Auto import, figure, wheel, etc.

.env

@@ -0,0 +1,4 @@
+REPO=test
+PREFIX=test
+TCP_PORT=
+SSL_PORT=4064:

Dockerfile

@@ -1,8 +1,10 @@
 FROM centos:centos7
+ARG CREATED=unknown
+ARG REVISION=unknown
 LABEL maintainer="[email protected]"
-LABEL org.opencontainers.image.created="unknown"
-LABEL org.opencontainers.image.revision="unknown"
-LABEL org.opencontainers.image.source="https://github.com/openmicroscopy/omero-server-docker"
+LABEL org.opencontainers.image.created="${CREATED}"
+LABEL org.opencontainers.image.revision="${REVISION}"
+LABEL org.opencontainers.image.source="https://github.com/ome/omero-server-docker"
 
 RUN mkdir /opt/setup
 WORKDIR /opt/setup

docker-compose.yml

@@ -0,0 +1,54 @@
+version: "3.3"
+#
+# Compose for the development of this docker image
+#
+services:
+  database:
+    image: "postgres:9.6"
+    environment:
+      - POSTGRES_USER=omero
+      - POSTGRES_DB=omero
+      - POSTGRES_PASSWORD=omero
+    networks:
+      - omero
+    volumes:
+      - "database:/var/lib/postgresql/data"
+
+  minimal:
+    image: ${REPO}/omero-server-minimal:${PREFIX}
+    build:
+      context: .
+      args:
+        - OMEGO_ADDITIONAL_ARGS="--ci=https://merge-ci.openmicroscopy.org/jenkins/"
+        - OMERO_VERSION="OMERO-build"
+    entrypoint: "true"
+
+  omero:
+    image: ${REPO}/omero-server:${PREFIX}
+    build:
+      context: extended
+      args:
+        - PARENT_IMAGE=${REPO}/omero-server-minimal:${PREFIX}
+    environment:
+      - CONFIG_omero_db_host=database
+      - CONFIG_omero_db_user=omero
+      - CONFIG_omero_db_pass=omero
+      - CONFIG_omero_db_name=omero
+      - ROOTPASS=omero
+    networks:
+      - omero
+    ports:
+      - "${TCP_PORT}4063"
+      - "${SSL_PORT}4064"
+    volumes:
+      - "omero:/OMERO"
+      - "./:/src:ro"
+    depends_on:
+      - minimal
+
+networks:
+  omero:
+
+volumes:
+  database:
+  omero:

extended/95-background.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+set -eu
+
+omero=/opt/omero/server/OMERO.server/bin/omero
+cd /opt/omero/server
+echo "Running importer in the background"
+sh -c "/tools/wait-on-login && /tools/import-all" &
+echo "Starting OMERO.server"
+exec $omero admin start --foreground

extended/Dockerfile

@@ -0,0 +1,8 @@
+ARG PARENT_IMAGE=openmicroscopy/omero-server-minimal:latest
+FROM ${PARENT_IMAGE}
+
+USER root
+ADD wait-on-login import-all /tools/
+ADD 95-background.sh /startup/
+RUN mkdir /import && touch /import/test.fake
+USER omero-server

extended/import-all

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import atexit
+import os
+import socket
+import sys
+import time
+
+
+OMERO_DIST = os.environ.get("OMERO_DIST", "/opt/omero/server/OMERO.server")
+if not os.path.exists(OMERO_DIST):
+	OMERO_DIST = "/opt/omero/web/OMERO.web"
+
+sys.path.append("/".join([OMERO_DIST, "lib/python"]))
+import omero
+from omero.cli import cli_login
+from omero.util.import_candidates import as_dictionary
+
+
+OMERO_HOST = os.environ.get("OMERO_HOST", "localhost")
+OMERO_USER = os.environ.get("OMERO_USER", "root")
+OMERO_PASS = os.environ.get("OMERO_PASS", "omero")
+OMERO_PORT = int(os.environ.get("OMERO_PORT", "4064"))
+SLEEP_TIME = int(os.environ.get("SLEEP_TIME", "30"))
+
+
+with cli_login("-s", OMERO_HOST,
+               "-u", OMERO_USER,
+               "-p", str(OMERO_PORT),
+               "-w", OMERO_PASS) as cli:
+
+    for k, v in as_dictionary(("/import",)).items():
+        cli.onecmd(["import", k])

extended/wait-on-login

@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+import atexit
+import os
+import socket
+import sys
+import time
+
+
+OMERO_DIST = os.environ.get("OMERO_DIST", "/opt/omero/server/OMERO.server")
+if not os.path.exists(OMERO_DIST):
+	OMERO_DIST = "/opt/omero/web/OMERO.web"
+
+sys.path.append("/".join([OMERO_DIST, "lib/python"]))
+import omero
+
+OMERO_HOST = os.environ.get("OMERO_HOST", "localhost")
+OMERO_USER = os.environ.get("OMERO_USER", "root")
+OMERO_PASS = os.environ.get("OMERO_PASS", "omero")
+OMERO_PORT = int(os.environ.get("OMERO_PORT", "4064"))
+SLEEP_TIME = int(os.environ.get("SLEEP_TIME", "30"))
+
+
+def end():
+    print "travis_fold:end:wait-on-login"
+
+atexit.register(end)
+
+print "travis_fold:start:wait-on-login"
+
+
+def port_is_open():
+    rc = socket.socket(socket.AF_INET, socket.SOCK_STREAM).connect_ex((OMERO_HOST, OMERO_PORT))
+    return (rc == 0)
+
+
+for x in range(1, 31):
+    if port_is_open():
+        break
+    else:
+        time.sleep(1.0)
+        print "waiting on port: #%s" % x
+
+
+# HACK: This 'ready' detection is still not working. Adding a hard sleep to be safe.
+print "Sleeping for", SLEEP_TIME
+time.sleep(SLEEP_TIME)
+
+# Second: try to login
+for x in range(1, 6):
+    # https://trello.com/c/rPstbt4z/216-open-ssl-110
+    client = omero.client(OMERO_HOST, OMERO_PORT)
+    try:
+        client.createSession(OMERO_USER, OMERO_PASS)
+        break
+    except:
+        print "Login attempt %s failed. Trying again in %s seconds" % (x, x+1)
+        time.sleep(x+1)
+    finally:
+        client.__del__()

playbook.yml

@@ -4,9 +4,37 @@
   vars:
     ice_version: "3.6"
     ice_install_devel: False
+    ice_python_wheel: https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.1.0/zeroc_ice-3.6.4-cp27-cp27mu-linux_x86_64.whl
     omero_server_database_manage: False
     omero_server_systemd_setup: False
     omero_server_system_uid: 1000
-    # You can reduce the size of the image by providing the URL to a
-    # precompiled Ice Python wheel
-    #ice_python_wheel:
+
+  # TODO: copied from https://github.com/openmicroscopy/prod-playbooks/blob/bd5b837c740ae79806d911893ace38701c204381/ome-dundeeomero.yml
+  # Should be part of a figure-server role
+  tasks:
+    - name: OMERO.figure server-side prerequisites, script prerequisites + web server for decoupled OMERO.web
+      become: yes
+      yum:
+        name: "{{ item }}"
+        state: present
+      with_items:
+        - python-reportlab
+        - python-markdown
+
+    - name: Create a figure scripts directory
+      become: yes
+      file:
+        path: /opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts
+        state: directory
+        mode: 0755
+        recurse: yes
+        owner: root
+
+    - name: Download the Figure_To_Pdf.py script
+      become: yes
+      get_url:
+        url: https://raw.githubusercontent.com/ome/omero-figure/{{ omero_figure_tag | default("master") }}/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
+        dest: /opt/omero/server/OMERO.server/lib/scripts/omero/figure_scripts/Figure_To_Pdf.py
+        mode: 0644
+        owner: root
+        checksum: "{{ omero_figure_pdfscript_checksum | default(omit) }}"