Project-MONAI
diff --git a/‎.github/containerscan/allowedlist.yaml
Lines changed: 1 addition & 0 deletions b/‎.github/containerscan/allowedlist.yaml
Lines changed: 1 addition & 0 deletions
diff --git a/‎.github/workflows/ci.yml
Lines changed: 15 additions & 14 deletions b/‎.github/workflows/ci.yml
Lines changed: 15 additions & 14 deletions
diff --git a/‎.licenserc.yaml
Lines changed: 4 additions & 0 deletions b/‎.licenserc.yaml
Lines changed: 4 additions & 0 deletions
diff --git a/‎Dockerfile
Lines changed: 3 additions & 0 deletions b/‎Dockerfile
Lines changed: 3 additions & 0 deletions
diff --git a/‎doc/dependency_decisions.yml
Lines changed: 42 additions & 59 deletions b/‎doc/dependency_decisions.yml
Lines changed: 42 additions & 59 deletions
diff --git a/‎docker-compose/.env
Lines changed: 28 additions & 0 deletions b/‎docker-compose/.env
Lines changed: 28 additions & 0 deletions
diff --git a/‎docker-compose/README.md
Lines changed: 42 additions & 0 deletions b/‎docker-compose/README.md
Lines changed: 42 additions & 0 deletions
@@ -15,3 +15,4 @@
 general:
   vulnerabilities:
     - CVE-2018-8292
+    - CVE-1999-1278
@@ -45,7 +45,7 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: "6.0.x"
 
@@ -76,20 +76,21 @@ jobs:
       with:
         fetch-depth: 0
 
-    - uses: actions/setup-dotnet@v2
+    - uses: actions/setup-dotnet@v3
       with:
         dotnet-version: "6.0.x"
 
     - name: Enable Homebrew
       run: echo "/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin" >> $GITHUB_PATH
 
     - name: Install License Finder tool with Homebrew
-      uses: tecoli-com/actions-use-homebrew-tools@v0
+      uses: tecoli-com/actions-use-homebrew-tools@v0.4
       with:
         tools: licensefinder
+        cache: yes
 
     - name: Enable NuGet cache
-      uses: actions/[email protected].8
+      uses: actions/[email protected].10
       with:
         path: ~/.nuget/packages
         key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
@@ -140,12 +141,12 @@ jobs:
           distribution: zulu
           java-version: '11'
 
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: "6.0.x"
 
       - name: Enable NuGet cache
-        uses: actions/[email protected].8
+        uses: actions/[email protected].10
         with:
           path: ~/.nuget/packages
           key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
@@ -218,12 +219,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: "6.0.x"
 
       - name: Enable NuGet cache
-        uses: actions/[email protected].8
+        uses: actions/[email protected].10
         with:
           path: ~/.nuget/packages
           key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
@@ -283,12 +284,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: "6.0.x"
 
       - name: Enable NuGet cache
-        uses: actions/[email protected].8
+        uses: actions/[email protected].10
         with:
           path: ~/.nuget/packages
           key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
@@ -396,12 +397,12 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-dotnet@v2
+      - uses: actions/setup-dotnet@v3
         with:
           dotnet-version: "6.0.x"
 
       - name: Enable NuGet cache
-        uses: actions/[email protected].8
+        uses: actions/[email protected].10
         with:
           path: ~/.nuget/packages
           key: ${{ runner.os }}-nuget-${{ hashFiles('**/packages.lock.json') }}
@@ -423,8 +424,8 @@ jobs:
 
       - name: Update docs version
         run: |
-          sed -i -e "s,v0.0.0,v$SEMVER,g" ./docs/docfx.json
-          sed -i -e "s,v0.0.0,v$SEMVER,g" ./docs/index.md
+          sed -i -e "s,v0.0.0,v${{ env.SEMVER }},g" ./docs/docfx.json
+          sed -i -e "s,v0.0.0,v${{ env.SEMVER }},g" ./docs/index.md
 
       - name: Build Docs
         working-directory: docs
 
@@ -32,9 +32,13 @@ header:
     - 'src/Monai.Deploy.InformaticsGateway.sln'
     - 'src/Database/Migrations/**'
     - 'demos/**/.env/**'
+    - 'demos/**/*.txt'
+    - 'doc/dependency_decisions.yml'
+    - 'docker-compose/configs/kibana.ndjson'
     - 'docs/templates/**'
     - 'tests/Integration.Test/*.dev'
     - 'tests/Integration.Test/data/**'
+    - 'guidelines/diagrams/*.txt'
 
   comment: on-failure
 
 
@@ -28,7 +28,10 @@ RUN dotnet publish -c Release -o out --nologo src/InformaticsGateway/Monai.Deplo
 # Build runtime image
 FROM mcr.microsoft.com/dotnet/aspnet:6.0-jammy
 
+# Enable elastic client compatibility mode
+ENV ELASTIC_CLIENT_APIVERSIONING=true
 ENV DEBIAN_FRONTEND=noninteractive
+
 RUN apt-get clean \
  && apt-get update \
  && apt-get install -y --no-install-recommends \
 
@@ -1,17 +1,3 @@
-# Copyright 2022 MONAI Consortium
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
 ---
 - - :approve
   - AWSSDK.Core
@@ -60,7 +46,7 @@
   - :who: mocsharp
     :why: MIT (https://github.com/Cysharp/ConsoleAppFramework/raw/master/LICENSE)
     :versions:
-    - 4.2.2
+    - 4.2.4
     :when: 2022-08-16 23:05:31.110052610 Z
 - - :approve
   - Crayon
@@ -336,21 +322,9 @@
     :why: MIT (https://github.com/microsoft/vstest/raw/main/LICENSE)
     :versions:
     - 17.1.0
-    :when: 2022-08-16 23:05:48.342748414 Z
-- - :approve
-  - Microsoft.CodeCoverage
-  - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/main/LICENSE)
-    :versions:
     - 17.2.0
-    :when: 2022-08-16 23:05:48.787754812 Z
-- - :approve
-  - Microsoft.CodeCoverage
-  - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/main/LICENSE)
-    :versions:
-    - 17.3.1
-    :when: 2022-09-01 23:05:49.229587689 Z
+    - 17.3.2
+    :when: 2022-08-16 23:05:48.342748414 Z
 - - :approve
   - Microsoft.Data.Sqlite.Core
   - :who: mocsharp
@@ -725,7 +699,7 @@
   - :who: mocsharp
     :why: MIT (https://raw.githubusercontent.com/microsoft/vstest/main/LICENSE)
     :versions:
-    - 17.3.1
+    - 17.3.2
     :when: 2022-09-01 23:06:13.008314524 Z
 - - :approve
   - Microsoft.NETCore.Platforms
@@ -775,42 +749,25 @@
     :why: MIT (https://github.com/microsoft/vstest/raw/v17.1.0/LICENSE)
     :versions:
     - 17.1.0
-    :when: 2022-08-16 23:06:16.175705981 Z
-- - :approve
-  - Microsoft.TestPlatform.ObjectModel
-  - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/v17.2.0/LICENSE)
-    :versions:
     - 17.2.0
-    :when: 2022-08-16 23:06:16.642573372 Z
-- - :approve
-  - Microsoft.TestPlatform.ObjectModel
-  - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/v17.3.1/LICENSE)
-    :versions:
-    - 17.3.1
-    :when: 2022-09-01 23:06:17.198633634 Z
+    - 17.3.2
+    :when: 2022-08-16 23:06:16.175705981 Z
 - - :approve
   - Microsoft.TestPlatform.TestHost
   - :who: mocsharp
     :why: MIT (https://github.com/microsoft/vstest/raw/v17.1.0/LICENSE)
     :versions:
     - 17.1.0
-    :when: 2022-08-16 23:06:17.671459450 Z
-- - :approve
-  - Microsoft.TestPlatform.TestHost
-  - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/v17.2.0/LICENSE)
-    :versions:
     - 17.2.0
-    :when: 2022-08-16 23:06:18.130472318 Z
+    - 17.3.2
+    :when: 2022-08-16 23:06:17.671459450 Z
 - - :approve
-  - Microsoft.TestPlatform.TestHost
+  - Microsoft.Toolkit.HighPerformance
   - :who: mocsharp
-    :why: MIT (https://github.com/microsoft/vstest/raw/v17.3.1/LICENSE)
+    :why: MIT (https://github.com/CommunityToolkit/WindowsCommunityToolkit/raw/main/License.md)
     :versions:
-    - 17.3.1
-    :when: 2022-09-01 23:06:18.619013325 Z
+    - 7.1.2
+    :when: 2022-09-20 00:42:18.619013325 Z
 - - :approve
   - Microsoft.Toolkit.HighPerformance
   - :who: mocsharp
@@ -851,14 +808,14 @@
   - :who: mocsharp
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 0.1.5
+    - 0.1.8
     :when: 2022-08-16 23:06:21.051573547 Z
 - - :approve
   - Monai.Deploy.Messaging.RabbitMQ
   - :who: mocsharp
     :why: Apache-2.0 (https://github.com/Project-MONAI/monai-deploy-messaging/raw/main/LICENSE)
     :versions:
-    - 0.1.5
+    - 0.1.8
     :when: 2022-08-16 23:06:21.511789690 Z
 - - :approve
   - Monai.Deploy.Storage
@@ -1737,7 +1694,6 @@
     :versions:
     - 4.7.2
     :when: 2022-08-16 23:07:19.845361666 Z
-
 - - :approve
   - System.Text.Json
   - :who: mocsharp
@@ -2413,4 +2369,31 @@
     :versions:
     - 4.0.1
     :when: 2022-08-16 23:10:21.184627612 Z
-    
+- - :approve
+  - NLog
+  - :who: mocsharp
+    :why: BSD 3-Clause License (https://github.com/NLog/NLog/raw/dev/LICENSE.txt)
+    :versions:
+    - 5.0.4
+    :when: 2022-10-12 03:14:06.538744982 Z
+- - :approve
+  - NLog.Extensions.Logging
+  - :who: mocsharp
+    :why: BSD 2-Clause Simplified License (https://github.com/NLog/NLog.Extensions.Logging/raw/master/LICENSE)
+    :versions:
+    - 5.0.4
+    :when: 2022-10-12 03:14:06.964203977 Z
+- - :approve
+  - NLog.Web.AspNetCore
+  - :who: mocsharp
+    :why: BSD 3-Clause License (https://github.com/NLog/NLog.Web/raw/master/LICENSE)
+    :versions:
+    - 5.1.4
+    :when: 2022-10-12 03:14:07.396706995 Z
+- - :approve
+  - fo-dicom.NLog
+  - :who: mocsharp
+    :why: Microsoft Public License (https://github.com/fo-dicom/fo-dicom/raw/development/License.txt)
+    :versions:
+    - 5.0.3
+    :when: 2022-10-12 03:14:08.789273776 Z
@@ -0,0 +1,28 @@
+# Copyright 2022 MONAI Consortium
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+ELASTIC_VERSION=8.4.2
+
+
+# Elastic Search
+# User 'elastic' (built-in)
+ELASTIC_PASSWORD='monai'
+
+# Logstash
+# User 'logstash_internal' (custom)
+LOGSTASH_INTERNAL_PASSWORD='monai'
+
+# Kibana
+# User 'kibana_system' (built-in)
+KIBANA_SYSTEM_PASSWORD='monai'
@@ -0,0 +1,42 @@
+<!-- 
+Copyright 2022 MONAI Consortium
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License. 
+-->
+
+# MONAI Deploy Informatics Gateway
+
+The [docker-compose.yml](./docker-compose.yml) file includes the following services to run the Informatics Gateway.
+
+* MinIO
+* RabbitMQ
+* ElasticSearch (optional)
+* LogStash (optional)
+* Kibana (optional)
+
+
+## Running docker compose
+
+To start all Informatics Gateway dependencies, run `docker compose up`.
+
+Before running Informatics Gateway, ensure the following environment variables are exported:
+
+```bash
+export DOTNET_ENVIRONMENT=Development # if using appsettings.Development.json
+export LOGSTASH_URL=tcp://localhost:50000 # this tells Informatics Gateway to export logs to LogStash at tcp://localhost:5000
+```
+IMPORTANT: for Linux users, before running `docker compose up`, please run `init.sh` to create directories with the correct permissions first. Otherwise, ElasticSearch will not be able to start.
+
+### Kibana
+
+A default search is imported to Kibana at startup. To load the saved search, go to Analytics > Discover from the 🍔 menu. From the top right click *Open* and select *MONAI-Default*.