holger-stenzhorn
commented
3 years ago @joundso Can you provide your .env here so that we have all information on how to reproduce your issue in one place?
Closed joundso closed 3 years ago
holger-stenzhorn
commented
3 years ago @joundso Can you provide your .env here so that we have all information on how to reproduce your issue in one place?
holger-stenzhorn
commented
3 years ago Fixed. Please retry with the updated image.
P.S.: If you want you do not need to explicitly specify the actual version of the ODM2FHIR image, e.g. 0.3.0-alpha-snapshot, but simply leave it out as the image is always automatically tagged as latest.
joundso
commented
3 years ago @holger-stenzhorn: The .env file is in the repo. The error occurred while producing local files, NOT while connecting to the FHIR server and still occurs with the new version with tag 0.3.0 from 30 minutes ago.
odm2fhir | 2021-02-02 09:15:17.841 INFO 1 --- [ main] ca.uhn.fhir.context.FhirContext : Creating new FHIR context for FHIR version [R4]
odm2fhir | 2021-02-02 09:15:17.976 INFO 1 --- [ main] d.d.uds.odm2fhir.ODM2FHIRApplication : Started ODM2FHIRApplication in 1.275 seconds (JVM running for 1.697)
odm2fhir | 2021-02-02 09:15:17.980 INFO 1 --- [ main] d.d.uds.odm2fhir.odm.reader.ODMReader : Reading ODM from file '/workspace/input/ODM.xml'...
odm2fhir | 2021-02-02 09:15:18.565 INFO 1 --- [ main] ca.uhn.fhir.util.XmlUtil : FHIR XML procesing will use StAX implementation 'Woodstox' version '6.2.3'
odm2fhir | 2021-02-02 09:15:19.381 ERROR 1 --- [ main] d.d.uds.odm2fhir.ODM2FHIRApplication : Failed to retrieve the server metadata statement during client initialization. URL used was /metadata
odm2fhir |
odm2fhir | ca.uhn.fhir.rest.client.exceptions.FhirClientConnectionException: Failed to retrieve the server metadata statement during client initialization. URL used was /metadataTo reproduce:
git clone https://github.com/miracum/odm-2-fhir-job.git
cd odm-2-fhir-job
## Change version tag in `.env` file from `0.2.2-alpha-snapshot` to `0.3.0-alpha-snapshot`:
sed -i 's/0.2.2-alpha-snapshot/0.3.0-alpha-snapshot/g' .env
docker-compose up@joundso Of course, the mentioned .env file is in your repository but it is a different repository which is not under our "control" and so that .env file could become out of sync as you only have a master branch and no tags there. Besides that it is always best to have all information on how to reproduce an error in the actual issue report. So could you drop your .env file here? Thanks! 🤝
joundso
commented
3 years ago OK, here is the docker-compose.yml and .env file form the repo above
version: "3.7"
services:
odm2fhir:
container_name: odm2fhir
# image: docker.pkg.github.com/num-codex/odm2fhir/odm2fhir:${IMAGE_TAG}
image: ghcr.io/num-codex/odm2fhir:${IMAGE_TAG}
restart: "no"
# environment:
# - odm.redcap.api.url=${odm_redcap_api_url}
# - odm.redcap.api.token=${odm_redcap_api_token}
# - fhir.server.url=${fhir_server_url}
# - fhir.server.basicauth.username=${fhir_server_basicauth_username}
# - fhir.server.basicauth.password=${fhir_server_basicauth_password}
# - fhir.server.oauth2.token.url=${fhir_server_oauth2_token_url}
# - fhir.server.oauth2.client.id=${fhir_server_oauth2_client_id}
# - fhir.server.oauth2.client.secret=${fhir_server_oauth2_client_secret}
volumes:
- ${ODM_FILE_PATH}:/workspace/input/ODM.xml
- ${FHIR_BUNDLES_FOLDER_PATH}:/workspace/output## Image-Tag (see here: https://github.com/num-codex/odm2fhir/packages):
IMAGE_TAG=0.2.2-alpha-snapshot
## REDCap API:
# odm_redcap_api_url=https://redcap.hospital.com/api/
## API-Key:
# odm_redcap_api_token=123456abcd
## Path to input file:
ODM_FILE_PATH=./in/demo.xml
## Path for output files:
FHIR_BUNDLES_FOLDER_PATH=./out
# fhir_server_url=url
# fhir_server_basicauth_username=username
# fhir_server_basicauth_password=password
# fhir_server_oauth2_token_url=url
# fhir_server_oauth2_client_id=id
# fhir_server_oauth2_client_secret=secret
cron="0 0 0 0 * *"@joundso Code and image updated. Could you please retry?
joundso
commented
3 years ago @joundso Code and image updated. Could you please retry?
Now it works. Thanks!
Describe the bug Using the new version
0.3.0-alpha-snapshotthe container did not create output files. This happened while converting a local xml file to local FHIR bundles as well while extracting data from the REDCap API to local FHIR bundles.Main Error text
2021-02-02 07:36:21.206 ERROR 1 --- [ main] d.d.uds.odm2fhir.ODM2FHIRApplication : Failed to retrieve the server metadata statement during client initialization. URL used was /metadataTo Reproduce Steps to reproduce the behavior: Working version (0.2.2):
Error version (0.3.0):
Details
Error log