PODP mode and local data mode

[CunliangGeng]

To enable local mode and podp mode, the pipeline of arranging data is redesigned. The pipeline will be implemented in a new class DatasetArranger.

flowchart LR

    ConfigError[Dynaconf config validation error]
    DataError[Data validation error]
    UseIt[Use the data]
    Download[Download or generate, and remove existing data if relevent]

    A[GNPS, antiSMASH and BigSCape] --> B{Pass Dynaconf config validation?}
    B -->|No | ConfigError
    
    B -->|Yes| G{Is the mode PODP?}
    
    G -->|No, local mode| G1{Does local data dir exist?}
    G1 -->|No | DataError
    G1 -->|Yes| H{Pass data validation?}
    H --> |No | DataError
    H --> |Yes| UseIt 

    G -->|Yes, podp mode| G2{Does local data dir exist?}
    G2 --> |No | Download
    G2 --> |Yes | J{Pass data validation?}
    J -->|No | Download --> |try max 2 times| J
    J -->|Yes| UseIt

 
    Mibig[mibig - always download, users not allowed to provide local data] --> M0{Pass Dynaconf config validation?}
    M0 -->|No | M01[Dynaconf config validation error]
    M0 -->|Yes | MibigDownload[Remove existing data if applicable and download data]


    podp[PODP project json file] --> P{Does the file exist?}
    P --> |No | P0[Download the file] --> P1
    P --> |Yes| P1[Validate the file]

    StrainMappings[Strain mappings file - required] --> SM{Is the mode PODP?}
    SM --> |No |SM0[Validate the file]
    SM --> |Yes|SM1[Generate the file] --> SM0

    StrainsSelected[Strains selected file - optional] --> SS[Validate the file if it exists]

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