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In some occasions, the analytics team may need to take specific actions to check or update changes in the datamarts. Examples in which this may happen may include the following:

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     2. If records are returned, then the datamart needs a refresh (section 2.4 below). Note the FLOWCELL_BARCODE of any records returned.

1.3. Check whether PDO Interesting Products list is updated

1. In some cases, PDOs will not appear in PDO_STAR or SLXRE_READGROUP_METADATA (such as Genotyping sequencing products and Sample Initiation products). These cases can be reviewed in the pdo_interesting_products table

2. Log in to COGNOS@SEQPROD on SQL Navigator and run the following query:

   Code Block
   language sql
   SELECT ip.product_part_number interesting_product, pdos.* FROM cognos.mercurydw_pdo_samples pdos , cognos.pdo_interesting_products ip WHERE pdos.pdo_sample_id IN ( 'SM-ID1', 'SM-ID2', ) AND pdos.product_part_number = ip.product_part_number(+)

   
   

   1. If the PRODUCT_FAMILY_NAME for one of these products is Whole Genome Genotyping, log in to REPORTING@SEQPROD on SQL Navigator and run the following query:

      Code Block
      language sql
      SELECT DISTINCT "Collab. sample ID", "PTID", "Collab. PTID", "PDO", "PDO sample ID" FROM arrays_mercloud_w_unmarked_rw WHERE "PDO sample ID" IN ('SM-ID1','SM-ID2')

      
      

   2. If the Collaborator Sample ID is "Deleted per Client Request", the datamart is up to date.

1.4. Check whether there's updated data to be added

1.  Check for metrics in DB with the following queries:

   Code Block
   language sql
   SELECT * FROM analytics.bsp_sample WHERE collaborator_sample_id IN 'oldcollabSMID1, oldcollabSMID2' ; SELECT * FROM metrics.basecalling_analysis ba WHERE ba.flowcell_barcode IN ('HTH3KBBXX') AND ba.metrics_type IN ('Indexed', 'Unindexed') ; SELECT * FROM metrics.picard_analysis ba WHERE ba.flowcell_barcode IN ('HTH3KBBXX') AND ba.metrics_type IN ('Indexed', 'Unindexed') ; --Understand when flowcells were updated in Analytics DM SELECT * FROM slxre_rghqs_targets t WHERE t.flowcell_barcode = --'HTH3KBBXX' ;

   
   

1.

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5. Check aggregations

1.  Check for aggregations in DB with the following queries:

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NOTE: is_latest should be 2 for anything with consent withdrawn (2 signifies BAM is deleted)

1.

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6 Check whether Sample datamarts have been refreshed

1. If refreshes aren't showing updated data, it may be because the sample ETL is down. If LIMS team has done their part, but the bsp.analytics_sample and analytics.bsp_sample DMs are not updated, check the ETL agent here: http://analytics:8090/etl_runs?status=Succeeded&status=Failed&status=Running&status=Abandoned&agent=analytics.tiger.agents.BspSample&action=Refresh

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1. Rerun the PDO_STAR query above. This refresh is immediate, so you can run the query right away.
2. If it returns nothing, the DM is all set.
3. If it still returns records, ensure that that is unexpected behavior and try the refresh again. (occasionally, there are other samples that need to remain with the "old" IDs, as is usually the case in sample swaps)
   1. If it still returns unexpected records, talk with Nasko.

2.4. Refreshing the ReadgroupMetadata DM in SEQPROD Database

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