m2ms · boriskovar-m2ms · Sep 5, 2022 · Sep 15, 2022 · Sep 15, 2022 · Sep 15, 2022
diff --git a/.dockerignore b/.dockerignore
@@ -1 +1,2 @@
 .github/
+.git/
diff --git a/.github/workflows/build-main.yaml b/.github/workflows/build-main.yaml
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
-.idea
+.idea
+
+data/
diff --git a/Dockerfile b/Dockerfile
@@ -1,72 +1,59 @@
 ARG BE_NAMESPACE=xchem
 ARG BE_IMAGE_TAG=latest
-FROM ${BE_NAMESPACE}/fragalysis-backend:${BE_IMAGE_TAG}
+ARG FE_NAMESPACE=xchem
+ARG FE_IMAGE_TAG=latest
+ARG STACK_NAMESPACE=xchem
+ARG STACK_VERSION=0.0.0
+# Start with the frontend container image AS 'frontend'.
+# As part of the build we will copy the contents of its '/frontend' directory
+# into the backend image that we also pull in.
+FROM ${FE_NAMESPACE}/fragalysis-frontend:${FE_IMAGE_TAG} AS frontend
 
 # We have to repeat the ARG assignments...
 # ARGs are reset during the FROM action
+# See https://docs.docker.com/engine/reference/builder/#understand-how-arg-and-from-interact
 
 # Us
-ARG STACK_NAMESPACE=xchem
-# Backend origin (a container)
-ARG BE_NAMESPACE=xchem
-ARG BE_IMAGE_TAG=latest
-# By default this is hosted on the xchem project's master branch
-# but it can be redirected with a couple of build-args.
-ARG FE_NAMESPACE=xchem
-ARG FE_BRANCH=master
+ARG STACK_NAMESPACE
+ARG STACK_VERSION
+# Backend image identity
+ARG BE_NAMESPACE
+ARG BE_IMAGE_TAG
+# Frontend image identity
+ARG FE_NAMESPACE
+ARG FE_IMAGE_TAG
+
+# Get the backend image
+# (we'll copy the pre-compiled frontend into it)
+FROM ${BE_NAMESPACE}/fragalysis-backend:${BE_IMAGE_TAG}
+
+# We have to repeat the ARG assignments...
+ARG STACK_NAMESPACE
+ARG STACK_VERSION
+ARG BE_NAMESPACE
+ARG BE_IMAGE_TAG
+ARG FE_NAMESPACE
+ARG FE_IMAGE_TAG
 
 # Set the container ENV to record the origin of the b/e and f/e
+# (for diagnostic purposes)
 ENV BE_NAMESPACE ${BE_NAMESPACE}
 ENV BE_IMAGE_TAG ${BE_IMAGE_TAG}
 ENV FE_NAMESPACE ${FE_NAMESPACE}
-ENV FE_BRANCH ${FE_BRANCH}
+ENV FE_IMAGE_TAG ${FE_IMAGE_TAG}
 ENV STACK_NAMESPACE ${STACK_NAMESPACE}
+ENV STACK_VERSION ${STACK_VERSION}
 
 ENV APP_ROOT /code
-ENV APP_USER_ID 2000
 
-RUN useradd -c 'Container user' --user-group --uid ${APP_USER_ID} --home-dir ${APP_ROOT} -s /bin/bash frag
-RUN apt-get update -y &&\
-  apt-get install -y wget gnupg bzip2 &&\
-  apt-get clean
+# Copy the frontend code from the frontend container
+WORKDIR ${APP_ROOT}/frontend
+WORKDIR ${APP_ROOT}/static
 
-# Install yarn (instead of npm)
-RUN curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | apt-key add -
-RUN echo "deb https://dl.yarnpkg.com/debian/ stable main" | tee /etc/apt/sources.list.d/yarn.list
-RUN apt-get update -y && apt-get install -y yarn && apt-get clean
-
-# Install nodejs
-RUN wget -q https://nodejs.org/download/release/v12.22.11/node-v12.22.11-linux-x64.tar.gz &&\
-  mkdir -p /usr/local/lib/nodejs &&\
-  tar -xf node-v12.22.11-linux-x64.tar.gz -C /usr/local/lib/nodejs &&\
-  rm node-v12.22.11-linux-x64.tar.gz
-ENV PATH /usr/local/lib/nodejs/node-v12.22.11-linux-x64/bin:$PATH
-
-# Add in the frontend code
-RUN git clone https://github.com/${FE_NAMESPACE}/fragalysis-frontend ${APP_ROOT}/frontend
-RUN cd ${APP_ROOT}/frontend && git checkout ${FE_BRANCH}
-
-# Now build the code
-RUN cd ${APP_ROOT}/frontend && yarn install
-RUN cd ${APP_ROOT}/frontend && yarn run build
-
-ADD docker-entrypoint.sh ${APP_ROOT}/docker-entrypoint.sh
-
-# Symlink these
-RUN mkdir ${APP_ROOT}/static
+COPY --from=frontend /frontend ${APP_ROOT}/frontend
 RUN ln -s ${APP_ROOT}/frontend/bundles/ ${APP_ROOT}/static/bundles
 
-RUN chmod 755 ${APP_ROOT}/docker-entrypoint.sh
-RUN chmod 755 ${APP_ROOT}/makemigrations.sh
-RUN chmod 755 ${APP_ROOT}/launch-stack.sh
-
-#RUN chown -R ${APP_USER_ID} ${APP_ROOT} /run /var
-
-# The VSERION file records the origin of the stack
-# and is set by the corresponding GitHub Action
-COPY LICENSE /LICENSE
-COPY README.md /README.md
-COPY VERSION /code/VERSION
-
 WORKDIR ${APP_ROOT}
+# The entrypoint is a responsibility of the backend image
+
 CMD ["./docker-entrypoint.sh"]
diff --git a/LICENSE b/LICENSE
@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright {yyyy} {name of copyright owner}
+   Copyright 2025 Diamond Light Source
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

diff --git a/README.md b/README.md
@@ -1,9 +1,81 @@
 [![build main](https://github.com/xchem/fragalysis-stack/actions/workflows/build-main.yaml/badge.svg)](https://github.com/xchem/fragalysis-stack/actions/workflows/build-main.yaml)
 
-[![experimental](http://badges.github.io/stability-badges/dist/experimental.svg)](http://github.com/xchem/fragalysis-stack)
-[![Version](http://img.shields.io/badge/version-0.0.1-blue.svg?style=flat)](https://github.com/xchem/fragalysis-stack)
+![GitHub tag (latest SemVer pre-release)](https://img.shields.io/github/v/tag/xchem/fragalysis-stack)
 [![License](http://img.shields.io/badge/license-Apache%202.0-blue.svg?style=flat)](https://github.com/xchem/fragalysis-stack/blob/master/LICENSE.txt)
 
 # Fragalysis stack
-Docker setup for building a Django, RDKit and Postgres stack with neo4j 
-Simply run docker-compose up
+
+Docker setup for building a Django, RDKit and Postgres stack with neo4j.
+
+>   There is no application code in this repository, it is a repository where the
+    stack application is *assembled* using environment variables that define the
+    origin of the [Backend] and [Frontend] container images.
+
+The stack is built and orchestrated using GitHub Actions and is deployed
+to *staging* and *production* installations (**Namespaces** in a designated
+Kubernetes cluster).
+
+The build variables `DOCKERHUB_USERNAME` and `TRIGGER_AWX` must be defined
+for orchestration to take place. Staging deployments take place on every downstream
+build (frontend and backend) and tag, and production deployments take place on every tag.
+
+You **MUST** make sure the Action variables that select the backend and frontend
+container images are updated prior to every production release so the stack
+uses the appropriate backend and frontend code. You will find these variables
+in the `.github/workflows/build-main.yaml` action file: -
+
+- `BE_IMAGE_TAG`
+- `FE_IMAGE_TAG`
+
+[More information on pushing to production](README.md#pushing-a-release-to-production)
+
+## Local development
+
+A docker-compose file provides a convenient way of launching the stack locally.
+The suitability of the various docker-compose files is the responsibility of
+the developer.
+
+Check the compose file, adjust accordingly, then: -
+
+    docker-compose up -d
+
+>   Containers in the docker-compose generally store persistent data in
+    the `./data` directory of this repository. These directories
+    are created automatically if they do not exist.
+
+When you're done you can tear everything down with: -
+
+    docker-compose down
+
+## Pushing a release to production
+
+1. Create new releases for the [Frontend] and [Backend].
+
+    * [Create a new release for the frontend](https://github.com/xchem/fragalysis-frontend/releases/new)
+        * Create a new tag with the format: `YYYY.MM.#` where:
+            * `YYYY` is the current year
+            * `MM` is the current month
+            * `#` is the patch number (positive integer)
+        * Choose a target: `staging` or `production`
+        * Title the release
+        * Describe the release
+    * [Create a new release for the backend](https://github.com/xchem/fragalysis-backend/releases/new)
+        * Same as the frontend
+
+ 2. Update [build-main.yaml](.github/workflows/build-main.yaml) with the new tags
+    * Change `FE_IMAGE_TAG` to the desired Frontend tag
+    * Change `BE_IMAGE_TAG` to the desired Backend tag
+    * Commit the changes to a new branch and start a pull request
+    * Wait for review and approval
+    * Wait for the [GitHub action](https://github.com/xchem/fragalysis-stack/actions) to complete (~10-20mins)
+
+> N.B. you can get the current Frontend, Backend, and Stack tags from the bottom of the Fragalysis menu
+
+3. Create a new release for [fragalysis-stack](https://github.com/xchem/fragalysis-stack/releases/new)
+   * Use the same tag convention as for the Frontend and Backend.
+   * Tags do not need to agree across the three repositories!
+
+---
+
+[backend]: https://github.com/xchem/fragalysis-backend
+[frontend]: https://github.com/xchem/fragalysis-frontend
diff --git a/VERSION b/VERSION
diff --git a/changelog.md b/changelog.md
@@ -1,4 +1,70 @@
 # Changelog (from 22/07/2021)
+
+
+## 16/12/2022 - version 2022.12.1
+Job launcher release
+### Frontend ([PR #335](https://github.com/xchem/fragalysis-frontend/pull/320)). 
+:heavy_plus_sign: Job table shows running jobs, and autoreloads
+:heavy_plus_sign: Improved snapshot loading
+
+### Backend ([PR #349-#361 #365 #367](https://github.com/xchem/fragalysis-backend/pull/347)). 
+:heavy_plus_sign: Bug fixing: backend timeout, error report
+
+### Resolved tickets. 
+[#977](https://github.com/m2ms/fragalysis-frontend/issues/917),[#996](https://github.com/m2ms/fragalysis-frontend/issues/996),[#979](https://github.com/m2ms/fragalysis-frontend/issues/979),[#1003](https://github.com/m2ms/fragalysis-frontend/issues/1003),[#1011](https://github.com/m2ms/fragalysis-frontend/issues/1011),[#935](https://github.com/m2ms/fragalysis-frontend/issues/935),[#995](https://github.com/m2ms/fragalysis-frontend/issues/995),
+
+
+## 29/09/2022 - version 2022.09.0
+Job launcher release
+### Frontend ([PR #300 #302 #306-#312 #314-#320](https://github.com/xchem/fragalysis-frontend/pull/320)). 
+:heavy_plus_sign: New functionality: Job Launcher
+:heavy_plus_sign: Improved performance
+:heavy_plus_sign: Bug fixing: Layout, filters, snapshots
+
+### Backend ([PR #330 #331 #334 #336-#347](https://github.com/xchem/fragalysis-backend/pull/347)). 
+:heavy_plus_sign: New functionality: Job Launcher
+:heavy_plus_sign: Improved container building
+
+### Resolved tickets. 
+[#917](https://github.com/m2ms/fragalysis-frontend/issues/917), [#862](https://github.com/m2ms/fragalysis-frontend/issues/862), [#936](https://github.com/m2ms/fragalysis-frontend/issues/936), [#859](https://github.com/m2ms/fragalysis-frontend/issues/859), [#959](https://github.com/m2ms/fragalysis-frontend/issues/959), [#960](https://github.com/m2ms/fragalysis-frontend/issues/960), [#870](https://github.com/m2ms/fragalysis-frontend/issues/870), [#949](https://github.com/m2ms/fragalysis-frontend/issues/949), [#932](https://github.com/m2ms/fragalysis-frontend/issues/932), [#867](https://github.com/m2ms/fragalysis-frontend/issues/867), [#933](https://github.com/m2ms/fragalysis-frontend/issues/933), [#934](https://github.com/m2ms/fragalysis-frontend/issues/934), [#906](https://github.com/m2ms/fragalysis-frontend/issues/906), [#878](https://github.com/m2ms/fragalysis-frontend/issues/978), [#911](https://github.com/m2ms/fragalysis-frontend/issues/911), [#991](https://github.com/m2ms/fragalysis-frontend/issues/991), [#703](https://github.com/m2ms/fragalysis-frontend/issues/703), [#875](https://github.com/m2ms/fragalysis-frontend/issues/875), [#868](https://github.com/m2ms/fragalysis-frontend/issues/868), [#942](https://github.com/m2ms/fragalysis-frontend/issues/942), [#887](https://github.com/m2ms/fragalysis-frontend/issues/887), [#966](https://github.com/m2ms/fragalysis-frontend/issues/966), [#889](https://github.com/m2ms/fragalysis-frontend/issues/889), [#939](https://github.com/m2ms/fragalysis-frontend/issues/939), [#926](https://github.com/m2ms/fragalysis-frontend/issues/926), [#796](https://github.com/m2ms/fragalysis-frontend/issues/796), [#869](https://github.com/m2ms/fragalysis-frontend/issues/869), [#885](https://github.com/m2ms/fragalysis-frontend/issues/885), [#883](https://github.com/m2ms/fragalysis-frontend/issues/883), [#904](https://github.com/m2ms/fragalysis-frontend/issues/904), [#958](https://github.com/m2ms/fragalysis-frontend/issues/958), [#946](https://github.com/m2ms/fragalysis-frontend/issues/946), [#973](https://github.com/m2ms/fragalysis-frontend/issues/973), [#957](https://github.com/m2ms/fragalysis-frontend/issues/957), [#947](https://github.com/m2ms/fragalysis-frontend/issues/947), [#969](https://github.com/m2ms/fragalysis-frontend/issues/969), [#864](https://github.com/m2ms/fragalysis-frontend/issues/864), [#873](https://github.com/m2ms/fragalysis-frontend/issues/873), .....
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+
 
 
 ## 20/07/2022 - version 2.7.1.
@@ -18,7 +84,7 @@ Quick fix
 ### Frontend ([PR #299](https://github.com/xchem/fragalysis-frontend/pull/299)). 
 :heavy_plus_sign: Bug fixed: RHS F button crashing
 
-### Backend ([PR #325,#327,#328,#329](https://github.com/xchem/fragalysis-backend/pull/314)). 
+### Backend ([PR #325,#327,#328,#329](https://github.com/xchem/fragalysis-backend/pull/329)). 
 :heavy_plus_sign: Bug fixed: download sdf files
 :heavy_plus_sign: Crystal ids in the sdf files
 

diff --git a/docker-compose.dev.yml b/docker-compose.dev.yml
@@ -1,3 +1,4 @@
+---
 version: '3'
 
 services:

diff --git a/docker-compose.test.yml b/docker-compose.test.yml
-Original file line number
+Diff line change
@@ -1 +1,3 @@
-    .idea
+    .idea
+    data/