Hi Kostas,
> I remember. However, I revisited it because I am getting different
> results when I run it with the client from when I run it in the
> workbench. Since it doesn't happen with inputs without the quotes I
> assume that the escaping did not work exactly as we liked... actually
> it is treated the same as without the quotes:
> transmembrane proteins AND amyloid
>
> If you use the above in WB it will provide the same results as the client.
>
> You can check the validated protein output to see the differences
> between the results.
Hmm, yes I see your point now!
I tried quoting like this and I think I got the results you are looking for:
"\"\"transmembrane proteins\" AND amyloid\""
I have attached the results I got for you to have a look at - are they OK?
The problem seems to be in trying to get ones head around where the escaping
should be done and, crucially, how to do it consistently. Clearly it would be
nice if the user could type "transmembrane proteins" AND amyloid and then have
the client library do the correct escaping to end up with "\"\"transmembrane
proteins\" AND amyloid\"" internally. But this is impossible when the shell
eats all of the unescaped quotes before the client library even sees them!
Cheers,
Rob
Created run with uuid: e03805bf-bd5f-433a-b707-d737a378f8fd
Created at Mon Feb 21 15:06:18 +0000 2011
Set input 'Query' to ""transmembrane proteins" AND amyloid"
Set input 'maxHits_parameter' to 3
Started at Mon Feb 21 15:06:18 +0000 2011
Running..................................
Finished at Mon Feb 21 15:06:53 +0000 2011
Exitcode: 0
Stdout:
ERROR 2011-02-21 15:06:19,123
(net.sf.taverna.raven.appconfig.ApplicationUserHome:152) - User home not a
valid directory: /usr/share/tomcat5.5
WARN 2011-02-21 15:06:19,128
(net.sf.taverna.raven.appconfig.ApplicationRuntime:137) - Could not determine
application's user home, using temporary dir
/tmp/taverna-cmd-2.2.0-201007063139113560869593166home
Outputs will be saved to the directory:
/usr/local/tomcat6.0/apache-tomcat-6.0.26/temp/fae01c61-9c08-4a2e-8350-2af66ea613a6/out
Outputs:
UniProtID -> [[[["P04154", "P07207", "P46531", "Q01705", "Q06007",
"Q07008", "Q59ED8", "Q5SXM3", "Q61905", "Q99JC2", "Q9QW58", "Q9R0X7",
"Q9W4T8"]], [["P15943", "Q06335", "Q06481", "Q13861", "Q14594", "Q14662",
"Q71U10", "Q7M4L3", "Q9BT36", "Q9TVV0", "Q9U4H3", "Q9W5F1", "P05067", "P08592",
"P09000", "P12023", "P78438", "P97487", "P97942", "Q10651", "Q13764", "Q13778",
"Q13793", "Q16011", "Q16014", "Q16019", "Q16020", "Q18583", "Q547B7", "Q6GSC0",
"Q8WZ99", "Q95ZX1", "Q99K32", "Q9BT38", "Q9UC33", "Q9UCA9", "Q9UCB6", "Q9UCC8",
"Q9UCD1", "Q9UQ58"]], [["P15943", "Q06335", "Q06481", "Q13861", "Q14594",
"Q14662", "Q71U10", "Q7M4L3", "Q9BT36", "Q9TVV0", "Q9U4H3", "Q9W5F1", "P05067",
"P08592", "P09000", "P12023", "P78438", "P97487", "P97942", "Q10651", "Q13764",
"Q13778", "Q13793", "Q16011", "Q16014", "Q16019", "Q16020", "Q18583", "Q547B7",
"Q6GSC0", "Q8WZ99", "Q95ZX1", "Q99K32", "Q9BT38", "Q9UC33", "Q9UCA9", "Q9UCB6",
"Q9UCC8", "Q9UCD1", "Q9UQ58"]], [], [], [], [], [], [], [], [["A6NL69",
"O00213", "O08642", "P46933", "Q3TPU0", "Q8BNF4", "Q8BSR9", "Q96A93", "Q99MK3",
"Q9QXJ1"]], [["O97425", "Q08649", "Q13430", "Q17RW5", "Q5XI16", "Q6GSE8",
"Q8CGZ3", "Q8CGZ4", "Q8CHK4", "Q8VIH0", "Q92993", "Q960X4", "Q99MK2", "Q9BWK7",
"Q9TYU5"]], [], [], [], [], [], [], [], []], [[], [["P15943", "Q06335",
"Q06481", "Q13861", "Q14594", "Q14662", "Q71U10", "Q7M4L3", "Q9BT36", "Q9TVV0",
"Q9U4H3", "Q9W5F1", "P05067", "P08592", "P09000", "P12023", "P78438", "P97487",
"P97942", "Q10651", "Q13764", "Q13778", "Q13793", "Q16011", "Q16014", "Q16019",
"Q16020", "Q18583", "Q547B7", "Q6GSC0", "Q8WZ99", "Q95ZX1", "Q99K32", "Q9BT38",
"Q9UC33", "Q9UCA9", "Q9UCB6", "Q9UCC8", "Q9UCD1", "Q9UQ58"]], [], [["O88731",
"O88732", "P70350", "Q03600", "Q13683", "Q24247", "Q5HZX9", "Q61737", "Q61738",
"Q61741", "Q63026", "Q63027", "Q63258", "Q8SY51", "Q9NY89", "Q9UET0", "Q9UEV2",
"Q9VYF6", "O95465", "P49768", "P49769", "P52166", "P97529", "P97887", "Q14762",
"Q15719", "Q15720", "Q20076", "Q4JIM4", "Q90X08", "Q91WK6", "Q96P33", "Q9JLP9",
"Q9U9C7", "Q9UIF0", "Q9W6T7", "O02194", "O02395", "O08947", "O35546", "O54977",
"O76802", "O88777", "O96340", "P49810", "P97934", "P97935", "Q61144", "Q90X07",
"Q90ZE4", "Q91VS3", "Q96P32", "Q9D616", "Q9I991", "Q9TY80", "Q9V3L9",
"Q9V3S1"]], [["O88731", "O88732", "P70350", "Q03600", "Q13683", "Q24247",
"Q5HZX9", "Q61737", "Q61738", "Q61741", "Q63026", "Q63027", "Q63258", "Q8SY51",
"Q9NY89", "Q9UET0", "Q9UEV2", "Q9VYF6", "O95465", "P49768", "P49769", "P52166",
"P97529", "P97887", "Q14762", "Q15719", "Q15720", "Q20076", "Q4JIM4", "Q90X08",
"Q91WK6", "Q96P33", "Q9JLP9", "Q9U9C7", "Q9UIF0", "Q9W6T7", "O02194", "O02395",
"O08947", "O35546", "O54977", "O76802", "O88777", "O96340", "P49810", "P97934",
"P97935", "Q61144", "Q90X07", "Q90ZE4", "Q91VS3", "Q96P32", "Q9D616", "Q9I991",
"Q9TY80", "Q9V3L9", "Q9V3S1"]], [["P15943", "Q06335", "Q06481", "Q13861",
"Q14594", "Q14662", "Q71U10", "Q7M4L3", "Q9BT36", "Q9TVV0", "Q9U4H3", "Q9W5F1",
"P05067", "P08592", "P09000", "P12023", "P78438", "P97487", "P97942", "Q10651",
"Q13764", "Q13778", "Q13793", "Q16011", "Q16014", "Q16019", "Q16020", "Q18583",
"Q547B7", "Q6GSC0", "Q8WZ99", "Q95ZX1", "Q99K32", "Q9BT38", "Q9UC33", "Q9UCA9",
"Q9UCB6", "Q9UCC8", "Q9UCD1", "Q9UQ58"]], [["Q9VL09", "B2R6T5", "P04629",
"P08119", "P35739", "Q15655", "Q15656", "Q3UFB7", "Q5D056", "Q5VZS2", "Q7Z5C3",
"Q9UIU7"]], [["O88731", "O88732", "P70350", "Q03600", "Q13683", "Q24247",
"Q5HZX9", "Q61737", "Q61738", "Q61741", "Q63026", "Q63027", "Q63258", "Q8SY51",
"Q9NY89", "Q9UET0", "Q9UEV2", "Q9VYF6", "O95465", "P49768", "P49769", "P52166",
"P97529", "P97887", "Q14762", "Q15719", "Q15720", "Q20076", "Q4JIM4", "Q90X08",
"Q91WK6", "Q96P33", "Q9JLP9", "Q9U9C7", "Q9UIF0", "Q9W6T7", "O02194", "O02395",
"O08947", "O35546", "O54977", "O76802", "O88777", "O96340", "P49810", "P97934",
"P97935", "Q61144", "Q90X07", "Q90ZE4", "Q91VS3", "Q96P32", "Q9D616", "Q9I991",
"Q9TY80", "Q9V3L9", "Q9V3S1"]]], [[["Q5K3A6", "Q5TC28", "Q5VUT1", "Q6N027",
"Q6ST50", "Q71JF2", "Q8BGR4", "Q8VHS2", "Q8WWY0"]], [["Q6P6N1", "Q80YA8",
"Q5IJ48", "Q5JS41", "Q5JS43", "Q6ZTA9", "Q6ZWI6"]], [["Q8N0V8", "Q8QZT4",
"Q8WVA0", "Q9BUF7"]], [], [], [["Q08423", "Q3TVE6", "Q63467", "A0AV67",
"P06756", "P12080", "P26008", "P43406", "Q53SK4", "Q59EB7", "Q6LD15", "Q9VXB6",
"B2RD16", "O75340", "P12815", "P53238", "Q545I0", "Q5TZS0", "Q61145", "O95465",
"P49768", "P49769", "P52166", "P97529", "P97887", "Q14762", "Q15719", "Q15720",
"Q20076", "Q4JIM4", "Q90X08", "Q91WK6", "Q96P33", "Q9JLP9", "Q9U9C7", "Q9UIF0",
"Q9W6T7", "O02194", "O02395", "O08947", "O35546", "O54977", "O76802", "O88777",
"O96340", "P49810", "P97934", "P97935", "Q61144", "Q90X07", "Q90ZE4", "Q91VS3",
"Q96P32", "Q9D616", "Q9I991", "Q9TY80", "Q9V3L9", "Q9V3S1"]], [["Q6TQU2",
"Q6TQU3", "O45876", "Q8BVF7", "Q8JHE9", "Q8R1T3", "Q91VL5", "Q9VQG2"]],
[["B2R5L9", "Q6QI68", "Q86BE9", "Q8MUT4", "Q9NZ42", "Q9U357", "P52295",
"Q24431", "Q95R96", "Q9VL45", "Q9CQR7", "Q568W9", "Q8JHF0"]], [], [],
[["P15943", "Q06335", "Q06481", "Q13861", "Q14594", "Q14662", "Q71U10",
"Q7M4L3", "Q9BT36", "Q9TVV0", "Q9U4H3", "Q9W5F1", "P05067", "P08592", "P09000",
"P12023", "P78438", "P97487", "P97942", "Q10651", "Q13764", "Q13778", "Q13793",
"Q16011", "Q16014", "Q16019", "Q16020", "Q18583", "Q547B7", "Q6GSC0", "Q8WZ99",
"Q95ZX1", "Q99K32", "Q9BT38", "Q9UC33", "Q9UCA9", "Q9UCB6", "Q9UCC8", "Q9UCD1",
"Q9UQ58"]], [], [], [], [], [], [["Q6P6N1", "Q80YA8", "Q5IJ48", "Q5JS41",
"Q5JS43", "Q6ZTA9", "Q6ZWI6"]], [["Q8N0V8", "Q8QZT4", "Q8WVA0", "Q9BUF7"]],
[["P15943", "Q06335", "Q06481", "Q13861", "Q14594", "Q14662", "Q71U10",
"Q7M4L3", "Q9BT36", "Q9TVV0", "Q9U4H3", "Q9W5F1", "P05067", "P08592", "P09000",
"P12023", "P78438", "P97487", "P97942", "Q10651", "Q13764", "Q13778", "Q13793",
"Q16011", "Q16014", "Q16019", "Q16020", "Q18583", "Q547B7", "Q6GSC0", "Q8WZ99",
"Q95ZX1", "Q99K32", "Q9BT38", "Q9UC33", "Q9UCA9", "Q9UCB6", "Q9UCC8", "Q9UCD1",
"Q9UQ58"]], [["Q5K3A6", "Q5TC28", "Q5VUT1", "Q6N027", "Q6ST50", "Q71JF2",
"Q8BGR4", "Q8VHS2", "Q8WWY0"]], [["Q6P6N1", "Q80YA8", "Q5IJ48", "Q5JS41",
"Q5JS43", "Q6ZTA9", "Q6ZWI6"]], [["Q8N0V8", "Q8QZT4", "Q8WVA0", "Q9BUF7"]],
[["Q5K3A6", "Q5TC28", "Q5VUT1", "Q6N027", "Q6ST50", "Q71JF2", "Q8BGR4",
"Q8VHS2", "Q8WWY0"]], [["Q6P6N1", "Q80YA8", "Q5IJ48", "Q5JS41", "Q5JS43",
"Q6ZTA9", "Q6ZWI6"]], [["Q8N0V8", "Q8QZT4", "Q8WVA0", "Q9BUF7"]], [], []]]
ValidatedProtein -> [[["Notch1"], ["APP"], ["APP"], [], [], [], [],
[], [], [], ["Fe65"], ["Tip60"], [], [], [], [], [], [], [], []], [[], ["APP"],
[], ["PS1"], ["PS1"], ["APP"], ["Trk"], ["PS1"]], [["CRB1"], ["CRB2"],
["CRB3"], [], [], ["PS2"], ["Aph1"], ["Pen2"], [], [], ["APP"], [], [], [], [],
[], ["CRB2"], ["CRB3"], ["APP"], ["CRB1"], ["CRB2"], ["CRB3"], ["CRB1"],
["CRB2"], ["CRB3"], [], []]]
> On 15 February 2011 17:54, Robert Haines <[email protected]> wrote:
>> Hi Kostas,
>>
>> Apologies for the delay in replying!
>>
>>> When I try to run the workflow below in the workbench
>>>
>>> http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml?version=3
>>>
>>> with inputs:
>>>
>>> "transmembrane proteins" AND amyloid
>>> 3
>>>
>>> it works fine.
>>>
>>> When I try via the ruby client:
>>>
>>> $ t2-run-workflow -w 74.t2flow -i Query:"\"transmembrane proteins\"
>>> AND amyloid" -i maxHits_parameter:3
>>> http://localhost:8980/taverna-server > tmptmptmp
>>>
>>> I get an error (see tmptmptmp).
>>>
>>> I tried escaping differently but I still get the same problem.
>>>
>>> Any ideas what is going wrong?
>>
>> If you remember, we saw this problem a while back (either just before or
>> just after Christmas I think) and we solved it with careful escaping.
>> Remember that the shell will consume an escape each time and that the double
>> quotes still need to be escaped after the shell has processed the line, and
>> slashes themselves must be escaped! So three slashes are needed rather than
>> one:
>>
>>> $ t2-run-workflow -w 74.t2flow -i Query:"\\\"transmembrane proteins\\\"
>>> AND amyloid" -i maxHits_parameter:3
>>> http://localhost:8980/taverna-server > tmptmptmp
>>
>>
>>
>> Best wishes,
>> Rob
>>
>> --
>> Robert Haines
>> myGrid Team
>> School of Computer Science
>> University of Manchester
>>
>>
>> ------------------------------------------------------------------------------
>> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
>> Pinpoint memory and threading errors before they happen.
>> Find and fix more than 250 security defects in the development cycle.
>> Locate bottlenecks in serial and parallel code that limit performance.
>> http://p.sf.net/sfu/intel-dev2devfeb
>> _______________________________________________
>> taverna-users mailing list
>> [email protected]
>> [email protected]
>> Web site: http://www.taverna.org.uk
>> Mailing lists: http://www.taverna.org.uk/about/contact-us/
>>
>
> ------------------------------------------------------------------------------
> The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
> Pinpoint memory and threading errors before they happen.
> Find and fix more than 250 security defects in the development cycle.
> Locate bottlenecks in serial and parallel code that limit performance.
> http://p.sf.net/sfu/intel-dev2devfeb
> _______________________________________________
> taverna-users mailing list
> [email protected]
> [email protected]
> Web site: http://www.taverna.org.uk
> Mailing lists: http://www.taverna.org.uk/about/contact-us/
--
Robert Haines
myGrid Team
School of Computer Science
University of Manchester
------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/about/contact-us/
