Table of Contents

Introduction

OpenSpecimen allows to configure graphical dashboards

Table of Contents

Introduction

OpenSpecimen allows configuring graphical dashboards with various counters and graphs. This helps users to get a summary view of the data collected for the protocol. A default dashboard is shipped with OpenSpecimen which is set for all protocols. But users can change this to update the dashlets as per requirement. Dashboard feature is available as an enterprise plugin.

Default dashboard

When OpenSpecimen is deployed with dashboard plugin, all protocols are set with a default dashboard with the below elements:

Metrics(Counts)
1. Total participants
2. Total primary specimens
3. Total available specimens
4. Total distributed specimens
Graphs
1. Specimens by type
2. Specimens by anatomic site
3. Specimens collected vs distributed in previous quarter
4. Specimens stored by freezer

Creating dashlets

Each of the above elements - metrics and graphs are considered as dashlets. These dashlets can either be created using query interface or REST API.

Create dashlet via UI

For details on creating using query interface, refer to Dashboard changes using query.

Create dashlet via API

URL: http[s]:<host>:<port>/openspecimen/rest/ng/dashlet-configs

URL

http://<host>:<port>/openspecimen/rest/ng/dashlet-configsMethodPOSTRequestapplication/jsonExample json

Method

POST

Request

application/json

Example 1 JSON for Metric

Dashlet to include metric : Count of completed visits

Code Block

collapsetrue


{ "name":"visit_count", "title":"Visits",


    "type":"COUNTER",
	"dataSource":{
		"options":{
			"criteria":" SpecimenCollectionGroup.activityStatus = \"Active\" and  SpecimenCollectionGroup.collectionStatus = \"Complete\" and  Specimen.collectionStatus = \"Collected\"  ",
			"metric":{
				"expr":"count(distinct SpecimenCollectionGroup.name)",
				"title":"Visits"
			}
		},
		"type":"AQL"
	},
	"chartOpts":{},
	"activityStatus":"Active"
}

Example

json

2 JSON for graph

Dashlet to include graph: Available aliquots by type

Code Block

collapsetrue

  {
    "name": "dash_1_20161215_0251537",
    "title": "Available aliquots by type",
    "type": "CHART",
    "dataSource": {
      "options": {
        "criteria": " Specimen.collectionStatus = \"Collected\" and  Specimen.lineage = \"Aliquot\" and  Specimen.specimenPosition.containerName exists   ",
        "metric": {
          "expr": "count(distinct Specimen.id)",
          "title": "Aliquots"
        },
        "category": {
          "expr": "Specimen.type",
          "title": "Type"
        }
      },
      "type": "AQL"
    },
    "chartOpts": {

"type":

"Pie"

},{ "name": "specimensByAnatomicSiteGroup", "title": "Collected specimens by anatomic site group", "type": "CHART", "dataSource": {

,"showSectionValuePct":true},
    "activityStatus": "Active"
  }

Example JSON for SQL based count dashlet

Code Block

collapse	true

  {
    "name": "dash-sys-active-dps",
    "title": "Distribution Protocols",
    "type": "COUNTER",
    "dataSource": {
      "type":"SQL", 
      "options": {
        "metrics": [{"columnIndex": 0,"title": "Active Distribution Protocols"}],  
        "sql": "select count(dp.identifier) from catissue_distribution_protocol dp  where dp.activity_status = 'Active'"
      }
    },
    "chartOpts": {},
    "activityStatus": "Active"
  }

Example JSON for SQL based graph dashlet Code Block

collapse	true

name: unique name to identify the dashlet
title: caption to display on chart or counter
type: specifies whether the dashlet represents a counter or chart
datasource: specifies how the data required for rendering the dashlet should be queried
1. type: specifies the data source type. At present, AQL and SQL data sources are supported out of the box
2. options: varies according to the chosen data source.
  1. criteria: specifies the condition on the records to be used for displaying counter or chart.
  2. category: specifies the field to categorise the records. In above example, records are categorised based on specimen type field
  3. metric: specifies the counter value or category value
  4. expr: Any valid temporal expression
  5. title: category or metric caption
chartOpts: type of dashlet chart to display

Example 3 JSON for graph

Dashlet to include graph: Count of participants by specimen type

Code Block

{
  "name" : "dash_4973_20201023_1242657",
  "title" : "Count of participants by specimen type",
  "type" : "CHART",
  "dataSource" : {
    "options" : {
      "criteria" : "Participant.vitalStatus in (\"Alive\",\"Dead\") and  Specimen.type any  and  Specimen.type exists  and  CollectionProtocol.Title in (\"Test_CP_1\",\"Test_CP_2\",\"Test_CP_3\",\"Kidney Disease\")",
      "metric" : {
        "

type

expr" :

"SQL

 "count(distinct Participant.participantId)",
        "

options

title" : "Participants"

{

   },
      "category" : {

"columnIndex":0,"title":"Anatomic Site"}


        "expr" : "Specimen.type",
        "

metrics

title" :

[{"columnIndex":1,"title":"Collected Specimens"}],

 "Specimen Type"
      }
    },
    "

sql

type" : "

select a.value, count(s.identifier) from catissue_specimen s inner join catissue_collection_protocol cp on cp.identifier = s.collection_protocol_id inner join catissue_permissible_value pv on pv.value = s.tissue_site inner join os_pvs_hierarchy h on h.descendant_id = pv.identifier inner join catissue_permissible_value a on a.identifier = h.ancestor_id where %sql_cp_restriction% and (a.parent_identifier is null and s.collection_status = 'Collected' and s.lineage = 'Aliquot' and s.available_quantity > 0 and pv.public_id = 'anatomic_site' and a.public_id = 'anatomic_site' and s.activity_status != 'Disabled') group by a.value order by count(s.identifier) desc", "restrictionOpts":{"type":"sql_cp_restriction","opts":{"cpIdExpr":"cp.identifier"}} }

AQL"
  },
  "chartOpts": {"type":"Pie", "showLegendValuePct" : true},
  "activityStatus": "Active"
}

Example 4 JSON for SQL based count dashlet

Code Block

  {
    "name": "dash-sys-active-dps",
    "title": "Distribution Protocols",
    "type": "COUNTER",
    "dataSource": {
      "type":"SQL", 
      "options": {
        "metrics": [{"columnIndex": 0,"title": "Active Distribution Protocols"}],  
        "sql": "select count(dp.identifier) from catissue_distribution_protocol dp  where dp.activity_status = 'Active'"
      }
    },
    "chartOpts": {

"type

},
    "activityStatus": "

Pie","showSectionValuePct":true}

Active"
  }

Example 5 JSON for SQL based graph dashlet

Code Block
{ "name": "specimensByAnatomicSiteGroup", "

activityStatus": "Active" }columnIndex in category and metrics specify what column of SQL result set should be used. In above example, first column of result set (i.e. columnIndex: 0) is used to create categories and second column of result set is used to show the count of each category.

title": "Collected specimens by anatomic site group",
    "type": "CHART",
    "dataSource": {
      "type":"SQL",
      "options": {
        "category": {"columnIndex":0,"title":"Anatomic Site"},
        "metrics":[{"columnIndex":1,"title":"Collected Specimens"}],
        "sql": "select a.value, count(s.identifier) from catissue_specimen s inner join catissue_collection_protocol cp on cp.identifier = s.collection_protocol_id inner join catissue_permissible_value pv on pv.value = s.tissue_site inner join os_pvs_hierarchy h on h.descendant_id = pv.identifier inner join catissue_permissible_value a on a.identifier = h.ancestor_id where %sql_cp_restriction% and (a.parent_identifier is null and s.collection_status = 'Collected' and s.lineage = 'Aliquot' and s.available_quantity > 0 and pv.public_id = 'anatomic_site' and a.public_id = 'anatomic_site' and s.activity_status != 'Disabled') group by a.value order by count(s.identifier) desc",
        "restrictionOpts":{"type":"sql_cp_restriction","opts":{"cpIdExpr":"cp.identifier"}} 
      } 
    },
    "chartOpts": {"type":"Pie","showSectionValuePct":true},
    "activityStatus": "Active"
  }

columnIndex in category and metrics specify what column of SQL result set should be used. In above example, first column of result set (i.e. columnIndex: 0) is used to create categories and second column of result set is used to show the count of each category.

Info
To edit existing dashlets, use 'Get' method to get the dashlets. Edit the JSON code for the specific dashlet section and use 'Put' to update it.

When 'showSectionValuePct' is set to true like Example 2 above, it shows the percent of each section. See below graph:

Image Added

When 'showLegendValuePct' is set to true like Example 3 above, it shows the percent of each section in the legends. See below graph:

Image Added

Configuring dashboards to CP

Different dashboards can be set per CP. To change settings per CP, go to individual protocol settings and edit the dashlets to be included or excluded.

...

URL http://<host>:<port>/openspecimen/rest/ng/dashboards/{dashboardId}

Method PUT

Request application/json

Example json

true

Code Block

collapse

{
  "view": "CollectionProtocol",
  "viewParams": {
    "cpId": "-1"
  },
  "dashlets": [
    {
      "config": {
        "name": "dash-sys-participants"
      },
      "sortOrder": 1
    },
    {
      "config": {
        "name": "visit_count"
      },
      "sortOrder": 2
    },
    {
      "config": {
        "name": "dash_1_20161214_0406950"
      },
      "sortOrder": 3
    },
    {
      "config": {
        "name": "dash_1_20161214_0357273"
      },
      "sortOrder": 4
    },
    {
      "config": {
        "name": "dash_1_20161215_0251537"
      },
      "sortOrder": 5
    },
    {
      "config": {
        "name": "dash-spmns-by-anatomic"
      },
      "sortOrder": 6
    },
    {
      "config": {
        "name": "dash-sys-coll-dist"
      },
      "sortOrder": 7
    },
{
      "config": {
        "name": "dash-sys-coll-dist-yr"
      },
      "sortOrder": 8
    },
    {
      "config": {
        "name": "dash-spmns-by-path"
      },
      "sortOrder": 9
    }
  ],
  "activityStatus": "Active"
}

Configuring dashboards to SpecimenCatalog

Query existing dashboard set for public SpecimenCatalog:

...

Versions Compared

Old Version 6

New Version Current

Key

Introduction

Introduction

Default dashboard

Creating dashlets

Create dashlet via UI

Create dashlet via API

Configuring dashboards to CP

Configuring dashboards to SpecimenCatalog

Page Comparison

Versions Compared

Old Version 6

New Version Current

Key

Introduction

Introduction

Default dashboard

Creating dashlets

Create dashlet via UI

Create dashlet via API

Configuring dashboards to CP

Configuring dashboards to SpecimenCatalog