Motivation
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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. |
| 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)
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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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- take user_name out of items (see authentication above)
- take out PDO-, SM- prefixes resp from PDO, PDO_SAMPLE. SAW will automatically add them back as needed.
- parameters which are pertinent to all samples (for example source=RQC) should be moved to standalone extra_info parameter. SAW will disperse it to PARAMS column of all samples involved.
- regarding parameters which are sample-specific (for example xShort=123;yLong=567)
- move all keys to standalone params_fields url-parameter as colon-separated-list-of-keys
- in the items/samples parameter leave only the semicolon-separated-list-of-valuesSAW will pair back keys/values accordingly and insert it into PARAMS column.
- In item's data_type, encode Exome with E (resp.WGS with W)
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