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Open-Cann / hypercerts-on-bos

BOS native Hypercerts leveraging a standardized type schema.

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Hypercerts on BOS

Built using Hyperfiles: https://github.com/flowscience/hyperfiles

About

An implementation of Hypercerts using Near Protocol's Blockchain Operating System (BOS). Hypercerts on BOS (HoB) is a decentralized front-end stored entirely on-chain that interacts with both the Near socialDB contract as well as the Hypercert contract on Optimism to enable minting on either network. The entire application can be integrated into any BOS gateway deployment such as near.org, near.social, and opencann.net with a single line of code. BOS native Hypercerts leveraging a standardized type schema. Standardized fields can make Hypercerts composable with other implementations of impact certificates (e.g. to aggregate & analyze metadata like scope, dates, contributors, etc).

Docs https://www.notion.so/opencann/Hypercerts-on-BOS-a779c2abf7e54e4bb5782e569dd14419

Demo https://near.org/flowscience.near/widget/create.hypercert

Built during Funding The Commons, Public Goods Hackathon (Aug 2023) https://app.buidlbox.io/projects/hypercerts-on-bos

https://www.youtube.com/watch?v=uu6ABkJSqsI

Core Types

metadata: redundant fields applicable to any type or thing

  • description (s)
  • image (s)
  • backgroundImage (s)

file: a collection of records

  • fileName (str, s)
  • fileFormat (thing, s)
  • records (thing, m)
  • owner (str, s)
  • permissions (thing, s)

fileformat: standard types for files

  • formatName (str, s)
  • fields (thing, m)
  • fileNames (thing, m)

field: primitives that compose into fileFormats

  • fieldName (str, s)
  • primitive (str, s)
  • fileFormats (thing, m)

record: individual pieces of data (a datum)

  • recordName (str, s)
  • fields (str, m)
  • recordValues (str, m)
  • recordOwner (str, s)
  • isEncrypted (bool, s)
  • permissions (thing, s)

permissions:

  • TBD
  • sking.near/widget/DAO.Permissions

Core fileformat Types

These enable files to be used for decentralized compute over Bacalhau via PLEX.

See example Colab notebook for off-chain demo.

job: an “.io file” to specify job type and input/output dir

  • jobName (str, s)
  • jobType (thing, s)
  • inputfiles (thing, m)
  • CID (str, s)
  • owner (str, s)
[
  {
    "outputs": {
      "outdata": {
        "class": "File",
        "filepath": "testdata_fastqc.zip",
        "ipfs": "QmXXKpKz2w1b992MXpSo3Dmohu46d4V4Y2WXLQZtWa9AKR"
      },
      "report": {
        "class": "File",
        "filepath": "testdata_fastqc.html",
        "ipfs": "QmWw6oevnbPqxJGVBMmAVPsRCfHEHcf8D6TFxThXENdx1b"
      }
    },
    "tool": {
      "name": "fastqc",
      "ipfs": "QmRsqab1yXAc8GPipkXkBjTjJq7VpXSRv5qdthLymm4Mzm"
    },
    "inputs": {
      "reads": {
        "class": "File",
        "filepath": "testdata.fastq",
        "ipfs": "QmUvALPCVL5ZgnRWyvfqjrTSK9UgLW1JJTLsisFooRpcGD"
      }
    },
    "state": "completed",
    "errMsg": "",
    "userId": "",
    "bacalhauJobId": "0581f011-8070-4ddb-959b-f6bc2c43e2ed"
  }
]

jobtype: standard types for jobs

Is this redundant with toolconfig???

  • jobType (str, s)
  • toolConfigFile (thing, s)
  • jobFiles (thing, m)

toolconfig: specify container path and jobtype parameters

Enforce input file formats are of the appropriate type (so the job will work).

Designate output file formats to enable composability in pipeline builder.

  • configName (str, s)
  • inputfileFormats (thing, m)
  • outputfileFormats (thing, m)
  • class
  • name
  • description
  • baseCommand:

Tested working toolConfigFiles can be found on Github (see example below).

https://github.com/Open-Cann/plex/blob/main/tools/fastqc/fastqc.json

{
  "class": "Tool",
  "name": "fastqc",
  "description": "Comprehensive quality control tool for high-throughput sequence data",
  "doi": "https://doi.org/10.48550/arXiv.2202.05146",
  "baseCommand": ["/bin/bash", "-c"],
  "arguments": [
    "fastqc $(inputs.reads.filepath) --outdir=/outputs/"
  ],
  
  "dockerPull": "staphb/fastqc:0.12.1@sha256:f5d8f72753269e0cee071fe198c89a59a1f8071445739b3398f7818f7cb039ae",
  "gpuBool": false,
  "networkBool": false,

  "inputs": {
    "reads": {
      "type": "File",
      "glob": ["*.bam", "*.sam", "*.fastq"]
    }
  },

  "outputs": {
    "report": {
      "type": "File",
      "glob": ["*.html"]
    },      
    "outdata": {
      "type": "File",
      "glob": ["*.zip"]
    }
  }
}
{
  "class": "CommandLineTool",
  "name": "equibind",
  "description": "Docking of small molecules to a protein",
  "baseCommand": ["/bin/bash", "-c"],
  "arguments": [
    "mkdir -p /tmp-inputs/tmp;",
    "mkdir -p /tmp-outputs/tmp;",
    "cp /inputs/* /tmp-inputs/tmp/;",
    "ls /tmp-inputs/tmp;",
    "cd /src && python /src/inference.py --config=/src/configs_clean/bacalhau.yml;",
    "mv /tmp-outputs/tmp/* /outputs/;",
    "mv /outputs/lig_equibind_corrected.sdf /outputs/$(inputs.protein.basename)_$(inputs.small_molecule.basename)_docked.$(inputs.small_molecule.ext);",
    "mv /tmp-inputs/tmp/*.pdb /outputs/;"],
  "dockerPull": "ghcr.io/labdao/equibind:main@sha256:21a381d9ab1ff047565685044569c8536a55e489c9531326498b28d6b3cc244f",
  "gpuBool": false,
  "networkBool": false,
  "inputs": {
    "protein": {
      "type": "File",
      "item": "",
      "glob": ["*.pdb"]
    },
    "small_molecule": {
      "type": "File",
      "item": "",
      "glob": ["*.sdf", "*.mol2"]
    }
  },
  "outputs": {
    "best_docked_small_molecule": {
      "type": "File",
      "item": "",
      "glob": ["*_docked.sdf", "*_docked.mol2"]
    },
    "protein": {
      "type": "File", 
      "item": "",
      "glob": ["*.pdb"]
    }
  }
}

Lists of Things

metadata

files

Core

  • every.file
  • every.fileformat
  • every.record
  • every.field
  • every.job
  • every.jobtype
  • every.toolconfig
  • {accountId}/thing/impact.file

Featured

  • every.hypercert

fileformats

fileformat.hypercert

  • impact

fileformat.impact

  • fileformat.job
  • fileformat.jobType
  • fileformat.toolConfig

types = fileformats = types???

type:artist

type:DAO

fields

records

  • hypercert.1
  • file.1
  • job.1

jobs

  • TBD

jobTypes

  • TBD

About

BOS native Hypercerts leveraging a standardized type schema.

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