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SELECT DISTINCT a.pdo_name||','||a.pdo_sample_id FROM ... a WHERE ...

Request a refresh for PdoStar5Agent by issuing SQL like this in SEQPROD.COGNOS:

INSERT INTO pdo_star_special_refreshes VALUES('PDO-1', 'SM-12345', sysdate);

Issue/Error: Once a week (1am on Fri) PdoStar5 goes through 1y-refresh. Sometime you might want to trigger it earlier.

Diagnosis: 

Remedy:  Connect to "analytics" server using your favorite SSH tool and run the following line:

/home/unix/analytics/TigerETL3/runEtlAgent.sh Task task=etlObject agentName=analytics.tiger.agents.PdoStar db=analyticsetl 'delta=MillisDelta.loadFromDb(365d,0d)'

Connect remotely to "analytics-etl" and run following command. Make sure that regular schedule will not interfere with your run (which takes ~50 minutes)

C:\AnalyticsETL\runEtlScript.bat C:\AnalyticsETL\scripts\PdoStarEtl.scala "1y-refresh=true"

Issue: How to make PDO_STAR5 ETL pick a new product ?

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Remedy: Follow the instructions  here for blacklist runfolder from RunMercury/RghqsLoader agents

Blacklist it by issuing SQL like this in SEQPROD.COGNOS:

UPDATE slxre_rghqs_targets a SET a.blacklist_timestamp=SYSDATE WHERE a.run_name='run123'

Issue: How to whitelist a FC for processing by Run Mercury and RGHQS agents.

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SELECT DISTINCT SAMPLE FROM (
SELECT a.project, a.SAMPLE, a.LIBRARY, a.data_type
FROM metrics.aggregation a 
WHERE   nvl(a.modified_at, a.workflow_end_date) >= to_date(<START Date from ETL dashboard>, 'yyyy-Mon-dd hh24:mi:ss')
    AND nvl(a.modified_at, a.workflow_end_date) <  to_date(<END Date from ETL dashboard>, 'yyyy-Mon-dd hh24:mi:ss')
    AND a.is_latest <>0 
GROUP BY a.project, a.SAMPLE, a.LIBRARY, a.data_type
HAVING count(*)>1
)

Issue: Designation ETL fails with "ORA-30926: unable to get a stable set of rows in the source tables" error

Diagnosis: This is usually caused by a flowcell with 2 runs valid run, one of which should have been cancelled. Run the query below to determine the trouble flowcell:

SELECT r.flowcell_barcode, count(*)
FROM slxre2_organic_run r
WHERE r.is_cancelled =0
AND r.run_date >= '1-jan-2017'
AND r.run_type ='PRODUCTION'
GROUP BY r.flowcell_barcode
HAVING count(*)>1

Remedy: Contact Tammy, Andrew B. , Mike DaSilva or John W. to clear the bad run from their dashboard. Designation ETl will recover as soon as the run is cleared. 

Issue: Scala ETL ERROR: analytics.etl.DeckEventAgent$ (Most likely 'lcSet' tag is missing)

Diagnosis: Sometimes this Squid web-service returns no LcSet. Comment about this incident is automatically posted in IPI-61224 and ticket reopened.

Remedy: Just follow up with LIMS team. Our DeckEventAgent will catch up as soon as LIMS service is fixed. No other intervention is needed.

Issue: analytics.etl.PkViolationWarning. unique constraint (COGNOS.RGHQS_METADATA_PK) violated

Diagnosis: This happens when 2+ readgroups having same (fc, lane, mol_index) try to get into datamart. Picard calls it "CLASH". RunMercuryAgent would ignore abusing readgroups and move on with the rest of 'good' ones. Email would give you detailed troubleshooting info.

Remedy: There isn't much for us to do. If upstream issues are resolved you can request a ReadgroupMetadata refresh for the whole run/fc (see above). You can search for the RG in GPINFOJIRA by searching the FC ID to see if it has been blacklisted and already handled upstream.

Issue/Error: ETL: DB error, server: (thorium or vorarestore), Error: ORA-12008: error in materialized view refresh path, ORA-25153: Temporary Tablespace is Empty

Diagnosis: This happens when the DB team is doing some kind of backup or transfer.

Remedy: These errors can be ignored. Everything is actually fine.

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