Database

LabPipe Server works with MongoDB.

Required collections

Collection	Description
ACCESS_TOKENS	Access tokens
ROLES	Roles
CLIENT_SETTINGS	To provide parameter list for the client
API_ACCESS_ROLES	API endpoint roles
OPERATORS	Operators, can be used for login on the client
STUDIES	Research studies
FORMS	Dynamic form templates to be retrieved on the client
REPORT_TEMPLATES	Report html templates for record notification email
INSTRUMENTS	Instruments
COLLECTORS	Devices attached to instruments for collection
SAMPLE_TYPES	Sample types
LOCATIONS	Locations
EMAIL_GROUPS	Email groups for notification email

ACCESS_TOKENS

Parameter	Format	Required
token	string	Yes
keyhash	string	Yes
roles	string[]	No

Example

{
  "token": "token",
  "keyhash": "$2a$10$oSnRBce/gDbLWsVv2wOx8.Rhv88zMPLCMRZb6j0gtZwKZvvohJWIa",
  "roles": [
    "general-token"
  ]
}

ROLES

Parameter	Format	Required
identifier	string	Yes
name	string	Yes

Example

{
  "identifier": "general-token",
  "name": "Accessible by all token"
}

CLIENT_SETTINGS

Parameter	Format	Required	Value
identifier	string	Yes	client_init
name	string	Yes
value	string[]	No

Example

{
  "identifier": "client_init",
  "name": "Parameter list for client init",
  "value": [
    "LOCATIONS",
    "OPERATORS",
    "STUDIES",
    "INSTRUMENTS",
    "COLLECTORS"
  ]
}

API_ACCESS_ROLES

Parameter	Format	Required
url	string	Yes
roles	string[]	Yes

Example

{
  "url": "/api/general/connect/auth",
  "roles": [
    "general-auth"
  ]
}

OPERATORS

Parameter	Format	Required
name	string	Yes
passwordHash	string	Yes
username	string	Yes
email	string	Yes
active	boolean	Yes
projects	string[]	No
notificationGroup	string[]	No
roles	string[]	No

Example

{
  "name": "Test User",
  "passwordHash": "$2a$10$QC4LEBrdfLvMoy0TetVKWeA2p4tbhv3mPhiYRdSbfjdXMJ3.ErtUC",
  "username": "testuser",
  "email": "[email protected]",
  "active": true,
  "projects": [
    "project1",
    "project2"
  ],
  "notificationGroup": [
    "test-email-group"
  ],
  "roles": [
    "general-auth"
  ]
}

STUDIES

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
config	object	Yes

Example

{
  "code": "EMBER",
  "name": "East Midlands Breathomics Pathology Node",
  "config": {
    "participant_id": {
      "prefix": [
        "AAA"
      ],
      "length": 4
    },
    "visit_id": [
      "A",
      "B"
    ],
    "location": [
      "LOC1",
      "LOC2"
    ],
    "instrument": [
      "PTR",
      "R"
    ],
    "collector": [
      "R"
    ],
    "sample_type": [
      {
        "identifier": "BS",
        "name": "BBBSSS",
        "available_at": [
          {
            "instrument": [
              "PTR"
            ],
            "collector": [
              "R"
            ]
          },
          {
            "instrument": [
              "R"
            ]
          }
        ]
      },
      {
        "identifier": "RP",
        "name": "RRRPPP",
        "available_at": [
          {
            "instrument": [
              "R"
            ]
          }
        ]
      }
    ]
  }
}

FORMS

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
studyIdentifier	string	Yes
instrumentIdentifier	string	Yes
template	object	Yes
url	string	Yes
notificationStyle	string	Yes

Example

{
  "identifier": "ember-form-1",
  "name": "Test Form",
  "studyIdentifier": "EMBER",
  "instrumentIdentifier": "R",
  "template": {
    "title": "Sample",
    "pages": [
      {
        "title": "Sample Information",
        "navTitle": "Sample Infomation",
        "requireValidForm": true,
        "order": 1,
        "questions": [
          {
            "key": "participant_id_prefix",
            "label": "Participant ID Prefix",
            "required": "true",
            "order": 1,
            "controlType": "select",
            "options": "__config::participant_id::prefix__",
            "helperText": "SN for screening visit only. Once enrolled, use STP."
          },
          {
            "key": "participant_id_number",
            "label": "Participant ID Number",
            "required": true,
            "order": 2,
            "controlType": "input",
            "type": "text",
            "helperText": "Participant ID number part, e.g. [0001] in [XXX0001]",
            "pattern": "__config::participant_id::length__"
          },
          {
            "key": "visit_id",
            "label": "Visit ID",
            "required": true,
            "order": 3,
            "controlType": "select",
            "type": "text",
            "helperText": "0 for screening visit only.",
            "options": "__config::visit_id__"
          }
        ],
        "formValidProcess": [
          {
            "newField": "participant_id",
            "processType": "concat",
            "dataField": "-::participant_id_prefix::participant_id_number",
            "required": true,
            "allowCopy": true
          },
          {
            "newField": "sample_id",
            "processType": "concat",
            "dataField": "-::participant_id_prefix::participant_id_number::visit_id::--R::--RP",
            "required": true,
            "allowCopy": true
          }
        ],
        "key": "p_sample_info"
      },
      {
        "title": "File Upload",
        "key": "p_file",
        "navTitle": "File",
        "requireValidForm": "true",
        "order": "3",
        "questions": [
          {
            "key": "file",
            "label": "Sample File",
            "required": false,
            "order": 1,
            "controlType": "file",
            "helperText": "Select file to upload",
            "target": "file",
            "multiple": true,
            "filter": [
              {
                "name": "HDF5 file",
                "extensions": [
                  "h5"
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "url": "/api/record/add",
  "notification_style": "ADMIN_ONLY"
}

REPORT_TEMPLATES

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
formIdentifier	string	Yes
text	string	No
html	object[]	Yes
active	boolean	Yes

Example

{
  "code": "test",
  "name": "Test Report",
  "form_code": "test",
  "text": "",
  "html": [
    {
      "type": "REPORT_TITLE",
      "source": "STATIC",
      "method": "VALUE",
      "value": "Test LabPipe Report Title",
      "order": 1
    },
    {
      "type": "SECTION_TITLE",
      "source": "STATIC",
      "method": "VALUE",
      "value": "Section 1 table for different objects",
      "order": 2
    },
    {
      "type": "TABLE_KEYVALUE",
      "source": "FORM_DATA",
      "method": "PROPERTY",
      "value": "p_basic",
      "order": 3
    },
    {
      "type": "SECTION_TITLE",
      "source": "STATIC",
      "method": "VALUE",
      "value": "Section 2 table for same type objects"
    },
    {
      "type": "TABLE_LOOP",
      "source": "FORM_DATA",
      "method": "PROPERTY",
      "value": "p_file.file",
      "order": 4
    },
    {
      "type": "SECTION_TITLE",
      "source": "STATIC",
      "method": "VALUE",
      "value": "Section 3 list",
      "order": 5
    },
    {
      "type": "LIST",
      "source": "FORM_DATA",
      "method": "PROPERTY",
      "value": "p_file.file",
      "order": 6
    },
    {
      "type": "REPORT_TITLE",
      "source": "FORM_CONFIG",
      "method": "PROPERTY",
      "value": "study_code",
      "order": 7
    },
    {
      "type": "SECTION_TITLE",
      "source": "FORM_CONFIG",
      "method": "PROPERTY",
      "value": "instrument_code",
      "order": 8
    }
  ],
  "active": true
}

INSTRUMENTS

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
realtime	boolean	Yes
fileType	string[]	Yes

Example

{
  "identifier": "R",
  "name": "ReCIVA",
  "realtime": true,
  "fileType": [
    "h5"
  ]
}

COLLECTORS

TBA.

SAMPLE_TYPES

TBA.

LOCATIONS

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
type	string[]	No

Example

{
  "identifier": "LOC1",
  "name": "Location 1",
  "type": []
}

EMAIL_GROUPS

Parameter	Format	Required
identifier	string	Yes
name	string	Yes
studyIdentifier	string	Yes
formIdentifier	string	Yes
admin	string[]	No
member	string[]	No

Example

{
  "identifier": "test-email-group",
  "studyIdentifier": "ember",
  "formIdentifier": "test",
  "name": "Test Email Group Wahaha",
  "admin": [
    "bo.zhao"
  ],
  "member": []
}