Cleanup and config change for GPhL-specific file

dev/Ubuntu_qt5/Dockerfile

@@ -0,0 +1,44 @@
+FROM ubuntu:focal
+
+# Set terminal and time zone, to catch installer interactoin attempts
+ENV TERM linux
+ENV TZ Europe/London
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+
+# Install system packages - from Marcus O mxcub3
+RUN apt-get update && apt-get -y upgrade && \
+    apt-get install -y apt-utils curl git sudo wget python
+RUN apt-get install -y build-essential
+
+# Install 'top-level' packages
+RUN apt-get install -y python3-scipy
+RUN apt-get install -y python3-pyqtgraph
+
+# NB numpy, matplotlib, Pillow, PyQt5, and sip
+# are installed at this point
+
+# Get and update pip
+RUN apt-get install python3-pip -y
+RUN pip install --upgrade pip
+
+# From requirement list
+#RUN pip install greenlet==0.4.16
+#RUN pip install gevent==1.3.7
+RUN pip install gevent
+RUN pip install suds-py3
+RUN pip install jsonpickle
+RUN pip install ruamel.yaml
+RUN pip install PyDispatcher
+RUN pip install pylint
+RUN pip install lxml
+RUN pip install jsonschema
+
+# Global Phasing requirements
+# Python-Java bridge - needed for GPhL workflow:
+# Install as root, otherwise not found in xml parsing
+#RUN pip install py4j==0.10.6
+RUN pip install py4j
+# Needed for GPhL simcal and stratcal
+RUN pip install f90nml
+# Needed for GPhL stratcal rotation matrices
+RUN pip install mgen

dev/gphl/Debian9_qt4/Dockerfile

@@ -1,10 +1,23 @@
-FROM mx3_deb9_qt4
+FROM mx3_deb9b_qt4
 
 RUN apt-get update
 
 RUN apt-get install python-pip -y
 RUN pip install --upgrade pip
 
+# To get rid of error, that the ps command cannot be found
+RUN apt-get install procps -y
+
+# Additional requirements - temporarily put here
+RUN apt-get install python-jsonschema -y
+RUN apt-get install python-pyqtgraph -y
+
+# Needed for new configuration from July 2019
+RUN pip install ruamel.yaml
+
+# Not used by gphl in dockers, but avoids constant error message
+RUN pip install redis
+
 # Python-Java bridge - needed for GPhL workflow:
 # Install as root, otehrwise not found in xml parsing
 RUN pip install py4j
@@ -18,20 +31,21 @@ RUN pip install mgen
 
 # Add user and group so files on main machine get to belong to user instead of root
 # NB this must be adjusted to the test user. TODO move to separate docker
-RUN groupadd -g 3001 gphl
+# RUN groupadd -g 3001 gphl
 #RUN useradd -g gphl -m -s /bin/tcsh -u 1158 rhfogh
 # No longer makes home directory - this must be mounted externally at startup
-RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
+# RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
 
 # Directories:
 #
 # /MXCuBE/mxcube - MXCuBE code location is made in mx3_deb9_qt4
 #
 # GPhL code locations. Name is should match external directory structure,
 # so that the same directory names work inside and outside the docker.
-RUN mkdir -p /archive
-RUN mkdir -p /scratch_fs1
-RUN mkdir -p /public/xtal
+# RUN mkdir -p /archive
+# RUN mkdir -p /scratch_fs1
+# RUN mkdir -p /public/xtal
+RUN mkdir -p /mnt/scrstch
 
 
 # Used instead of Entrypoint to allow alternative commands to be run

dev/gphl/Debian9_qt4/start_mxcube2

@@ -1,18 +1,21 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl2
+CONTAINER=mx3_deb9_qt4_gphl5
 
 # The following variables should be checked and (re)set as needed
 
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
-# HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+HO_CONFIGURATION=${HO_SERVER}/configuration
+# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/embl_hh_p14"
-CUSTOM_HARDWARE_OBJECTS_PATH=""
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address
@@ -21,8 +24,9 @@ CUSTOM_BRICKS_PATH=""
 MAC_ADDRESS="54:ee:75:b6:8e:d3"
 #
 # User for docker - for giving correct file ownership.
-# DOCKER_USER_ID="1000:100"
-DOCKER_USER_ID="1158:3001"
+DOCKER_USER_ID="1000:100"
+# DOCKER_USER_ID="1158:3001"
+# CONSIDER SOMETHING LKE --user $(id -u):$(id -g)
 # User name - used only for file names etc.
 USER_NAME="test_user"
 
@@ -38,18 +42,20 @@ OUTPUT_HOME="/home/rhfogh/dockerhome/"
 # GPHL-specific directories for mounting
 # Note: These are the same from insisde and outside the docker
 # and so must be either identical or used on only one side.
-GPHL_RELEASE_ROOT="/public/xtal/"
-GPHL_SETUP_ROOT="/archive/rhfogh/mxcube/"
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/GPhL/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/GPhL/mxcube_setup/"
 
 # Location for output data - must be the same inside and outside docker
-DATA_ROOT="/scratch_fs1/"
+DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
 
 
 # End of settable parameters.
 
 
 xhost +local:
 # Command needed to run GPhL workflows
+# Add in this for debug
+# -p 8050:8050 \
 exec docker run -it \
 --mac-address $MAC_ADDRESS \
 -p 25333:25333 \

dev/gphl/Ubuntu_focal_qt5/Dockerfile

@@ -0,0 +1,25 @@
+FROM ubuntu_focal_qt5
+
+RUN apt-get update
+
+RUN mkdir -p /MXCuBE
+WORKDIR /MXCuBE
+
+# Add user and group so files on main machine get to belong to user instead of root
+# NB this must be adjusted to the test user. TODO move to separate docker
+# RUN groupadd -g 3001 gphl
+#RUN useradd -g gphl -m -s /bin/tcsh -u 1158 rhfogh
+# No longer makes home directory - this must be mounted externally at startup
+# RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
+
+# Directories:
+#
+# GPhL code locations. Name is should match external directory structure,
+# so that the same directory names work inside and outside the docker.
+# RUN mkdir -p /archive
+# RUN mkdir -p /scratch_fs1
+# RUN mkdir -p /public/xtal
+RUN mkdir -p /mnt/scratch
+
+# Used instead of Entrypoint to allow alternative commands to be run
+CMD ["python3",  "/MXCuBE/mxcube/mxcubeqt/__main__.py", "--pyqt5", "--mockupMode"]

dev/gphl/Ubuntu_focal_qt5/start_mxcube

@@ -0,0 +1,75 @@
+#!/usr/bin/env bash
+
+CONTAINER=mxcube_ubuntu_focal_qt5
+
+# The following variables should be checked and (re)set as needed
+#
+MXCUBE_BASE="/MXCuBE"
+MXCUBE_CORE="${MXCUBE_BASE}/mxcubecore/mxcubecore"
+CUSTOM_BRICKS_PATH=""
+CUSTOM_HARDWARE_OBJECTS_PATH="${MXCUBE_CORE}/HardwareObjects/mockup"
+
+MOCKUP_XML_PATH="${MXCUBE_CORE}/configuration/mockup"
+MXCUBE_CORE_CONFIG_PATH="${MOCKUP_XML_PATH}/gphl:${MOCKUP_XML_PATH}/qt:${MOCKUP_XML_PATH}"
+
+# SOLEIL:
+MXCUBE_CORE_CONFIG_PATH="${MXCUBE_CORE_CONFIG_PATH}:${MXCUBE_CORE}/configuration/soleil/px2/mockups"
+
+# User and mac address
+#
+# Mac address for docker - nededed for GPhL license
+MAC_ADDRESS="54:ee:75:b6:8e:d3"
+#
+# User for docker - for giving correct file ownership.
+DOCKER_USER_ID="1000:100"
+# DOCKER_USER_ID="1158:3001"
+# CONSIDER SOMETHING LKE --user $(id -u):$(id -g)
+# User name - used only for file names etc.
+USER_NAME="test_user"
+
+# Directories set-up
+#
+# MXCuBE installation is in /MXCuBE/mxcube, as per standard
+#
+# Home directory, used for e.g. .config and .ssh. Externally mounted.
+DOCKER_HOME="/home/rhfogh/"
+OUTPUT_HOME="/home/rhfogh/dockerhome/"
+# GPhL software.
+
+# GPHL-specific directories for mounting
+# Note: These are the same from insisde and outside the docker
+# and so must be either identical or used on only one side.
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/GPhL/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/GPhL/mxcube_setup/"
+
+# Location for output data - must be the same inside and outside docker
+DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
+
+# End of settable parameters.
+
+
+xhost +local:
+# Command needed to run GPhL workflows
+# Add in this for debug
+# -p 8050:8050 \
+exec docker run -it \
+--mac-address $MAC_ADDRESS \
+-p 25333:25333 \
+-p 25334:25334 \
+-h=$CONTAINER \
+-u $DOCKER_USER_ID \
+-e HOME=$DOCKER_HOME \
+-e USER=$USER_NAME \
+-e DISPLAY=$DISPLAY \
+-e QT_X11_NO_MITSHM=1 \
+-e MXCUBE_CORE_CONFIG_PATH=$MXCUBE_CORE_CONFIG_PATH \
+-e CUSTOM_HARDWARE_OBJECTS_PATH=$CUSTOM_HARDWARE_OBJECTS_PATH \
+-e CUSTOM_BRICKS_PATH=$CUSTOM_BRICKS_PATH \
+-e PYTHONPATH=$MXCUBE_BASE/mxcube:$MXCUBE_BASE/mxcubecore \
+-v $MXCUBE_ROOT:/MXCuBE \
+-v $GPHL_RELEASE_ROOT:$GPHL_RELEASE_ROOT \
+-v $GPHL_SETUP_ROOT:$GPHL_SETUP_ROOT \
+-v $DATA_ROOT:$DATA_ROOT \
+-v $OUTPUT_HOME:$DOCKER_HOME \
+-v /tmp/.X11-unix:/tmp/.X11-unix \
+$CONTAINER