Example for external tools with zip and unzip
Created: 2012-04-05 16:42:09
Last updated: 2012-04-05 16:42:10
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/
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Authors (1)
Steffen Moeller
Alan Williams |
![header=[] body=[These are the descriptive titles embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Titles (1)
Example for external tools with zip and unzip |
![header=[] body=[These are the descriptions embedded within the workflow version] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Descriptions (1)
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/
|
![header=[] body=[These are the listed dependencies of the workflow] cssheader=[boxoverTooltipHeader] cssbody=[boxoverTooltipBody] delay=[200] Information](/images/famfamfam_silk/information.png?1680607579)
Dependencies (0)
Processors (5)
Name |
Type |
Description |
zip |
externaltool |
|
unzip |
externaltool |
|
Get_Web_Page_from_URL |
localworker |
Scriptif ((url == void) || (url == null)) {
throw new RuntimeException("The url must be specified");
}
URL inputURL = null;
if (base != void) {
inputURL = new URL(new URL(base), url);
}
else {
inputURL = new URL(url);
}
URLConnection con = inputURL.openConnection();
InputStream in = con.getInputStream();
StringBuffer result = new StringBuffer();
BufferedReader reader;
String encoding = con.getContentEncoding();
if (encoding == null) {
reader = new BufferedReader(new InputStreamReader(in));
} else {
reader = new BufferedReader(new InputStreamReader(in, encoding));
}
String line = null;
String NEWLINE = System.getProperty("line.separator");
while ((line = reader.readLine()) != null) {
result.append(line);
result.append(NEWLINE);
}
reader.close();
contents = result.toString();
|
url_value |
stringconstant |
Valuehttp://www.myexperiment.org/files/135/download/franck.txt |
diff |
externaltool |
|
Outputs (9)
Name |
Description |
Original_File |
Parameter file for GROMACS downloaded directly from http://md.chem.rug.nl/~mdcourse/minim.mdp
Any file would do for this example.
|
Unzipped_File |
The compressed file is uncompressed again.
|
unzip_STDERR |
Empty if executing normally.
|
unzip_STDOUT |
Always empty.
|
zip_STDERR |
Empty if executing normally.
|
zip_STDOUT |
Always empty.
|
diff_STDERR |
|
diff_STDOUT |
|
Zipped_file |
|
Datalinks (14)
Source |
Sink |
Get_Web_Page_from_URL:contents |
zip:file_to_zip |
zip:zipped_file |
unzip:zipped_file |
url_value:value |
Get_Web_Page_from_URL:url |
Get_Web_Page_from_URL:contents |
diff:file1 |
unzip:unzipped_file |
diff:file2 |
Get_Web_Page_from_URL:contents |
Original_File |
unzip:unzipped_file |
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 |
zip:zipped_file |
Zipped_file |
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