Mercurial > repos > yhoogstrate > ega_download_streamer
comparison ega_download_streamer.xml @ 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 |
comparison
equal
deleted
inserted
replaced
2:4a8332665db3 | 3:a1f6611f0533 |
---|---|
19 #set $random_request_uid = 'request_'+str($ega_file_identifier)+'_'+''.join(random.SystemRandom().choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for _ in range(64)) | 19 #set $random_request_uid = 'request_'+str($ega_file_identifier)+'_'+''.join(random.SystemRandom().choice(string.ascii_uppercase + string.ascii_lowercase + string.digits) for _ in range(64)) |
20 | 20 |
21 echo \$user > credentials.txt && | 21 echo \$user > credentials.txt && |
22 echo \$pass >> credentials.txt && | 22 echo \$pass >> credentials.txt && |
23 | 23 |
24 echo "Creating an encryption request at server" && | 24 echo "Creating an encryption request at server:" && |
25 java -jar | 25 |
26 if java -jar | |
26 "\$JAVA_JAR_PATH/EgaDemoClient.jar" | 27 "\$JAVA_JAR_PATH/EgaDemoClient.jar" |
27 -pf "credentials.txt" | 28 -pf "credentials.txt" |
28 -rf "$ega_file_identifier" | 29 -rf "$ega_file_identifier" |
29 -re "$encryption_key" | 30 -re "$encryption_key" |
30 -label "${random_request_uid}" | grep -v "Login failed" && | 31 -label "${random_request_uid}" | grep -v "Login failed" > request.log ; then |
32 | |
33 cat request.log && | |
34 echo "" && | |
35 echo "" && | |
36 echo "" && | |
37 echo "Downloading request:" && | |
38 | |
39 if java -jar | |
40 "\$JAVA_JAR_PATH/EgaDemoClient.jar" | |
41 -pf "credentials.txt" | |
42 -dr "${random_request_uid}" | |
43 -nt 7 > download.log ; then | |
44 | |
45 cat download.log && | |
46 | |
47 ## Commands below may fail if authentication was not a success | |
48 ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) && | |
49 DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} && | |
50 | |
51 echo "" && | |
52 echo "" && | |
53 echo "" && | |
54 echo "Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME:" && | |
55 | |
56 if java -jar | |
57 "\$JAVA_JAR_PATH/EgaDemoClient.jar" | |
58 -pf credentials.txt | |
59 -dc "\$ENCRYPTED_FILES_NAME" | |
60 -dck "$encryption_key" > decrypt.log ; then | |
61 | |
62 cat decrypt.log && | |
63 | |
64 if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip\$; then | |
65 | |
66 echo "" && | |
67 echo "" && | |
68 echo "" && | |
69 echo "Unpacking because it is an archive" && | |
70 gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ; | |
71 | |
72 else | |
73 mv "\$DECRYPTED_FILES_NAME" "$output" ; | |
74 fi ; | |
75 | |
76 else | |
77 echo "Error: decrypting failed:" 1>&2 && | |
78 cat decrypt.log && | |
79 exit 1 ; | |
80 fi ; | |
81 | |
82 else | |
83 echo "Error: downloading the request failed:" 1>&2 && | |
84 cat download.log && | |
85 exit 1 ; | |
86 fi ; | |
31 | 87 |
32 echo "\n\n\nDownloading request" && | 88 else |
33 java -jar | 89 echo "Error: making the request failed" 1>&2 && |
34 "\$JAVA_JAR_PATH/EgaDemoClient.jar" | 90 cat request.log && |
35 -pf "credentials.txt" | 91 exit 1 ; |
36 -dr "${random_request_uid}" | 92 fi && |
37 -nt 7 > download.log && | |
38 | 93 |
39 cat download.log && | |
40 | |
41 ## Commands below may fail if authentication was not a success | |
42 ENCRYPTED_FILES_NAME=\$(grep -oE "Completed Download Target:[ ]+(.*?)\.cip" download.log | sed -r "s/^Completed Download Target:[ ]+//" ) && | |
43 DECRYPTED_FILES_NAME=\${ENCRYPTED_FILES_NAME%.cip} && | |
44 | |
45 echo "\n\n\n Decrpyting \$ENCRYPTED_FILES_NAME to \$DECRYPTED_FILES_NAME" && | |
46 java -jar | |
47 "\$JAVA_JAR_PATH/EgaDemoClient.jar" | |
48 -pf credentials.txt | |
49 -dc "\$ENCRYPTED_FILES_NAME" | |
50 -dck "$encryption_key" && | |
51 | |
52 if file --mime-type "\$DECRYPTED_FILES_NAME" | grep -q /gzip$; then | |
53 echo "Unpacking as well" && | |
54 gunzip -cf "\$DECRYPTED_FILES_NAME" > "$output" ; | |
55 else | |
56 mv "\$DECRYPTED_FILES_NAME" "$output" ; | |
57 fi ; | |
58 | 94 |
59 echo "Cleaning up credentials" && | 95 echo "Cleaning up credentials" && |
60 echo "overwriten" > "credentials.txt" && | 96 echo "overwriten" > "credentials.txt" && |
61 rm "credentials.txt" | 97 rm "credentials.txt" |
62 ]]></command> | 98 ]]></command> |