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Issue #2086 - Change default bulkdata directory #2425

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May 25, 2021
Merged

Issue #2086 - Change default bulkdata directory #2425

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8b53f38
Issue #2086 - Change default bulkdata directory
tbieste May 24, 2021
3226b96
Issue #2086 - Update after review comments
tbieste May 24, 2021
cd9530e
Issue #2086 - Update after review comments
tbieste May 24, 2021
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4 changes: 2 additions & 2 deletions docs/src/pages/guides/FHIRServerUsersGuide.md
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Original file line number Diff line number Diff line change
Expand Up @@ -1320,7 +1320,7 @@ The Bulk Data web application writes the exported FHIR resources to an IBM Cloud
"storageProviders": {
"default" : {
"type": "file",
"fileBase": "${WLP_OUTPUT_DIR}/fhir-server/output",
"fileBase": "/output/bulkdata",
"exportPublic": true,
"disableOperationOutcomes": true,
"duplicationCheck": false,
Expand Down Expand Up @@ -2071,7 +2071,7 @@ This section contains reference information about each of the configuration prop
|`fhirServer/bulkdata/storageProviders/<source>/location`|string|Object store location |
|`fhirServer/bulkdata/storageProviders/<source>/endpointInternal`|string|Object store end point url used to read/write from COS |
|`fhirServer/bulkdata/storageProviders/<source>/endpointExternal`|string|Object store end point url used in the constructed download URLs|
|`fhirServer/bulkdata/storageProviders/<source>/fileBase`|string| The absolute path of the output directory |
|`fhirServer/bulkdata/storageProviders/<source>/fileBase`|string| The absolute path of the output directory. It is recommended not to mount this to the root file system or the share a direct volume mount. For instance, if the volume is /output/bulkdata, use /output/bulkdata/data to ensure a failed mount does not result in writing to the root file system.|
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|`fhirServer/bulkdata/storageProviders/<source>/validBaseUrls`|list|The list of supported urls which are approved for the fhir server to access|
|`fhirServer/bulkdata/storageProviders/<source>/disableBaseUrlValidation`|boolean|Disables the URL checking feature, allowing all URLs to be imported|
|`fhirServer/bulkdata/storageProviders/<source>/exportPublic`|boolean|Whether or not the server is configured to support export to parquet; to properly enable it the administrator must first make spark and stocator available to the fhir-bulkdata-webapp (e.g through the shared lib at `wlp/user/shared/resources/lib`)|
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3 changes: 2 additions & 1 deletion fhir-install/Dockerfile
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Expand Up @@ -52,7 +52,8 @@ RUN features.sh

COPY --chown=1001:0 --from=base /opt/ol/wlp/usr /opt/ol/wlp/usr

RUN configure.sh
RUN configure.sh && \
mkdir -p /output/bulkdata

COPY --chown=1001:0 --from=base /opt/ibm-fhir-server /opt/ibm-fhir-server

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2 changes: 1 addition & 1 deletion fhir-server/liberty-config/config/default/fhir-server-config.json
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Expand Up @@ -170,7 +170,7 @@
"type": "file",
"_type": "ibm-cos|aws-s3|file|https",
"validBaseUrls": [],
"fileBase": "/fhir-server/output",
"fileBase": "/output/bulkdata",
"bucketName": "fhir-performance",
"location": "us",
"endpointInternal": "https://s3.us-east.cloud-object-storage.appdomain.cloud",
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