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i2b2 to PCORnet Common Data Model Transformation - requires i2b2 PCORnet ontology
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Lab transform inserts invalid values into SPECIMEN_SOURCE #72

Closed jklann closed 5 years ago

jklann commented 6 years ago

From @sguptawustl --

Some more issues have occurred with labs i2p procedure and ontology. Please note that the new value set for specimen_source does not contain the following values anymore: "BLOOD" "SR_PLS" or "SERUM, PLASMA, or SR_PLS"

Attached is the new list. Looks like the following code in labs transform is insufficient and results in populating values outside of CDM specification (got this error in edc report).

jklann commented 6 years ago

We’re not supporting new specimen_source values since PCORnet doesn’t provide us a list correlating to LOINC codes anymore. But the old ones should not be broken.

Temporary fix just set all to NI, Matt already checked in and integrated into both versions but NOT tested in Oracle 081f17d5e2964f7060b01561a7df2f639c86f870 (oracle) and 90090467b6d7460644af2e11486d9ed16cb48561 (mssql)

jklann commented 6 years ago

Oracle additional fix: 570a900f3ec644fcbdda020a3eff5a968e50f3f4

Tested on demodata in Oracle and it worked.

Leaving issue open because it would be better to insert specimen_source when we have it rather than ignoring it.

jklann commented 6 years ago

The issue has resurfaced! SR_PLS is not correctly changed to SER_PLAS

jklann commented 6 years ago

Update, SR_PLS does not appear in specimen_source in the v4.1 ontology, only in the Partners version. This should not affect current users. We will fix the transform anyway for compatibility. MSSQL: 3b84d5b9c6437646811e16e67ac8a3937c34caeb

jklann commented 6 years ago

Resurfaced issue fixed in Oracle. Still open, due to need for better fix.

2d47f5662e67c16545c4f6377e50f73494d33fb5

jklann commented 6 years ago

ffa6fe2e4d6da0c66bd24ae0fa8b05303b339010 fixed in MSSQL

jklann commented 5 years ago

Appears Matt fixed in Oracle in commit 136c23f0dc297f68d9a79599b51ffdc39703e799