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Change from always inserting 'BI' to referencing the originfact table for the insert.
…b2 to pcori. - Old code was joining the fact table with a mapping table that did not have 1 to 1 mappings, which resulted in duplicate facts (one representing the fact as an ICD9 and one representing the fact as an ICD10) - Picks ICD10s over ICD9 after 2015-10 and ICD9s over ICD10 before 2015-10
Schema updates 4745
Remove bad NDC code if present
_TIME fields were switched to using 24 hour clock
Fix mislabeled dx type and remove duplicate dx facts
Adjust DX_ORIGIN insertion
Add OS to encounter_type coalesce 4710
Result num fix
Break out result of enc_type coalesce before merge to `visit_dimension`
Replace SCILHS lab normal ranges with KUMC normal ranges
…as revised, Luigi support files were copied from Heron, Oracle and Luigi libraries were updated and spot fixes were performed in Python code.
https://github.com/kumc-bmi/heron/tree/para_etl_3985/heron_tasks 21fa46c on Dec 13, 2017
Added create table statement for hash_token
Added code to populate obs_gen table with naaccr data
Harvest updates 5885
Encounter facility 5886
… doesnt have any records in it
Added DX_DATE column to the diagnosis table
Removed the select statements from the cdm_status table as hash_token…
Cdm lab result cm v5 updates 5876
Obs clin 5875
Song consolidated a new payer_map.csv file to include IDX payers
removing hard coded references to the schema pcornet_cdm
... to avoid ORA-00001: unique constraint
SQLAlchemy got more strict? DictReader changed? ``` sqlalchemy.exc.ArgumentError: Column must be constructed with a non-blank name or assign a non-blank .name before adding to a Table. ```
- leave `insert into cdm_status` to the task framework - separate with / only, not both ; and / - drop before creating
fixes for harvest_local, obs_gen, obs_clin, payer_map LP, SC and co are cool with merging this.
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