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Table of Contents

Executing Any AQL

...

Item

Value

HTTP Method

POST

URI

/rest/ng/query

Body

Code Block
{ "cpId": <cpId>, "aql": <AQL>, "wideRowMode": <OFF\|SHALLOW\|DEEP>, "outputColumnExprs": <true\|false>, "outputIsoDateTime": <true\|false>, "timeoutInSeconds": <integer> }

Response

JSON containing desired results

...

Parameter	Description
cpId	Collection protocol ID. If specified, limits the results to specified CP records. Useful when AQL contains CP specific custom fields.
aql	Valid AQL string that needs to be executed
wideRowMode	Specifies whether multi-valued attributes result in a single row or one row per value. Default value is OFF. Other permitted values are SHALLOW and DEEP. Try out to see what fits best for your use case.
outputColumnExprs	Specifies whether the column labels or AQL expression needs to be included in the query response. By default, user friendly column labels are included in query response.
outputIsoDateTime	Specifies how the date column values needs to be serialised in the query response. If true, then date/time values are serialised using ISO format: yyyy-MM-dd'T'HH:mm:ss. Otherwise, date/time values are serialised using the format specified in OS locale settings

Example

Given below is an example query request to obtain count of aliquots by visit dates:

...

timeoutInSeconds

Specifies how long to wait for the query to complete before aborting it. When not specified, this field defaults to 55 seconds. This is a guard against the run away query that hog the system resources, eventually resulting in service disruption.

To wait forever for the query to complete, use -1. This should be avoided unless you are aware about the consequences of allowing a runaway query.

Example

Given below is an example query request to obtain count of aliquots by visit dates:

Code Block

language	js

{
	"cpId": 1,
	"aql": "select Participant.ppid, SpecimenCollectionGroup.collectionDate, count(distinct Specimen.id) where Specimen.lineage = \"Aliquot\"",
	"outputIsoDateTime": true
}

...

Item	Value
HTTP Method	GET
URI	/rest/ng/saved-queries
Response	JSON containing detailed list of saved queries

Parameters

Parameter	Description
cpId	The cpId is used to filter the saved queries based on the CP. This is helpful in running the queries in background using scheduled jobs for initialisation of CP specific custom fields/forms. Note: This is the CP that you select in the top-left dropdown of the add/edit query wizard.
searchString	Matches a substring in the title of the saved query.
start	Used for paginating the results. If start=5, the output result will start from row number 5.
max	Used for paginating the results. If max=10, the output result will be maximum 10 rows
countReq	Boolean type parameter, if specified as 'true' output will show the total number of saved-queries. Otherwise it won't.

Sample response

Get URL: 'rest/ng/saved-queries?countReq=true&start=0&max=10'

Code Block

language	js
collapse	true

{
    "count": 23,
    "queries": [
        {
            "id": 23,
            "title": "Show details of tissue specimen having frozen event",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273075000
        },
        {
            "id": 22,
            "title": "Show list of tissue specimens frozen within 15 mins of received time",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273075000
        },
        {
            "id": 21,
            "title": "Show specimens stored in a Container",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273075000
        },
        {
            "id": 20,
            "title": "Show list of Specimens based on SCG Label",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273075000
        },
        {
            "id": 19,
            "title": "Show list of specimens based on participant demographics",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273074000
        },
        {
            "id": 18,
            "title": "Show list of Specimens based on participant info (PPID or MRN)",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273074000
        },
        {
            "id": 17,
            "title": "Show specimen information based on Specimen Label",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273074000
        },
        {
            "id": 16,
            "title": "Specimen kit report query",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273074000
        },
        {
            "id": 15,
            "title": "Specimen Catalog",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273073000
        },
        {
            "id": 14,
            "title": "Show list of specimens based on specimen details",
            "createdBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedBy": {
                "id": 1,
                "type": null,
                "firstName": "System",
                "lastName": null,
                "loginName": null,
                "domain": null,
                "emailAddress": null,
                "instituteName": null,
                "primarySite": null,
                "admin": null,
                "instituteAdmin": null,
                "manageForms": null,
                "cpCount": 0,
                "creationDate": null,
                "activityStatus": null
            },
            "lastModifiedOn": 1575273073000
        }
    ]
}

...

Item

Value

HTTP Method

POST

URI

/rest/ng/query/{savedQueryId}

Body

Code Block

language	js

{
	"drivingForm":"Participant",
	"wideRowMode": "DEEP",
	"startAt": 0,
	"maxResults": 20
}

Response

JSON containing the output of the saved queries

...

Parameter	Description	Allowed Values
drivingForm	Driving form determines the search perspective. When left empty, it defaults to Participant. (For example when drivingForm is Participant, the root table is 'catissue_coll_prot_reg' which is then used to join with the other tables.Similarly when drivingForm is Specimen, the root table will be catissue_specimen, which will be joined with the other tables.)	Participant, Specimen
startAt	Used for paginating the results. If startAt=5, the output result will startAt from row number 5.	Integer
maxResults	Used for paginating the results. If maxResults=10, the output result will be maximum 10 rows	Integer
wideRowMode	Specifies whether multi-valued attributes result in a single row or one row per value. Default value is OFF. Other permitted values are SHALLOW and DEEP. Try out to see what fits best for your use case.	DEEP, SHALLOW, OFF

Sample response

Code Block

language	js
collapse	true

{
    "columnMetadata": [
        {
            "expr": "CollectionProtocol.Title",
            "aggregate": false
        },
        {
            "expr": "Participant.ppid",
            "aggregate": false
        },
        {
            "expr": "Participant.gender",
            "aggregate": false
        },
        {
            "expr": "Participant.medicalRecord.medicalRecordNumber",
            "aggregate": false
        },
        {
            "expr": "Participant.medicalRecord.mrnSiteName",
            "aggregate": false
        },
        {
            "expr": "Participant.race",
            "aggregate": false
        },
        {
            "expr": "SpecimenCollectionGroup.name",
            "aggregate": false
        },
        {
            "expr": "SpecimenCollectionGroup.clinicalDiagnosis",
            "aggregate": false
        },
        {
            "expr": "SpecimenCollectionGroup.site",
            "aggregate": false
        },
        {
            "expr": "Specimen.label",
            "aggregate": false
        },
        {
            "expr": "Specimen.extensions.SpecimenCollectionEvent.time",
            "aggregate": false
        },
        {
            "expr": "Specimen.class",
            "aggregate": false
        },
        {
            "expr": "Specimen.type",
            "aggregate": false
        },
        {
            "expr": "Specimen.specimenPosition.containerName",
            "aggregate": false
        },
        {
            "expr": "Specimen.specimenPosition.positionDimensionOneString",
            "aggregate": false
        },
        {
            "expr": "Specimen.specimenPosition.positionDimensionTwoString",
            "aggregate": false
        },
        {
            "expr": "Specimen.pathologicalStatus",
            "aggregate": false
        },
        {
            "expr": "Specimen.tissueSite",
            "aggregate": false
        },
        {
            "expr": "Specimen.availableQty",
            "aggregate": false
        }
    ],
    "columnLabels": [
        "Collection Protocol# Title",
        "Participant# PPID",
        "Participant# Gender",
        "Participant# MRN",
        "Participant# MRN Site",
        "Participant# Race",
        "Visit# Name",
        "Visit# Clinical Diagnosis (Deprecated)",
        "Visit# Visit Site",
        "Specimen# Specimen Label",
        "Specimen# Collection Event# Date and Time",
        "Specimen# Class",
        "Specimen# Type",
        "Specimen# Container Name",
        "Specimen# Container Column",
        "Specimen# Container Row",
        "Specimen# Pathological Status",
        "Specimen# Anatomic Site",
        "Specimen# Available Quantity"
    ],
    "columnTypes": [
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "DATE",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "STRING",
        "FLOAT"
    ],
    "columnUrls": [
        "#/object-state-params-resolver?stateName=cp-detail.overview&objectName=collection_protocol&key=title&value={{$value}}",
        "#/object-state-params-resolver?stateName=participant-detail.overview&objectName=collection_protocol_registration&key=id&value={{$cprId}}",
        null,
        null,
        "#/object-state-params-resolver?stateName=site-detail.overview&objectName=site&key=name&value={{$value}}",
        null,
        "#/object-state-params-resolver?stateName=visit-detail.overview&objectName=visit&key=name&value={{$value}}",
        null,
        "#/object-state-params-resolver?stateName=site-detail.overview&objectName=site&key=name&value={{$value}}",
        "#/object-state-params-resolver?stateName=specimen-detail.overview&objectName=specimen&key=id&value={{$specimenId}}",
        null,
        null,
        null,
        "#/object-state-params-resolver?stateName=container-detail.locations&objectName=storage_container&key=name&value={{$value}}",
        null,
        null,
        null,
        null,
        null
    ],
    "rows": [
        [
            "TCP",
            "$$cp_reg_1$$",
            null,
            null,
            null,
            null,
            "$$cp_visit_1$$",
            null,
            "Pune Site",
            "0000004",
            "02-12-2019 16:03",
            "Fluid",
            "Buffy Coat",
            "test_box1",
            "4",
            "1",
            "Not Specified",
            "Not Specified",
            "6.00"
        ]
    ],
    "columnIndices": null,
    "dbRowsCount": 1
}

Exporting Query Data

Request

Method

POST

URL

rest/ng/query/export

Body

Code Block

language	js

{
  "aql": "select Participant.ppid, Participant.regDate, Participant.gender, Participant.race, Specimen.label, Specimen.type where  Participant.participantId exists",
  "wideRowMode": "DEEP"
}

Response

Code Block

language	js

{
  "dataFile": "query_0_61e59bc2-9350-47db-9af8-a1e7a3b65bc2",
  "completed": false
}

Parameters

aql	Valid AQL query whose output needs to be exported to a CSV file
dataFile	Handle or file ID to use for downloading the exported CSV file
completed	Boolean indicating whether the exported CSV file can be downloaded right away

Download Exported Data File

Request

Method

GET

URL

rest/ng/query/export?fileId=<dataFile>

Response

Scenario 1: When the exported data file is not ready

HTTP 400 with the following error message in the response body

Code Block

language	js

[
  {
    "code":"QUERY_EXPORT_DATA_IN_PROGRESS",
    "message":"The query result data export is in progress. Retry downloading the file after some time."
  }
]

Scenario 2: When the exported data file is ready

HTTP 200 with the ZIP binary stream in the response body

Parameters

fileId

The handle or file ID returned by the export API

Query Export in Action

Initiate Export

Image Added

Download Exported File - Attempt 1 of N

Image Added

Download Exported File

Image Added

FAQ

Let’s assume we've the following data:

A specimen record with label L
Specimen L has 2 biohazards - H1, H2
Specimen L has 2 frozen events F1, F2
Output includes specimen label (L), biohazards, and one or more fields of frozen event.

What does OFF, SHALLOW and DEEP do? What are the differences between them?
Let's assume we've a specimen record L with biohazards H1 and H2. Also, let's assume the specimen L has 2 frozen events F1 and F2.Using above, it is easy to explain the various wide row modes:
1. wideRowMode = OFF. There will be one row for each combination of biohazard and frozen event. That is -
  (L, H1, F1), (L, H1, F2), (L, H2, F1), (L, H2, F2)
2. wideRowMode = SHALLOW. There will be one row for each frozen event. That is -
  (L, H1, H2, F1), (L, H1, H2, F2)
3. wideRowMode = DEEP. There will be one row for each specimen irrespective of the number of biohazards and frozen events. That is -
  (L, H1, H2, F1, F2)
Why is it so hard to get the same results from the same query in both the API and in OpenSpecimen?
The UI uses either SHALLOW or DEEP. It does not use OFF.
When the “Enable Wide Rows” checkbox is ticked, the wideRowMode=DEEP. When it is unticked, wideRowMode=SHALLOW.

Versions Compared

Old Version 7

New Version Current

Key

Executing Any AQL

Example

Example

Parameters

Sample response

Sample response

Exporting Query Data

Request

Parameters

Download Exported Data File

Request

Parameters

Query Export in Action

Initiate Export

Download Exported File - Attempt 1 of N

Download Exported File

FAQ