move /srv/webknossos to /webknossos in the dockerfiles (#5843)

* move /srv/webknossos to /webknossos in the dockerfiles
* Merge branch 'master' into docker-directory
* add umask to dockerfiles
* Merge branch 'docker-directory' of github.com:scalableminds/webknossos into docker-directory
* Merge branch 'master' into docker-directory
* fix entrypoint
* docs
* pr feedback
* Merge branch 'master' into docker-directory
* remove newrelic env vars

CHANGELOG.unreleased.md

@@ -14,7 +14,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Added a new bounding box tool that allows resizing and creating bounding boxes more easily. Additionally, the context menu now contains options to modify the bounding box close to the clicked position. [#5767](https://github.com/scalableminds/webknossos/pull/5767)
 
 ### Changed
--
+- The docker setup has been restructured, which requires changes to existing docker-compose setups. See the migration guide for details. [#5843](https://github.com/scalableminds/webknossos/pull/5843) 
 
 ### Fixed
 - Fixed a bug where admins could not share annotations with teams they were not explicitly a member of. [#5845](https://github.com/scalableminds/webknossos/pull/5845)

Dockerfile

@@ -1,10 +1,10 @@
 FROM openjdk:8-jdk
 RUN apt-get update \
-    && apt-get -y install postgresql-client \
-    && rm -rf /var/lib/apt/lists/*
+  && apt-get -y install postgresql-client \
+  && rm -rf /var/lib/apt/lists/*
 
-RUN mkdir -p /srv/webknossos
-WORKDIR /srv/webknossos
+RUN mkdir -p /webknossos
+WORKDIR /webknossos
 
 COPY target/universal/stage .
 COPY webknossos-datastore/lib/native target/universal/stage/lib/native
@@ -17,6 +17,9 @@ RUN addgroup --system --gid 999 webknossos \
   && chmod go+x bin/webknossos \
   && chmod go+w .
 
+RUN echo '#!/bin/bash\numask 002\nbin/webknossos "$@"\n' > /docker-entrypoint.sh \
+  && chmod +x /docker-entrypoint.sh
+
 HEALTHCHECK \
   --interval=1m --timeout=5s --retries=10 \
   CMD curl --fail http://localhost:9000/api/buildinfo || exit 1
@@ -25,4 +28,4 @@ USER webknossos
 
 EXPOSE 9000
 
-ENTRYPOINT [ "bin/webknossos" ]
+ENTRYPOINT [ "/docker-entrypoint.sh" ]

MIGRATIONS.unreleased.md

@@ -7,7 +7,8 @@ User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 ## Unreleased
 
-- 
+- The docker files now place the webKnossos installation under `/webknossos` instead of `/srv/webknossos`. All mounts, most importantly `/srv/webknossos/binaryData`, need to be changed accordingly.
+- The entrypoint of the docker files have changed. Therefore, any existing `docker-compose.yml` setups need to be adapted. In most cases, only the `entrypoint: bin/webknossos` lines need to be removed (if existant).
 
 ### Postgres Evolutions:
 

docker-compose.yml

@@ -32,7 +32,7 @@ services:
       # - -Dplay.modules.enabled-="com.scalableminds.webknossos.datastore.DataStoreModule"
       # - -Dplay.http.router="noDS.Routes"
     volumes:
-      - ./binaryData:/srv/webknossos/binaryData
+      - ./binaryData:/webknossos/binaryData
     environment:
       - POSTGRES_URL=jdbc:postgresql://postgres/webknossos
     user: ${USER_UID:-1000}:${USER_GID:-1000}
@@ -42,9 +42,8 @@ services:
     image: scalableminds/webknossos-datastore:${DOCKER_TAG:-master}
     ports:
       - "9090:9090"
-    entrypoint: bin/webknossos-datastore
     volumes:
-      - ./binaryData:/srv/webknossos-datastore/binaryData
+      - ./binaryData:/webknossos-datastore/binaryData
     command:
       - -J-Xmx20G
       - -J-Xms1G
@@ -58,7 +57,6 @@ services:
     image: scalableminds/webknossos-tracingstore:${DOCKER_TAG:-master}
     ports:
       - "9050:9050"
-    entrypoint: bin/webknossos-tracingstore
     command:
       - -J-Xmx20G
       - -J-Xms1G

docs/datasets.md

@@ -52,7 +52,7 @@ services:
   webknossos:
     ...
     volumes:
-      - ./data:/srv/webknossos/binaryData
+      - ./data:/webknossos/binaryData
       - /cluster:/cluster
 ...
 ```