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


  2. Code Block
    languagebash
    themeEmacs
    titleRun etlShell
    /home/unix/analytics/TigerETL3/runEtlShell.sh


  3. run etl-commands as you see fit

...

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._
analytics.tiger.utils.CognosDB("analytics.tiger.agents.PicardAggregator.
Manual
Samples",
deltaETL(Set
regSamples("
ALCH
JB-
ABSQ
0236-
TTP1-A-12-0-D-A489-36","ALCH-ABSQ-NB1-A-1-0-D-A489-36
T-02,TCGA-HU-A4H5-11A-11D-A25E-08"))
flatMap DataSetEtl() flatMap


 Manual Refresh of Picard Aggregations using a query (Research)


Code Block
languagescala
import analytics.tiger.agents.PicardAggregator
.Regular.pipeline)		 Manual Refresh of Picard Aggregations using a query
._
analytics.tiger.utils.CognosDB("analytics.tiger.agents.PicardAggregator.
fromSQL
FromSql",
deltaFromSql
 regFromSql(
"
"
"
SELECT a.SAMPLE
FROM 
 FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = '
CAD-JDV-098'""")flatMap DataSetEtl() flatMap 
NWD725917'"))


Manual Refresh of Picard Aggregations for a list of samples (CRSP)

DEPRECATED (use RunETL tool instead)

Code Block
languagescala
import analytics.tiger.agents.PicardAggregator._
analytics.tiger.utils.AnalyticsEtlDB("analytics.tiger.agents.PicardAggregator.
Regular.pipeline
CRSP.Samples", crspSamples("SM-INAAG,SM-INAAL"))


Manual Refresh of Picard Aggregations for using a list of samples query (CRSP)


 AnalyticsEtlDB
Code Block
languagescala
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


Code Block
CognosDB("analytics.tiger.agents.RapidQcAggregator.Manual",
 deltaETL(Set("
SM-HXT86
NWD581810")) flatMap DataSetEtl() flatMap analytics.tiger.agents.
PicardAggregator
RapidQcAggregator.
CRSP.pipeline
mainPipeline)


Manual Refresh of Picard RapidQC Aggregations using a query (CRSP) AnalyticsEtlDB


Code Block
CognosDB("analytics.tiger.agents.
PicardAggregator.CRSP
RapidQcAggregator.fromSQL",
 deltaFromSql("""SELECT a.
SAMPLE FROM cognos.slxre2_pagg_sample a WHERE a.SAMPLE = 'SM-HUTAC
bsp_collaborator_sample_id FROM pdo_star5_aux a WHERE a.pdo_sample = 'SM-HQV67'""")
 flatMap DataSetEtl() flatMap analytics.tiger.agents.
PicardAggregator
RapidQcAggregator.
CRSP.pipeline
mainPipeline)