use yq to parse yaml value

sda-download/.github/integration/setup/common/20_tools.sh

@@ -5,4 +5,4 @@ C4GH_VERSION="$(curl --retry 100 -sL https://api.github.com/repos/neicnordic/cry
 curl --retry 100 -sL https://github.com/neicnordic/crypt4gh/releases/download/"${C4GH_VERSION}"/crypt4gh_linux_x86_64.tar.gz | sudo tar -xz -C /usr/bin/ &&
         sudo chmod +x /usr/bin/crypt4gh
 
-sudo apt install -y jq s3cmd
+sudo apt install -y jq s3cmd yq

sda-download/.github/integration/tests/common/50_check_endpoint.sh

@@ -85,7 +85,7 @@ echo "expected file found"
 # Test file can be decrypted
 ## test also the files endpoint
 
-C4GH_PASSPHRASE=$(grep -F passphrase config.yaml | tail -1 | sed -e 's/.* //' -e 's/"//g')
+C4GH_PASSPHRASE=$(yq '.c4gh.passphrase' config.yaml)
 export C4GH_PASSPHRASE
 
 crypt4gh decrypt -s c4gh.sec.pem -f dummy_data.c4gh && mv dummy_data old-file.txt

sda-download/.github/integration/tests/common/70_check_download.sh

@@ -11,7 +11,7 @@ token=$(curl -s --cacert certs/ca.pem "https://localhost:8000/tokens" | jq -r  '
 dataset="https://doi.example/ty009.sfrrss/600.45asasga"
 file="dummy_data"
 expected_size=1048605
-C4GH_PASSPHRASE=$(grep -F passphrase config.yaml | tail -1 | sed -e 's/.* //' -e 's/"//g')
+C4GH_PASSPHRASE=$(yq '.c4gh.passphrase' config.yaml)
 export C4GH_PASSPHRASE
 
 # download decrypted full file,  check file size

sda-download/.github/integration/tests/s3notls/52_check_endpoint.sh

@@ -70,7 +70,7 @@ echo "expected file found"
 # Test file can be decrypted
 ## test also the files endpoint
 
-C4GH_PASSPHRASE=$(grep -F passphrase config.yaml | tail -1 | sed -e 's/.* //' -e 's/"//g')
+C4GH_PASSPHRASE=$(yq '.c4gh.passphrase' config.yaml)
 export C4GH_PASSPHRASE
 
 crypt4gh decrypt -s c4gh.sec.pem -f dummy_data.c4gh && mv dummy_data old-file.txt

sda-download/dev_utils/run_integration_test.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-for c in s3cmd jq
+for c in s3cmd jq yq
 do
     if ! command -v $c
     then
@@ -194,7 +194,7 @@ echo "expected file found"
 # Test file can be decrypted
 ## test also the files endpoint
 
-C4GH_PASSPHRASE=$(grep -F passphrase config.yaml | tail -1 | sed -e 's/.* //' -e 's/"//g')
+C4GH_PASSPHRASE=$(yq '.c4gh.passphrase' config.yaml)
 export C4GH_PASSPHRASE
 
 crypt4gh decrypt --sk c4gh.sec.pem < dummy_data.c4gh > old-file.txt

sda-download/dev_utils/run_integration_test_no_tls.sh

@@ -1,6 +1,6 @@
 #!/bin/sh
 
-for c in s3cmd jq
+for c in s3cmd jq yq
 do
     if ! command -v $c
     then
@@ -152,7 +152,7 @@ echo "expected file found"
 # Test file can be decrypted
 ## test also the files endpoint
 
-C4GH_PASSPHRASE=$(grep -F passphrase config.yaml | tail -1 | sed -e 's/.* //' -e 's/"//g')
+C4GH_PASSPHRASE=$(yq '.c4gh.passphrase' config.yaml)
 export C4GH_PASSPHRASE
 
 crypt4gh decrypt --sk c4gh.sec.pem < dummy_data.c4gh > old-file.txt