"make build_concepts" does not work.

[elmonten]

Hi!

I'm trying to install the staging branch and I keep having troubles at the early steps. I got stuck on the Step 4.

I have changed the environmental variables to:

export DBUSER=postgres
export DBNAME=mimic
export SCHEMA=mimiciii
export HOST=localhost
export DBSTRING="dbname=$DBNAME options=--search_path=$SCHEMA"

and it launches this error:

(mimic_extract_py36) user@computer:~/Documents/MIMIC_Extract-staging/utils$ make build_concepts
{ \
source setup_user_env.sh; \
[ -e ../../mimic-code/buildmimic/postgres/Makefile ] || git clone https://github.com/MIT-LCP/mimic-code/ ../../mimic-code/; \
}
{ \
source setup_user_env.sh; \
cd ../../mimic-code/concepts; \
psql -U  "" -h  -f ./make-concepts.sql; \
cd ../../MIMIC_Extract-staging/utils; \
}
psql: could not translate host name "-f" to address: Name or service not known
{ \
source ./setup_user_env.sh; \
psql -U  "" -h  -f ./niv-durations.sql; \
psql -U  "" -h  -f ./crystalloid-bolus.sql; \
psql -U  "" -h  -f ./colloid-bolus.sql; \
}
psql: could not translate host name "-f" to address: Name or service not known
psql: could not translate host name "-f" to address: Name or service not known
psql: could not translate host name "-f" to address: Name or service not known
Makefile:46: recipe for target 'build_extra_concepts' failed
make: *** [build_extra_concepts] Error 2

Does anyone have any solution? Thank you very much in advance :)

[BXL3243]

Hi!

I'm trying to install the staging branch and I keep having troubles at the early steps. I got stuck on the Step 4.

I have changed the environmental variables to:

export DBUSER=postgres
export DBNAME=mimic
export SCHEMA=mimiciii
export HOST=localhost
export DBSTRING="dbname=$DBNAME options=--search_path=$SCHEMA"

and it launches this error:

(mimic_extract_py36) user@computer:~/Documents/MIMIC_Extract-staging/utils$ make build_concepts
{ \
source setup_user_env.sh; \
[ -e ../../mimic-code/buildmimic/postgres/Makefile ] || git clone https://github.com/MIT-LCP/mimic-code/ ../../mimic-code/; \
}
{ \
source setup_user_env.sh; \
cd ../../mimic-code/concepts; \
psql -U  "" -h  -f ./make-concepts.sql; \
cd ../../MIMIC_Extract-staging/utils; \
}
psql: could not translate host name "-f" to address: Name or service not known
{ \
source ./setup_user_env.sh; \
psql -U  "" -h  -f ./niv-durations.sql; \
psql -U  "" -h  -f ./crystalloid-bolus.sql; \
psql -U  "" -h  -f ./colloid-bolus.sql; \
}
psql: could not translate host name "-f" to address: Name or service not known
psql: could not translate host name "-f" to address: Name or service not known
psql: could not translate host name "-f" to address: Name or service not known
Makefile:46: recipe for target 'build_extra_concepts' failed
make: *** [build_extra_concepts] Error 2

Does anyone have any solution? Thank you very much in advance :)

I also have the same problem, have you fixed it? Thanks so much

[elmonten]

Hello,

No, sorry, I have not fixed it yet. I might try to install the tool again, but I have to focus on other things as of now. If you can fix it, I'd truly appreciate you share it.

[mmcdermott]

Apologies for the slow response. MIMIC modified their code-base rendering our README instructions insufficient to build concepts. We've just pushed a new release, with new instructions, which we believe should have fixed this and all outstanding issues. Please re-open if you encounter any new issues.