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  1. 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.
  2. Run etlShell
    /home/unix/analytics/TigerETL3/runEtlShell.sh
  3. run etl-commands as you see fit


ETL Tasks

TASK descriptionCOMMAND

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)
import analytics.tiger.agents.PdoStar._
AnalyticsEtlDB("analytics.tiger.agents.PdoStar.fromSQL", collSamplesToPdoSamples(List("oldcollabSMID1","oldcollabSMID2")) flatMap DataSetEtl() flatMap pipeline)
Manual Refresh of Picard Aggregations for a list of samples (Research)
import analytics.tiger.agents.PicardAggregator._
import scala.collection.JavaConverters._
CognosDB("analytics.tiger.agents.PicardAggregator.Manual", deltaETL(Set("NWD725917","NWD622113")) flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineRegular").asScala, Map(), Map("DATA_ID" -> dataId))})
 Manual Refresh of Picard Aggregations using a query (Ressearch)
import analytics.tiger.agents.PicardAggregator._
import scala.collection.JavaConverters._

CognosDB("analytics.tiger.agents.PicardAggregator.fromSQL", deltaFromSql("""SELECT a.SAMPLE FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = 'NWD725917'""") flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineRegular").asScala, Map(), Map("DATA_ID" -> dataId))})
Manual Refresh of Picard Aggregations for a list of samples (CRSP)
import analytics.tiger.agents.PicardAggregator._
import scala.collection.JavaConverters._
AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.Manual", deltaETL(Set("SM-INAAF")) flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineCRSP").asScala, Map(), Map("DATA_ID" -> dataId))})
Manual Refresh of Picard Aggregations using a query (CRSP)
import analytics.tiger.agents.PicardAggregator._
import scala.collection.JavaConverters._

AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.fromSQL", deltaFromSql("""SELECT a.SAMPLE FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = 'SM-INAAF'""") flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineCRSP").asScala, Map(), Map("DATA_ID" -> dataId))})
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)
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