Merge pull request #103 from helenkirk/casa61-64

Casa61 64

science-containers/Dockerfiles/casa/centos7/Dockerfile

@@ -0,0 +1,16 @@
+FROM centos:7
+#This dockerfile makes a centos7 container with library dependencies needed
+# for casa versions
+
+RUN yum clean all -y
+RUN yum makecache -y
+RUN yum update -y
+RUN yum install -y freetype libSM libXi libXrender libXrandr \
+	libXfixes libXcursor libXinerama fontconfig \
+        libxslt xauth xorg-x11-server-Xvfb dbus-x11 \
+	tkinter ImageMagick-c++ xterm perl autoconf python-sphinx graphviz xz
+
+RUN yum install -y firefox
+
+RUN yum install -y sssd-client acl
+

science-containers/Dockerfiles/casa/centos7/Makefile

@@ -0,0 +1,28 @@
+
+VERSIONS = \
+	7
+
+
+DOCKER_REPO_BASE=images.canfar.net/skaha/centos
+
+.PHONY: build clean run 
+
+all: build
+
+build: 
+	@- $(foreach V,$(VERSIONS), \
+		docker build -t ${DOCKER_REPO_BASE}:$(V) .; \
+    	)
+
+clean:
+	@- $(foreach V,$(VERSIONS), \
+	  docker rmi ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+
+
+upload: build
+	@- $(foreach V,$(VERSIONS), \
+	  docker push ${DOCKER_REPO_BASE}:$(V) ; \
+	)
+clean_all: clean
+upload_all: upload

science-containers/Dockerfiles/casa/version-6.1-6.4/Dockerfile

@@ -1,20 +1,8 @@
-FROM centos:6
+FROM images.canfar.net/skaha/centos:7
 
 # xterm dependency is an extra to get the casa shell in the display
 # perl was added for casa later than 5
 
-# Override old repo info with current urls
-RUN rm /etc/yum.repos.d/CentOS-Base.repo
-ADD CentOS-Base.repo /etc/yum.repos.d/
-
-RUN yum clean all -y
-RUN yum makecache -y
-RUN yum update -y
-RUN yum install -y freetype libSM libXi libXrender libXrandr \
-	libXfixes libXcursor libXinerama fontconfig \
-        libxslt xauth xorg-x11-server-Xvfb dbus-x11 \
-	tkinter ImageMagick-c++ xterm perl autoconf python-sphinx graphviz xz
-
 # setup all required env variables
 ARG CASA_RELEASE
 ENV CASA_RELEASE=${CASA_RELEASE}
@@ -30,7 +18,6 @@ ADD ${CASA_RELEASE}.tar.xz /opt/
 # chown because the untarred casa has wrong owner/group
 RUN chown -R root:root /opt/${CASA_RELEASE%%-py*} && ln -s /opt/${CASA_RELEASE%%-py*} /opt/casa
 
-RUN yum install -y sssd-client acl
 
 # add the admit enhancement (issue #25)
 RUN yum install -y tcsh
@@ -53,6 +40,16 @@ RUN cd /opt/${CASA_RELEASE%%-py*} && \
     ln -s /arc/projects/casa-data-repository/ /opt/${CASA_RELEASE%%-py*}/${REPLACED_DATA}
 RUN rm -rf /arc
 
+#AnalysisUtils package
+RUN mkdir /opt/casa/analysisUtils
+RUN yum install -y wget
+RUN cd /opt/casa/analysisUtils && wget ftp://ftp.cv.nrao.edu/pub/casaguides/analysis_scripts.tar && tar -xvf analysis_scripts.tar
+#(if above doesn't work, can manually download the package and add as below)
+#ADD ./analysis_scripts.tar /opt/casa/analysisUtils/
+#NB: the analysisUtils path is added to the CASA startup file in the init.sh script
+# (needs access to user's $HOME)
+
+
 RUN mkdir /skaha
 ADD init.sh /skaha/
 
@@ -64,8 +61,6 @@ WORKDIR /opt
 COPY extract-casaviewer.sh .
 RUN bash extract-casaviewer.sh && rm extract-casaviewer.sh
 
-#RUN chmod 755 /opt/squashfs-root /opt/squashfs-root/usr /opt/squashfs-root/usr/*
-#COMMENTED BELOW LINE OUT ONLY FOR TESTING PURPOSES.  NEED TO INCLUDE!
 RUN chmod 777 -R /opt/squashfs-root /opt/squashfs-root/usr /opt/squashfs-root/usr/*
 
 CMD [ "/skaha/init.sh" ]

science-containers/Dockerfiles/casa/version-6.1-6.4/Makefile

@@ -9,9 +9,9 @@ VERSIONS_OLD = \
 # 	casa-6.3.0-48 #\
 
 VERSIONS_PIPELINE = \
-	casa-6.4.1-12-pipeline-2022.2.0.64-py3.6
+	casa-6.1.1-15-pipeline-2020.1.0.40
+#	casa-6.4.1-12-pipeline-2022.2.0.64-py3.6
 # 	casa-6.2.1-7-pipeline-2021.2.0.128
-#	casa-6.1.1-15-pipeline-2020.1.0.40
 
 #!NB >casa6.4.3 versions have a different directory naming structure
 VERSIONS = \

science-containers/Dockerfiles/casa/version-6.1-6.4/download.sh

@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+if [ $# -lt 2 ]
+then
+  echo "usage: $0 <version> <"old"|"current">"
+  exit 1
+fi
+
+RELEASE=$1
+FILE="${RELEASE}.tar.xz"
+
+if [ $2 == "old" ]; then
+  URL="https://casa.nrao.edu/download/distro/casa/release/rhel//${FILE}"
+elif [ $2 == "pipeline" ]; then
+  URL="https://casa.nrao.edu/download/distro/casa-pipeline/release/linux/${FILE}"
+else
+  URL="https://casa.nrao.edu/download/distro/casa/release/rhel/${FILE}"
+fi
+
+# make sure we are in the source folder
+HERE=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+cd $HERE
+
+if [ ! -e "$FILE" ]; then
+    curl -O  $URL
+else
+    echo "$FILE already downloaded."
+fi
+
+FILE="admit"
+URL="https://github.com/astroumd/${FILE}"
+if [ ! -e "$FILE" ]; then
+    git clone  $URL
+else
+    echo "$FILE already downloaded."
+fi

science-containers/Dockerfiles/casa/version-6.1-6.4/extract-casaviewer.sh

@@ -1,36 +1,59 @@
 #!/bin/bash
+#NB: needs to be edited for casa version in first coding line below
+# AppImage fix applies now too casaviewer, casaplotms
+# and new: casalogger, casaplotserver, casatablebrowser, casafeather
+
+#casavers=casa-6.5.4-9-pipeline-2023.1.0.124
+#casavers=casa-6.5.3-28-pipeline-2023.0.0.36
+#casavers=casa-6.4.1-12-pipeline-2022.2.0.64
+#casavers=casa-6.2.1-7-pipeline-2021.2.0.128
+casavers=casa-6.1.1-15-pipeline-2020.1.0.40
+#casavers=casa-6.3.0-48
+#casavers=casa-6.2.0-124
+#casavers=casa-6.1.0-118
+#casavers=casa-6.4.0-16
+#casavers=casa-6.4.3-27
+
+#pyvers=python3.8
+pyvers=python3.6
 
 pushd /opt
-casaviewer=$(python3 -m casaviewer --app-path 2> /dev/null | grep casaviewer)
-echo ${casaviewer}
+#below command was original way of structuring this, but not working anymore
+#manually inputting casavers above to get around this
+#casaviewer=$(python3 -m casaviewer --app-path 2> /dev/null | grep casaviewer)
+#echo ${casaviewer}
+casaviewer=/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage
 ${casaviewer} --appimage-extract 2> /dev/null
+
 mv /opt/casa/bin/casaviewer /opt/casa/bin/casaviewer.old
 ln -s /opt/squashfs-root/AppRun /opt/casa/bin/casaviewer
-#ln -s /opt/squashfs-root/AppRun /usr/local/bin/casaviewer
 
 #additional steps courtesy of CASA helpdesk
-mv /opt/casa/lib/py/lib/python3.6/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage /opt/casa/lib/py/lib/python3.6/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage.orig
-ln -s /opt/squashfs-root/usr/bin/casaviewer /opt/casa/lib/py/lib/python3.6/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage
-
-#additional steps below to fix a similar problem for plotms
-# Right now, need to uncomment out each specific version for the first
-# command to run.  Hopefully this can be tidied up to something similar to the
-# first set of commands above
-
-#---- Choose the correct line/version below & uncomment out ------
-#/opt/casa-6.1.0-118/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.2.0-124/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.3.0-48/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-/opt/casa-6.4.1-12-pipeline-2022.2.0.64/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.2.1-7-pipeline-2021.2.0.128/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.1.1-15-pipeline-2020.1.0.40/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.4.0-16/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.4.3-27/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#/opt/casa-6.4.4-31/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
-#----------------
-
-#the two commands below apply to all versions to finish fixing plotms
-mv /opt/casa/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage /opt/casa/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage.orig
-ln -s /opt/squashfs-root/usr/bin/casaplotms /opt/casa/lib/py/lib/python3.6/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage
+#NB: casa6.5 and higher use python3.8, only option
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage.orig
+ln -s /opt/squashfs-root/usr/bin/casaviewer /opt/casa/lib/py/lib/${pyvers}/site-packages/casaviewer/__bin__/casaviewer-x86_64.AppImage
+
+#Apply similar process for other packages
+#1) extract AppImage
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage --appimage-extract 2> /dev/null
+/opt/${casavers}/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage --appimage-extract 2> /dev/null
+
+#2a) move old AppImage
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage.orig
+mv /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage.orig
+
+#2b) link to new one
+ln -s /opt/squashfs-root/usr/bin/casaplotms /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotms/__bin__/casaplotms-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casalogger /opt/casa/lib/py/lib/${pyvers}/site-packages/casalogger/__bin__/casalogger-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casafeather /opt/casa/lib/py/lib/${pyvers}/site-packages/casafeather/__bin__/casafeather-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casaplotserver /opt/casa/lib/py/lib/${pyvers}/site-packages/casaplotserver/__bin__/casaplotserver-x86_64.AppImage
+ln -s /opt/squashfs-root/usr/bin/casatablebrowser /opt/casa/lib/py/lib/${pyvers}/site-packages/casatablebrowser/__bin__/casatablebrowser-x86_64.AppImage
+
 
 popd

science-containers/Dockerfiles/casa/version-6.1-6.4/init.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+echo "INIT START"
+echo "sourcing admit_start.sh"
+source /opt/admit/admit_start.sh
+echo "INIT DONE"

science-containers/Dockerfiles/casa/version-6.1-6.4/nsswitch.conf

@@ -0,0 +1,62 @@
+#
+# /etc/nsswitch.conf
+#
+# An example Name Service Switch config file. This file should be
+# sorted with the most-used services at the beginning.
+#
+# The entry '[NOTFOUND=return]' means that the search for an
+# entry should stop if the search in the previous entry turned
+# up nothing. Note that if the search failed due to some other reason
+# (like no NIS server responding) then the search continues with the
+# next entry.
+#
+# Valid entries include:
+#
+#	nisplus			Use NIS+ (NIS version 3)
+#	nis			Use NIS (NIS version 2), also called YP
+#	dns			Use DNS (Domain Name Service)
+#	files			Use the local files
+#	db			Use the local database (.db) files
+#	compat			Use NIS on compat mode
+#	hesiod			Use Hesiod for user lookups
+#	[NOTFOUND=return]	Stop searching if not found so far
+#
+
+# To use db, put the "db" in front of "files" for entries you want to be
+# looked up first in the databases
+#
+# Example:
+#passwd:    db files nisplus nis
+#shadow:    db files nisplus nis
+#group:     db files nisplus nis
+
+passwd:     sss files
+shadow:     files sss
+group:      sss files
+
+#hosts:     db files nisplus nis dns
+hosts:      files dns
+
+# Example - obey only what nisplus tells us...
+#services:   nisplus [NOTFOUND=return] files
+#networks:   nisplus [NOTFOUND=return] files
+#protocols:  nisplus [NOTFOUND=return] files
+#rpc:        nisplus [NOTFOUND=return] files
+#ethers:     nisplus [NOTFOUND=return] files
+#netmasks:   nisplus [NOTFOUND=return] files
+
+bootparams: nisplus [NOTFOUND=return] files
+
+ethers:     files
+netmasks:   files
+networks:   files
+protocols:  files
+rpc:        files
+services:   files
+
+netgroup:   nisplus
+
+publickey:  nisplus
+
+automount:  files nisplus
+aliases:    files nisplus

science-containers/Dockerfiles/casa/version-6.1-6.4/update-data.patch

@@ -0,0 +1,27 @@
+#!/usr/bin/perl
+##
+## move rsync point from svn.cv.nrao.edu to casa.nrao.edu
+##
+use File::Find;
+
+if ( scalar(@ARGV) < 1 ) { die "$0 requires path to CASA installation to be patched..." }
+if ( scalar(@ARGV) > 1 ) { die "$0 requires only one parameter which is the path to CASA installation to be patched..." }
+
+unless ( -d $ARGV[0] ) { die "$0 requires path to CASA installation (which should be a directory) to be patched..." }
+
+sub locate_script {
+    if ( -f $_ && $_ eq "update-data" ) {
+        print "substituting $File::Find::dir/$_\n";
+        open( CONTENTS, "< $_" );
+        my @contents = <CONTENTS>;
+        close( CONTENTS );
+        open( CONTENTS, "> $_" );
+        foreach my $x ( @contents ) {
+            $x =~ s@(?:rsync://svn.cv.nrao.edu/casa-data|rsync://casa.nrao.edu/casa-data)@rsync://casa-rsync.nrao.edu/casa-data@g;
+            print CONTENTS "$x";
+        }
+        close( CONTENTS );
+    }
+}
+
+find( { wanted => \&locate_script }, $ARGV[0] );