diff --git a/Makefile b/Makefile index 7cd90e6f..473ccba8 100644 --- a/Makefile +++ b/Makefile @@ -6,7 +6,7 @@ PYTHON_CMD := $(shell command -v python3 2> /dev/null) BUILDAH_CMD := $(shell command -v buildah 2> /dev/null) DOCKER_CMD := $(shell command -v docker 2> /dev/null) ELIXIR_CLOUD_REGISTRY := docker.io/elixircloud -DOCKER_FILE_PATH := containers +DOCKER_FILE_PATH := deployment/containers # Define arguments IMAGE ?= filer diff --git a/README.md b/README.md index ff0d377c..bfe644ad 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ - + -An implementation of a task execution engine based on the [TES standard](https://github.com/ga4gh/task-execution-schemas) running on `Kubernetes`. For more details on `TES`, see the (very) brief [introduction to TES](documentation/tesintro.md). +An implementation of a task execution engine based on the [TES standard](https://github.com/ga4gh/task-execution-schemas) running on `Kubernetes`. For more details on `TES`, see the (very) brief [introduction to TES](deployment/documentation/tesintro.md). For organisational reasons, this project is split into 3 repositories: - This one, which contains documentation and deployment files @@ -10,15 +10,16 @@ For organisational reasons, this project is split into 3 repositories: If the API is running on your cluster it will pull the images from our `docker.io` repository automatically. -`TESK` is designed with the goal to support any `Kubernetes` cluster, for its deployment please refer to the [deployment](documentation/deployment.md) page. +`TESK` is designed with the goal to support any `Kubernetes` cluster, for its deployment please refer to the [deployment](deployment/documentation/deployment.md) page. -The technical documentation is available in the [documentation](documentation) folder. +The technical documentation is available in the [documentation](deployment/documentation) folder. ## Architecture As a diagram: -![TESK architecture](documentation/img/architecture.png) +# TODO: Change the image remove tomcat, change naming etc +![TESK architecture](deployment/documentation/img/architecture.png) **Description**: The first pod in the task lifecycle is the API pod, a pod which runs a web server (`Tomcat`) and exposes the `TES` specified endpoints. It consumes `TES` requests, validates them and translates them to `Kubernetes` jobs. The API pod then creates a `task controller` pod, or `taskmaster`. @@ -30,4 +31,4 @@ After the last executor, the `filer` is called once more to process the outputs - A working [Kubernetes](https://kubernetes.io/) cluster version 1.9 and later. - If you want TESK to handle tasks with I/O (and you probably want), you additionally need: - A default storage class, which TESK will use to create temporary PVCs. It is enough that the storage class supports the RWO mode. -- And, if you want TESK to integrate with workflow managers, you additionally need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](documentation/deployment.md) page). +- And, if you want TESK to integrate with workflow managers, you additionally need either an FTP account or a PVC that can be accessed from within or from outside of the cluster by the workflow manager (more in the [deployment](deployment/documentation/deployment.md) page). diff --git a/charts/tesk/.gitignore b/deployment/charts/tesk/.gitignore similarity index 100% rename from charts/tesk/.gitignore rename to deployment/charts/tesk/.gitignore diff --git a/charts/tesk/.helmignore b/deployment/charts/tesk/.helmignore similarity index 100% rename from charts/tesk/.helmignore rename to deployment/charts/tesk/.helmignore diff --git a/charts/tesk/Chart.yaml b/deployment/charts/tesk/Chart.yaml similarity index 100% rename from charts/tesk/Chart.yaml rename to deployment/charts/tesk/Chart.yaml diff --git a/charts/tesk/README.md b/deployment/charts/tesk/README.md similarity index 100% rename from charts/tesk/README.md rename to deployment/charts/tesk/README.md diff --git a/charts/tesk/ftp/.netrc-TEMPLATE b/deployment/charts/tesk/ftp/.netrc-TEMPLATE similarity index 100% rename from charts/tesk/ftp/.netrc-TEMPLATE rename to deployment/charts/tesk/ftp/.netrc-TEMPLATE diff --git a/charts/tesk/s3-config/config-TEMPLATE b/deployment/charts/tesk/s3-config/config-TEMPLATE similarity index 100% rename from charts/tesk/s3-config/config-TEMPLATE rename to deployment/charts/tesk/s3-config/config-TEMPLATE diff --git a/charts/tesk/s3-config/credentials-TEMPLATE b/deployment/charts/tesk/s3-config/credentials-TEMPLATE similarity index 100% rename from charts/tesk/s3-config/credentials-TEMPLATE rename to deployment/charts/tesk/s3-config/credentials-TEMPLATE diff --git a/charts/tesk/service-info/service-info.yaml b/deployment/charts/tesk/service-info/service-info.yaml similarity index 100% rename from charts/tesk/service-info/service-info.yaml rename to deployment/charts/tesk/service-info/service-info.yaml diff --git a/charts/tesk/templates/common/oauth-client-secret.yaml b/deployment/charts/tesk/templates/common/oauth-client-secret.yaml similarity index 100% rename from charts/tesk/templates/common/oauth-client-secret.yaml rename to deployment/charts/tesk/templates/common/oauth-client-secret.yaml diff --git a/charts/tesk/templates/common/service-info-cm.yaml b/deployment/charts/tesk/templates/common/service-info-cm.yaml similarity index 100% rename from charts/tesk/templates/common/service-info-cm.yaml rename to deployment/charts/tesk/templates/common/service-info-cm.yaml diff --git a/charts/tesk/templates/common/taskmaster-rbac.yaml b/deployment/charts/tesk/templates/common/taskmaster-rbac.yaml similarity index 100% rename from charts/tesk/templates/common/taskmaster-rbac.yaml rename to deployment/charts/tesk/templates/common/taskmaster-rbac.yaml diff --git a/charts/tesk/templates/common/tesk-deployment.yaml b/deployment/charts/tesk/templates/common/tesk-deployment.yaml similarity index 100% rename from charts/tesk/templates/common/tesk-deployment.yaml rename to deployment/charts/tesk/templates/common/tesk-deployment.yaml diff --git a/charts/tesk/templates/common/tesk-svc.yaml b/deployment/charts/tesk/templates/common/tesk-svc.yaml similarity index 100% rename from charts/tesk/templates/common/tesk-svc.yaml rename to deployment/charts/tesk/templates/common/tesk-svc.yaml diff --git a/charts/tesk/templates/ftp/ftp-endpoint.yaml b/deployment/charts/tesk/templates/ftp/ftp-endpoint.yaml similarity index 100% rename from charts/tesk/templates/ftp/ftp-endpoint.yaml rename to deployment/charts/tesk/templates/ftp/ftp-endpoint.yaml diff --git a/charts/tesk/templates/ftp/ftp-secret.yaml b/deployment/charts/tesk/templates/ftp/ftp-secret.yaml similarity index 100% rename from charts/tesk/templates/ftp/ftp-secret.yaml rename to deployment/charts/tesk/templates/ftp/ftp-secret.yaml diff --git a/charts/tesk/templates/ftp/ftp-service.yaml b/deployment/charts/tesk/templates/ftp/ftp-service.yaml similarity index 100% rename from charts/tesk/templates/ftp/ftp-service.yaml rename to deployment/charts/tesk/templates/ftp/ftp-service.yaml diff --git a/charts/tesk/templates/ftp/netrc-secret.yaml b/deployment/charts/tesk/templates/ftp/netrc-secret.yaml similarity index 100% rename from charts/tesk/templates/ftp/netrc-secret.yaml rename to deployment/charts/tesk/templates/ftp/netrc-secret.yaml diff --git a/charts/tesk/templates/ingress/ingress-rules.yaml b/deployment/charts/tesk/templates/ingress/ingress-rules.yaml similarity index 100% rename from charts/tesk/templates/ingress/ingress-rules.yaml rename to deployment/charts/tesk/templates/ingress/ingress-rules.yaml diff --git a/charts/tesk/templates/openshift/oc-route.yaml b/deployment/charts/tesk/templates/openshift/oc-route.yaml similarity index 100% rename from charts/tesk/templates/openshift/oc-route.yaml rename to deployment/charts/tesk/templates/openshift/oc-route.yaml diff --git a/charts/tesk/templates/storage/aws-secret.yaml b/deployment/charts/tesk/templates/storage/aws-secret.yaml similarity index 100% rename from charts/tesk/templates/storage/aws-secret.yaml rename to deployment/charts/tesk/templates/storage/aws-secret.yaml diff --git a/charts/tesk/templates/storage/openstack.yaml b/deployment/charts/tesk/templates/storage/openstack.yaml similarity index 100% rename from charts/tesk/templates/storage/openstack.yaml rename to deployment/charts/tesk/templates/storage/openstack.yaml diff --git a/charts/tesk/tls_secret_name.yml-TEMPLATE b/deployment/charts/tesk/tls_secret_name.yml-TEMPLATE similarity index 100% rename from charts/tesk/tls_secret_name.yml-TEMPLATE rename to deployment/charts/tesk/tls_secret_name.yml-TEMPLATE diff --git a/charts/tesk/values.yaml b/deployment/charts/tesk/values.yaml similarity index 100% rename from charts/tesk/values.yaml rename to deployment/charts/tesk/values.yaml diff --git a/containers/filer.Dockerfile b/deployment/containers/filer.Dockerfile similarity index 100% rename from containers/filer.Dockerfile rename to deployment/containers/filer.Dockerfile diff --git a/containers/taskmaster.Dockerfile b/deployment/containers/taskmaster.Dockerfile similarity index 100% rename from containers/taskmaster.Dockerfile rename to deployment/containers/taskmaster.Dockerfile diff --git a/documentation/deployment.md b/deployment/documentation/deployment.md similarity index 100% rename from documentation/deployment.md rename to deployment/documentation/deployment.md diff --git a/documentation/img/TESKlogo.png b/deployment/documentation/img/TESKlogo.png similarity index 100% rename from documentation/img/TESKlogo.png rename to deployment/documentation/img/TESKlogo.png diff --git a/documentation/img/TESKlogowfont.png b/deployment/documentation/img/TESKlogowfont.png similarity index 100% rename from documentation/img/TESKlogowfont.png rename to deployment/documentation/img/TESKlogowfont.png diff --git a/documentation/img/architecture.png b/deployment/documentation/img/architecture.png similarity index 100% rename from documentation/img/architecture.png rename to deployment/documentation/img/architecture.png diff --git a/documentation/img/project-architecture.png b/deployment/documentation/img/project-architecture.png similarity index 100% rename from documentation/img/project-architecture.png rename to deployment/documentation/img/project-architecture.png diff --git a/documentation/integrated_wes_tes.md b/deployment/documentation/integrated_wes_tes.md similarity index 100% rename from documentation/integrated_wes_tes.md rename to deployment/documentation/integrated_wes_tes.md diff --git a/documentation/local_ftp.md b/deployment/documentation/local_ftp.md similarity index 100% rename from documentation/local_ftp.md rename to deployment/documentation/local_ftp.md diff --git a/documentation/tesintro.md b/deployment/documentation/tesintro.md similarity index 100% rename from documentation/tesintro.md rename to deployment/documentation/tesintro.md diff --git a/examples/inputFile.json b/deployment/examples/inputFile.json similarity index 100% rename from examples/inputFile.json rename to deployment/examples/inputFile.json diff --git a/examples/inputHelloWorld.json b/deployment/examples/inputHelloWorld.json similarity index 100% rename from examples/inputHelloWorld.json rename to deployment/examples/inputHelloWorld.json diff --git a/examples/inputHttp.json b/deployment/examples/inputHttp.json similarity index 100% rename from examples/inputHttp.json rename to deployment/examples/inputHttp.json diff --git a/examples/localftp/taskWithIO.json b/deployment/examples/localftp/taskWithIO.json similarity index 100% rename from examples/localftp/taskWithIO.json rename to deployment/examples/localftp/taskWithIO.json diff --git a/examples/resources/cpu.json b/deployment/examples/resources/cpu.json similarity index 100% rename from examples/resources/cpu.json rename to deployment/examples/resources/cpu.json diff --git a/examples/resources/more_cpu_than_nodes.json b/deployment/examples/resources/more_cpu_than_nodes.json similarity index 100% rename from examples/resources/more_cpu_than_nodes.json rename to deployment/examples/resources/more_cpu_than_nodes.json diff --git a/examples/taskCreate b/deployment/examples/taskCreate similarity index 100% rename from examples/taskCreate rename to deployment/examples/taskCreate diff --git a/examples/taskList b/deployment/examples/taskList similarity index 100% rename from examples/taskList rename to deployment/examples/taskList diff --git a/examples/transferPvc/Readme.md b/deployment/examples/transferPvc/Readme.md similarity index 100% rename from examples/transferPvc/Readme.md rename to deployment/examples/transferPvc/Readme.md diff --git a/examples/transferPvc/clean b/deployment/examples/transferPvc/clean similarity index 100% rename from examples/transferPvc/clean rename to deployment/examples/transferPvc/clean diff --git a/examples/transferPvc/minikubeStart b/deployment/examples/transferPvc/minikubeStart similarity index 100% rename from examples/transferPvc/minikubeStart rename to deployment/examples/transferPvc/minikubeStart diff --git a/examples/transferPvc/pod.yaml b/deployment/examples/transferPvc/pod.yaml similarity index 100% rename from examples/transferPvc/pod.yaml rename to deployment/examples/transferPvc/pod.yaml diff --git a/examples/transferPvc/pv.yaml b/deployment/examples/transferPvc/pv.yaml similarity index 100% rename from examples/transferPvc/pv.yaml rename to deployment/examples/transferPvc/pv.yaml diff --git a/examples/transferPvc/pvc.yaml b/deployment/examples/transferPvc/pvc.yaml similarity index 100% rename from examples/transferPvc/pvc.yaml rename to deployment/examples/transferPvc/pvc.yaml