aline notebook throws error

[suriyan3]

Prerequisites

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Description

I am running my postgres db in docker. I have loaded the data which i have downloaded from https://physionet.org/content/mimiciii-demo/1.4/.
When I am trying to run this python notebook D:\mimic-code\mimic-iii\notebooks\aline especially this query
queries = [
'sepsis/angus.sql',
'durations/weight-durations.sql',
'demographics/heightweight.sql',
'aline_vaso_flag.sql'
]

for query_file in queries:
# load in the text of the query
f = os.path.join(concepts_path, query_file)
with open(f) as fp:
query = ''.join(fp.readlines())
query = query.replace('`', '"')

# Execute the query
print('Generating materialized view using {} ...'.format(f),end=' ')
execute_query_safely(query_schema + query, con)
print('done.')

It throws below error 
relation "physionet-data.mimiciii_clinical.diagnoses_icd" does not exist

LINE 32: from "physionet-data.mimiciii_clinical.diagnoses_icd"

when i checked in mimic database I have this table diagnoses_icd. How to fix this issue.

[alistairewj]

Ah the aline notebook looks out of date. We converted the original script it is calling to BigQuery syntax. If you change the path from "concepts" to "concepts_postgres" it should work.

[suriyan3]

Hi @alistairewj ,

Thanks for the quick response. I have changed those values. It is throwing error when executing this line

inner join echo_data ec

relation "echo_data" does not exist and I have also checked in the list of tables it is not there.

[alistairewj]

Odd, maybe the echo data script isn't called by the postgres build script, or more likely there was an error in building the table. It's here though so you can build it yourself and maybe fix any errors that come up: https://github.com/MIT-LCP/mimic-code/blob/main/mimic-iii%2Fconcepts_postgres%2Fecho_data.sql

[suriyan3]

Hi @alistairewj ,

Ok I will load that sql file. I have made the initial setup by loading postgres_create_tables.sql and postgres_load_data.sql from location D:\mimic-code\mimic-iii\buildmimic\postgres. So just want to know am I missing anything in the setup or do i have to run any other script which will do all the setup.