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openspecimen/rest/ng/collection-protocols

Use this resource to create new collection protocol in the openSpecimen application. Use HTTP POST method to call this API by passing the below details in JSON format.

 

Below are the attributes which need to be sent in the request body:

Parameter
Details
title Collection protocol title.Unique in the application
shortTitle

Collection protocol short title. Unique in the application

startDateCollection protocol starting date
endDate[optional]Collection protocol end date. If given then, the endDate should not be later than startDate.
investigator

Principal investigator on CP

Mainly contains following  parameters :

loginName :  User login name. For this specified user must be present in application.

domainName: Name of domain to which user belongs to. By default it will be catissue.

activityStatusActivity status of a collection protocol
cpType[optional]Collection protocol type
labelFormat[optional]CP label format
derivedLabelFormat[optional]Derived label format
aliquotLabelFormat[optional]Aliquot label format
ppIdFormat[optional]PPId format
cpSiteRoles[optional]

It is collection of Sites and Roles with respect to CP. By default it will be none. i.e. Blank collection.

Mainly contains following  parameters :

roleName :  Role of user like Scientist, Admin etc. For this attribute role must be present in application.

siteName: Site name. For this attribute Site must be present in application.

 

 

http[s]:<host>:<port>/openspecimen/rest/ng/collection-protocols

Use this URL to add collection protocol in openSpecimen application.

Result:

The response of this request will contains the details of the created collection protocol.

Below is the example of the create collection protocol:

...

Response

{
id: 158
title: "LiverCancer Study"
shortTitle: "LCS"
cpType: "Parent"
startDate: 1391299200000
endDate: null
activityStatus: "Active"
labelFormat: null
derivedLabelFormat: null
aliquotLabelFormat: null
ppIdFormat: null
cpeDetails:    
 
{
id: 1038
collectionPointLabel: "First Follow-up"
studyCalendarEventPoint: null
labelFormat: null
activityStatus: "Active"
defaultSiteName: null
specimenRequirementDetails:    
 
{
id: 14295
collectionTimestamp: 1410480000000
collector: 
{
loginName: "admin@admin.com"
domainName: "catissue"
}
collectionComments: null
collectionProcedure: "Needle Aspirate"
collectionContainer: "Frizeer"
receivedQuality: "Acceptable"
receivedTimestamp: null
receiver: 
{
loginName: "admin@admin.com"
domainName: "catissue"
}
receivedComments: null
collectionProtocolEvent: null
childSpecimenRequirementCollection: 
 {
id: 14296
collectionTimestamp: 1410480000000
collector: 
{
loginName: "admin@admin.com"
domainName: "catissue"
}
collectionComments: null
collectionProcedure: "Needle Aspirate"
collectionContainer: "container"
receivedQuality: "Acceptable"
receivedTimestamp: null
receiver: 
{
loginName: "admin@admin.com"
domainName: "catissue"
}
receivedComments: null
collectionProtocolEvent: null
childSpecimenRequirementCollection: 
[0]
tissueSite: null
tissueSide: null
pathologicalStatus: null
lineage: "Aliquot"
initialQuantity: null
specimenClass: null
specimenType: null
labelFormat: null
specimenRequirementLabel: null
activityStatus: "Active"
}
tissueSite: null
tissueSide: null
pathologicalStatus: null
lineage: "New"
initialQuantity: null
specimenClass: null
specimenType: null
labelFormat: null
specimenRequirementLabel: null
activityStatus: "Active"
}
}
coordinators: 
[0 ]
investigator: 
{
loginName: "admin@admin.com"
domainName: "catissue"
}

...

openspecimen/rest/ng/collection-protocols

Use this resource to create new collection protocol in the openSpecimen application. Use HTTP POST method to call this API by passing the below details in JSON format.


Below are the attributes which need to be sent in the request body:

Parameter
Details
title

Full title of the collection protocol, which is normally used in the regulatory approval documents.

shortTitle

User friendly short string to uniquely identify the collection protocol.

code [optional]A short code to uniquely identify the CP in the system.
startDate [optional]Collection protocol starting date
endDate [optional]Collection protocol end date. If given then, the endDate should be later than start date.
principalInvestigator

Principal investigator of CP

Mainly contains following  parameters :

loginName :  User login name. For this specified user must be present in application.

domainName: Name of domain to which user belongs to. By default it will be catissue.

coordinators [optional]

Collection of coordinators. It is collection of user info mainly contains following parameters :

loginName :  User login name. For this specified user must be present in application.

domainName: Name of domain to which user belongs to. By default it will be catissue.

irbId [optional]Ethics approval id
anticipatedParticipantsCount [optional]Anticipated participants count. This is ignored for specimen centric CPs.
activityStatusActivity status of a collection protocol
visitNameFmt [optional]Visit name format. This is ignored for specimen centric CPs.
specimenLabelFmt [optional]Specimen label format
derivedLabelFormat [optional]Derived label format
aliquotLabelFormat [optional]Aliquot label format
ppidFmt [optional]PPID format. This is ignored for specimen centric CPs.
cpSites

Array of sites at which the collection protocol is being run or active.

Mainly contains following  parameters :

siteName: Site name.

code[optional]: Site code


manualPpidEnabled [optional]When enabled, users have to manually enter the participant PPID.
manualVisitNameEnabled [optional]When enabled, users have to manually enter the visit names.
manualSpecLabelEnabled [optional]When enabled, users have to manually enter the specimen (primary, derived, aliquot) labels.
specimenCentric

Boolean indicating whether the CP is participant or specimen centric. When the value of this attribute is null or false, a participant centric CP is created. However, when the value is true, a specimen centric CP is created.

Note: This flag is effective only when a CP is being created. The value of this attribute is ignored in the CP update APIs.

In other words, a participant centric CP cannot be converted to specimen centric and vice-versa.


http[s]:<host>:<port>/openspecimen/rest/ng/collection-protocols

Use this URL to add collection protocol in openSpecimen application.

Result:

The response of this request will contains the details of the created collection protocol.

Below is the example of the create collection protocol:

URLhttp://<host>:<port>/openspecimen/rest/ng/collection-protocols
MethodPOST
Requestapplication/json
json
{
   "shortTitle": "A Planned Clinical Study FD",
   "title": "Planned Clinical Study",
   "code": null,
   "principalInvestigator": { 
     "loginName": "admin@admin.com",
     "domain": "openspecimen"
   },
   "startDate": 1427653800000,
   "endDate": 1454178600000,
   "ppidFmt": "DWP%05d",
   "manualPpidEnabled": false,
   "coordinators": [],
   "cpSites": [ {
     "siteName": "Arkansas Repository",
     "code": "CS_123"
   }, {
     "siteName": "Arkansas Hospital",
     "code": "CS_34"
   } ],
   "consentsWaived": false,
   "irbId": "65465",
   "anticipatedParticipantsCount": null,
   "descriptionUrl": null,
   "specimenLabelFmt": "%PPI%.%SP_TYPE%.%SYS_UID%",
   "derivativeLabelFmt": "%PPI%.%SP_TYPE%.%SYS_UID%",
   "aliquotLabelFmt": "%PSPEC_LABEL%.%PSPEC_UID%",
   "visitNameFmt": null,
   "manualVisitNameEnabled": false,
   "manualSpecLabelEnabled": true,
   "aliquotsInSameContainer": null,
   "activityStatus": "Active"
}
Response
{
   "id": 2,
   "shortTitle": "A Planned Clinical Study FD",
   "title": "Planned Clinical Study",
   "code": null,
   "principalInvestigator": {
     "id": 1,
     "firstName": "Admin",
     "lastName": "Admin",
     "loginName": "admin@admin.com",
     "domain": "openspecimen",
     "emailAddress": "openspecimendemo@gmail.com",
     "admin": true,
     "cpCount": 0,
     "creationDate": null
   },
   "startDate": 1427653800000,
   "endDate": 1454178600000,
   "participantCount": null,
   "specimenCount": null,
   "ppidFmt": "DWP%05d",
   "manualPpidEnabled": false,
   "coordinators": [],
   "cpSites": [ {
     "id": 2,
     "siteName": "Arkansas Repository",
     "code": "CS_123"
   }, {
     "id": 25,
     "siteName": "Arkansas Hospital",
     "code": "CS_34"
   } ],
   "consentsWaived": false,
   "irbId": "65465",
   "anticipatedParticipantsCount": null,
   "descriptionUrl": null,
   "specimenLabelFmt": "%PPI%.%SP_TYPE%.%SYS_UID%",
   "derivativeLabelFmt": "%PPI%.%SP_TYPE%.%SYS_UID%",
   "aliquotLabelFmt": "%PSPEC_LABEL%.%PSPEC_UID%",
   "visitNameFmt": null,
   "manualVisitNameEnabled": false,
   "manualSpecLabelEnabled": true,
   "aliquotsInSameContainer": null,
   "activityStatus": "Active",
   "consents": null,
   "events": null
}

 Error Cases :

code
Applies to
Status Message
200All resourcesCollection Protocol has been created successfully
400All requestsInvalid parameters, e.g  duplicate CP title, blank CP title etc
401All requestsAuthorization failed, user doesn’t have authority
500All requestsInternal server error, encountered server error while performing operations

...