services:archive:soaplab:guide [2013/02/28 17:03]
hpm (172.22.68.212) Archive Soaplab pages. |
services:archive:soaplab:guide [2013/04/23 16:39] (current)
hpm (172.22.68.212) |
| | ====== Calling Soaplab based EMBOSS Web Services====== | | ====== Calling Soaplab based EMBOSS Web Services====== |
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| - | For [[http://www.ebi.ac.uk/Tools/webservices/tutorials/06_programming| programmatic access]] to Soaplab based [[http://www.ebi.ac.uk/soaplab/| EMBOSS Web Services]] most of the standard Web Services client libraries/tools can be used, alternatively when programming in Java it is possible to use [[http://soaplab.sourceforge.net/soaplab2/BuildClientGuide.html| Soaplab Client Library]] distributed as part of Soaplab. | + | For [[http://www.ebi.ac.uk/Tools/webservices/tutorials/06_programming|programmatic access]] to Soaplab based [[http://www.ebi.ac.uk/soaplab/|EMBOSS Web Services]] most of the standard Web Services client libraries/tools can be used, alternatively when programming in Java it is possible to use [[http://soaplab.sourceforge.net/soaplab2/BuildClientGuide.html|Soaplab Client Library]] distributed as part of Soaplab. |
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| - | EBI Soaplab Web Services have two interfaces. | + | EMBL-EBI Soaplab Web Services have two interfaces. |
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| - | * [[http://www.ebi.ac.uk/soaplab/typed/services/information.wossname| Typed interface]]; input/output types are defined at WSDL/XSD level | + | * [[http://www.ebi.ac.uk/soaplab/typed/services/information.wossname|Typed interface]]; input/output types are defined at WSDL/XSD level |
| - | * [[http://www.ebi.ac.uk/soaplab/services| Generic interface]]; input/output types can be queried by making webservices calls | + | * [[http://www.ebi.ac.uk/soaplab/services|Generic interface]]; input/output types can be queried by making webservices calls |
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| - | You can find below an [[#writing_your_client_in_perl| example Perl script]] that use the typed interface to call two example EMBOSS Web Services. If you decide to use Soaplab client library there is an [[#using_soaplab_client_library| example Java program]] below that lists all available Web Services categories in the EBI Soaplab server and retrieves an example Uniprot entry using the seqret Web Service. | + | |
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| | + | You can find below an [[#writing_your_client_in_perl|example Perl script]] that use the typed interface to call two example EMBOSS Web Services. If you decide to use Soaplab client library there is an [[#using_soaplab_client_library|example Java program]] below that lists all available Web Services categories in the EMBL-EBI Soaplab server and retrieves an example UniProtKB entry using the seqret Web Service. |
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| | Alternative ways of accessing to Soaplab Web Services that requires no programming effort would be listed as follows | | Alternative ways of accessing to Soaplab Web Services that requires no programming effort would be listed as follows |
| - | * [[http://www.ebi.ac.uk/soaplab/| Spinet web interface]], call EMBOSS programs through usual HTML forms | + | * [[http://www.ebi.ac.uk/soaplab/|Spinet web interface]], call EMBOSS programs through usual HTML forms |
| - | * [[http://soaplab.sourceforge.net/soaplab2/CmdLineClient.html| Soaplab client script]], distributed as part of Soaplab, example usage is given [[#using_soaplab_command-line_client_script| below]] | + | * [[http://soaplab.sourceforge.net/soaplab2/CmdLineClient.html|Soaplab client script]], distributed as part of Soaplab, example usage is given [[#using_soaplab_command-line_client_script| below]] |
| - | * [[http://taverna.sourceforge.net/| Taverna workbench]], design and execute workflows that can consume Soaplab Web Services | + | * [[http://taverna.sourceforge.net/|Taverna workbench]], design and execute workflows that can consume Soaplab Web Services |
| - | * Tools similar to [[http://www.soapui.org/| soapUI]], in this case we recommend use of the typed interface | + | * Tools similar to [[http://www.soapui.org/|soapUI]], in this case we recommend use of the typed interface |
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| | ===== Writing your client in Perl ===== | | ===== Writing your client in Perl ===== |
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| - | The following example Perl script demonstrates use of the EBI EMBOSS Web Services. It first calls the [[http://www.ebi.ac.uk/soaplab/typed/services/alignment_global.needle?wsdl| needle]] Web Service to calculate global(overlap) alignment of two input sequences and then calls the [[http://www.ebi.ac.uk/soaplab/typed/services/alignment_multiple.plotcon?wsdl| plotcon]] Web Service to draw a plot of the sequence conservation within windows over the alignment. | + | The following example Perl script demonstrates use of the EMBL-EBI EMBOSS Web Services. It first calls the [[http://www.ebi.ac.uk/soaplab/typed/services/alignment_global.needle?wsdl|needle]] Web Service to calculate global(overlap) alignment of two input sequences and then calls the [[http://www.ebi.ac.uk/soaplab/typed/services/alignment_multiple.plotcon?wsdl|plotcon]] Web Service to draw a plot of the sequence conservation within windows over the alignment. |
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| | <code> | | <code> |
| | ===== Using Soaplab command-line client script ===== | | ===== Using Soaplab command-line client script ===== |
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| - | Soaplab-2 [[http://soaplab.sourceforge.net/soaplab2/CmdLineClient.html|command-line client]] is a typical testing tool that covers the most functionality of the Soaplab features. Although its user-friendliness is limited it can be used for batch and automated Soaplab services calls. It supports both Soaplab-1 and Soaplab-2 servers. You need to install [[http://soaplab.sourceforge.net/soaplab2/BuildClientGuide.html| Soaplab clients module]] to have the Soaplab command-line client script installed in your system. | + | Soaplab-2 [[http://soaplab.sourceforge.net/soaplab2/CmdLineClient.html|command-line client]] is a typical testing tool that covers the most functionality of the Soaplab features. Although its user-friendliness is limited it can be used for batch and automated Soaplab services calls. It supports both Soaplab-1 and Soaplab-2 servers. You need to install [[http://soaplab.sourceforge.net/soaplab2/BuildClientGuide.html|Soaplab clients module]] to have the Soaplab command-line client script installed in your system. |
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| | In order to see the list of options, type: | | In order to see the list of options, type: |
| | build/run/run-cmdline-client -help | | build/run/run-cmdline-client -help |
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| - | To access the list service running at the EBI Soaplab server you may try to use: | + | To access the list service running at the EMBL-EBI Soaplab server you may try to use: |
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| | build/run/run-cmdline-client -l\ | | build/run/run-cmdline-client -l\ |
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| | where (1) shows where to go, (2) says what service to invoke, (3) and (4) are named input data, (5) means "create a job, start it and wait for its completion", and finally (6) says "give me all results". | | where (1) shows where to go, (2) says what service to invoke, (3) and (4) are named input data, (5) means "create a job, start it and wait for its completion", and finally (6) says "give me all results". |
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| | build/run/run-cmdline-client \ | | build/run/run-cmdline-client \ |
| | ===== Using Soaplab client library ===== | | ===== Using Soaplab client library ===== |
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| - | This example uses Soaplab2 API for getting available service categories from the EBI Soaplab server, and also retrieves an example Uniprot entry using the seqret Web Service: | + | This example uses Soaplab2 API for getting available service categories from the EMBL-EBI Soaplab server, and also retrieves an example UniProtKB entry using the seqret Web Service: |
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| | <code java> | | <code java> |
