Fix docker uid/gid + binaryData permissions. Persist postgres db

.gitignore

@@ -26,6 +26,7 @@ binaryData
 tracingData/
 backup/
 ./data/
+fossildb-dev/
 boot/
 .idea/
 .tmp/

CHANGELOG.md

@@ -20,6 +20,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 ### Fixed
 
 - Fixed a bug where the initial onboarding setup failed if automatic initial data was disabled. [#3421](https://github.com/scalableminds/webknossos/pull/3421)
+- Fixed a permission issue in the try setup
 - Fixed a bug where the guessed bounding box for datasets that do not start at (0,0,0) was too large [#3437](https://github.com/scalableminds/webknossos/pull/3437)
 - Fixed a bug where dataset list refresh failed when datasets for non-existing organizations were reported. [#3438](https://github.com/scalableminds/webknossos/pull/3438)
 - Fixed a bug where the form values when editing TaskTypes were missing [#3451](https://github.com/scalableminds/webknossos/pull/3451)

Dockerfile

@@ -11,7 +11,11 @@ COPY target/universal/stage .
 RUN addgroup --system --gid 999 webknossos \
   && adduser --system --uid 999 --ingroup webknossos webknossos \
   && mkdir disk \
-  && chown -R webknossos .
+  && chown -R webknossos . \
+  && chmod go+x bin/webknossos \
+  && chmod go+w .
+
+
 
 USER webknossos
 

README.md

@@ -1,11 +1,11 @@
 # webKnossos
-Cellular-resolution connectomics is currently substantially limited by the throughput and efficiency of data analysis. 
-Current solutions require an efficient integration of automated image analysis with massive manual data annotation. 
-To scale such annotation efforts it is decisive to be able to crowd source data analysis online. 
+Cellular-resolution connectomics is currently substantially limited by the throughput and efficiency of data analysis.
+Current solutions require an efficient integration of automated image analysis with massive manual data annotation.
+To scale such annotation efforts it is decisive to be able to crowd source data analysis online.
 Here we present **webKnossos**.
 
-> Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter  
-webKnossos: efficient online 3D data annotation for connectomics.  
+> Boergens, Berning, Bocklisch, Bräunlein, Drawitsch, Frohnhofen, Herold, Otto, Rzepka, Werkmeister, Werner, Wiese, Wissler and Helmstaedter
+webKnossos: efficient online 3D data annotation for connectomics.
 [Nature Methods (2017) DOI:10.1038/NMETH.4331.](https://www.nature.com/articles/nmeth.4331)
 
 ![webKnossos logo](https://webknossos.brain.mpg.de/assets/images/oxalis.svg)
@@ -32,16 +32,18 @@ webKnossos: efficient online 3D data annotation for connectomics.
 
 ## Development setup
 ### Docker
-This is the fastest way to try webKnossos. 
-Docker CE 17+ and Docker Compose 1.18+ is required. 
-This is only recommended for testing. 
+This is the fastest way to try webKnossos.
+Docker CE 17+ and Docker Compose 1.18+ is required.
+This is only recommended for testing.
 [For production](https://github.com/scalableminds/webknossos/wiki/Production-setup), a more elaborate setup with persistent file mounts and HTTPS reverse proxy is recommended.
 
 ```bash
-docker-compose pull webknossos
-docker-compose up webknossos
+./start-docker.sh
 ```
 
+See the [wiki](https://github.com/scalableminds/webknossos/wiki/Try-setup) for instructions on updating this try setup.
+
+
 ### Dependencies
 
 * [Oracle JDK 8+](http://www.oracle.com/technetwork/java/javase/downloads/index.html) or [Open JDK 8+](http://openjdk.java.net/) (full JDK, JRE is not enough)
@@ -124,18 +126,18 @@ See: http://www.scala-sbt.org/release/docs/Getting-Started/Setup.html
 ```bash
 sbt run
 ```
-Will fetch all Scala, Java and node dependencies and run the application on Port 9000. 
+Will fetch all Scala, Java and node dependencies and run the application on Port 9000.
 Make sure that the PostgreSQL service is running before you start sbt.
 
 ### Run on a remote machine
 ```bash
 sbt "run -Dhttp.uri=http://<remote address>:9000"
 ```
-Will fetch all Scala, Java and node dependencies and run the application on Port 9000. 
+Will fetch all Scala, Java and node dependencies and run the application on Port 9000.
 Make sure that the PostgreSQL service is running before you start sbt.
 
-Make sure to open port `9000` in your firewall. 
-This is only recommended for development purposes. 
+Make sure to open port `9000` in your firewall.
+This is only recommended for development purposes.
 See below for a recommended production setup.
 
 ## Production setup
@@ -173,7 +175,7 @@ Contact us at [[email protected]](mailto:[email protected]).
 
 ### Thanks
 * [CircleCI](https://circleci.com/gh/scalableminds/webknossos) for letting us run builds and tests on their CI
-* [Browser Stack](https://www.browserstack.com/) for letting us test WebKnossos on a variety of different devices  
+* [Browser Stack](https://www.browserstack.com/) for letting us test WebKnossos on a variety of different devices
 <a href="https://www.browserstack.com/"><img src="https://p14.zdusercontent.com/attachment/1015988/wustfygoUpQ0faC7tIiaOpJUM?token=eyJhbGciOiJkaXIiLCJlbmMiOiJBMTI4Q0JDLUhTMjU2In0..TpDEVjDPeSTDWdmL0pu6Mw.pdawodFlbAuP4ZbKn5Ucpyq69pCh3bUXv_XH_yJk7CdAzi6IIi7Az6VWriflXVKOyTWtqA8JkxqPu11s9R56jC2I5JwCc1DJILtD_j9fT4rAIth-hvnST0eA_LqBdXpRYKMHtxookA-dZ9pbvHBTFb-JG2PEKl1IXZCw5GlIRgW2Oxieg9xXtFpBN7R6_Q5yRiwuviemrK0ide1ygC8HTMDgdgdbCLuhHDDeNyluU7tR9kVtV7KZDsVd2WIBId-fSyzInofDhlk196_fHwR0WQd1pN7GDVIdfRhxTTTNWTw.g0PCM6T1kBG7AtBwKZmfzQ" width=100 alt="Browserstack Logo"></a>
 
 # License

conf/evolutions/reversions/033-tasktype-recommendedConfiguration.sql

@@ -1,7 +1,7 @@
 START TRANSACTION;
 
 DROP VIEW webknossos.taskTypes_;
-ALTER TABLE webknossos.taskTypes DROP COLUMN recommendedConfiguration JSONB;
+ALTER TABLE webknossos.taskTypes DROP COLUMN recommendedConfiguration;
 
 
 CREATE VIEW webknossos.taskTypes_ AS SELECT * FROM webknossos.taskTypes WHERE NOT isDeleted;

docker-compose.yml

@@ -7,10 +7,9 @@ services:
     ports:
       - "9000:9000"
     links:
-      - fossildb
-      - postgres
+      - fossildb-persisted
+      - postgres-persisted
     command:
-      - -Djava.io.tmpdir=disk
       - -Dconfig.file=conf/application.conf
       - -Djava.net.preferIPv4Stack=true
       - -Dhttp.address=0.0.0.0
@@ -21,10 +20,12 @@ services:
       # the following lines disable the integrated datastore:
       # - -Dplay.modules.enabled-="com.scalableminds.webknossos.datastore.DataStoreModule"
       # - -Ddatastore.enabled=false
+      # - -Dplay.http.router="noDS.Routes"
     volumes:
       - ./binaryData:/srv/webknossos/binaryData
     environment:
       - POSTGRES_URL=jdbc:postgresql://postgres/webknossos
+    user: ${USER_UID:-1000}:${USER_GID:-1000}
 
   webknossos-datastore:
     build: webknossos-datastore
@@ -168,6 +169,12 @@ services:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
 
+  postgres-persisted:
+    extends:
+      service: postgres
+    volumes:
+      - "./pg/db:/var/lib/postgresql/data/"
+
   postgres-dev:
     extends:
       service: postgres
@@ -178,25 +185,41 @@ services:
 
   psql:
     extends: postgres
-    command: psql -h postgres -U postgres webknossos
+    command: psql -h postgres-persisted -U postgres webknossos
     links:
-      - postgres
+      - postgres-persisted
+    environment:
+      PGPASSWORD: postgres
+    volumes:
+      - ./conf/evolutions/:/evolutions/
+
+  drop-db:
+    extends: postgres
+    command: psql -h postgres-persisted -U postgres postgres -c "DROP DATABASE webknossos"
+    links:
+      - postgres-persisted
     environment:
       PGPASSWORD: postgres
 
+
   fossildb:
     image: scalableminds/fossildb:master__337
     command:
       - fossildb
       - -c
-      - skeletons,skeletonUpdates,volumes,volumeData
+      - skeletons,skeletonUpdates,volumes,volumeData,volumeUpdates
     user: ${USER_UID:-fossildb}:${USER_GID:-fossildb}
 
-  fossildb-dev:
+  fossildb-persisted:
     extends:
       service: fossildb
-    ports:
-      - "7155:7155"
     volumes:
       - "./fossildb/data:/fossildb/data"
       - "./fossildb/backup:/fossildb/backup"
+
+  fossildb-dev:
+    extends:
+      service: fossildb
+    volumes:
+      - "./fossildb-dev/data:/fossildb/data"
+      - "./fossildb-dev/backup:/fossildb/backup"

start-docker.sh

@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+set -Eeuo pipefail
+
+USER_UID=$(id -u) USER_GID=$(id -g) docker-compose up webknossos