merge tmp branch with original files to the monorepo feature branch

.gitignore

@@ -126,4 +126,4 @@ docs/_build/
 target/
 
 # Ipython Notebook
-.ipynb_checkpoints
+.ipynb_checkpoints

apps/sage/otel-collector/Dockerfile

@@ -0,0 +1,5 @@
+FROM public.ecr.aws/aws-observability/aws-otel-collector:latest as aws-otel
+
+FROM otel/opentelemetry-collector-contrib:0.113.0
+
+COPY --from=aws-otel /healthcheck /healthcheck

apps/sage/otel-collector/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 T. Thyer
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

apps/sage/otel-collector/README.md

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+# Purpose
+
+As discussed in this Github Issue: <https://github.com/open-telemetry/opentelemetry-collector-contrib/issues/30798#issuecomment-2009233014>
+The official opentelemetry (OTEL) collector image does not contain cURL or related shell
+commands required to do container level health checks. It is reliant on external
+services such as the application load balancer in AWS to perform these checks. This is
+problematic with our deployment of the OTEL collector as we are using AWS
+service connect with AWS ECS to allow other containers within the namespace to connect
+to the collector. As such, there is no load balancer in-front of the container to handle
+its lifecycle. Within ECS, the recommended way from AWS to handle container level health
+checks is to let ECS perform commands in the container.
+Source: <https://docs.aws.amazon.com/AmazonECS/latest/APIReference/API_HealthCheck.html>
+
+Since the OTEL collector does not have a shell, nor cURL available we need to accomplish
+this another way. In the official AWS OTEL collector distro they accomplish this by
+compiling a golang script down into a binary that can be run within the container.
+Unfortunately we cannot use the AWS OTEL collector because they are not supporting the
+`oauth2clientauthextension`: <https://github.com/aws-observability/aws-otel-collector/issues/1492>.
+
+For our purposes we are creating a new image based off the `otel/opentelemetry-collector-contrib` image,
+but with the addition of the healthcheck binary from the AWS OTEL distro. This
+combination lets us use the oauth2 extension, and have container level health checks.
+
+## Creating a new image (To automate later on)
+
+As new base images are updated we will need to in-turn create a new otel collector
+image that we deploy to ECS.
+
+1. Update values in the `Dockerfile`
+2. Run `docker build -t ghcr.io/sage-bionetworks/sage-otel-collector:vX.X.X .` (Replace the version)
+3. Run `docker push ghcr.io/sage-bionetworks/sage-otel-collector:vX.X.X` (Replace the version)
+
+Once a new image is built and pushed, then you'll want to update the values in the CDK
+scripts to use the new image version.