Re: [gpc-informatics] #579: Data Characterization - Cycle 3 Tracking

[GPC Informatics]

#579: Data Characterization - Cycle 3 Tracking
--+-
 Reporter:  lv|   Owner:  mprittie
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  cdm-cycle3
Component:  data-stds |  Resolution:
 Keywords:  CDM v3, DCQ, EDC  |  Blocked By:
 Blocking:|
--+-

Comment (by hangs008):

 Replying to [comment:9 dconnolly]:
 Thanks Dan, I added a new issue to their tracker.
 Here are the UMN run times:
 - Oracle -> SQL Server CDM Load: 31 Hours
 - DCQ: ~50.5 Hours
 - EDC: < 5 Minutes

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gpc-informatics 
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Re: [gpc-informatics] #579: Data Characterization - Cycle 3 Tracking

[GPC Informatics]

#579: Data Characterization - Cycle 3 Tracking
--+-
 Reporter:  lv|   Owner:  mprittie
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  cdm-cycle3
Component:  data-stds |  Resolution:
 Keywords:  CDM v3, DCQ, EDC  |  Blocked By:
 Blocking:|
--+-

Comment (by mprittie):

 KUMC CDM Cycle 3 Refresh 2 ETL run times:
  - i2p-transform: ~40 hrs
 {{{
 PCORNetDemographic  0.45 hrs
 PCORNetEncounter1.33 hrs
 PCORNetDiagnosis12.56 hrs
 PCORNetCondition3.82 hrs
 PCORNetProcedure5.48 hrs
 PCORNetVital11.11 hrs
 PCORNetEnroll   0.07 hrs
 PCORNetLabResultCM  2.91 hrs
 PCORNetPrescribing  3.29 hrs
 PCORNetDispensing   0.86 hrs
 PCORNetDeath0 hrs
 PCORNetHarvest  0 hrs
 }}}
  - DCQ: between 3-4 hrs
  - EDC: < 5 mins

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Re: [gpc-informatics] #579: Data Characterization - Cycle 3 Tracking

[GPC Informatics]

#579: Data Characterization - Cycle 3 Tracking
--+-
 Reporter:  lv|   Owner:  mprittie
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  cdm-cycle3
Component:  data-stds |  Resolution:
 Keywords:  CDM v3, DCQ, EDC  |  Blocked By:
 Blocking:|
--+-

Comment (by dconnolly):

 Nobody in gpc-dev has write access to the curation query. I suggest you
 contact the authors via https://github.com/CDMFORUM/CDM-GUIDANCE/issues

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Re: [gpc-informatics] #579: Data Characterization - Cycle 3 Tracking

[GPC Informatics]

#579: Data Characterization - Cycle 3 Tracking
--+-
 Reporter:  lv|   Owner:  mprittie
 Type:  problem   |  Status:  assigned
 Priority:  major |   Milestone:  cdm-cycle3
Component:  data-stds |  Resolution:
 Keywords:  CDM v3, DCQ, EDC  |  Blocked By:
 Blocking:|
--+-

Comment (by hangs008):

 Running the XTBL_L3_MISMATCH query takes ~12 hours through SAS at UMN. I
 wrote equivalent queries directly against the DBMS and was able to gather
 the results in under 4 minutes. Would it be possible to re-factor the
 curation query to leverage the database engine for those of us who hold
 our data in a DB? We have indices on our ENCOUNTERIDs and our PATIDs so
 most of the counts can be handled directly at the index level instead of
 pulling in the whole data set.

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