First draft of an environment file for fish shell (#359)

environment.fish

@@ -0,0 +1,81 @@
+# -*- Mode: shell-script -*-
+#
+# Copyright (C) 2013-2016 DNAnexus, Inc.
+#
+# This file is part of dx-toolkit (DNAnexus platform client libraries).
+#
+#   Licensed under the Apache License, Version 2.0 (the "License"); you may not
+#   use this file except in compliance with the License. You may obtain a copy
+#   of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+#   WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+#   License for the specific language governing permissions and limitations
+#   under the License.
+#
+#
+# Source this file in a fish shell to initialize DNAnexus environment
+# variables:
+# $ source environment.fish
+
+if test ! -n "$version" -a -n "(echo $SHELL | grep -q fish)"
+    echo "You are not using fish shell. Try 'environment' or 'environment.csh' instead."
+    exit
+end
+
+set SOURCE (status --current-filename)
+
+while test -L "$SOURCE"
+  set SOURCE (readlink "$SOURCE")
+end
+
+switch (uname)
+  case Darwin FreeBSD NetBSD DragonFly
+    set -x DNANEXUS_HOME ( dirname (realpath "$SOURCE" ) )
+  case Linux
+    set -x DNANEXUS_HOME ( cd -P ( dirname "$SOURCE" ) ; pwd )
+  case '*'
+    echo "It doesn't look like you're on a linux system"
+end
+
+# Get RHEL version
+if test -e /etc/redhat-release
+  set RHEL_MAJOR_VERSION (grep -o "Red Hat Enterprise Linux .* release [0-9]\+" /etc/redhat-release | sed -e "s/Red Hat Enterprise Linux .* release //")
+end
+
+# Detect system installation of dx-toolkit
+if [ "$DNANEXUS_HOME" = "/etc/profile.d" ]
+  set -x DNANEXUS_HOME "/usr/share/dnanexus"
+  # Private Python packages. We really ought not pollute PYTHONPATH with these though.
+  set -xg PYTHONPATH /usr/share/dnanexus/lib/python2.7/site-packages $PYTHONPATH
+  set -xg CLASSPATH /usr/share/java/dnanexus-api-0.1.0.jar $CLASSPATH
+else
+  set -x PATH $DNANEXUS_HOME/bin $PATH
+  set -xg CLASSPATH $DNANEXUS_HOME/lib/java/*/ $CLASSPATH
+
+  if [ "$RHEL_MAJOR_VERSION" = "7" ]
+    set -xg PYTHONPATH $DNANEXUS_HOME/share/dnanexus/lib/python2.7/site-packages:$DNANEXUS_HOME/lib64/python2.7/site-packages $PYTHONPATH
+  else
+    set -xg PYTHONPATH $DNANEXUS_HOME/share/dnanexus/lib/python2.7/site-packages:$DNANEXUS_HOME/lib/python2.7 $PYTHONPATH
+  end
+end
+
+# Note: The default I/O stream encoding in Python 2.7 (as configured on ubuntu) is ascii, not UTF-8 or the system locale
+# encoding. We reset it here to avoid having to set it for every I/O operation explicitly.
+set -x PYTHONIOENCODING UTF-8
+
+# Clean up old session files
+if [ $HOME != "" ]
+    for session_dir in "$HOME/.dnanexus_config/sessions/"*
+        if test ! 'ps -p (basename "$session_dir") &> /dev/null'
+            rm -rf "$session_dir"
+        end
+    end
+end
+
+if test -z "$DX_SECURITY_CONTEXT" -a -n "$DX_AUTH_TOKEN"
+    set -x DX_SECURITY_CONTEXT "{\"auth_token_type\":\"Bearer\",\"auth_token\":\"$DX_AUTH_TOKEN\"}"
+end