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Update documentation for HL7 support (#114)
* gh-102 HL7 docs * Update docfx.json to support net6.0 properly * Build solution before buildign docs * Use windows to build docs * Updat4e NuGetDefense to continue on error * Allow retries for HL7 test feature Signed-off-by: Victor Chang <vicchang@nvidia.com>
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‎.github/workflows/ci.yml‎

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working-directory: ./src
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- name: NuGetDefense Scanning
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continue-on-error: true
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run: |
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sed -i "s/OSSINDEXAPI_TOKEN/$OSSINDEXAPI_TOKEN/g" NuGetDefense.json
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sed -i "s/OSSINDEXAPI_USERNAME/$OSSINDEXAPI_USERNAME/g" NuGetDefense.json
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run: echo "::set-output name=${{ matrix.os }}-TAG::${{ fromJSON(steps.meta.outputs.json).labels['org.opencontainers.image.version'] }}"
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docs:
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runs-on: ubuntu-latest
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runs-on: windows-latest
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needs: [calc-version]
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env:
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SEMVER: ${{ needs.calc-version.outputs.semVer }}
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restore-keys: |
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${{ runner.os }}-nuget
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- name: Setup DocFX
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uses: crazy-max/ghaction-chocolatey@v1
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with:
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args: install docfx
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- name: Restore dependencies
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run: dotnet restore
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working-directory: ./src
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- name: Build Solution
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run: dotnet build -c ${{ env.BUILD_CONFIG }} --nologo ${{ env.SOLUTION }}
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working-directory: ./src
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- name: Update docs version
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run: |
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sed -i -e "s,v0.0.0,v$SEMVER,g" ./docs/docfx.json
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sed -i -e "s,v0.0.0,v$SEMVER,g" ./docs/index.md
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- uses: nikeee/docfx-action@v1.0.0
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name: Build Docs
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with:
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args: docs/docfx.json
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- name: Build Docs
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working-directory: docs
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run: docfx docfx.json
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continue-on-error: false
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- name: Package docs
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run: |
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mkdir ~/release
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pushd docs/_site
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zip -r ~/release/mig-docs-${{ env.SEMVER }}.zip *
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popd
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ls -lR ~/release
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mkdir ~\release
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Compress-Archive -Path docs\_site\* -DestinationPath ~\release\mig-docs-${{ env.SEMVER }}.zip
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Get-ChildItem ~\release -Recurse
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- name: Upload docs
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uses: actions/upload-artifact@v2.3.1

‎docs/changelog.md‎

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## 0.3.0
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[Github Milestone 0.3.0](https://github.com/Project-MONAI/monai-deploy-informatics-gateway/milestone/3)
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- Adds HL7 (MLLP) service to enable triggering of workflow requests using HL7 messages.
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- Breaking changes with how Informatics Gateway handles incoming data and uploading to the storage service.
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All incoming data are now immediately queued for upload to the storage service instead of saving to the local disk.
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Therefore, if Informatics Gateway restarts or crashes during upload, any queued or incomplete uploads are lost.
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In addition, during the Informatics Gateway startup, the payload assembly service removes any payloads containing
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any pending files. Files that were successfully uploaded to the temporary location (`storage>temporary`) in the
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bucket (`storage>temporaryBucketName`) are then moved to the payload bucket (`storage>bucketName`) before sending a workflow request.
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bucket (`storage>temporaryBucketName`) are then moved to the payload bucket (`storage>bucketName`) before sending a workflow request.
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## 0.2.0
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‎docs/compliance/hl7.md‎

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<!--
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~ Copyright 2022 MONAI Consortium
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~
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~ Licensed under the Apache License, Version 2.0 (the "License");
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~ you may not use this file except in compliance with the License.
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~ You may obtain a copy of the License at
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~
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~ http://www.apache.org/licenses/LICENSE-2.0
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~
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~ Unless required by applicable law or agreed to in writing, software
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~ distributed under the License is distributed on an "AS IS" BASIS,
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~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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~ See the License for the specific language governing permissions and
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~ limitations under the License.
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-->
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# HL7 (Health Level 7)
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The following reference describes the connectivity capabilities of MONAI Deploy SDK out of the box.
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Users implementing the MONAI Deploy SDK must update their HL7 Conformance Statement according
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to the actual capabilities of their application.
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## HL7 MLLP Listener
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The HL7 listener adheres to the Minimal Lower Layer Protocol (MLLP) which accepts Health Level 7
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messages via TCP/IP connections at port 2575 (default). The Informatics Gateway provides basic syntax validation
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based on [HL7-dotnetcore](https://github.com/Efferent-Health/HL7-dotnetcore) toolkit. All validated messages are stored
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regardless of the message types.
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### Communication
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The Informatics Gateway allows concurrent connections for the HL7 listener and allows multiple messages to be transmitted
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in a single connection or in a single command. Messages received are immediately assembled into a payload for the
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[MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) to consume.
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### Configurations
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The HL7 listener can be configured in the `appsettings.json` file. Refer to [Configuration](../setup/schema.md) for additional details.
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### Acknowledgement Mode
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The listener supports the acknowledgment mode dictated in the MSH.15 field. If no value is specified, the listener defaults to the configuration option `sendAck`.
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### Supported Character Sets
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The HL7 listener supports Unicode UTF8 or any 8-bit character sets.

‎docs/compliance/toc.md‎

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-->
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# [DICOM](dicom.md)
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# [HL7](hl7.md)
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# [Open Source Licenses](open-source-licenses.md)

‎docs/docfx.json‎

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{
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"metadata": [{
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"src": [{
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"files": [
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"Api/Monai.Deploy.InformaticsGateway.Api.csproj",
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"Client/Monai.Deploy.InformaticsGateway.Client.csproj",
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"Client.Common/Monai.Deploy.InformaticsGateway.Client.Common.csproj",
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"Common/Monai.Deploy.InformaticsGateway.Common.csproj",
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"Configuration/Monai.Deploy.InformaticsGateway.Configuration.csproj",
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"DicomWebClient/Monai.Deploy.InformaticsGateway.DicomWeb.Client.csproj"
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"metadata": [
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{
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"src": [
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{
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"files": [
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"Api/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.Api.dll",
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"Client/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.Client.dll",
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"Client.Common/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.Client.Common.dll",
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"Common/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.Common.dll",
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"Configuration/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.Configuration.dll",
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"DicomWebClient/bin/Release/net6.0/Monai.Deploy.InformaticsGateway.DicomWeb.Client.dll"
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],
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"exclude": [
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"**/obj/**",
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"**Test/**",
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"_site/**"
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],
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"src": "../src"
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}
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],
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"exclude": [
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"**/bin/**",
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"**/obj/**",
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"Test/**",
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"_site/**"
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],
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"src": "../src"
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}],
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"dest": "obj/api/dotnet",
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"filter": "filterConfig.yml"
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}],
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"dest": "obj/api/dotnet",
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"filter": "filterConfig.yml",
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"properties": {
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"TargetFramework": "net6.0"
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}
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}
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],
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"build": {
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"content": [{
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"content": [
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{
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"files": [
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"**/*.yml"
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],
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]
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}
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],
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"resource": [{
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"files": [
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"images/**"
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],
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"exclude": [
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"obj/**",
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"_site/**"
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]
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}],
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"resource": [
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{
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"files": [
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"images/**"
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],
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"exclude": [
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"obj/**",
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"_site/**"
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]
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}
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],
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"globalMetadata": {
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"_appTitle": "MONAI Deploy Informatics Gateway v0.0.0",
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"_enableSearch": true,

‎docs/index.md‎

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## Services
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MIG contains the following standard protocols to communicate with medical devices:
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MIG contains the following standard protocols for communicating with medical devices:
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* **DICOM SCP**: C-ECHO, C-STORE
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* **DICOM SCU**: C-STORE
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* **HL7 Server**: A HL7 MLLP listener.
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* **ACR DSI API**: [The American College of Radiology’s Data Science Institute API](https://www.acrdsi.org/-/media/DSI/Files/ACR-DSI-Model-API.pdf)
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* **DICOMweb client**: QIDO-RS, WADO-RS, STOW-RS
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* **FHIR client**: GET
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[!Note]
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The DICOMweb client and FHIR client are called using the ACR DSI API.
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The ACR DSI API uses the DICOMweb client and FHIR client.
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### DICOM SCP
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The *DICOM SCP Service* accepts standard DICOM C-ECHO and C-STORE commands, which receive DICOM instances for processing. The received instances are stored immediately to the configured temporary storage location (`InformaticsGateway>storage>temporary`) and then uploaded to the shared storage for the [MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) to consume. All DICOM instances are stored on disk as-is using the original transfer syntax described in
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the [DICOM Interface](./compliance/dicom.md#dicom-scp) section. The MONAI Deploy application developer must handle any encoding/decoding of the DICOM files within the applications. Please refer to the [MONAI Deploy App SDK](https://github.com/Project-MONAI/monai-deploy-app-sdk) for further information.
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The *DICOM SCP Service* accepts standard DICOM C-ECHO and C-STORE commands, which receive DICOM instances for processing. In addition, the Informatics Gateway groups received DICOM instances by the study or series based on the configuration. Once DICOM instances are grouped, they are assembled into a payload for the [MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) to consume.
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### DICOM SCU
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### DICOMWeb STOW-RS
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The *DICOMWeb STOW-RS Service* allows users to trigger a new workflow request by uploading a DICOM dataset.
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The *DICOMWeb STOW-RS Service* allows users to trigger a new workflow request by uploading a DICOM dataset. The entire DICOM dataset is assembled into a payload for the [MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) to consume.
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It provides options to trigger a workflow with or without specifying a workflow ID/name. See the
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[DICOMWeb STOW-RS](./api/rest/dicomweb-stow.md) section for more information.
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### HL7 MLLP Server
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The *HL7 MLLP Server* accepts Health Level 7 messages via the MLLP (Minimal Lower Layer Protocol). The received messages are validated and assembled into a payload for the [MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) to consume.
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### ACR DSI API
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The ACR DSI API allows users to trigger inference requests via RESTful calls, utilizing DICOMweb and FHIR to
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retrieve data specified in the request. Upon data retrieval, the Informatics Gateway uploads the data to the
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shared storage and generates an `md.workflow.request` event, which notifies the
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[MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager) for processing.
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#### DICOMweb Export
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### DICOMweb Export
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A DICOMweb export agent can export any user-generated DICOM content to configured DICOM destinations. The agent
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subscribes to the `md.export.request.monaidicomweb` events generated by the [MONAI Deploy Workflow Manager](https://github.com/Project-MONAI/monai-deploy-workflow-manager)

‎docs/setup/schema.md‎

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| dicomWeb | DICOMweb service configuration options | [DicomWebConfiguration](xref:Monai.Deploy.InformaticsGateway.Configuration.DicomWebConfiguration) |
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| export | Export service configuration options | [DataExportConfiguration](xref:Monai.Deploy.InformaticsGateway.Configuration.DataExportConfiguration) |
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| fhir | FHIR service configuration options | [FhirConfiguration](xref:Monai.Deploy.InformaticsGateway.Configuration.FhirConfiguration) |
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| hl7 | HL7 listener configuration options | [Hl7Configuration](xref:Monai.Deploy.InformaticsGateway.Configuration.Hl7Configuration) |
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| storage | Storage configuration options, including storage service and disk usage monitoring | [StorageConfiguration](xref:Monai.Deploy.InformaticsGateway.Configuration.StorageConfiguration) |
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| messaging | Message broker configuration options | [MessageBrokerConfiguration](xref:Monai.Deploy.InformaticsGateway.Configuration.MessageBrokerConfiguration) |
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| Cli | The configuration used by the CLI | - |
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}
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},
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"messaging": {
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"publisherServiceAssemblyName":"Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessagePublisherService, Monai.Deploy.Messaging.RabbitMQ",
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"publisherServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessagePublisherService, Monai.Deploy.Messaging.RabbitMQ",
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"publisherSettings": {
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"endpoint": "localhost",
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"username": "username",
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"password": "password",
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"virtualHost": "monaideploy",
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"exchange": "monaideploy"
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},
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"subscriberServiceAssemblyName":"Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
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"subscriberServiceAssemblyName": "Monai.Deploy.Messaging.RabbitMQ.RabbitMQMessageSubscriberService, Monai.Deploy.Messaging.RabbitMQ",
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"subscriberSettings": {
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"endpoint": "localhost",
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"username": "username",
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}
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},
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"storage": {
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"temporary": "/payloads",
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"bufferRootPath": "./temp",
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"tempStorageRootPath": "/incoming",
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"bucketName": "monaideploy",
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"storageRootPath": "/payloads",
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"temporaryBucketName": "monaideploy",
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"serviceAssemblyName": "Monai.Deploy.Storage.MinIO.MinIoStorageService, Monai.Deploy.Storage.MinIO",
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"settings": {
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"endpoint": "localhost:9000",
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"accessKey": "admin",
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"accessToken": "password",
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"securedConnection": false,
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"region": "local"
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"region": "local",
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"executableLocation": "/bin/mc",
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"serviceName": "MinIO"
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}
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},
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"hl7": {
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"port": 2575,
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"maximumNumberOfConnections": 10,
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"clientTimeout": 60000,
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"sendAck": true
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}
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},
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"Logging": {

‎tests/Integration.Test/Features/HealthLevel7.feature‎

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| 2.6 |
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| 2.8 |
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@messaging_workflow_request @messaging
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@messaging_workflow_request @messaging @retry(10)
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Scenario Outline: Ability to receive and store multiple messages in a single batch
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Given HL7 messages in version <version>
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When the message are sent to Informatics Gateway in one batch

‎tests/Integration.Test/data/hl7/2.5.1-/002.txt‎ renamed to ‎tests/Integration.Test/data/hl7/2.5.1/002.txt‎

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‎tests/Integration.Test/data/hl7/2.5.1-/003.txt‎ renamed to ‎tests/Integration.Test/data/hl7/2.5.1/003.txt‎

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