Fix bugs for liberty tools

README.md

@@ -1,31 +1,30 @@
-# Galaxy Show and Tell
+# MCFE Galaxy
 
-This repository serves as an example for RSEs to self host Galaxy. The repository contains a `docker-compose.yml` file that can be used to start a Galaxy instance with a few tools pre-installed.
+## Triggering events
 
-Some guides are given below to help you get started!
+Randall includes services which listen for events on a MQTT broker. 
+These events cause further events to be triggered which may include:
+- updating the metadata in Fuseki
+- running workflows on Galaxy
 
-If you are interested in some context for this repo some slides [are available](https://uomresearchit.github.io/Galaxy-Show-And-Tell/).
+To see an example of this in action you can run the following command:
 
-## Tutorials
+```bash
+mosquitto_pub -u {{YOUR_USER}} -P {{YOUR_PASS}} -t '/parameter/update/01234' -m '{"MajorRadius": "8.5"}
+```
 
-[Tutorial: From bootstrap to workflows! Getting started with Galaxy](docs/getting-started.md)
+If you want to see the logs of the Crater service, you can do so by running:
 
-## How to guides
+```bash
+mosquitto_sub -u {{YOUR_USER}} -P {{YOUR_PASS}} -t '/#' -v
+```
 
-[How to: Add tools to your Galaxy](docs/add-tools.md)
+## Useful web interfaces
 
-[How to: Add public workflows your Galaxy](docs/add-workflows.md)
-
-## Useful resources 
-
-The best introductions to Galaxy are given by the Galaxy project itself. You may choose to start your Galaxy journey by reading the following:
-[Introduction to Galaxy Analyses](https://training.galaxyproject.org/training-material/topics/introduction/)
-
-If you are an RSE looking to develop tooling for Galaxy then generic documentation can be found at: [Developing Galaxy Tools](https://training.galaxyproject.org/training-material/topics/dev/#st-tooldev)
-
-You could also explore the Galaxy training material for coaching Galaxy administrators, however, this is not necessary to get started and the techniques may not necessarily apply to a self-hosted instance (the Galaxy Training Network assume deployment through Ansible, we use Docker Compose).
-https://training.galaxyproject.org/training-material/topics/admin/
-
-## Technical reference
-
-The `.env` file is self documented via the `env.template` file. 
+Randall is made of serveral tools which provide web interfaces. These include:
+- Fuseki: http://fuseki.localhost (default username: `admin`, default password: `admin`)
+  * This is a triplestore which stores the metadata
+- Galaxy: http://galaxy.localhost (username and password from .env file)
+  * This is a workflow manager which runs workflows
+- Traefik: http://localhost:8888 (no authentication)
+  * This is a reverse proxy which routes traffic to the appropriate service

docker-compose.yml → compose.yaml

@@ -26,10 +26,11 @@ services:
         USER root
         RUN apt update && apt -y install docker.io
         USER galaxy
-        COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+        COPY --from=ghcr.io/astral-sh/uv:0.8.15 /uv /uvx /bin/
         ENV HOME=/tmp
         ENV UV_CACHE=/tmp/uv_cache
-        RUN uv add boto3
+        RUN sed -i '/wheels.galaxyproject.org/d' pyproject.toml
+        RUN uv add boto3 --index https://pypi.org/simple
     restart: unless-stopped
     group_add:
       - ${DOCKER_GID}
@@ -49,8 +50,9 @@ services:
       - ./galaxy/tusd:/usr/local/sbin/tusd
       # Populate the instance
       - ./galaxy/tools:/galaxy/server/tools/
+      - ./galaxy/lib/mcfe_datatypes.py:/galaxy/server/lib/galaxy/datatypes/mcfe_datatypes.py
       # Add custom configuration files
-      - ./galaxy/config/tool_conf.xml:/galaxy/server/config/tool_conf.xml.sample
+      - ./galaxy/config/tool_conf.xml:/galaxy/server/config/tool_conf.xml
       - ./galaxy/config/datatypes_conf.xml:/galaxy/server/config/datatypes_conf.xml
       # Provide docker-in-docker
       - /var/run/docker.sock:/var/run/docker.sock:ro
@@ -86,11 +88,13 @@ services:
     build:
       context: .
       dockerfile_inline: |
-        FROM alpine:3.22
-        RUN apk update && apk add gettext bash
+        FROM ubuntu:22.04
+        RUN apt update && apt install -y gettext
         COPY ./galaxy/init/template.sh /template.sh
     container_name: ${PROJECT_NAME}-galaxy-template-eval
     env_file: .env
+    environment:
+      REPO_PATH: ${PWD}
     volumes:
       - ./galaxy/config/:/work
       - galaxy-store:/galaxy/server/
@@ -146,7 +150,6 @@ services:
       minio:
         condition: service_healthy
     volumes:
-      - ./minio/init/bootstrap.sh:/bootstrap.sh
       - ./minio/data:/data:ro      
     networks:
       - galaxy

env.template

@@ -6,9 +6,6 @@
 # ------------------------------------------------------------------------------
 # Parameters to configure the Galaxy instance
 
-# The path to this repo
-REPO_PATH=/home/owool/Projects/2025/RSE-Galaxy
-
 # The group ID of the docker group on the host machine, to allow the Galaxy
 # container to access the docker socket.
 
@@ -23,7 +20,8 @@ GALAXY_ADMIN_PASS={{adminadmin}}
 GALAXY_API_KEY={{iamanadminyouknow}}
 
 # Galaxy config
-GALAXY_VERSION=25.0.2
+GALAXY_VERSION={{25.0.2}}
+GALAXY_URL={{https://mygalaxy.org}}
 
 # ------------------------------------------------------------------------------
 # General configuration parameters

galaxy/config/datatypes_conf.xml

@@ -694,6 +694,10 @@
     <datatype extension="oxligl" type="galaxy.datatypes.binary:OxliGraphLabels" mimetype="application/octet-stream" display_in_upload="true"/>
     <!-- Constructive solid geometry datatypes -->
     <datatype extension="stl" type="galaxy.datatypes.constructive_solid_geometry:STL" display_in_upload="true"/>
+    <datatype extension="vtu" type="galaxy.datatypes.mcfe_datatypes:vtu" display_in_upload="true" />
+    <datatype extension="pvtu" type="galaxy.datatypes.mcfe_datatypes:pvtu" display_in_upload="true"/>
+    <datatype extension="vtp" type="galaxy.datatypes.mcfe_datatypes:vtp" display_in_upload="true"/>
+
     <datatype extension="plyascii" type="galaxy.datatypes.constructive_solid_geometry:PlyAscii" display_in_upload="true"/>
     <datatype extension="plybinary" type="galaxy.datatypes.constructive_solid_geometry:PlyBinary" display_in_upload="true"/>
     <datatype extension="vtkascii" type="galaxy.datatypes.constructive_solid_geometry:VtkAscii" display_in_upload="true"/>

galaxy/config/galaxy.yml.template

@@ -2,17 +2,16 @@ gravity:
   gunicorn:
     bind: 0.0.0.0:8080
     workers: 2
-    extra_ars: '--forwarded-allow-ips="*"'
+    extra_args: '--forwarded-allow-ips="*"'
     preload: true
   celery:
     concurrency: 2
     loglevel: WARNING
   tusd:
     enable: true
-    host: 0.0.0.0
-    port: 1080
     tusd_path: /usr/local/sbin/tusd
     upload_dir: /galaxy/server/data/tus/
+    extra_args: '-verbose'
   # handlers:
   #   handler:
   #     processes: 2
@@ -28,12 +27,15 @@ gravity:
 
 galaxy:
   # Main config
-  admin_users:
-   - admin@example.org
+  admin_users: admin@example.org
   bootstrap_admin_api_key: '$GALAXY_API_KEY'
   id_secret: 'morestufftoreplace'
   log_level: WARNING
 
+  # Use remote users
+  use_remote_user: true
+  remote_user_maildomain: example.org
+
   # Watch file changes 
   watch_tools: 'true'
   watch_job_rules: 'true'
@@ -61,7 +63,7 @@ galaxy:
   new_user_dataset_access_role_default_private: true
 
   # TUS
-  galaxy_infrastructure_url: "http://localhost:8080"
+  galaxy_infrastructure_url: "$GALAXY_URL"
   tus_upload_store: /galaxy/server/data/tus/
 
   # SQL Performance
@@ -75,7 +77,6 @@ galaxy:
   retry_job_output_collection: 3
 
   # Debugging
-  cleanup_job: onsuccess
   allow_user_impersonation: true
 
   # Object Store
@@ -117,7 +118,7 @@ galaxy:
   shed_data_manager_config_file: /galaxy/server/config/shed_data_manager_conf.xml
   shed_tool_config_file: /galaxy/server/config/shed_tool_conf.xml
   shed_tool_data_table_config: /galaxy/server/config/shed_tool_data_table_conf.xml
-  tool_config_file: /galaxy/server/config/tool_conf.xml.sample
+  tool_config_file: /galaxy/server/config/tool_conf.xml
   job_config_file: /galaxy/server/config/job_conf.xml
   tool_data_path: /galaxy/server/database/tool_data
   tool_data_table_config_path: /galaxy/server/config/tool_data_table_conf.xml.sample

galaxy/config/job_conf.xml.template

@@ -20,11 +20,16 @@
     </destination>
     <destination id="docker_root" runner="local">
       <param id="docker_enabled">true</param>
-      <param id="docker_volumes">galaxy-store:/galaxy/server</param>
-      <param id="docker_sudo">true</param>
+      <param id="docker_volumes">galaxy-store:/galaxy/server,$REPO_PATH/galaxy/tools:/galaxy/server/tools</param>
+      <param id="docker_sudo">false</param>
+      <param id="docker_set_user">0</param>
       <param id="docker_auto_rm">true</param> 
+      <param id="docker_run_extra_arguments">--entrypoint '' --env PATH=/opt/openmpi/bin:/opt/rh/gcc-toolset-12/root/usr/bin:$PATH </param>
+
     </destination>
   </destinations>
   <tools>
+   <tool id="tmap8" destination="docker_root" />
+   <tool id="moose" destination="docker_root" />
   </tools>
 </job_conf>

galaxy/config/tool_conf.xml

@@ -60,4 +60,80 @@
     <tool file="plotting/boxplot.xml" hidden="true" />
     <tool file="maf/vcf_to_maf_customtrack.xml" />
   </section>
+  <section id="MCFE_OpenMC" name="MCFE OpenMC Tools">
+    <tool file="openmc/openmc.xml" />
+  </section>
+  <section id="MCFE_CAD_Converters" name="MCFE CAD Converters">
+    <tool file="USD_to_h5m/USD_to_h5m.xml" />
+    <tool file="h5m_to_vtk/h5m_to_vtk.xml" />
+    <tool file="obj_to_USD/obj_to_USD.xml" />
+    <tool file="vtp_to_obj/vtp_to_obj.xml" />
+    <tool file="stp_to_stl/stp_to_stl.xml" />
+    <tool file="stl_to_h5m/stl_to_h5m.xml" />
+    <tool file="h5m_to_stl/h5m_to_stl.xml" />
+    <tool file="stl_to_obj/stl_to_obj.xml" />
+    <tool file="tracks_to_vtp/tracks_to_vtp.xml" />
+  </section>
+  <section id="MCFE_Other_Converters" name="MCFE Converter Tools">
+    <tool file="normalise_tallies/normalise_tallies.xml" />
+    <tool file="h5m_materials/h5m_materials.xml" />
+    <tool file="flatten_USD/flatten_USD.xml" />
+    <tool file="extract_openmc_tallies/extract_openmc_tallies.xml" />
+    <tool file="json_string_to_file/json_string_to_file.xml" />
+    <tool file="json_file_to_string/json_file_to_string.xml" />
+  </section>
+  <section id="MCFE_Parametric_Tools" name="MCFE Parametric Tools">
+    <tool file="capella_paramak_generator/capella_paramak_generator.xml" />
+    <tool file="capella_openmc/capella_openmc.xml" />
+  </section>
+  <section id="MCFE_PINN_Tools" name="MCFE PINN Tools">
+    <tool file="heatflux_to_PINN/heatflux_to_PINN.xml" />
+    <tool file="paramak_to_PINN/paramak_to_PINN.xml" />
+    <tool file="sample_points_PINN/sample_points_PINN.xml" />
+    <tool file="visualisation_PINN/visualisation_PINN.xml" />
+    <tool file="modulus/modulus.xml" />
+  </section>
+  <section id="MCFE_Data" name="MCFE Data">
+    <tool file="minio_push/minio_push.xml" />
+    <tool file="minio_pull/minio_pull.xml" />
+  </section>
+  <section id="MCFE_Unstructured_Mesh_Tools" name="MCFE Unstructured Mesh Tools">
+    <tool file="unstructured_convert_heating/unstructured_convert_heating.xml" />
+    <tool file="unstructured_mesh_openmc/unstructured_mesh_openmc.xml" />
+    <tool file="unstructured_heatflux_to_PINN/unstructured_heatflux_to_PINN.xml" />
+  </section>
+  <section id="MCFE_Misc" name="MCFE Misc Tools">
+    <tool file="save-output-rocrate/save_output_rocrate.xml" />
+    <tool file="tile_paramak/tile_paramak.xml" />
+    <tool file="tile_openmc/tile_openmc.xml" />
+    <tool file="trained_PINN/trained_PINN.xml" />
+    <tool file="MQTT_pub/MQTT_pub.xml" />
+  </section>
+  <section id="MCFE_Deprecated" name="MCFE Deprecated Tools">
+    <tool file="paramak_generator/paramak_generator.xml" />
+    <tool file="openmc_parametric/openmc_parametric.xml" />
+    <tool file="paramak_generator_noplasma/paramak_generator_noplasma.xml" />
+  </section>
+  <section id="nTtau_Tools" name="nTtau Digital Tools">
+    <tool file="containment_vessel/containment_vessel.xml" />
+    <tool file="cylinder_gen/cylinder_gen.xml" />
+    <tool file="CylinderBCMesh/CylinderBCMesh.xml" />
+    <tool file="get_bounding_box/get_bounding_box.xml" />
+    <tool file="sphere_gen/sphere_gen.xml" />
+    <tool file="sphereBCMesh/sphereBCMesh.xml" />
+    <tool file="step_to_vtk/step_to_vtk.xml" />
+    <tool file="tokamak_gen/tokamak_gen.xml" />
+  </section>
+  <section id="LIBRTI_Tools" name="LIBRTI Tools">
+    <tool file="moose/moose.xml" />
+    <tool file="tmap8/tmap8.xml" />
+    <tool file="moose_postprocess/moose_postprocess.xml" />
+    <tool file="tmap_postprocess/tmap_postprocess.xml" />
+    <tool file="create_sample_msh/create_sample_msh.xml" />
+    <tool file="tmap_extract_flow/tmap_extract_flow.xml" />
+    <tool file="upload_file_to_nucleus/upload_file_to_nucleus.xml" />
+  </section>
+  <section id="Test" name="Test Tools">
+    <tool file="test.xml" />
+  </section>
 </toolbox>

galaxy/lib/mcfe_datatypes.py

@@ -0,0 +1,74 @@
+"""
+Classes for MCFE added datatypes
+"""
+
+from galaxy.datatypes import data
+from galaxy.datatypes.metadata import MetadataElement
+
+import os
+import logging
+
+log = logging.getLogger(__name__)
+
+class vtp(data.Data):
+    file_ext = "vtp"
+
+class vtk(data.Data):
+    file_ext = "vtk"
+
+class vtu(data.Data):
+    file_ext = "vtu"
+
+class pvtu(data.Data):
+    file_ext = "pvtu"
+
+class usd(data.Data):
+    file_ext = "usd"
+
+class usda(data.Data):
+    file_ext = "udsa"
+
+class usdc(data.Data):
+    file_ext = "usdc"
+
+class usdz(data.Data):
+    file_ext = "usdz"
+
+class obj(data.Data):
+    file_ext = "obj"
+
+class stp(data.Data):
+    file_ext = "stp"
+
+class step(data.Data):
+    file_ext = "step"
+
+class h5(data.Data):
+    file_ext = "h5"
+
+class h5m(data.Data):
+    file_ext = "h5m"
+
+class out(data.Data):
+    file_ext = "out"
+
+class xml(data.Data):
+    file_ext = "xml"
+
+class stl(data.Data):
+    file_ext = "stl"
+
+class npz(data.Data):
+    file_ext = "npz"
+
+class yaml(data.Data):
+    file_ext = "yaml"
+
+class odb(data.Data):
+    file_ext = "odb"
+
+class inp(data.Data):
+    file_ext = "inp"
+
+class pth(data.Data):
+    file_ext = "pth"