Tiger3 ETL Shell Commands (refreshes, etc.)

ssh-connect to "analytics" server using your favorite SSH tool. For Windows SecureCRT is offered as standard ssh-software to Broadies. For Mac you can connect through the command line in Terminal.

Run etlShell

/home/unix/analytics/TigerETL3/runEtlShell.sh

run etl-commands as you see fit

ETL Tasks

TASK description	COMMAND
Manually push into GitHub by providing CSV-list of dbObjects and optional commit message. Note that dbObjects are specified by (dbname.schema.objectname) triplets where dbname is: seqprod, labopsjira or bsp If no explicit commit-message is provided then built-into-your-code comments would be picked */ GITHUBCOMMENT:** RPT-1234 */	analytics.tiger.agents.OracleVCS.main(Array("labopsjira.REPORTING.ZZZAB_METADATA_TRANSITIONS,seqprod.COGNOS.ACTIVE_LAB", "Monads are great"))
blacklist runfolder from RunMercury/RghqsLoader agents	CognosDB("RunfolderAPI.blacklist", RunfolderAPI.blacklistRun("runfolder1,runfolder2"))
whitelist runfolder from RunMercury/RghqsLoader agents	CognosDB("RunfolderAPI.whitelist", RunfolderAPI.whitelistRun("runfolder1,runfolder2"))
Manual Refresh in PDO Star5 using a query (using PDO_NAMEs)	AnalyticsEtlDB("analytics.tiger.agents.PdoStar.fromSQL", deltaFromSql("""SELECT DISTINCT a.pdo_name\|\|','\|\|a.pdo_sample_id FROM cognos.pdo_star5 a WHERE a.pdo_name = 'PDO-14680'""") flatMap DataSetEtl() flatMap analytics.tiger.agents.PdoStar.pipeline)
Manual Refresh in PDO Star5 using a query (alternate method using "Old" Collaborator Sample IDs)	DEPRECATED (use RunETL tool instead) import analytics.tiger.agents.PdoStar._ AnalyticsEtlDB("analytics.tiger.agents.PdoStar.CollaboratorSamples", collSamplesToPdoSamples(List("oldcollabSMID1","oldcollabSMID2")) flatMap DataSetEtl() flatMap pipeline)
Manual Refresh of Picard Aggregations for a list of samples (Research)	DEPRECATED (use RunETL tool instead) import analytics.tiger.agents.PicardAggregator._ analytics.tiger.utils.CognosDB("analytics.tiger.agents.PicardAggregator.Samples", regSamples("JB-0236-T-02,TCGA-HU-A4H5-11A-11D-A25E-08"))
Manual Refresh of Picard Aggregations using a query (Research)	import analytics.tiger.agents.PicardAggregator._ analytics.tiger.utils.CognosDB("analytics.tiger.agents.PicardAggregator.FromSql", regFromSql("SELECT a.SAMPLE FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = 'NWD725917'"))
Manual Refresh of Picard Aggregations for a list of samples (CRSP)	DEPRECATED (use RunETL tool instead) import analytics.tiger.agents.PicardAggregator._ analytics.tiger.utils.AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.Samples", crspSamples("SM-INAAG,SM-INAAL"))
Manual Refresh of Picard Aggregations using a query (CRSP)	import analytics.tiger.agents.PicardAggregator._ analytics.tiger.utils.AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.FromSql", crspFromSql("SELECT a.SAMPLE FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = 'SM-INAAL'"))
Manual Refresh of RapidQC Aggregations for a list of samples	CognosDB("analytics.tiger.agents.RapidQcAggregator.Manual", deltaETL(Set("NWD581810")) flatMap DataSetEtl() flatMap analytics.tiger.agents.RapidQcAggregator.mainPipeline)
Manual Refresh of RapidQC Aggregations using a query	CognosDB("analytics.tiger.agents.RapidQcAggregator.fromSQL", deltaFromSql("""SELECT a.bsp_collaborator_sample_id FROM pdo_star5_aux a WHERE a.pdo_sample = 'SM-HQV67'""") flatMap DataSetEtl() flatMap analytics.tiger.agents.RapidQcAggregator.mainPipeline)

Tiger3 ETL Shell Commands (refreshes, etc.)

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