Bug fixes acgh and rnaseq upload pipeline (TMART-188)

Indeed, this is obvious not in line anymore with the other stored procedures. It should be removed.
Should I remove the lines?



From: Gustavo Lopes [mailto:notifications@github.com]
Sent: maandag 20 oktober 2014 16:03
To: transmart/transmart-data
Cc: Jonge, C de
Subject: Re: [transmart-data] Bug fixes acgh and rnaseq upload pipeline (TMART-188) (#42)


In ddl/oracle/tm_cz/procedures/i2b2_process_acgh_data.sql:

> @@ -515,6 +515,17 @@ BEGIN

>       i2b2_fill_in_tree(TrialId, r_addNodes.leaf_node, jobID);

>    END LOOP;

>

> +  -- set sourcesystem_cd, c_comment to null if any added upper-level nodes

> +

> +  update i2b2 b

> +     set sourcesystem_cd=null,c_comment=null

> +     where b.sourcesystem_cd = TrialId

> +       and length(b.c_fullname) < length(topNode);

> +

> +  stepCt := stepCt + 1;

> +  cz_write_audit(jobId,databaseName,procedureName,'Set sourcesystem_cd to null for added upper level nodes',SQL%ROWCOUNT,stepCt,'Done');

> +  commit;

> +

@forus<https://github.com/forus> has recently removed a bunch of (needless to say, copy pasted) code that looks like this. See 996256c<https://github.com/transmart/transmart-data/commit/996256cdafc14f7768f8295ed431dc1cd603b42f>. I'm guessing this shouldn't be included.

—
Reply to this email directly or view it on GitHub<https://github.com/transmart/transmart-data/pull/42/files#r19085680>.

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