Mercurial > repos > yhoogstrate > ega_download_streamer
changeset 3:a1f6611f0533 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/ega_client_galaxy_wrapper commit 056cdfa2329a82d02640ccaf6364005d40decafa
| author | yhoogstrate |
|---|---|
| date | Tue, 29 Mar 2016 07:44:25 -0400 |
| parents | 4a8332665db3 |
| children | 42fbce72bc07 |
| files | ega_download_streamer.xml |
| diffstat | 1 files changed, 64 insertions(+), 28 deletions(-) [+] |
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--- a/ega_download_streamer.xml Tue Mar 29 05:45:20 2016 -0400 +++ b/ega_download_streamer.xml Tue Mar 29 07:44:25 2016 -0400 @@ -21,40 +21,76 @@ echo \$user > credentials.txt && echo \$pass >> credentials.txt && - echo "Creating an encryption request at server" && - java -jar + echo "Creating an encryption request at server:" && + + if java -jar "\$JAVA_JAR_PATH/EgaDemoClient.jar" -pf "credentials.txt" -rf "$ega_file_identifier" -re "$encryption_key" - -label "${random_request_uid}" | grep -v "Login failed" && - - echo "\n\n\nDownloading request" && - java -jar - "\$JAVA_JAR_PATH/EgaDemoClient.jar" - -pf "credentials.txt" - -dr "${random_request_uid}" - -nt 7 > download.log && + -label "${random_request_uid}" | grep -v "Login failed" > request.log ; then + + cat request.log && + echo "" && + echo "" && + echo "" && + echo "Downloading request:" && + + if java -jar + "\$JAVA_JAR_PATH/EgaDemoClient.jar" + -pf "credentials.txt" + -dr "${random_request_uid}" + -nt 7 > download.log ; then + + cat download.log && + + ## Commands below may fail if authentication was not a success + ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) && + DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} && + + echo "" && + echo "" && + echo "" && + echo "Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME:" && + + if java -jar + "\$JAVA_JAR_PATH/EgaDemoClient.jar" + -pf credentials.txt + -dc "\$ENCRYPTED_FILES_NAME" + -dck "$encryption_key" > decrypt.log ; then + + cat decrypt.log && + + if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip\$; then + + echo "" && + echo "" && + echo "" && + echo "Unpacking because it is an archive" && + gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ; + + else + mv "\$DECRYPTED_FILES_NAME" "$output" ; + fi ; + + else + echo "Error: decrypting failed:" 1>&2 && + cat decrypt.log && + exit 1 ; + fi ; + + else + echo "Error: downloading the request failed:" 1>&2 && + cat download.log && + exit 1 ; + fi ; - cat download.log && - - ## Commands below may fail if authentication was not a success - ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) && - DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} && + else + echo "Error: making the request failed" 1>&2 && + cat request.log && + exit 1 ; + fi && - echo "\n\n\n Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME" && - java -jar - "\$JAVA_JAR_PATH/EgaDemoClient.jar" - -pf credentials.txt - -dc "\$ENCRYPTED_FILES_NAME" - -dck "$encryption_key" && - - if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip$; then - echo "Unpacking as well" && - gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ; - else - mv "\$DECRYPTED_FILES_NAME" "$output" ; - fi ; echo "Cleaning up credentials" && echo "overwriten" > "credentials.txt" &&