| Table of Contents |
|---|
Executing Any AQL
Below API can be used to execute any AQL and obtain the desired results. AQL is custom query language built-in OpenSpecimen to allow power users perform complex queries on data without requiring to know anything about the OpenSpecimen data model.
...
| Code Block | ||
|---|---|---|
| ||
{
"cpId": 1,
"aql": "select Participant.ppid, SpecimenCollectionGroup.collectionDate, count(distinct Specimen.id) where Specimen.lineage = \"Aliquot\"",
"outputIsoDateTime": true
} |
Sample response
...
| Code Block | ||
|---|---|---|
| ||
{
"columnMetadata": [
{
"expr": "Participant.ppid",
"aggregate": false
},
{
"expr": "SpecimenCollectionGroup.collectionDate",
"aggregate": false
},
{
"expr": "count ( distinct Specimen.id )",
"aggregate": true
}
],
"columnLabels": [
"Participant# PPID",
"Visit# Visit Date",
"Column"
],
"columnTypes": [
"STRING",
"DATE",
"INTEGER"
],
"columnUrls": [
"#/object-state-params-resolver?stateName=participant-detail.overview&objectName=collection_protocol_registration&key=id&value={{$cprId}}",
null,
null
],
"rows": [
[
"OPSMN-0001-TCP",
"2015-06-04T00:00:00",
"184"
],
[
"OPSMN-0001-TCP",
"2016-06-30T11:30:00",
"25"
],
[
"OPSMN-0003-TCP",
"2015-05-05T00:00:00",
"107"
],
[
"OPSMN-0003-TCP",
"2015-05-19T00:00:00",
"17"
],
[
"OPSMN-0003-TCP",
"2015-07-24T00:00:00",
"4"
],
[
"OPSMN-0003-TCP",
"2015-08-17T00:00:00",
"5"
],
...
]
} |
...
| Item | Value |
|---|---|
| HTTP Method | GET |
| URI | /rest/ng/saved-queries |
| Response | JSON containing detailed list of saved queries |
Parameters
| Parameter | Description |
|---|---|
| cpIdCollection protocol ID. If specified, <Find out and add here what happens> | 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 | ||||
|---|---|---|---|---|
| ||||
{
"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
}
]
} |
...
Executing a saved-query
...
Request Details
| Item | Value | |||||
|---|---|---|---|---|---|---|
| HTTP Method | POST | |||||
| URI | /rest/ng/query/{id} | |||||
| Body |
| |||||
| Response | JSON containing the output of the saved queries |
Parameters
| Parameter | Description | Allowed Values |
|---|
runType
drivingForm
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 | ||||
|---|---|---|---|---|
| ||||
{
"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
} |
...