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Mariela Mihaleva

Atanas Mihalev

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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 */



Code Block
languagescala
analytics.tiger.agents.OracleVCS.main(Array("labopsjira.REPORTING.ZZZAB_METADATA_TRANSITIONS,seqprod.COGNOS.ACTIVE_LAB", "Monads are great"))


blacklist runfolder from RunMercury/RghqsLoader agents


Code Block
languagescala
CognosDB("RunfolderAPI.blacklist", RunfolderAPI.blacklistRun("runfolder1,runfolder2"))


whitelist runfolder from RunMercury/RghqsLoader agents


Code Block
languagescala
CognosDB("RunfolderAPI.whitelist", RunfolderAPI.whitelistRun("runfolder1,runfolder2"))


Manual Refresh in PDO Star5 using a query (using PDO_NAMEs)


Code Block
languagescala
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)

Code Block
languagescala
import analytics.tiger.agents.PdoStar._
AnalyticsEtlDB("analytics.tiger.agents.PdoStar.
fromSQL
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)

Code Block
languagescala
import analytics.tiger.agents.PicardAggregator._
import scala
analytics.
collection
tiger.
JavaConverters
utils.
_ 
CognosDB("analytics.tiger.agents.PicardAggregator.
Manual
Samples",
deltaETL
regSamples(
Set("NWD725917","NWD622113")) flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineRegular").asScala, Map(), Map("DATA_ID" -> dataId))}) 
"JB-0236-T-02,TCGA-HU-A4H5-11A-11D-A25E-08"))


 Manual Refresh of Picard Aggregations using a query (RessearchResearch)


Code Block
languagescala
import analytics.tiger.agents.PicardAggregator._
import scalaanalytics.collectiontiger.JavaConvertersutils._
CognosDB("analytics.tiger.agents.PicardAggregator.fromSQLFromSql", deltaFromSqlregFromSql("""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)

DEPRECATED (use RunETL tool instead)

Code Block
languagescala
import analytics.tiger.agents.PicardAggregator._
import scala
analytics.
collection
tiger.
JavaConverters
utils.
_ 
AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.
Manual
Samples",
deltaETL(Set
crspSamples("SM-
INAAF")) flatMap DataSetEtl() flatMap {(dataId: Int) => scriptETL(conf.getConfigList("mainPipelineCRSP").asScala, Map(), Map("DATA_ID" -> dataId))}
INAAG,SM-INAAL"))


Manual Refresh of Picard Aggregations using a query (CRSP)


Code Block
languagescala
import analytics.tiger.agents.PicardAggregator._
import scalaanalytics.collectiontiger.JavaConvertersutils._
AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.CRSP.fromSQLFromSql", deltaFromSqlcrspFromSql("""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))}INAAL'"))


Manual Refresh of RapidQC Aggregations for a list of samples


Code Block
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


Code Block
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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