16578: Copy bwa tutorial from jutro to local cluster

[arvados.git] / tools / copy-tutorial / copy-tutorial.sh

diff --git a/tools/copy-tutorial/copy-tutorial.sh b/tools/copy-tutorial/copy-tutorial.sh
index bdc75da2e1df428009a1a5113d1db81eca0fbf37..8d8d2d5e39774c1838e3f6c3be23cff466721f4e 100755 (executable)
--- a/tools/copy-tutorial/copy-tutorial.sh
+++ b/tools/copy-tutorial/copy-tutorial.sh
@@ -1,25 +1,58 @@
-#!/bin/sh
+#!/bin/bash
 # Copyright (C) The Arvados Authors. All rights reserved.
 #
 # SPDX-License-Identifier: AGPL-3.0
 
-set -e
+set -e -o pipefail
 
 if test -z "$1"  ; then
   echo "$0: Copies Arvados tutorial resources from public data cluster (jutro)"
   echo "Usage: copy-tutorial.sh <dest>"
-  echo "<dest> is destination cluster configuration that can be found in ~/.config/arvados"
+  echo "<dest> is 5-character cluster id of the destination"
   exit
 fi
 
-echo "Copying from public data cluster (jutro) to $1"
+src=jutro
+dest=$1
 
-for a in $(cat $HOME/.config/arvados/$1.conf) ; do export $a ; done
+if ! test -f $HOME/.config/arvados/${dest}.conf ; then
+    echo "Please create $HOME/.config/arvados/${dest}.conf with the following contents:"
+    echo "ARVADOS_API_HOST=<${dest} host>"
+    echo "ARVADOS_API_TOKEN=<${dest} token>"
+    exit 1
+fi
+
+if ! test -f $HOME/.config/arvados/jutro.conf ; then
+    # Set it up with the anonymous user token.
+    echo "ARVADOS_API_HOST=jutro.arvadosapi.com" > $HOME/.config/arvados/jutro.conf
+    echo "ARVADOS_API_TOKEN=v2/jutro-gj3su-e2o9x84aeg7q005/22idg1m3zna4qe4id3n0b9aw86t72jdw8qu1zj45aboh1mm4ej" >> $HOME/.config/arvados/jutro.conf
+    exit 1
+fi
+
+for a in $(cat $HOME/.config/arvados/${dest}.conf) ; do export $a ; done
+
+echo
+echo "Copying bwa mem example from public data cluster (jutro) to $dest"
+echo
 
-project_uuid=$(arv --format=uuid group create --group '{"name":"User guide resources", "group_class": "project"}')
+set -x
+
+project_uuid=$(arv --format=uuid group list --filters '[["name", "=", "User guide resources"]]')
+if test -z "$project_uuid" ; then
+    project_uuid=$(arv --format=uuid group create --group '{"name":"User guide resources", "group_class": "project"}')
+    arv link create --link '{"link_class": "permission", "name": "can_read", "tail_uuid": "'$dest'-j7d0g-anonymouspublic", "head_uuid": "'$project_uuid'"}'
+fi
+
+if ! arv-keepdocker | grep "arvados/jobs *latest" ; then
+    arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-4zz18-sxmit0qs6i9n2s4
+fi
 
 # Bwa-mem workflow
-arv-copy --src jutro --dst $1 --project-uuid=$project_uuid f141fc27e7cfa7f7b6d208df5e0ee01b+59
-arv-copy --src jutro --dst $1 --project-uuid=$project_uuid jutro-7fd4e-mkmmq53m1ze6apx
+arv-copy --src jutro --dst $dest --project-uuid=$project_uuid f141fc27e7cfa7f7b6d208df5e0ee01b+59
+arv-copy --src jutro --dst $dest --project-uuid=$project_uuid jutro-7fd4e-mkmmq53m1ze6apx
+
+set +x
 
-echo "Data copied to \"User guide resources\" at $project_uuid"
+echo
+echo "Finished, data copied to \"User guide resources\" at $project_uuid"
+echo