Schema Examples

Requests and Responses

These are the Server-Server and Server-Client messages that are used to transmit data, job requests and results throughout the Grassroots system. All messages are sent as JSON-based messages and are described in depth in the Schema guide.

1. A Client queries the Operations that a Server can provide. An operation_id with the value get_all_services is the one for asking for all of its possible Operations.

{
  "header": {
    "schema": {
      "major": 0,
      "minor": 10
    }
    }
    "operations": {
        "operation_id": "get_all_services"
    }
}

1. The Server sends its response. In this example, it has 2 Operations: “Foobar Contig Search service” and “Foobar Keyword Search service”

{
 "header": {
    "schema": {
      "major": 0,
      "minor": 10
    }
  },
  "services": [
    {
      "service_name": "SamTools service",
      "provider": {
        "name": "grassroots-2",
        "description": "Grassroots 2 running the Grassroots Infrastructure",
        "uri": "https://grassroots.tools"
      },
      "description": "A service using SamTools",
      "operations": {
        "operation_id": "SamTools service",
        "description": "A service using SamTools",
        "parameter_set": {
          "parameters": [
            {
              "param": "input_file",
              "current_value": "Chinese Spring",
              "type": "string",
              "grassroots_type": "xsd:string",
              "level": "all",
              "description": "The available databases",
              "name": "Indexes",
              "default_value": "Chinese Spring",
              "enum": [
                {
                  "description": "Chinese Spring",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_CS42_TGACv1_all.fa"
                },
                {
                  "description": "Cadenza",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_Cadenza_EIv1.1.fa"
                },
                {
                  "description": "Kronos",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_turgidum_Kronos_EIv1.1.fa"
                },
                {
                  "description": "Paragon",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_Paragon_EIv1.1.fa"
                },
                {
                  "description": "Robigus",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_Robigus_EIv1.1.fa"
                },
                {
                  "description": "Claire",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_Claire_EIv1.1.fa"
                },
                {
                  "description": "CS42 cDna",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_CS42_TGACv1_scaffold.annotation.gff3.cdna.fa"
                },
                {
                  "description": "CS42 cds",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Triticum_aestivum_CS42_TGACv1_scaffold.annotation.gff3.cds.fa"
                },
                {
                  "description": "Aegilops tauschii",
                  "value": "/mnt/ngs_data/references/assembly/aegilops_tauschii/GCA_000347335.1/Aegilops_tauschii.GCA_000347335.1.26.dna.genome.fa"
                },
                {
                  "description": "CS42 cDNA",
                  "value": "/mnt/ngs_data/databases/blast/triticum_aestivum/brenchley_CS42/allCdnaFinalAssemblyAllContigs_vs_TREPalle05_notHits_gt100bp"
                },
                {
                  "description": "CS42 5x Liverpool 454 assembly",
                  "value": "/mnt/ngs_data/databases/blast/triticum_aestivum/brenchley_CS42/CS_5xDNA_all"
                },
                {
                  "description": "CS42 orthologous group sub-assemblies",
                  "value": "/mnt/ngs_data/references/assembly/triticum_aestivum/brenchley_CS42/subassemblies_TEcleaned_Hv80Bd75Sb70Os70_30aa_firstBestHit_assembly_ml40_mi99.fa"
                },
                {
                  "description": "WGSCv2.0",
                  "value": "/mnt/ngs_data/references/assembly/triticum_aestivum/IWGSC/v2/IWGSCv2.0.fa"
                },
                {
                  "description": "A-genome progenitor Triticum urartu",
                  "value": "/mnt/ngs_data/references/assembly/triticum_urartu/GCA_000347455.1/Triticum_urartu.GCA_000347455.1.26.dna.genome.fa"
                },
                {
                  "description": "Synthetic W7984",
                  "value": "/mnt/ngs_data/references/assembly/triticum_aestivum/W7984/w7984.meraculous.scaffolds.Mar28_contamination_removed.fa"
                },
                {
                  "description": "Wild winter wheat G3116",
                  "value": "/mnt/ngs_data/references/assembly/triticum_monococcum/spp_aegilopoides/TmG3116_cDNA.fa"
                },
                {
                  "description": "Domesticated spring wheat",
                  "value": "/mnt/ngs_data/references/assembly/triticum_monococcum/spp_monococcum/TmDV92_cDNA.fa"
                },
                {
                  "description": "Barley Golden Promise",
                  "value": "/home/ubuntu/Applications/grassroots-0/grassroots/extras/blast/databases/Hordeum_vulgare_Golden_promise_EIv1.fa"
                }
              ]
            },
            {
              "param": "Scaffold",
              "current_value": "",
              "type": "string",
              "grassroots_type": "xsd:string",
              "level": "all",
              "description": "The name of the scaffold to find",
              "name": "Scaffold name",
              "default_value": ""
            },
            {
              "param": "Scaffold line break index",
              "current_value": 60,
              "type": "integer",
              "grassroots_type": "params:signed_integer",
              "level": "advanced",
              "description": "If this is greater than 0, then add a newline after each block of this many letters",
              "name": "Max Line Length",
              "default_value": 60
            }
          ],
          "groups": []
        },
        "synchronous": true,
        "icon_uri": "https://grassroots.tools/grassroots-test/2/images/Search%20service"
      }
    }
  ]
}

1. The user decides to run the “Foobar Contig Search service” with contig_name set to BC000000100 but not to run the “Foobar Keyword Search service. The Client’s request back to the Server would be:

{
    "services": [{
        "service_name": "Foobar Keyword Contig service",
        "start_service": true,
        "parameter_set": {
            "parameters": [{
                "param": "contig_name",
                "current_value": "BC000000100",
                "grassroots_type": "params:keyword"
            }]
        }
    }, {
        "service_name": "Foobar Keyword Search service",
        "start_service": false
    }]
}

1. The Server can run the requested Operations. In this case, the results are available straight away as the Operations run synchronously.

{
    "service_name": "Foobar Keyword Contig service",
    "status": 3,
    "description": "An operation to obtain contig information using SNP or Contig names",
    "uri": "http://foobar.com/search_by_contig",
    "results": [{
        "protocol": "inline",
        "title": "item title",
        "data": "item data"
    }, {
        "protocol": "http",
        "title": "item title",
        "data": "foobar.com/view_data_online/id1"
    }, {
        "protocol": "inline",
        "title": "item title",
        "data": {
            "format": "SNP",
            "custom key": "custom value"
        }
    }]
}