[DATA-1] Update_for_act references

[jklann]

While loading the CRC cell for the act project, I'm receiving errors from references to the ncats_demographics table (which exists) in the metadata schema.

This causes the previous inserts inside the "Update_for_act.sql" to fail as well, preventing the ICD9CM and ICD9PROC facts from being inserted.

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Buildfile: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/data_build.xml

init:

db_demodata_load_data:
[echo] Loading demodata -- may take a while; over 10 min
[unzip] Expanding: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/crcdata.zip into /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/Update_for_act.sql
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'vital_status_cd', c_operator = 'IN' , c_dimcode = '''Y'',''D''' where c_fullname like '\ACT\Demographics\Vital Status\Known Deceased\%'
[sql] org.postgresql.util.PSQLException: ERROR: relation "ncats_demographics" does not exist
[sql] Position: 9
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'sex_cd', c_operator = '=' , c_dimcode = 'F' where c_fullname like '\ACT\Demographics\Sex\Female\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'sex_cd', c_operator = '=' , c_dimcode = 'M' where c_fullname like '\ACT\Demographics\Sex\Male\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'race_cd', c_operator = 'IN' , c_dimcode = '''black'',''african american''' where c_fullname like '\ACT\Demographics\Race\Black or African American\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'race_cd', c_operator = 'IN' , c_dimcode = '''white''' where c_fullname like '\ACT\Demographics\Race\White\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'race_cd', c_operator = 'IN' , c_dimcode = '''indian''' where c_fullname like '\ACT\Demographics\Race\American Indian or Alaska Native\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Failed to execute: update ncats_demographics set c_facttablecolumn = 'patient_num', c_tablename = 'patient_dimension', c_columnname = 'race_cd', c_operator = 'IN' , c_dimcode = '''asian''' where c_fullname like '\ACT\Demographics\Race\Asian\%'
[sql] org.postgresql.util.PSQLException: ERROR: current transaction is aborted, commands ignored until end of transaction block
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/insert_crc_concept_dimension_DX_V2_tables.sql
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/insert_crc_concept_dimension_LAB_V2_tables.sql
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/insert_crc_concept_dimension_MEDS_V2_tables.sql
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/insert_crc_concept_dimension_PX_V2_tables.sql
[sql] Executing resource: /docker-entrypoint.d/workspace/master/NewInstall/Crcdata/scripts/act/postgresql/insert_crc_concept_dimension_V1_tables.sql
[sql] 2483946 of 2483953 SQL statements executed successfully

BUILD SUCCESSFUL
Total time: 11 minutes 14 seconds

---

db.type=postgresql
db.username=i2b2data
db.password=demodata
db.server=postgres::i2b2
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://postgres/i2b2?searchpath=i2b2data
db.project=act

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Imported from Jira

• Key: DATA-1
• ID: 10779
• Type: Bug
• Priority: Minor
• Status: To Do
• Reporter: Former user
• Created: 16/Dec/19 2:30 PM
• Updated: 16/Dec/19 2:30 PM
• Project: DATA—i2b2 Data
• Environment: c718238