Pack: Taverna localworker example pack

Description:

The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Description:

The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Description:

The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Description:

The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Description:

The beanshell converts the empty string '' to a byte array which is then converted back to the empty string '' by the Byte[]_to_string service.

Description:

The beanshell converts the string 'hello' to a byte array which is then converted back to the string 'hello' by the Byte[]_to_string service.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The choose service displays a dialog with no title or message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a'].

The choose service displays a dialog with 'Some title' and 'Some message'. The user is only able to choose the value 'a'. When the user presses OK 'a' is passed to the answer port of the choose service and so to the output of the workflow.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The choose service displays a dialog with 'Some title' and with 'Some message'. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The choose service displays a dialog with 'Some title' but no message. The user is able to choose from the values ['a','b','c','d',e']. When the user presses OK the value the user chose is passed to the answer port of the choose service and so to the output of the workflow.

Description:

The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell.

The create_temporary_file beanshell creates a file to which the concatentation can be written.

The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has been given a default value of 'true', the results are also copied to the results port of concatenate_files.

The temporary file to which the results were written is read by the read_text_file service and its contents output.

Both of the workflow outputs contain 'a b c d e' i.e. the contents of the concatenated files separated by a newline.

Description:

The split_string_into_string_list_by_regular_expresson outputs an empty list since the string to be split is defaulted to ''. As there are no input values, the create_and_populate_temporary_file generates an empty list.

The create_temporary_file beanshell creates a file to which the concatentation can be written.

The concatenate_files service does not write anything to the temporary output file. Because the displayresults port has been given a default value of 'true', the empty string is also copied to the results port of concatenate_files.

The temporary file to which the results were written is read by the read_text_file service and its contents output.

Both of the workflow outputs contain '' i.e. the empty string.

Description:

The workflow splits the string 'a,b,c,d,e' into its five elements and saves the individual strings to five temporary files. The file paths to those files are then output by the create_and_populate_temporary_file beanshell.

The create_temporary_file beanshell creates a file to which the concatentation can be written.

The concatenate_files service concatenates the five files and writes the result to the temporary output file. Because the displayresults port has no value, the results are not output by the service.

The temporary file to which the results were written is read by the read_text_file service and its contents output.

The workflow output contains 'a b c d e' i.e. the contents of the concatenated files separated by a newline.

Description:

The concatenate two strings service takes the strings 'good' and 'bye' and returns the result 'goodbye'.

Description:

The concatenate two strings service takes two empty strings and returns an empty string.

Description:

The create lots of strings service returns a list containing a large number of strings.

Description:

The decode base64 to byte[] service decodes the base64 string. The byte array is then converted into the string 'Hello world'.

Description:

The echo_with_occasional_failure service mostly echoes the string 'hello' to the out port. Sometimes, it throws a service failure.

Description:

The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Description:

Example file containing GenBank data so that it can be used for example Taverna workflows

Description:

Example SwissProt data to be used for Taverna examples.

Description:

XML file to be used for example workflows

Description:

XSLT file to be used for example workflows

Description:

Note that this workflow only works on Unix systems.

The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the create_and_populate_list beanshell which creates a list of '-R' and the path. The resultant list is passed to the args port of the Execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'.

The execute_cmd_line_app service runs the /bin/ls -R command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Description:

Note that this workflow only works on Unix systems.

The get_temporary_directory beanshell returns the path to the directory in which temporary files are held. This value is passed to the args port of the execute_cmd_line_app service. The command port of that service has been defaulted to '/bin/ls'.

The execute_cmd_line_app service runs the /bin/ls command on the temporary directory. The result is passed to its result port and then to the out port of the workflow.

Description:

The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and the default depth of 1, will output the list [['b','c'], ['f','g'],['j','k'],['n','o'']] as it is the list with depth 1 e.g. ['e','f','g','h'] that are considered.

Description:

The extract_elements_from_a_list is passed the list [['a','b','c', 'd'], ['e','f','g','h'],['i','j','k','l'],['m','n','o','p']] with fromIndex of 1 and toIndex of 3 and depth 2, will output the list [['e','f','g','h'],['i','j','k','l']] as it is the outermost list i.e. that with depth 2 that is considered.

Description:

The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 0 and the toIndex is 5, so the service outputs an identical list.

Description:

The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 2 and the toIndex is 3, so the service outputs the single element list ['c'].

Description:

The fail if true service throws an exception if given the value 'false'.

Description:

The fail if true service executes without an exception if given a non-false value such as 'fred'.

Description:

The fail if true service executes without an exception if given the value 'true'.

Description:

The fail if true service executes without an exception if given the value 'false'.

Description:

The fail if true service executes without an exception if given a value that is not true e.g. 'fred'.

Description:

The fail if true service throws an exception when passed the value true.

Description:

The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then that triple is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['abc', 'axy'] is output.

Description:

The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, the second character after the 'a' is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['c', 'y'] is output.

Description:

The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then the two characters after the 'a' are included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['bc', 'xy'] is output.

Description:

The workflow filters the five element list split from the first service and returns the three elements that match the regular expression.

Description:

The workflow filters the five element list split from the first service and returns an empty list as no elements match.

Description:

The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']],[['e']]] and, using a flatten depth of 3, outputs the list ['a', 'b', 'c', 'd','e'].

Description:

The flatten_list service takes the list [[['a']], [['b']], [['c']], [['d']]] and, using the default flatten depth of 2, outputs the list [['a'], ['b'], ['c'], ['d'], ['e']].

Description:

Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using just the url parameter

Description:

Retrieve the image at http://www.mygrid.org.uk/files/2008/09/dragon-workflow.png using both the url and base parameters

Description:

Retrieve the web page at http://www.mygrid.org.uk, examine it for images and output the images.

Description:

Retrieve the web page at http://www.mygrid.org.uk/usermanual1.7/user_gettings_started.html and examine it for images. The workflow should return an empty list.

Description:

Fetches a web page from http://www.mygrid.org.uk/tools using just the url parameter of the service. Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Description:

Fetches a web page from http://www.mygrid.org.uk/tools with the base parameter as "http://www.mygrid.org.uk" and the url as "/tools". Note that when viewed, the HTML may not be rendered correctly. However, the HTML may be viewed by rendering the result as plain text.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The empty directory is examined by the List_files_by_extension service. Since no files end in ".png", an empty list is output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_extension service. Since no files end in ".fred", an empty list is output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_extension service and the file paths to the three files ending in ".png" are output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_extension service and the file path to the one file ending in ".bin" is output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The empty directory is examined by the List_files_by_regex service. Since there are no files, an empty list is output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_regex service. Since no files match the regular expression 'x.*' i.e. no files have a name that starts with 'x', an empty list is output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_regex service and the file paths matching the regular expression '.*i.*', i.e. those containing an 'i', are output.

Description:

The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory.

The populate_directory beanshell creates several files within the temporary directory.

Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

Description:

The merge string list to string service takes the list ['a','b','c'] and using the separator ':' outputs the string 'a:b:c'.

Description:

The merge string list to string service takes the list ['a','b','c'] and outputs the string 'a b c'.

Description:

The merge string list to string service takes an empty list [] and outputs an empty string ''.

Description:

The pad numeral with leading 0s takes the input '12' and pads it to the default target length of 7, yielding the output '0000012'.

Description:

The pad numeral with leading 0s takes the input '12' and pads it to the specified target length of 4, yielding the output '0012'.

Description:

The pad numeral with leading 0s takes the input '12' and because the specified target length of 1 is too short, yields the output '12'.

Description:

The Get_web_page_from_URL downloads a file from myExperiment that contains GenBank data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_GenBank_file service. That service reads the file and converts the GenBank data into Agave format. The result is then sent to the workflow's out port.

Description:

The Get_web_page_from_URL downloads a file from myExperiment that contains SwissProt data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_SwissProt_file service. That service reads the file and converts the SwissProt data into Agave format. The result is then sent to the workflow's out port.

Description:

The beanshell write the string 'hello' to a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello'.

Description:

The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the empty string ''.

Description:

The beanshell write the string 'hello' four times separated by a new lineto a temporary file. The filepath to the temporary file is then passed to the Read_text_file service which reads the file and outputs the string 'hello hello hello hello'.

Description:

The remove duplicate strings service takes the list ['a','b','c','b','a','d'], strips out duplicate strings and outputs the result ['a','b','c','d'].

Description:

The remove duplicate strings service takes the empty list [] and outputs the result [].

Description:

The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The select service displays a dialog with no title but with 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The select service displays a dialog with no title or message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a' and outputs the list ['a'].

The select service displays a dialog with 'Some title' and 'Some message'. The user is only able to select the value 'a'. When the user presses OK 'a' is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The select service displays a dialog with ''Some title' and 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Description:

The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e'].

The select service displays a dialog with 'Some title' but no message. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Description:

The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression 'o' splits it into the list ['b','',':and:f']

Description:

The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression ':' splits it into the list ['boo','and','foo']

Description:

The split string into string list by regular expression takes the string 'a,b,c' and using the default regular expression ',' splits it into the list ['a','b','c']

Description:

The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].

Description:

The string list difference service takes in ['a','b','c'] and ['a','e','c'] and returns the list ['b','e'].

Description:

The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].

Description:

The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].

Description:

The string list union service takes in two empty lists [] and [] and returns an empty list [].

Description:

The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Description:

The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Description:

The tell service displays an informative dialog with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Description:

The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Description:

The tell service displays an informative dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Description:

The test always fails service generates a service failure when no parameter values are supplied.

Description:

The test always fails service generates a service failure when one parameter value is supplied.

Description:

The test always fails service generates a service failure when two parameter values are supplied.

Description:

The Transcribe DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding transcribed RNA sequence, in this example, 'gauccuccau'.

Description:

The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML.

The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port of Transform_XML.

The create_temporary_file beanshell creates a temporary file to which the transformed XML is to be written. The file path to this file is passed to the outFileURL port of Transform_XML.

The Transform_XML service transforms the XML using the specified XSLT and sends the resultant XML document to its outputStr port and so to the workflow's out port. The transformed XML document is also written to the file whose path is passed to the outFileURL port.

To check the content of the output file, its file path is passed to the Read_Text_File service. Once the Transform_XML service has finished, the Read_Text_File service reads the output file and echoes its content to the contents_of_output_file port of the workflow.

Description:

The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML.

The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port of Transform_XML.

The Transform_XML service transforms the XML using the specified XSLT and sends the resultant XML document to its outputStr port and so to the workflow's out port.

Description:

The get_xml_file_from_web service downloads an example xml from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xml_file. The path to the temporary file is passed to the inFileURL port of Transform_XML.

The get_xslt_file_from_web service downloads an example xslt file from myExperiment. The content of that file is then saved to a temporary file by create_and_populate_xslt_file. The path to the temporary file is passed to the xslFileURL port of Transform_XML.

The Transform_XML service transforms the XML using the specified XSLT and sends the resultant XML document to its outputStr port and so to the workflow's out port. The Transform_XML_service has the default for outputExt set to 'out' so the transformed XML document is also written to the file whose path is the same as that of the inFileURL but with '.out' as the extension.

To check the content of the output file, its file path is calculated by calls of Filter_list_of_strings_extracting_match_to_a_regex and Concatenate_two_strings. The file path is passed to the Read_Text_File service. Once the Transform_XML service has finished, the Read_Text_File service reads the output file and echoes its content to the contents_of_output_file port of the workflow.

Description:

The warn service displays a warning dialog with no title but message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Description:

The warn service displays a prompt with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Description:

The warn service displays a warning dialog with 'Some title' and message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Description:

The warn service displays a warning dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Description:

The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes the empty string '' into the file. '' is also output by the service.

Description:

The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file A service which writes the string 'hello' into the file. After service A has run, service B writes 'goodbye' into the file. The file is then read by the Read_Text_File service and its content, 'goodbye', output by the workflow.

Description:

The beanshell creates an empty temporary file. The filepath to the temporary file is then passed to the Write_text_file service which writes 'hello' into the file. 'hello' is also output by the service.