[tests] move checker functions to separate file

also clean up minor typos etc

.github/integration/scripts/checkers.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+set -e
+
+# Function checking that file(s) were encrypted
+function check_encrypted_file {
+    for k do
+        echo "working with $k"
+        output=$(head -c 8 "$k")
+
+        if [[ "$output" == "crypt4gh" ]]; then
+            echo "Encrypted data file: $k"
+        else
+            echo "Failed to encrypt file: $k"
+            exit 1
+        fi
+    done
+}
+
+
+# Function checking that a file was uploaded to the S3 backend
+function check_uploaded_file {
+    if s3cmd -c testing/directS3 ls s3://"$1" | grep -q "$2"; then
+        echo "Uploaded encrypted file to s3 backend"
+    else
+        echo "Failed to upload file to s3 backend"
+        exit 1
+    fi
+}

.github/integration/tests/10_encrypt_decrypt.sh

@@ -1,24 +1,7 @@
 #!/bin/bash
 set -e
-
-# Function checking that a file was encrypted
-function check_encypted_file() {
-
-    for k in $1
-    do
-        output=$(head -c 8 "$k")
-
-        if [[ "$output" = "crypt4gh"  ]]; then
-            echo "Encrypted data file"
-        else
-            echo "Failed to encrypt file"
-            exit 1
-        fi
-    done
-}
-
-# inferred from access_key in testing/s3cmd.conf
-user=test_dummy.org
+test_dir=$(dirname "$0")
+source "$test_dir/../scripts/checkers.sh"
 
 # Create random file
 dd if=/dev/urandom of=data_file count=1 bs=1M
@@ -34,16 +17,15 @@ fi
 # Encrypt a file
 ./sda-cli encrypt -key sda_key.pub.pem data_file
 
-files="data_file.c4gh"
-check_encypted_file $files
+check_encrypted_file data_file.c4gh
 
 
 # Create folder and encrypt files in it
 cp data_file data_file1
 mkdir data_files_enc
 ./sda-cli encrypt -key sda_key.pub.pem -outdir data_files_enc data_file data_file1
 
-check_encypted_file "data_files_enc/data_file.c4gh data_files_enc/data_file1.c4gh"
+check_encrypted_file data_files_enc/data_file.c4gh data_files_enc/data_file1.c4gh
 
 # Test multiple pub key encryption
 
@@ -55,7 +37,7 @@ do
     else
         echo "Failed to create key pair for encryption"
         exit 1
-fi
+    fi
 done
 
 # Create file with concatenated pub keys
@@ -67,7 +49,7 @@ cp data_file data_file_keys
 
 # Encrypt with multiple key flag calls
 ./sda-cli encrypt -key sda_key.pub.pem -key sda_key2.pub.pem data_file_keys
-check_encypted_file "data_file_keys.c4gh"
+check_encrypted_file data_file_keys.c4gh
 # Decrypt file with both keys, one at the time
 for key in sda_key sda_key2
 do
@@ -86,7 +68,7 @@ rm data_file_keys.c4gh
 
 # Encrypt with a single key and with a concatenated key file
 ./sda-cli encrypt -key sda_key.pub.pem -key sda_keys data_file_keys
-check_encypted_file "data_file_keys.c4gh"
+check_encrypted_file data_file_keys.c4gh
 
 # Decrypt file with all three keys
 for key in sda_key sda_key1 sda_key2
@@ -105,7 +87,7 @@ rm data_file_keys.c4gh
 
 # Encrypt with concatenated key file
 ./sda-cli encrypt -key sda_keys data_file_keys
-check_encypted_file "data_file_keys.c4gh"
+check_encrypted_file data_file_keys.c4gh
 
 # Decrypt file with all keys
 for key in sda_key1 sda_key2

.github/integration/tests/20_upload.sh

@@ -1,38 +1,12 @@
 #!/bin/bash
 set -e
+test_dir=$(dirname "$0")
+source "$test_dir/../scripts/checkers.sh"
+
 # inferred from access_key in testing/s3cmd.conf
 user=test_dummy.org
 
 
-# Function checking that a file was encrypted
-function check_encypted_file() {
-
-    for k in $1
-    do
-        output=$(head -c 8 "$k")
-
-        if [[ "$output" = "crypt4gh"  ]]; then
-            echo "Encrypted data file"
-        else
-            echo "Failed to encrypt file"
-            exit 1
-        fi
-    done
-}
-
-# Function checking that a file was uploaded to the S3 backend
-function check_uploaded_file() {
-    # TODO if emtpy, this will fail silently
-    output=$(s3cmd -c testing/directS3 ls s3://"$1" | grep -q "$2")
-    if $output ; then
-        echo "Uploaded encrypted file to s3 backend"
-    else
-        echo "Failed to upload file to s3 backend"
-        exit 1
-    fi
-}
-
-
 # Create folder with subfolder structure and add some encrypted files
 mkdir data_files_enc/dir1 data_files_enc/dir1/dir2
 cp data_files_enc/data_file.c4gh data_files_enc/data_file3.c4gh
@@ -47,7 +21,7 @@ check_uploaded_file "test/$user/data_file.c4gh" data_file.c4gh
 
 
 # Try to upload a file twice with the --force-overwrite flag
-output=$(./sda-cli -config testing/s3cmd.conf upload --force-overwrite data_file.c4gh)
+./sda-cli -config testing/s3cmd.conf upload --force-overwrite data_file.c4gh
 
 
 # Test upload all files from a folder, one by one
@@ -105,7 +79,7 @@ cp data_file data_files_unenc/. && cp data_file data_files_unenc/dir1/data_file1
 uploadDir="testEncryptUpload"
 ./sda-cli -config testing/s3cmd.conf upload -encrypt-with-key sda_key.pub.pem -r data_files_unenc -targetDir "$uploadDir"
 
-check_encypted_file "data_files_unenc/data_file.c4gh" "data_files_unenc/dir1/data_file1.c4gh"
+check_encrypted_file data_files_unenc/data_file.c4gh data_files_unenc/dir1/data_file1.c4gh
 
 for k in data_files_unenc/data_file.c4gh data_files_unenc/dir1/data_file1.c4gh
 do