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num-codex / num-knoten

This repository contains the deployment package for the CODEX NUM-Knoten.
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invalid script `05_execute-fhir-to-i2b2.sh` #55

Open cerbelding opened 3 years ago

cerbelding commented 3 years ago

Expected Behavior

Run script, (download docker image), run container

Actual Behavior

Docker image can't be reached as .env file within fhir-to-i2b2 isn't used when running the shell script. Error Message: 

erbelding_c@num-codex-int-02:/opt/num-knoten$ sh 05_execute-fhir-to-i2b2.sh
: not foundfhir-to-i2b2.sh: 2:
: not foundfhir-to-i2b2.sh: 5:
WARNING: The IMAGE_TAG variable is not set. Defaulting to a blank string.
WARNING: The WRITE_TO_FILE variable is not set. Defaulting to a blank string.
WARNING: The WRITE_TO_PSQL variable is not set. Defaulting to a blank string.
WARNING: The DATA_METHOD variable is not set. Defaulting to a blank string.
ERROR: no such image: docker.miracum.org/miracum-etl/fhir-to-i2b2:: invalid reference format

Steps to Reproduce the Problem

  1. $ sh 05_execute-fhir-to-i2b2.sh

Working alternative:

omit shell script, direct docker-compose

$ docker-compose -f fhir-to-i2b2/docker-compose.yml --env-file fhir-to-i2b2/.env up

Specifications