Issues running demo code

[jbains223]

Prerequisites

• [ x] Put an X between the brackets on this line if you have done all of the following:
  • Checked the online documentation: https://mimic.physionet.org/about/mimic/
  • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
  • Checked online common solutions: https://opendata.stackexchange.com/questions/tagged/mimic-iii

Description

I am currently using a Mac and trying to set up the database using Postgresql as instructed in the tutorial on the MIMIC III database website. I have loaded the demo data into a file /buildmimic/postgres/data/ and have been trying to run make from /buildmimic/postgres/. However, every time I try to run make, it tells me "Unable to find /Data/ADMISSIONS.csv - exiting before build.
make: *** [mimic-check] Error 1"

I have checked multiple times and the file is certainly there. Am I placing the data in the wrong place? I have checked online for any resources regarding this but I have not been able to solve this issue. Can you please help me. Thank you.

[alistairewj]

Can you run ls /buildmimic/postgres/data/ ? Interested to see what files you have there. We have a few demos, and the make file requires the CSV files.

The error is telling you that the /Data/ADMISSIONS.csv file does not exist. You can fix this by (1) changing the data directory, as detailed in the README, to a folder containing the data files such as ADMISSIONS.csv, or (2) move the data files to the /Data/ subfolder.

[jbains223]

I can't run ls /buildmimic/postgres/data/ but when I go into the /buildmimic/postgres/data file and ls, I get the list of data files.

I have all the data files listed under /buildmimic/postgres/data/

Jazmins-MacBook-Pro:postgres j.bains$ ls
Data postgres_checks.sql
Makefile postgres_create_tables.sql
README.md postgres_create_tables_pg10.sql
create_mimic_user.sh postgres_load_data.sql
postgres_add_comments.sql postgres_load_data_7zip.sql
postgres_add_constraints.sql postgres_load_data_gz.sql
postgres_add_indexes.sql
Jazmins-MacBook-Pro:postgres j.bains$ cd Data
Jazmins-MacBook-Pro:Data j.bains$ ls
ADMISSIONS.csv D_ICD_DIAGNOSES.csv NOTEEVENTS.csv
CALLOUT.csv D_ICD_PROCEDURES.csv OUTPUTEVENTS.csv
CAREGIVERS.csv D_ITEMS.csv PATIENTS.csv
CHARTEVENTS.csv D_LABITEMS.csv PRESCRIPTIONS.csv
CPTEVENTS.csv ICUSTAYS.csv PROCEDUREEVENTS_MV.csv
DATETIMEEVENTS.csv INPUTEVENTS_CV.csv PROCEDURES_ICD.csv
DIAGNOSES_ICD.csv INPUTEVENTS_MV.csv SERVICES.csv
DRGCODES.csv LABEVENTS.csv TRANSFERS.csv
D_CPT.csv MICROBIOLOGYEVENTS.csv
Jazmins-MacBook-Pro:Data j.bains$

[alistairewj]

Then, as detailed here https://github.com/MIT-LCP/mimic-code/blob/master/buildmimic/postgres/README.md

.. specify the datadir to the folder you put the data in, i.e. /buildmimic/postgres/data/

[jbains223]

I have attempted that prior and did the same thing again and this is what comes up:

Jazmins-MacBook-Pro:postgres j.bains$ ls
Data postgres_checks.sql
Makefile postgres_create_tables.sql
README.md postgres_create_tables_pg10.sql
create_mimic_user.sh postgres_load_data.sql
postgres_add_comments.sql postgres_load_data_7zip.sql
postgres_add_constraints.sql postgres_load_data_gz.sql
postgres_add_indexes.sql
Jazmins-MacBook-Pro:postgres j.bains$ make create-user mimic datadir="/buildmimic/postgres/Data/"

-- Creating user, database, schema --

MIMIC_USER="postgres" MIMIC_DB="mimic" MIMIC_PASSWORD="postgres" MIMIC_SCHEMA="mimiciii" DBHOST="" DBPORT="" ./create_mimic_user.sh
MIMIC_PASSWORD is set
MIMIC_DB is set to 'mimic'
User is set to 'postgres'
DROP DATABASE
CREATE DATABASE
CREATE SCHEMA

---

-- Checking for data --

Data path: /buildmimic/postgres/Data/
Unable to find /buildmimic/postgres/Data/ADMISSIONS.csv - exiting before build.
make: *** [mimic-check] Error 1
Jazmins-MacBook-Pro:postgres j.bains$

[young310]

Hi @jbains223 ,

I am also using mac, and it looks like you place data in different directory.
Could you try using the following command and give me the results?

1. make create-user mimic datadir="Data/"
2. pwd

[jbains223]

Thank you for the suggestion @young310. I will try this as soon as I can but for some reason I am having trouble compressing my data files into a zip file. There's too much data and it's taking up too much space on my computer. Is there another way of doing this?

[young310]

You can place the mimic data files in anywhere you want, for me, I just put them on an external hard drive. Then you have to use datadir="/Volume/your external driver/data". You can also use csv files to build the database, so you don't need to do extra compression jobs.

[jbains223]

Hi @young310,
Thank you so much!! When I ran the above make create-user mimic datadir="Data/", it ran and all the tables came back as PASSED.

One other question:
I am using Postgres.app and downloaded the pgAdmin4 for the GUI aspect. However, since I downloaded that, Postgres.app is refusing to run on Port 5432 which is the default stating that there is already a server running on that port. Is there some way to troubleshoot this? I changed the port to 5433 and it worked fine. However, when I went to try to use the database in pgAdmin4 it didn't pull up for me to access. Did I do something wrong?

[young310]

@jbains223 I never use "Postgres.app" before, and I guess you have installed more than one postgre server instance. For now, it's hard to help you without access to your computer. sorry.

[jbains223]

Oh ok. No worries. @young310 what server or application are you using to run and build the database?

[young310]

@jbains223 I am currently using docker, and had install server using the installer provided by by ENTERPRISEDB before.