From bea5e9b99009c6490fef4ddb817a0274b0b64914 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 11:30:37 +0000 Subject: [PATCH 01/17] switch to rocky9 --- Dockerfile | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index 75de8ed..7e33628 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM centos:centos7.9.2009@sha256:be65f488b7764ad3638f236b7b515b3678369a5124c47b8d32916d6487418ea4 +FROM rockylinux:9 LABEL maintainer="ome-devel@lists.openmicroscopy.org.uk" ENV LANG en_US.utf-8 @@ -7,10 +7,9 @@ RUN mkdir /opt/setup WORKDIR /opt/setup ADD playbook.yml requirements.yml /opt/setup/ -RUN yum -y install epel-release \ - && yum -y install ansible sudo \ +RUN dnf -y install ansible sudo \ && ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ - && yum -y clean all \ + && dnf -y clean all \ && rm -fr /var/cache RUN ansible-playbook playbook.yml \ @@ -18,7 +17,7 @@ RUN ansible-playbook playbook.yml \ && rm -fr /var/cache RUN curl -L -o /usr/local/bin/dumb-init \ - https://github.com/Yelp/dumb-init/releases/download/v1.2.0/dumb-init_1.2.0_amd64 && \ + https://github.com/Yelp/dumb-init/releases/download/v1.2.5/dumb-init_1.2.5_amd64 && \ chmod +x /usr/local/bin/dumb-init ADD entrypoint.sh /usr/local/bin/ ADD 50-config.py 60-default-web-config.sh 98-cleanprevious.sh 99-run.sh /startup/ From cd679664b32ce330b98cf6a7957e04ceb08146d1 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 11:33:26 +0000 Subject: [PATCH 02/17] update roles --- requirements.yml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/requirements.yml b/requirements.yml index a113d60..5ec1fc4 100644 --- a/requirements.yml +++ b/requirements.yml @@ -1,13 +1,14 @@ # External Ansible roles required by this repository - name: ome.basedeps - version: 1.2.0 + src: https://github.com/pwalczysko/ansible-role-basedeps/ + version: fix-repo-rhel - src: ome.java - version: 2.1.0 + version: 2.2.0 - src: ome.omero_common - version: 0.3.4 + version: 0.4.0 - name: ome.omero_web - version: 4.0.1 + version: 5.0.0 From 1010a9cf1a4df5d690bf7c463d55d073162f4273 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 12:39:50 +0000 Subject: [PATCH 03/17] set local --- Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7e33628..2bfe63b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,12 +1,15 @@ FROM rockylinux:9 LABEL maintainer="ome-devel@lists.openmicroscopy.org.uk" -ENV LANG en_US.utf-8 RUN mkdir /opt/setup WORKDIR /opt/setup ADD playbook.yml requirements.yml /opt/setup/ +RUN dnf -y install epel-release +RUN dnf install -y glibc-langpack-en +ENV LANG en_US.utf-8 + RUN dnf -y install ansible sudo \ && ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ && dnf -y clean all \ From 6598b78a730f879f591f60ec0b284a8d0d2a8e38 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 12:59:14 +0000 Subject: [PATCH 04/17] remove ice --- playbook.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/playbook.yml b/playbook.yml index 99121a4..5e622a9 100644 --- a/playbook.yml +++ b/playbook.yml @@ -3,10 +3,6 @@ - role: ome.omero_web - role: ome.java vars: - ice_version: "3.6" - ice_install_devel: False - ice_install_python: 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_web_systemd_setup: False omero_web_setup_nginx: False # These defaults can be overriden at runtime From e0f32a730ac99f8c4183604c0b56ae11d5682122 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 13:48:11 +0000 Subject: [PATCH 05/17] use interpreter --- Dockerfile | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2bfe63b..0a37a71 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,13 +10,15 @@ RUN dnf -y install epel-release RUN dnf install -y glibc-langpack-en ENV LANG en_US.utf-8 -RUN dnf -y install ansible sudo \ - && ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ +RUN dnf -y install ansible sudo + + +RUN ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ && dnf -y clean all \ && rm -fr /var/cache -RUN ansible-playbook playbook.yml \ - && yum -y clean all \ +RUN ansible-playbook playbook.yml -e 'ansible_python_interpreter=/usr/bin/python3' \ + && dnf -y clean all \ && rm -fr /var/cache RUN curl -L -o /usr/local/bin/dumb-init \ From 4c7a6cd75450491d8b04e61bb2255680c9235c34 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 13:48:40 +0000 Subject: [PATCH 06/17] install omero tagging/tagsearch from new account --- standalone/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/standalone/Dockerfile b/standalone/Dockerfile index 9fc8655..7294780 100644 --- a/standalone/Dockerfile +++ b/standalone/Dockerfile @@ -10,8 +10,8 @@ RUN /opt/omero/web/venv3/bin/pip install \ omero-fpbioimage \ omero-mapr \ omero-parade \ - omero-webtagging-autotag \ - omero-webtagging-tagsearch \ + omero-autotag \ + omero-tagsearch \ whitenoise ADD 01-default-webapps.omero /opt/omero/web/config/ From a374fae10eb39e9c1e265387edad093cdc91cd24 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Wed, 15 Nov 2023 13:55:51 +0000 Subject: [PATCH 07/17] configure autotag and tagsearch --- standalone/01-default-webapps.omero | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/standalone/01-default-webapps.omero b/standalone/01-default-webapps.omero index bf9e702..d928887 100644 --- a/standalone/01-default-webapps.omero +++ b/standalone/01-default-webapps.omero @@ -20,5 +20,15 @@ config append -- omero.web.mapr.config '{"menu": "anyvalue", "config":{"default" config append -- omero.web.apps '"omero_parade"' config append -- omero.web.ui.center_plugins '["Parade", "omero_parade/init.js.html", "omero_parade"]' +# Add autotag to webclient +config append omero.web.apps '"omero_autotag"' +config append omero.web.ui.center_plugins '["Auto Tag", "omero_autotag/auto_tag_init.js.html", "auto_tag_panel"]' + +# Add tagsearch to webclient +config append omero.web.apps '"omero_tagsearch"' + + # Top links config set -- omero.web.ui.top_links '[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}],["History", "history", {"title": "History"}], ["Mapr", {"viewname": "maprindex_anyvalue"}, {"title": "Find Any Value"}], ["Figure", "figure_index", {"title": "Open Figure in new tab", "target": "_blank"}], ["Help", "https://help.openmicroscopy.org/", {"title":"Open OMERO user guide in a new tab", "target":"new"}]]' + +config append omero.web.ui.top_links '["Tag Search", "tagsearch"]' From 1ed12c5f4b1963a13abbae1f7d75b1b1741f78f8 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 16 Nov 2023 09:38:01 +0000 Subject: [PATCH 08/17] fix install --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0a37a71..d8db502 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,8 +21,9 @@ RUN ansible-playbook playbook.yml -e 'ansible_python_interpreter=/usr/bin/python && dnf -y clean all \ && rm -fr /var/cache + RUN curl -L -o /usr/local/bin/dumb-init \ - https://github.com/Yelp/dumb-init/releases/download/v1.2.5/dumb-init_1.2.5_amd64 && \ + https://github.com/Yelp/dumb-init/releases/download/v1.2.5/dumb-init_1.2.5_x86_64 && \ chmod +x /usr/local/bin/dumb-init ADD entrypoint.sh /usr/local/bin/ ADD 50-config.py 60-default-web-config.sh 98-cleanprevious.sh 99-run.sh /startup/ From 726461791dc4d4cf004e8376da9dfc2f75031ad0 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 16 Nov 2023 21:51:58 +0000 Subject: [PATCH 09/17] remove dependency already included in omero-web role --- requirements.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements.yml b/requirements.yml index 5ec1fc4..dfa2488 100644 --- a/requirements.yml +++ b/requirements.yml @@ -7,8 +7,5 @@ - src: ome.java version: 2.2.0 -- src: ome.omero_common - version: 0.4.0 - - name: ome.omero_web version: 5.0.0 From 8ca5b565876ed03b745dd227f9d16b76ad547d34 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Fri, 17 Nov 2023 11:14:45 +0000 Subject: [PATCH 10/17] do not install from git repo --- requirements.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/requirements.yml b/requirements.yml index dfa2488..94f7bf8 100644 --- a/requirements.yml +++ b/requirements.yml @@ -1,9 +1,4 @@ # External Ansible roles required by this repository - -- name: ome.basedeps - src: https://github.com/pwalczysko/ansible-role-basedeps/ - version: fix-repo-rhel - - src: ome.java version: 2.2.0 From d95d7b9d1f38643972846c4e2dcf47f9e6f13c0a Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 20 Nov 2023 09:38:53 +0000 Subject: [PATCH 11/17] review installation of ansible --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d8db502..8bcb0d1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,7 +10,7 @@ RUN dnf -y install epel-release RUN dnf install -y glibc-langpack-en ENV LANG en_US.utf-8 -RUN dnf -y install ansible sudo +RUN dnf -y install ansible-core sudo RUN ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ From dea566429788053e12365ec5c3a74701f52c860b Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 20 Nov 2023 10:03:30 +0000 Subject: [PATCH 12/17] add ansible.posix --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8bcb0d1..433768e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,7 @@ RUN dnf install -y glibc-langpack-en ENV LANG en_US.utf-8 RUN dnf -y install ansible-core sudo - +RUN ansible-galaxy collection install ansible.posix RUN ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ && dnf -y clean all \ From 8d638b31cf27a10797de884e82374599aa784bfa Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Mon, 20 Nov 2023 10:25:19 +0000 Subject: [PATCH 13/17] install community.general --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 433768e..428f470 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,6 +12,7 @@ ENV LANG en_US.utf-8 RUN dnf -y install ansible-core sudo RUN ansible-galaxy collection install ansible.posix +RUN ansible-galaxy collection install community.general RUN ansible-galaxy install -p /opt/setup/roles -r requirements.yml \ && dnf -y clean all \ From 14e9d8e8e828642eb43905670c208e61297eea52 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 5 Dec 2023 13:44:17 +0000 Subject: [PATCH 14/17] update url --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index c67a111..594732e 100644 --- a/README.md +++ b/README.md @@ -29,8 +29,8 @@ This image also includes these OMERO.web plugins with a default configuration: The following plugins are installed but disabled: - [fpbioimage](https://pypi.org/project/omero-fpbioimage/) -- [autotag](https://pypi.org/project/omero-webtagging-autotag/) -- [tagsearch](https://pypi.org/project/omero-webtagging-tagsearch/) +- [autotag](https://pypi.org/project/omero-autotag/) +- [tagsearch](https://pypi.org/project/omero-webtagging-tagsearch) To enable them or to change the configuration of a default plugin see the relevant plugin documentation. From 11dc2d555438cdc1a79b9a07b721609b9fc4674d Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 5 Dec 2023 13:46:11 +0000 Subject: [PATCH 15/17] change base image in doc --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 594732e..657dd1b 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ OMERO.web Docker [![Actions Status](https://github.com/ome/omero-web-docker/workflows/Build/badge.svg)](https://github.com/ome/omero-web-docker/actions) -A CentOS 7 based Docker image for OMERO.web. +A RockyLinux 9 based Docker image for OMERO.web. Also see [SUPPORT.md](./SUPPORT.md) From 654bd820dc4508ecf5d47a51a3f07fb3b5edc952 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 5 Dec 2023 13:47:16 +0000 Subject: [PATCH 16/17] adjust example --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 657dd1b..a3c0eed 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,7 @@ To enable them or to change the configuration of a default plugin see the releva To run the Docker image you can set a single OMERO.server to connect to by defining `OMEROHOST`: - docker run -d --name omero-web \ + docker run -d --name omero-web-standalone \ -e OMEROHOST=omero.example.org \ -p 4080:4080 \ openmicroscopy/omero-web-standalone From cc49fa99b8b8bdf3ea21110edd2d3980fb901c74 Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Tue, 5 Dec 2023 13:50:48 +0000 Subject: [PATCH 17/17] clean up --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a3c0eed..fa15de1 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Also see [SUPPORT.md](./SUPPORT.md) Running OMERO with docker-compose --------------------------------- - The [omero-deployment-examples repository](https://github.com/ome/omero-deployment-examples/) repository +The [omero-deployment-examples repository](https://github.com/ome/omero-deployment-examples/) repository contains a number of different ways of deployment OMERO. Unless you are looking for something specific, *we suggest starting with [docker-example-omero](https://github.com/ome/docker-example-omero).* @@ -26,11 +26,12 @@ This image also includes these OMERO.web plugins with a default configuration: - [iviewer](https://www.openmicroscopy.org/omero/iviewer/) - [mapr](https://pypi.org/project/omero-mapr/) - [parade](https://pypi.org/project/omero-parade/) +- [autotag](https://pypi.org/project/omero-autotag/) +- [tagsearch](https://pypi.org/project/omero-webtagging-tagsearch) The following plugins are installed but disabled: - [fpbioimage](https://pypi.org/project/omero-fpbioimage/) -- [autotag](https://pypi.org/project/omero-autotag/) -- [tagsearch](https://pypi.org/project/omero-webtagging-tagsearch) + To enable them or to change the configuration of a default plugin see the relevant plugin documentation.