Introduction
OpenSpecimen allows to configure 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.
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When OpenSpecimen is deployed with dashboard plugin, all protocols are set with a default dashboard with the below elements:
- Metrics(Counts)
- Total participants
- Total primary specimens
- Total available specimens
- Total distributed specimens
- Graphs
- Specimens by type
- Specimens by anatomic site
- Specimens collected vs distributed in previous quarter
- Specimens stored by freezer
...
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 |
|
| Method | POST |
| Request | application/json |
Example1 | Example 1 json for Metric | Dashlet to include metric : Count of completed visits | Code Block |
|---|
{
"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"
} |
|
Example2 |
| Example 2 json for graph | Dashlet to include graph: Available aliquots by type | Code Block |
|---|
{
"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"
} |
- 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
- type: specifies the data source type. At present, AQL and SQL data sources are supported out of the box
- options: varies according to the chosen data source.
- criteria: specifies the condition on the records to be used for displaying counter or chart.
- category: specifies the field to categorise the records. In above example, records are categorised based on specimen type field
- metric: specifies the counter value or category value
- expr: Any valid temporal expression
- title: category or metric caption
- chartOpts: type of dashlet chart to display
|
Example3 JSON for | 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" : {
"expr" : "count(distinct Participant.participantId)",
"title" : "Participants"
},
"category" : {
"expr" : "Specimen.type",
"title" : "Specimen Type"
}
},
"type" : "AQL"
},
"chartOpts": {"type":"Pie","showSectionValuePct":true, "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": {},
"activityStatus": "Active"
} |
|
Example4 |
| Example 5 JSON for SQL based graph dashlet |
| Code Block |
|---|
{
"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. |
| 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. |
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| URL | http://<host>:<port>/openspecimen/rest/ng/dashboards/{dashboardId} |
| Method | PUT |
| Request | application/json |
| Example json |
| Code Block |
|---|
{
"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"
} |
|
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