Metadata-Version: 2.1
Name: synapsegenie
Version: 0.0.1
Summary: Synapse flat file validation and processing pipeline
Home-page: https://github.com/Sage-Bionetworks/synapsegenie
Author: Thomas Yu
Author-email: thomas.yu@sagebionetworks.org
License: MIT
Description: # Synapse Genie
        
        ## Introduction
        
        This package can deploy a AACR GENIE like project on Synapse and perform validation and processing of files.
        
        ## Installation
        
        Dependencies:
        - Python 3.6 or higher
        - [synapseclient](http://python-docs.synapse.org) (`pip install synapseclient`)
        - Python [pandas](http://pandas.pydata.org) (`pip install pandas`)
        
        ```
        pip install synapsegenie
        synapsegenie -v
        ```
        
        ## Usage
        
        ### Creating your own registry
        Please view the [example registry](example_registry) to learn how to utilize `synapsegenie`.  `synapsegenie` allows a user to create a registry package with a list of file formats.  Each of these file format classes should extend `synapsegenie.example_filetype_format.FileTypeFormat`.  Learn more about creating Python packages [here](https://packaging.python.org/tutorials/packaging-projects/).  Once you have installed your registry package, you can now use the `synapsegenie` command line client.
        
        ### synapsegenie Synapse project
        A `synapsegenie` Synapse project must exist for you to fully utilize this package.  There is now a command to create this infrastructure in Synapse.  If you already have an existing Synapse Project you would like to use, please use the `--project_id` parameter, otherwise please use the `--project_name` parameter to create a new Synapse project.
        
        ```
        synapsegenie bootstrap-infra --format_registry_packages example_registry \
                                     --project_name "My Project Name"
                                     --centers AAA BBB CCC
        ```
        
        If you decide to add centers at a later date, you can re-run this command and the center will be added
        
        ```
        synapsegenie bootstrap-infra --format_registry_packages example_registry \
                                     --project_id syn12345
                                     --centers AAA BBB CCC DDD
        ```
        
        ### File Validator
        The `synapsegenie` package also has a function to run the validator locally on all of your files. Please view the help to see how to run to validator.
        
        ```
        synapsegenie validate-single-file -h
        
        synapsegenie /path/to/file center_name \
                     --format_registry_packages example_registry \
                     --project_id syn12345 \ # Run bootstrap-infra to create a Synapse project
        ```
        
        ### Validation/Processing
        `synapsegenie` will validate and process all the files uploaded by centers.  Every valid file will be processed and uploaded into Synapse tables.
        
        ```
        synapsegenie process -h
        
        # only validate
        synapsegenie process --format_registry_packages example_registry \
                             --project_id syn12345
                             --only_validate
        
        # validate + process
        synapsegenie process --format_registry_packages example_registry \
                             --project_id syn12345
        ```
        
        ## Contributing
        
        To learn how to contribute, please read the [contributing guide](CONTRIBUTING.md)
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
