledgments
        
        * [National Institutes of Health](https://www.nih.gov/) - [Big Data to Knowledge Initiative](https://datascience.nih.gov/bd2k)
          * Grants: R01MD010362, 1UG1DA04030901, 1U54EB020404, 1R01CA190329, 1R01DE02524, R00MD010468, 3UH2DA041713, 10555SC
        * [National Science Foundation](https://www.nsf.gov/)
          * Grants: 1640813, 1722646
        * [Intelligence Advanced Research Projects Activity](https://www.iarpa.gov/)
          * Contract: 2017-17042800006
Keywords: mHealth machine-learning data-analysis
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: System :: Distributed Computing
