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Dashboard Configuration

Owned by Poornima Govindrao
Last updated: Oct 26, 2020 by Divya Prabhu (Unlicensed)
6 min read

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:

  1. Metrics(Counts)
    1. Total participants
    2. Total primary specimens
    3. Total available specimens
    4. Total distributed specimens
  2. 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
MethodPOST
Requestapplication/json
Example 1 JSON for Metric

Dashlet to include metric : Count of completed visits

{
	"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 2 JSON for graph

Dashlet to include graph: Available aliquots by type

  {
    "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","showSectionValuePct":true},
    "activityStatus": "Active"
  }
  1. name: unique name to identify the dashlet
  2. title: caption to display on chart or counter
  3. type: specifies whether the dashlet represents a counter or chart
  4. 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
  5. chartOpts: type of dashlet chart to display
Example 3 JSON for graph

Dashlet to include graph: Count of participants by specimen type

{
  "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" : {
        "expr" : "count(distinct Participant.participantId)",
        "title" : "Participants"
      },
      "category" : {
        "expr" : "Specimen.type",
        "title" : "Specimen Type"
      }
    },
    "type" : "AQL"
  },
  "chartOpts": {"type":"Pie", "showLegendValuePct" : true},
  "activityStatus": "Active"
}
Example 4 JSON for SQL based count dashlet
  {
    "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 5 JSON for SQL based graph dashlet
{
    "name": "specimensByAnatomicSiteGroup",
    "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.

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:

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

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.

To set default dashboard for all CPs, follow the below steps:

Step 1: Query existing default system level dashboard for all CPs:
GET <app_url>/rest/ng/dashboards?view=CollectionProtocol&viewKey=cpId&viewKeyValues=-1
Step 2: Use above API response to obtain dashboard ID, add make required changes.
URLhttp://<host>:<port>/openspecimen/rest/ng/dashboards/{dashboardId}
MethodPUT
Requestapplication/json
Example json
{
  "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:

Method: Get 

URL: http://<host>:<port>/rest/ng/dashboards?view=SpecimenCatalog

JSON for making changes to SpecimenCatalog dashboard is similar to CP dashboard. Only the 'view' has to be replaced with 'SpecimenCatalog'.


Got feedback or spotted a mistake?

Leave a comment at the end of this page or email contact@krishagni.com