[integration tests] handle some file errors

* missing file
* truncated file

.github/integration/tests/sda/92_handle_file_errors.sh

@@ -0,0 +1,155 @@
+#!/bin/bash
+set -e
+
+cd shared || true
+
+# clean ingest queue to simplify what is to come.
+curl -s -u guest:guest -XDELETE http://rabbitmq:15672/api/queues/sda/inbox/contents
+
+# encrypt file with wrong public key and upload to inbox
+yes | /shared/crypt4gh encrypt -p sync.pub.pem -f NA12878.bam
+s3cmd -c s3cfg put NA12878.bam.c4gh s3://test_dummy.org/bad.file.c4gh
+
+# truncate file to simulate storage issues
+dd if=NA12878_20k_b37.bam.c4gh bs=128 count=1024 of=truncated.c4gh
+s3cmd -c s3cfg put truncated.c4gh s3://test_dummy.org/
+
+## test starts here
+
+CORRID=$(
+    curl -s -X POST \
+        -H "content-type:application/json" \
+        -u guest:guest http://rabbitmq:15672/api/queues/sda/inbox/get \
+        -d '{"count":1,"encoding":"auto","ackmode":"ack_requeue_false"}' | jq -r .[0].properties.correlation_id
+)
+
+stream_size=$(curl -s -u guest:guest http://rabbitmq:15672/api/queues/sda/error_stream | jq '.messages_ready')
+
+properties=$(
+    jq -c -n \
+        --argjson delivery_mode 2 \
+        --arg correlation_id "$CORRID" \
+        --arg content_encoding UTF-8 \
+        --arg content_type application/json \
+        '$ARGS.named'
+)
+
+encrypted_checksums=$(
+    jq -c -n \
+        --arg sha256 "$(echo "aa" | sha256sum | cut -d ' ' -f1)" \
+        --arg md5 "$(echo "aa" | md5sum | cut -d ' ' -f1)" \
+        '$ARGS.named|to_entries|map(with_entries(select(.key=="key").key="type"))'
+)
+
+bad_file_payload=$(
+    jq -r -c -n \
+        --arg type ingest \
+        --arg user [email protected] \
+        --arg filepath test_dummy.org/bad.file.c4gh \
+        --argjson encrypted_checksums "$encrypted_checksums" \
+        '$ARGS.named|@base64'
+)
+
+bad_file=$(
+    jq -c -n \
+        --arg vhost sda \
+        --arg name sda \
+        --argjson properties "$properties" \
+        --arg routing_key "ingest" \
+        --arg payload_encoding base64 \
+        --arg payload "$bad_file_payload" \
+        '$ARGS.named'
+)
+
+curl -s -u guest:guest 'http://rabbitmq:15672/api/exchanges/sda/sda/publish' \
+    -H 'Content-Type: application/json;charset=UTF-8' \
+    -d "$bad_file" | jq
+
+sleep 10
+
+if [ $((stream_size++)) -eq "$(curl -s -u guest:guest http://rabbitmq:15672/api/queues/sda/error_stream | jq '.messages_ready')" ]; then
+    echo "Bad file not moved to error"
+    exit 1
+fi
+
+
+missing_file_payload=$(
+    jq -r -c -n \
+        --arg type ingest \
+        --arg user [email protected] \
+        --arg filepath test_dummy.org/missing.file.c4gh \
+        --argjson encrypted_checksums "$encrypted_checksums" \
+        '$ARGS.named|@base64'
+)
+
+missing_file=$(
+    jq -c -n \
+        --arg vhost sda \
+        --arg name sda \
+        --argjson properties "$properties" \
+        --arg routing_key "ingest" \
+        --arg payload_encoding base64 \
+        --arg payload "$missing_file_payload" \
+        '$ARGS.named'
+)
+
+curl -s -u guest:guest 'http://rabbitmq:15672/api/exchanges/sda/sda/publish' \
+    -H 'Content-Type: application/json;charset=UTF-8' \
+    -d "$missing_file" | jq
+
+sleep 10
+
+
+if [ $((stream_size++)) -eq "$(curl -s -u guest:guest http://rabbitmq:15672/api/queues/sda/error_stream | jq '.messages_ready')" ]; then
+    echo "missing file not moved to error"
+    exit 1
+fi
+
+CORRID=$(
+    curl -s -X POST \
+        -H "content-type:application/json" \
+        -u guest:guest http://rabbitmq:15672/api/queues/sda/inbox/get \
+        -d '{"count":1,"encoding":"auto","ackmode":"ack_requeue_false"}' | jq -r .[0].properties.correlation_id
+)
+
+properties=$(
+    jq -c -n \
+        --argjson delivery_mode 2 \
+        --arg correlation_id "$CORRID" \
+        --arg content_encoding UTF-8 \
+        --arg content_type application/json \
+        '$ARGS.named'
+)
+
+truncated_file_payload=$(
+    jq -r -c -n \
+        --arg type ingest \
+        --arg user [email protected] \
+        --arg filepath test_dummy.org/truncated.c4gh \
+        --argjson encrypted_checksums "$encrypted_checksums" \
+        '$ARGS.named|@base64'
+)
+
+truncated_file=$(
+    jq -c -n \
+        --arg vhost sda \
+        --arg name sda \
+        --argjson properties "$properties" \
+        --arg routing_key "ingest" \
+        --arg payload_encoding base64 \
+        --arg payload "$truncated_file_payload" \
+        '$ARGS.named'
+)
+
+curl -s -u guest:guest 'http://rabbitmq:15672/api/exchanges/sda/sda/publish' \
+    -H 'Content-Type: application/json;charset=UTF-8' \
+    -d "$truncated_file" | jq
+
+sleep 10
+
+if [ $((stream_size++)) -eq "$(curl -s -u guest:guest http://rabbitmq:15672/api/queues/sda/error_stream | jq '.messages_ready')" ]; then
+    echo "truncated file not moved to error"
+    exit 1
+fi
+
+echo "file errors test completed successfully"