Foundry API v1

This guide is aimed at introducing users to the Foundry API, with which one can interact with Metadata Tracker and Run Submission/Tracking through the command line as opposed to the console/user interface. You'll find sample requests and responses related to runs, projects, collections, fields, and data.

The Metadata Tracker API utilizes REST (Representational State Transfer) architecture for its communication. All API requests pull information from HTML pages, and all responses, including errors, are returned in JSON format. HTTP response status codes are used to indicate the success or failure of the API calls.

Authentication and authorization

Requests to the Metadata Tracker API are for both public and private information, so all endpoints require authentication.

After getting their access token, users can make a request to the Metadata Tracker API with the Authorization HTTP header. This header can be specified with the Bearer <your-access-token flag to authenticate a command as being given by a specific user and to confer the same permissions that that user already has onto the current request.

Here's how Metadata Tracker API users can retrieve an access token for the currently logged-in user.

Example request:

bash
$ curl -X POST 'https://www.viafoundry.com/vmeta/api/v1/users/login' \
-H 'Content-Type: application/json' \
-d '
    {
        "email":"your-email@mail.com",
        "password":"your-password"
    }'

Example response:

JSON
{
    "status": "success",
    "token": "eyJhbGciOiJSUz....",
    "data": {
        "user": {
            "role": "user",
            "_id": "b6c9a200168a225f39add38d",
            "email": "your-email@mail.com",
            "name": "test user",
            "scope": "*",
            "username": "yukseleo"
        }
    }
}

Runs

In Foundry, you can submit runs, track their statuses and get their run reports.

Get All Runs

This request retrieves a list of all the runs for the currently logged in user.

Example request:

 bash
 $ curl -X GET 'https://www.viafoundry.com/vpipe/api/service.php?data=getRuns' \
-H 'Authorization: Bearer <your-access-token>'

Example response:

 {
    "status": "success",
    "data": {
        "data": [
            {
                "name": "Build index (amazon)",
                "_id": "234"
            },
            {
                "name": "UMIextract",
                "_id": "249"
            },
            {
                "name": "test",
                "_id": "250"
            }
        ]
    }
}

Get a Run

Retrieve details of a single run.

Example request:

bash
$ curl -X GET \
'https://www.viafoundry.com/vpipe/api/service.php?data=getRun&id=4311' \
-H 'Authorization: Bearer <your-access-token>'

Example response:

 {
    "status": "success",
    "data": {
        "data": {
            "inputs": [
                {
                    "name": "gtfFilePath",
                    "type": "val",
                    "val": "/share/data/umw_biocore/genome_data/human/hg38_gencode_v34/ucsc.gtf"
                },
                {
                    "name": "mate",
                    "type": "val",
                    "val": "triple"
                },
                {
                    "name": "genome_build",
                    "type": "val",
                    "val": "human_hg38_gencode_v34"
                }
            ],
            "dmetaOutput": [
                {
                    "filename": "filename",
                    "feature": "row",
                    "target": "analysis",
                    "id": "g-109",
                    "name": "UMI_count_final_after_star"
                },
                {
                    "filename": "row",
                    "feature": "column",
                    "target": "sample_summary",
                    "id": "g-124",
                    "name": "summary"
                }
            ]
        }
    }
}

Create a Run

In this example, the term tmplt_id is used for template run id, reads represents an illustration for defining a collection as input. The global pipeline inputs include the parameters mate, genome, and run_STAR. Specifically, STAR_Module_Map_STAR.params_STAR is associated with the STAR_Module_Map_STAR process parameter. Notably, the process name (STAR_Module_Map_STAR) and variable name (params_STAR) are separated by the "." symbol.

In this illustration, the remaining pipeline parameters will be derived from the template run parameters.

Example request:

 bash
 $ curl -X POST \
'https://www.viafoundry.com/vpipe/api/service.php?run=startRun' \
-H 'Authorization: Bearer <your-access-token>' \
-H 'Content-Type: application/json' \
-d '
    {
        "doc": {
            "name": "New Run Name",
            "tmplt_id": 1314,
            "in": {
                "mate": "pair",
                "genome": "s3://viafoundry/run_data/genome_data/human/hg38/ensembl_v110/main/genome.fa",
                "run_STAR": "yes",
                "STAR_Module_Map_STAR.params_STAR": "--outSAMtype BAM SortedByCoordinate",
                "reads": [
                      {
                          "name": "exper_rep3",
                          "file_used": [[ "exper_rep3.1.gz","exper_rep3.2.gz"]],
                          "file_dir": [[ "/share/data/umw_biocore/genome_data/mousetest/mm10/gz"]], 
                          "google_cre_id": "",
                          "amazon_cre_id": "",
                          "file_type": "fastq",
                          "collection_type": "pair",
                          "archive_dir": ""
                      },
                      {
                          "name": "exper_rep2",
                          "file_used": [["exper_rep2.1.gz","exper_rep2.2.gz"]],
                          "file_dir": [["/share/data/umw_biocore/genome_data/mousetest/mm10/gz"]],
                          "google_cre_id": "",
                          "amazon_cre_id": "",
                          "file_type": "fastq",
                          "collection_type": "pair",
                          "archive_dir": ""
                      }]
            }
        }
    }'

Example response:

 {
    "status": "success",
    "data": {
        "data": {
            "status": "submitted",
            "id": 354,
            "creationDate": "2021-04-13T05:32:16.505Z",
            "message": "Run successfully submitted."
        }
    }
}

Projects

In Metadata Tracker, projects serve as your analysis hubs, acting as silos for your data and collections. Some important and frequently-used API requests include retrieving a user's project(s), as well as creating, updating, and deleting projects.

Get All Projects

This request retrieves a list of all the projects for the currently logged in user.

Example request:

bash
$ curl -X GET 'https://www.viafoundry.com/vmeta/api/v1/projects' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "results": 1,
    "data": {
        "data": [
            {
                "active": true,
                "creationDate": "2020-11-17T19:36:49.048Z",
                "lastUpdateDate": "2020-11-17T19:36:49.048Z",
                "_id": "5fb2b395c8c1e577fcb8ce6c",
                "restrictTo": {
                    "role": [
                        "admin"
                    ]
                },
                "name": "vitiligo",
                "label": "Vitiligo",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                },
            }
        ]
    }
}

Get a Project

Retrieve the metadata associated with a single project.

Example request:

bash
$ curl -X GET \
'https://www.viafoundry.com/vmeta/api/v1/projects/5fb2b395c8c1e577fcb8ce6c' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "results": 1,
    "data": {
        "data": [
            {
                "active": true,
                "creationDate": "2020-11-17T19:36:49.048Z",
                "lastUpdateDate": "2020-11-17T19:36:49.048Z",
                "_id": "5fb2b395c8c1e577fcb8ce6c",
                "restrictTo": {
                    "role": [
                        "admin"
                    ]
                },
                "name": "vitiligo",
                "label": "Vitiligo",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                },
            }
        ]
    }
}

Create a Project

POST request for creating a project:

Example request:

bash
$ curl -X POST \
'https://www.viafoundry.com/vmeta/api/v1/projects' \
-H 'Authorization: Bearer <your-access-token' \
-H 'Content-Type: application/json' \
-d '
    {
        "name": "vitiligo",
        "label": "Vitiligo"
    }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "active": true,
            "creationDate": "2021-03-31T02:04:27.474Z",
            "lastUpdateDate": "2021-03-31T02:04:27.474Z",
            "_id": "6063dbcfa50bb5fa9eb9cfba",
            "name": "vitiligo",
            "label": "Vitiligo",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22"
        }
    }
}

Update a Project

Update one or more metadata fields of an existing project.

Example request:

bash
$ curl \
  -X PATCH \
  -H "Authorization: Bearer <token" \
  https://www.viafoundry.com/vmeta/api/v1/projects/5fb2b395c8c1e577fcb8ce6c \
  -H "Content-Type: application/json" \
  -d '
      {
        "label": "Vitiligo"
      }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "active": true,
            "creationDate": "2020-11-17T19:36:49.048Z",
            "lastUpdateDate": "2020-11-17T19:36:49.048Z",
            "_id": "5fb2b395c8c1e577fcb8ce6c",
            "restrictTo": {
                "role": [
                    "admin"
                ]
            },
            "name": "vitiligo",
            "label": "Vitiligo",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            }
        }
    }
}

Delete a Project

Delete an existing project. NOTE: This action is irreversible, and should only be executed when absolutely certain of its intentions.

Example request:

bash
$ curl \
  -X DELETE \
  -H "Authorization: Bearer <token" \
  https://www.viafoundry.com/vmeta/api/v1/projects/5fb2b395c8c1e577fcb8ce6c

Example response:

JSON
{
    "status": "success",
    "data": {
        "doc": "Deleted!"
    }
}

Collections

Get All Collections

Retrieve a list of all the collections owned by the currently logged-in user.

Example request:

bash
$ curl -X GET 'https://www.viafoundry.com/vmeta/api/v1/collections' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{"status": "success",
    "results": 10,
    "data": {
        "data": [
            {
                "version": 1,
                "required": false,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.301Z",
                "lastUpdateDate": "2020-09-08T21:56:35.301Z",
                "_id": "5f57ffba35db5980ba020ff3",
                "restrictTo": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                },
                "name": "exp_series",
                "label": "Experiment Series",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "projectID": "5fb2b395c8c1e577fcb8ce6c",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                },
                "id": "5f57ffba35db5980ba020ff3"
            },
            {
                "version": 1,
                "required": false,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.301Z",
                "lastUpdateDate": "2020-09-08T21:56:35.301Z",
                "_id": "5f57ffe635db5980ba020ff4",
                "restrictTo": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                },
                "name": "exp",
                "label": "Experiments",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "projectID": "5fb2b395c8c1e577fcb8ce6c",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                },
                "id": "5f57ffe635db5980ba020ff4"
            }]
    }
}

Get a Collection

Retrieve the details of a single collection.

Example request:

bash
$ curl -X GET \
'https://www.viafoundry.com/vmeta/api/v1/collections/5f57ffe635db5980ba020ff4' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": [
            {
                "version": 1,
                "required": false,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.301Z",
                "lastUpdateDate": "2020-09-08T21:56:35.301Z",
                "_id": "5f57ffe635db5980ba020ff4",
                "restrictTo": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                },
                "name": "exp",
                "label": "Experiments",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "projectID": "5fb2b395c8c1e577fcb8ce6c",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                }
            }
        ]
    }
}

Create a Collection

This POST request is only allowed for users with the project-admin role.

Example request:

bash
$ curl -X POST \
'https://www.viafoundry.com/vmeta/api/v1/collections' \
-H 'Authorization: Bearer <your-access-token' \
-H 'Content-Type: application/json' \
-d '
    {
        "name": "analysis",
        "label": "Analysis",
        "projectID":"5fb2b395c8c1e577fcb8ce6c",
        "restrictTo": {"group":["5fb45793aa5adff6f407f2d2"]},
    }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "version": 1,
            "required": false,
            "active": true,
            "creationDate": "2021-03-31T02:26:17.087Z",
            "lastUpdateDate": "2021-03-31T02:26:17.087Z",
            "_id": "6063e3a33c195afbe6d5e036",
            "name": "analysis",
            "label": "Analysis",
            "restrictTo": {
                "group": [
                    "5fb45793aa5adff6f407f2d2"
                ]
            },
            "projectID": "5fb2b395c8c1e577fcb8ce6c",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            }
        }
    }
}

Update a Collection

Update an existing collection.

Example request:

bash
$ curl \
  -X PATCH \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/collections/6063e3a33c195afbe6d5e036 \
  -H "Content-Type: application/json" \
  -d '
      {
        "label": "Analysis"
      }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "version": 1,
            "required": false,
            "active": true,
            "creationDate": "2021-03-31T02:26:17.087Z",
            "lastUpdateDate": "2021-03-31T02:26:17.087Z",
            "_id": "6063e3a33c195afbe6d5e036",
            "name": "analysis",
            "label": "Analysis",
            "restrictTo": {
                "group": [
                    "5fb45793aa5adff6f407f2d2"
                ]
            },
            "projectID": "5fb2b395c8c1e577fcb8ce6c",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            }
        }
    }
}

Delete a Collection

Delete an existing collection. NOTE: This action is irreversible, and should only be executed when absolutely certain of its intentions.

Example request:

bash
$ curl \
  -X DELETE \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/collections/6063e3a33c195afbe6d5e036

Example response:

JSON
{
    "status": "success",
    "data": {
        "doc": "Deleted!"
    }
}

Fields

Get All Fields

Retrieve a list of fields for the currently logged in user.

Example request:

bash
$ curl -X GET 'https://www.viafoundry.com/vmeta/api/v1/fields' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "results": 2,
    "data": {
        "data": [
            {
                "type": "String",
                "required": true,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.406Z",
                "lastUpdateDate": "2020-09-08T21:56:35.406Z",
                "_id": "5f58518835db5980ba020ff7",
                "name": "name",
                "label": "Name",
                "collectionID": "5f57ffba35db5980ba020ff3",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                },
                "unique": true
            },
            {
                "type": "String",
                "required": false,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.406Z",
                "lastUpdateDate": "2020-09-08T21:56:35.406Z",
                "_id": "5f58559f35db5980ba020ff8",
                "name": "design",
                "label": "Design",
                "collectionID": "5f57ffba35db5980ba020ff3",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                }
            }]
        }
    }

Get a Field

Retrieve details of a single field.

Example request:

bash
$ curl -X GET \
'https://www.viafoundry.com/vmeta/api/v1/fields/5f58559f35db5980ba020ff8' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": [
            {
                "type": "String",
                "required": false,
                "active": true,
                "creationDate": "2020-09-08T21:56:35.406Z",
                "lastUpdateDate": "2020-09-08T21:56:35.406Z",
                "_id": "5f58559f35db5980ba020ff8",
                "name": "design",
                "label": "Design",
                "collectionID": "5f57ffba35db5980ba020ff3",
                "lastUpdatedUser": "5f39add38db6c9a200168a22",
                "owner": "5f39add38db6c9a200168a22",
                "perms": {
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    },
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    }
                }
            }
        ]
    }
}

Create a Field

This POST request is only enabled for users with the project-admin role.

Example request:

bash
$ curl -X POST \
'https://www.viafoundry.com/vmeta/api/v1/fields' \
-H 'Authorization: Bearer <your-access-token' \
-H 'Content-Type: application/json' \
-d '
    {
        "name": "clin_pheno",
        "label": "Clinical Phenotype",
        "type": "String",
        "collectionID":"5f74a0e05443973d2bfd870c"
    }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "type": "String",
            "required": false,
            "active": true,
            "creationDate": "2021-03-31T02:57:02.771Z",
            "lastUpdateDate": "2021-03-31T02:57:02.771Z",
            "_id": "6063e7c91bfc89fd1960ae5b",
            "name": "clin_pheno",
            "label": "Clinical Phenotype",
            "collectionID": "5f74a0e05443973d2bfd870c",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            },
            "id": "6063e7c91bfc89fd1960ae5b"
        }
    }
}

Update a Field

Update an existing field.

Example request:

bash
$ curl \
  -X PATCH \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/fields/6063e7c91bfc89fd1960ae5b \
  -H "Content-Type: application/json" \
  -d '
      {
        "ontology": {
            "create": true,
            "include": [
                "Dermatomyositis",
                "GVHD",
                "Healthy Control",
                "Lupus",
                "Psoriasis",
                "Vitiligo"
            ]
        }
      }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "type": "String",
            "required": false,
            "active": true,
            "creationDate": "2021-03-31T02:57:02.771Z",
            "lastUpdateDate": "2021-03-31T02:57:02.771Z",
            "_id": "6063e7c91bfc89fd1960ae5b",
            "name": "clin_pheno",
            "label": "Clinical Phenotype",
            "collectionID": "5f74a0e05443973d2bfd870c",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            },
            "ontology": {
                "create": true,
                "include": [
                    "Dermatomyositis",
                    "GVHD",
                    "Healthy Control",
                    "Lupus",
                    "Psoriasis",
                    "Vitiligo"
                    ]
            }
        }
    }
}

Delete a Field

Delete an existing field. NOTE: This action is irreversible, and should only be executed when absolutely certain of its intentions.

Example request:

bash
$ curl \
  -X DELETE \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/fields/6063e7c91bfc89fd1960ae5b

Example response:

JSON
{
    "status": "success",
    "data": {
        "doc": "Deleted!"
    }
}

Data

Pull All Data of a Project's Collection

Retrieve all data associated with a given collection in a project for the currently logged-in user.

Example request:

bash
$ curl -X GET 'https://www.viafoundry.com/vmeta/api/v1/projects/vitiligo/data/sample' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "results": 2,
    "data": {
        "data": [
            {
                "creationDate": "2020-12-17T16:42:06.252Z",
                "lastUpdateDate": "2020-12-17T16:42:06.252Z",
                "_id": "5fdb8c6ad6330eb80d503fe2",
                "name": "CL067_L2_V1_Bst_sc_iD",
                "sample_type": "scRNAseq",
                "technology": "inDrop",
                "status": "Processed",
                "contract": "scRNAseq",
                "bead_occup": "65-70%",
                "biosamp_id": "5fdb8820d6330eb80d503a31",
                "lastUpdatedUser": "5f92529b89c7d0b3bf31ac27",
                "owner": "5f92529b89c7d0b3bf31ac27",
                "perms": {
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    },
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    }
                },
                "DID": 1
            },
            {
                "creationDate": "2020-12-17T16:42:06.252Z",
                "lastUpdateDate": "2020-12-17T16:42:06.252Z",
                "_id": "5fdb8c6ad6330eb80d503fe4",
                "name": "VB071_L1_V1_Bst_sc_iD",
                "sample_type": "scRNAseq",
                "technology": "inDrop",
                "status": "Processed",
                "contract": "scRNAseq",
                "bead_occup": "33/50 (~65%)",
                "biosamp_id": "5fdb8820d6330eb80d503a33",
                "lastUpdatedUser": "5f92529b89c7d0b3bf31ac27",
                "owner": "5f92529b89c7d0b3bf31ac27",
                "perms": {
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    },
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    }
                },
                "DID": 2
            }]
        }
    }

Get a Data Value

Retrieve details of a single data field.

Example request:

bash
$ curl -X GET \
'https://www.viafoundry.com/vmeta/api/v1/projects/vitiligo/data/sample/5fdb8c6ad6330eb80d503fe2' \
-H 'Authorization: Bearer <your-access-token'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": [
                    {
                "creationDate": "2020-12-17T16:42:06.252Z",
                "lastUpdateDate": "2020-12-17T16:42:06.252Z",
                "_id": "5fdb8c6ad6330eb80d503fe2",
                "name": "CL067_L2_V1_Bst_sc_iD",
                "sample_type": "scRNAseq",
                "technology": "inDrop",
                "status": "Processed",
                "contract": "scRNAseq",
                "bead_occup": "65-70%",
                "biosamp_id": "5fdb8820d6330eb80d503a31",
                "lastUpdatedUser": "5f92529b89c7d0b3bf31ac27",
                "owner": "5f92529b89c7d0b3bf31ac27",
                "perms": {
                    "write": {
                        "group": [
                            "5fb45793aa5adff6f407f2d2"
                        ]
                    },
                    "read": {
                        "group": [
                            "5fb4575faa5adff6f407f2d1"
                        ]
                    }
                },
                "DID": 1
            }
        ]
    }
}

Create a Data Value

This POST request is only allowed for the users with Write permission.

Example request:

bash
$ curl -X POST \
'https://www.viafoundry.com/vmeta/api/v1/projects/vitiligo/data/sample' \
-H 'Authorization: Bearer <your-access-token' \
-H 'Content-Type: application/json' \
-d '
    {
        "name": "CL070_L2_V1_Bst_sc_iD",
        "sample_type": "scRNAseq",
        "technology": "inDrop",
        "status": "Sequenced",
        "contract": "scRNAseq",
        "bead_occup": "65-70%",
        "biosamp_id":"5fdb8820d6330eb80d503a31"
    }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "creationDate": "2021-03-31T03:16:58.503Z",
            "lastUpdateDate": "2021-03-31T03:16:58.503Z",
            "_id": "606453c0cb44bcfdbb84c6a2",
            "name": "CL070_L2_V1_Bst_sc_iD",
            "sample_type": "scRNAseq",
            "technology": "inDrop",
            "status": "Sequenced",
            "contract": "scRNAseq",
            "bead_occup": "65-70%",
            "biosamp_id": "5fdb8820d6330eb80d503a31",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            },
            "DID": 135
        }
    }
}

Update a Data Field

Update an existing data field.

Example request:

bash
$ curl \
  -X PATCH \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/projects/vitiligo/data/sample/606453c0cb44bcfdbb84c6a2 \
  -H "Content-Type: application/json" \
  -d '
      {
        "status":"Processed"
      }'

Example response:

JSON
{
    "status": "success",
    "data": {
        "data": {
            "creationDate": "2021-03-31T03:16:58.503Z",
            "lastUpdateDate": "2021-03-31T03:16:58.503Z",
            "_id": "606453c0cb44bcfdbb84c6a2",
            "name": "CL070_L2_V1_Bst_sc_iD",
            "sample_type": "scRNAseq",
            "technology": "inDrop",
            "status": "Processed",
            "contract": "scRNAseq",
            "bead_occup": "65-70%",
            "biosamp_id": "5fdb8820d6330eb80d503a31",
            "lastUpdatedUser": "5f39add38db6c9a200168a22",
            "owner": "5f39add38db6c9a200168a22",
            "perms": {
                "read": {
                    "group": [
                        "5fb4575faa5adff6f407f2d1"
                    ]
                },
                "write": {
                    "group": [
                        "5fb45793aa5adff6f407f2d2"
                    ]
                }
            },
            "DID": 135
        }
    }
}

Delete a Data Field

Delete an existing data value. NOTE: This action is irreversible, and should only be executed when absolutely certain of its intentions.

Example request:

bash
$ curl \
  -X DELETE \
  -H "Authorization: Bearer <your-access-token" \
  https://www.viafoundry.com/vmeta/api/v1/projects/vitiligo/data/sample/606453c0cb44bcfdbb84c6a2

Example response:

JSON
{
    "status": "success",
    "data": {
        "doc": "Deleted!"
    }
}

Foundry API v1

Authentication and authorization

User Login

Runs

Get All Runs

Get a Run

Create a Run

Projects

Get All Projects

Get a Project

Create a Project

Update a Project

Delete a Project

Collections

Get All Collections

Get a Collection

Create a Collection

Update a Collection

Delete a Collection

Fields

Get All Fields

Get a Field

Create a Field

Update a Field

Delete a Field

Data

Pull All Data of a Project's Collection

Get a Data Value

Create a Data Value

Update a Data Field

Delete a Data Field