Motivation
There have been situations where end users need to review a sample, check relevant metrics and trigger a specific Action - for example "for a given sample, IF RapidQC has completed AND LOD>0 THEN submit "FinalAggregation" request in Pipeline's JMS queue". All of these actions to be done/initiated from within Tableau. Beyond visualization, Tableau can't do much else in terms of maintaining a "workflow" in DB, talking to external web-services like JMS and so on. That's why these job is being outsourced to our "SampleAnalyticsWorkflow" web-service - it's written in Scala so there is virtually no limit what tasks it can do for you. Tableau utilize it's UrlAction gadget to make a URL call to SAW service when appropriate.
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| Column name | Data type | Description |
|---|---|---|
| PDO | VARCHAR2 | PDO |
| PDO_SAMPLE | VARCHAR2 | PDO SAMPLE |
| DATA_TYPE | VARCHAR2 | Exome, WGS |
| REQUEST_TYPE | NUMBER | "RequestFinalAggregation", "RequestTopOff", "RequestTopOffGroup", "RequestPoolCreated", "RequestSendToRework", "RequestHoldForTopOff", "RequestWaitingForNewRwData", "RequestReset", "RequestPCHoldForTopOff","RequestVolumeFinal" |
| USER_NAME | VARCHAR2 | who triggered this action/transition |
| PARAMS | VARCHAR2 | This is a free text where Tableau developers can store additional info re this transition which later can be used. Usually it's semicolon-separated-list-of-key=value-pairs |
| TIMESTAMP | DATE | when this action was triggered |
| IS_LATEST | NUMBER | Boolean (1 or 0), Is this the latest transition a given (PDO, PDO_SAMPLE, DATA_TYPE) has gone through. Every time new transition is recorded it comes with IS_LATEST=1 whereas previous latest transition is reset IS_LATEST=0 |
| IP_ADDRESS | VARCHAR2 | where (which IP) this request came from |
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- requestType is the text-representation of this request (RequestFinalAggregation, RequestTopOff, etc)
- each individual item is a quintuple representing a single sample like this pdo:pdo_sample:data_type:user_name:parameters (greens are optional)
parameters represents any piece of data you might want to attach to a given sample/transition. It is a semicolon-separated-list-of-key-=value-pairs. Gets recorded in PARAMS column.
Authentication
There are 3 alternative ways to provide a "user_name"
- repeat it in the quintuple. Very wasteful.
- standalone upfront URL-parameter "&user_name=JohnDoe" (economical and solid). Unfortunately as of now, Tableau's urlAction can't inject the username like this.
- 2-step the cookie-dance (economical but might be tricky to use from within Tableau)
- record the user_name-cookie in the browser environment by calling this URL http://analytics:8090/api/setCookie?cookies=sampleAnalyticsWorkflow.user_name=JohnDoe (you only need to do this once for your entire session). Cookie/credentials are configured to expire after 10 minutes.
- and then make the main SAW call as many times as you need
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- step1: JOIN cognos.slxre_readgroup_metadata ON (pdo, pdo_sample, data_type) and lookup (research_project_id,collaborator_sample_id) for a given sample
- step2: send message to appropriate JMS queue
Environments
2 separate environments are provided
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