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The default fhir-server-config file-based bulk storageProvider should point to an existing directory #2086

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lmsurpre opened this issue Mar 12, 2021 · 2 comments
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bulk-data configuration P2 Priority 2 - Should Have

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@lmsurpre
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lmsurpre commented Mar 12, 2021

Is your feature request related to a problem? Please describe.
Our default config has "fileBase": "/fhir-server/output". However, this location doesn't exist by default and so, to make it functional, a user must either:
A. change this default setting in fhir-server-config.json; or
B. create this absolute directory for the output

I believe that this was done so that our config would work in our CI across both windows and linux.

Describe the solution you'd like
Our docker container already has a symlink from /output to /opt/ol/wlp/usr/servers/fhir-server (with the proper user permissions I think), so maybe we can just create a directory name bulkdata in that location and set the default to /output/bulkdata?

Describe alternatives you've considered
Document steps for having a volume mount at the existing default directory instead: /fhir-server/output

Acceptance Criteria
1.
GIVEN [a precondition]
AND [another precondition]
WHEN [test step]
AND [test step]
THEN [verification step]
AND [verification step]

Additional context
Add the target directory to our docker image

@lmsurpre
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lmsurpre commented May 24, 2021

Paul recommended that we include an extra level to make it easier to do mounts properly.
For example, set the config to default to /output/bulkdata/data instead of /output/bulkdata.

@tbieste tbieste self-assigned this May 24, 2021
@tbieste tbieste added this to the Sprint 2021-07 milestone May 24, 2021
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
tbieste added a commit that referenced this issue May 24, 2021
Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>
prb112 added a commit that referenced this issue May 25, 2021
Issue #2086 - Change default bulkdata directory
@lmsurpre
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lmsurpre commented Jun 4, 2021

I built the latest docker image and then ran it with a command like this:

docker run -it -p 9443:9443 -v /tmp/derby:/output/derby -e BOOTSTRAP_DB=true ibmcom/ibm-fhir-server

I loaded a single patient and then invoked export. To my delight, it "just works" with the default config now. The exported file was available within the container under /output/bulkdata.

Next I added an additional volume mount as follows:

docker run -it -p 9443:9443 -v /tmp/derby:/output/derby -v /tmp/bulkdata:/output/bulkdata ibmcom/ibm-fhir-server

I repeated the export and now the export was under my host's /tmp/bulkdata directory. Awesome.

@lmsurpre lmsurpre closed this as completed Jun 4, 2021
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