SynBioHub Submit plugin draft

This is a simple FASTA -> SBOL submit plugin

Submit plugin architecture

1. SynBioHub sends a submit manifest to the /evaluate endpoint of the plugin
   • For each file in the submission, the manifest will have a filename, a url where the file can be accessed, and a edam type, which is a URL representing SynBioHub's best guess at the file type.
   • The plugin should respond with a list of needs for each file, with each need containing a filename, and a requirement, where the requirement is 0 if the plugin will ignore the file, 1 if the plugin will reference the file but not convert it to SBOL, and 2 if the plugin will convert the file to SBOL.
   • Demo: This plugin simply reads the first byte of the file, and if it is '>', it assumes that it is a FASTA file and says it will convert it to SBOL.
2. SynBioHub will decide which plugins will handle which files, and send an updated manifest to the /run endpoint of each plugin. The updated manifest will only contain the files which the plugin said it needed.
3. The plugin should convert its files into SBOL. It may create one or more SBOL files. It should also create a manifest file, which describes which input files were used to create which output files.
4. The manifest and all resulting plugin files should be zipped together by the plugin, and sent as a response to the /run request.

Example evaluate manifest

{
    "manifest": [{
        "url": "https://mineshaft.zach.network/4ccc8279-001a-440d-acc4-547ec51610ef.fasta",
        "filename": "zach.fasta",
        "edam": "http://edamontology.org/format_2330"
    }, {
        "url": "https://mineshaft.zach.network/ee8fc566-e416-4903-aaa7-9fce84fcd539.fasta",
        "filename": "jet.fasta",
        "edam": "http://edamontology.org/format_2330"
    }, {
        "url": "https://mineshaft.zach.network/49bc7acc-419a-47a0-9086-b4011e82f55d.sbol",
        "filename": "zach.sbol",
        "edam": "http://edamontology.org/format_2330"
    }]
}

Example evaluate response

{
    "manifest": [{
        "filename": "zach.fasta",
        "requirement": 2
    }, {
        "filename": "jet.fasta",
        "requirement": 2
    }, {
        "filename": "zach.sbol",
        "requirement": 0
    }]
}

Example run request

{
    "manifest": [{
        "url": "https://mineshaft.zach.network/4ccc8279-001a-440d-acc4-547ec51610ef.fasta",
        "filename": "zach.fasta",
        "edam": "http://edamontology.org/format_2330"
    }, {
        "url": "https://mineshaft.zach.network/ee8fc566-e416-4903-aaa7-9fce84fcd539.fasta",
        "filename": "jet.fasta",
        "edam": "http://edamontology.org/format_2330"
    }]
}

Example response manifest

{
    "results": [{
        "filename": "zach.fasta.converted",
        "sources": ["zach.fasta"]
    }, {
        "filename": "jet.fasta.converted",
        "sources": ["jet.fasta"]
    }]
}