PHP exec function error:

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chemcrack
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Posts: 4
Joined: Fri Jun 25, 2010 12:15 am

PHP exec function error:

Post by chemcrack »

I am trying to execute awk command in php ...
It works fine if i don't pipe the first output...
What's wrong with the code... :banghead:

Code: Select all

$descfile = "user.oddescriptors.txt";
$output = exec("awk 'FNR>186' "$descfile" |awk '{sub(/^/, "1, ")};1'|awk '{sub(/[ \,?]+$/, "")};1'|awk '{$116=$117=$118=$126=""}1'");
davex
Forum Contributor
Posts: 101
Joined: Sat Feb 27, 2010 4:10 pm
Location: Namibia

Re: PHP exec function error:

Post by davex »

Hi,

Well just on first look without digging any deeper I can see a problem with your quotes - in the string you are using "" within the awk command. This will need to be escaped for them to make sense in PHP or else PHP will read them as close-quotes. Oh I also see a backslash will will also need escaped:

Try:

Code: Select all

$descfile = "user.oddescriptors.txt";
$output = exec("awk 'FNR>186' ".$descfile." |awk '{sub(/^/, \"1, \")};1'|awk '{sub(/[ \\,?]+$/, \"\")};1'|awk '{$116=$117=$118=$126=\"\"}1'");
Which I think should exec the command:

awk 'FNR>186' user.oddescriptors.txt |awk '{sub(/^/,"1,")};1'| awk '{sub(/[ \,?]+$/,"")};1'| awk '{$116=$117=$118=$126=""}1'

But also I'm not sure if you might get stung and $116 etc will try and resolve as variables... Maybe echo the command out and see what is actually being committed.

Cheers,

Dave.
chemcrack
Forum Newbie
Posts: 4
Joined: Fri Jun 25, 2010 12:15 am

Re: PHP exec function error:

Post by chemcrack »

Hi Dave,

Thanks for noticing the error...it really helps ..i' ll take care of this..
hmm i tried with your code as well..but same problem this time tooo!!!

however, I solved this by putting the same in shell script and called them in php,,it works..
but it should have worked in awk as well...isnt???
anyway its solved.. thanks for helping me!!!!

myscript.sh:
awk 'FNR>186' $1 |awk '{sub(/^/, "1, ")};1'|awk '{sub(/[ \,?]+$/, "")};1'|awk '{$116=$117=$118=$126=""}1'>featurefile;

Code: Select all

<? 
 system("sh myscript.sh $name2");
?>
davex
Forum Contributor
Posts: 101
Joined: Sat Feb 27, 2010 4:10 pm
Location: Namibia

Re: PHP exec function error:

Post by davex »

Hi,

Well if it works then it works!

I would look at the command by putting it into a string and echoing before execing - something will probably stand out straight away. I don't see any reason it shouldn't work.

Cheers,

Dave.
chemcrack
Forum Newbie
Posts: 4
Joined: Fri Jun 25, 2010 12:15 am

Re: PHP exec function error:

Post by chemcrack »

I am not sure how to do that. Could you please elaborate.
I am pasting the input file for your reference. (as its not getting attached !!)
please bear with me for the long text..

thanks
sangeetha.


%
% molecular properties of user.sdf
% this file contains molecular descriptors computed by JOELib2 and the CDK
%
% authors: Georg Hinselmann, Nikolas Fechner
% University of Tuebingen, Germany
%
%
@RELATION 'molecule'
@ATTRIBUTE joelib2.feature.types.count.NumberOfAtoms NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfB NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfBr NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfC NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfCl NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfF NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfHal NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfI NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfN NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfO NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfP NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfS NUMERIC
@ATTRIBUTE joelib2.feature.types.FractionRotatableBonds NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NumberOfBonds NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HeavyBonds NUMERIC
@ATTRIBUTE joelib2.feature.types.count.AromaticBonds NUMERIC
@ATTRIBUTE joelib2.feature.types.MolecularWeight NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HeteroCycles NUMERIC
@ATTRIBUTE joelib2.feature.types.KierShape1 NUMERIC
@ATTRIBUTE joelib2.feature.types.KierShape2 NUMERIC
@ATTRIBUTE joelib2.feature.types.KierShape3 NUMERIC
@ATTRIBUTE WTPT-1 NUMERIC
@ATTRIBUTE WTPT-2 NUMERIC
@ATTRIBUTE WTPT-3 NUMERIC
@ATTRIBUTE WTPT-4 NUMERIC
@ATTRIBUTE WTPT-5 NUMERIC
@ATTRIBUTE joelib2.feature.types.TopologicalDiameter NUMERIC
@ATTRIBUTE joelib2.feature.types.GraphShapeCoefficient NUMERIC
@ATTRIBUTE chi0vC NUMERIC
@ATTRIBUTE chi1vC NUMERIC
@ATTRIBUTE Zagreb NUMERIC
@ATTRIBUTE SCH-3 NUMERIC
@ATTRIBUTE SCH-4 NUMERIC
@ATTRIBUTE SCH-5 NUMERIC
@ATTRIBUTE SCH-6 NUMERIC
@ATTRIBUTE VCH-3 NUMERIC
@ATTRIBUTE VCH-4 NUMERIC
@ATTRIBUTE VCH-5 NUMERIC
@ATTRIBUTE VCH-6 NUMERIC
@ATTRIBUTE SC-3 NUMERIC
@ATTRIBUTE SC-4 NUMERIC
@ATTRIBUTE SC-5 NUMERIC
@ATTRIBUTE SC-6 NUMERIC
@ATTRIBUTE VC-3 NUMERIC
@ATTRIBUTE VC-4 NUMERIC
@ATTRIBUTE VC-5 NUMERIC
@ATTRIBUTE VC-6 NUMERIC
@ATTRIBUTE SP-0 NUMERIC
@ATTRIBUTE SP-1 NUMERIC
@ATTRIBUTE SP-2 NUMERIC
@ATTRIBUTE SP-3 NUMERIC
@ATTRIBUTE SP-4 NUMERIC
@ATTRIBUTE SP-5 NUMERIC
@ATTRIBUTE SP-6 NUMERIC
@ATTRIBUTE SP-7 NUMERIC
@ATTRIBUTE VP-8 NUMERIC
@ATTRIBUTE VP-9 NUMERIC
@ATTRIBUTE VP-10 NUMERIC
@ATTRIBUTE VP-11 NUMERIC
@ATTRIBUTE VP-12 NUMERIC
@ATTRIBUTE VP-13 NUMERIC
@ATTRIBUTE VP-14 NUMERIC
@ATTRIBUTE VP-15 NUMERIC
@ATTRIBUTE SPC-4 NUMERIC
@ATTRIBUTE SPC-5 NUMERIC
@ATTRIBUTE SPC-6 NUMERIC
@ATTRIBUTE VPC-4 NUMERIC
@ATTRIBUTE VPC-5 NUMERIC
@ATTRIBUTE VPC-6 NUMERIC
@ATTRIBUTE WPATH NUMERIC
@ATTRIBUTE WPOL NUMERIC
@ATTRIBUTE chi0C NUMERIC
@ATTRIBUTE chi1C NUMERIC
@ATTRIBUTE ECCEN NUMERIC
@ATTRIBUTE nAtomLAC NUMERIC
@ATTRIBUTE nAtomLC NUMERIC
@ATTRIBUTE nAtomP NUMERIC
@ATTRIBUTE ATSc1 NUMERIC
@ATTRIBUTE ATSc2 NUMERIC
@ATTRIBUTE ATSc3 NUMERIC
@ATTRIBUTE ATSc4 NUMERIC
@ATTRIBUTE ATSc5 NUMERIC
@ATTRIBUTE ATSm1 NUMERIC
@ATTRIBUTE ATSm2 NUMERIC
@ATTRIBUTE ATSm3 NUMERIC
@ATTRIBUTE ATSm4 NUMERIC
@ATTRIBUTE ATSm5 NUMERIC
@ATTRIBUTE bpol NUMERIC
@ATTRIBUTE apol NUMERIC
@ATTRIBUTE GRAV-1 NUMERIC
@ATTRIBUTE GRAV-2 NUMERIC
@ATTRIBUTE GRAV-3 NUMERIC
@ATTRIBUTE GRAVH-1 NUMERIC
@ATTRIBUTE GRAVH-2 NUMERIC
@ATTRIBUTE GRAVH-3 NUMERIC
@ATTRIBUTE GRAV-4 NUMERIC
@ATTRIBUTE GRAV-5 NUMERIC
@ATTRIBUTE GRAV-6 NUMERIC
@ATTRIBUTE LOBMAX NUMERIC
@ATTRIBUTE LOBMIN NUMERIC
@ATTRIBUTE MOMI-X NUMERIC
@ATTRIBUTE MOMI-Y NUMERIC
@ATTRIBUTE MOMI-Z NUMERIC
@ATTRIBUTE MOMI-XY NUMERIC
@ATTRIBUTE MOMI-XZ NUMERIC
@ATTRIBUTE MOMI-YZ NUMERIC
@ATTRIBUTE MOMI-R NUMERIC
@ATTRIBUTE joelib2.feature.types.GeometricalDiameter NUMERIC
@ATTRIBUTE joelib2.feature.types.GeometricalRadius NUMERIC
@ATTRIBUTE Wlambda1.unity NUMERIC
@ATTRIBUTE Wlambda2.unity NUMERIC
@ATTRIBUTE Wlambda3.unity NUMERIC
@ATTRIBUTE Wnu1.unity NUMERIC
@ATTRIBUTE Wnu2.unity NUMERIC
@ATTRIBUTE Wgamma1.unity NUMERIC
@ATTRIBUTE Wgamma2.unity NUMERIC
@ATTRIBUTE Wgamma3.unity NUMERIC
@ATTRIBUTE Weta1.unity NUMERIC
@ATTRIBUTE Weta2.unity NUMERIC
@ATTRIBUTE Weta3.unity NUMERIC
@ATTRIBUTE WT.unity NUMERIC
@ATTRIBUTE WA.unity NUMERIC
@ATTRIBUTE WV.unity NUMERIC
@ATTRIBUTE WK.unity NUMERIC
@ATTRIBUTE WG.unity NUMERIC
@ATTRIBUTE WD.unity NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HBA1 NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HBA2 NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HBD1 NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HBD2 NUMERIC
@ATTRIBUTE joelib2.feature.types.count.AcidicGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.BasicGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.HydrophobicGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.AliphaticOHGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.AromaticOHGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.NO2Groups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.OSOGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.SO2Groups NUMERIC
@ATTRIBUTE joelib2.feature.types.count.SOGroups NUMERIC
@ATTRIBUTE joelib2.feature.types.MolarRefractivity NUMERIC
@ATTRIBUTE joelib2.feature.types.LogP NUMERIC
@ATTRIBUTE joelib2.feature.types.PolarSurfaceArea NUMERIC
@ATTRIBUTE joelib2.feature.types.GlobalTopologicalChargeIndex NUMERIC
@ATTRIBUTE PPSA-1 NUMERIC
@ATTRIBUTE PPSA-2 NUMERIC
@ATTRIBUTE PPSA-3 NUMERIC
@ATTRIBUTE PNSA-1 NUMERIC
@ATTRIBUTE PNSA-2 NUMERIC
@ATTRIBUTE PNSA-3 NUMERIC
@ATTRIBUTE DPSA-1 NUMERIC
@ATTRIBUTE DPSA-2 NUMERIC
@ATTRIBUTE DPSA-3 NUMERIC
@ATTRIBUTE FPSA-1 NUMERIC
@ATTRIBUTE FPSA-2 NUMERIC
@ATTRIBUTE FPSA-3 NUMERIC
@ATTRIBUTE FNSA-1 NUMERIC
@ATTRIBUTE FNSA-2 NUMERIC
@ATTRIBUTE FNSA-3 NUMERIC
@ATTRIBUTE WPSA-1 NUMERIC
@ATTRIBUTE WPSA-2 NUMERIC
@ATTRIBUTE WPSA-3 NUMERIC
@ATTRIBUTE WNSA-1 NUMERIC
@ATTRIBUTE WNSA-2 NUMERIC
@ATTRIBUTE WNSA-3 NUMERIC
@ATTRIBUTE RPCG NUMERIC
@ATTRIBUTE RNCG NUMERIC
@ATTRIBUTE RPCS NUMERIC
@ATTRIBUTE RNCS NUMERIC
@ATTRIBUTE THSA NUMERIC
@ATTRIBUTE TPSA NUMERIC
@ATTRIBUTE RHSA NUMERIC
@ATTRIBUTE RPSA NUMERIC
@ATTRIBUTE XLogP NUMERIC
@ATTRIBUTE LipinksiFailures NUMERIC
@ATTRIBUTE KI NUMERIC
@DATA
% NAME OF MOLECULE 1: 44199335
44.0, 0.0, 0.0, 15.0, 0.0, 0.0, 0.0, 0.0, 1.0, 6.0, 0.0, 0.0, 0.2174, 45.0, 23.0, 0.0, 312.342, 1.0, 18.3403, 6.8571, 2.922, 43.3222, 1.9692, 17.9281, 14.8864, 3.0417, 12.0, 11.0, 9.4223, 5.5908, 139.0, 0.0, 0.0, 0.0589, 0.3885, 0.0, 0.0, 0.0361, 0.1994, 2.2082, 0.2033, 1.5001, 0.4448, 1.146, 0.1006, 0.5297, 0.1384, 16.5436, 10.2857, 9.6801, 8.2726, 7.2839, 4.9582, 2.6106, 1.7283, 12.5276, 7.5207, 6.2826, 5.0096, 3.672, 2.3118, 1.1798, 0.7019, 6.2715, 11.9929, 16.8764, 2.8822, 4.3564, 5.1734, 920.0, 43.0, 9.8365, 6.0074, 330.0, 10.0, 45.0, 3.0, 1.1974, -0.6576, 0.0027, -0.0407, 0.146, 27.1688, 27.3805, 43.6461, 56.8724, 63.7556, 27.7198, 47.6482, 1737.9365, 41.6886, 12.023, 2004.6114, 44.7729, 12.6089, 4320.3114, 65.7291, 16.2869, 2.071, 1.9596, 3264.7591, 3129.1874, 832.4512, 1.0433, 3.9219, 3.759, 6.4, 12.6475, 0.9721, 1.4198, 2.0378, 10.8917, 0.0989, 0.142, ?, ?, ?, 0.4315, 0.3879, 0.4619, 14.3494, 40.5529, 86.4153, 0.3193, ?, 1.2813, 28.0, 7.0, 4.0, 5.0, 1.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0, 0.0, 97.8635, 1.6469, 129.92, 2.0061, 452.0649, 1189.1524, 40.2413, 152.5738, -401.344, -43.4179, 299.4911, 1590.4964, 83.6593, 0.7477, 1.9667, 0.0666, 0.2523, -0.6638, -0.0718, 273.336, 719.0076, 24.3315, 92.2521, -242.6682, -26.2522, 0.1085, 0.1504, 0.0205, 4.747, 354.1158, 250.523, 0.5857, 0.4143, 0.306, 0.0, ?
phptutor
Forum Newbie
Posts: 1
Joined: Wed Jun 16, 2010 8:36 am

Re: PHP exec function error:

Post by phptutor »

I can run this code correctly with out any prob

http://www.phptutor.net
davex
Forum Contributor
Posts: 101
Joined: Sat Feb 27, 2010 4:10 pm
Location: Namibia

Re: PHP exec function error:

Post by davex »

Hi,

Something like:

Code: Select all

$descfile = "user.oddescriptors.txt";
$command = "awk 'FNR>186' ".$descfile." |awk '{sub(/^/, \"1, \")};1'|awk '{sub(/[ \\,?]+$/, \"\")};1'|awk '{$116=$117=$118=$126=\"\"}1'";
echo $command;
$output = exec($command);
Cheers,

Dave.
chemcrack
Forum Newbie
Posts: 4
Joined: Fri Jun 25, 2010 12:15 am

Re: PHP exec function error:

Post by chemcrack »

Great!!!
Are you able to echo $output ...Please let me know..
But i am not able to see the echo $output in browser???why??

output should be something like :
1, 44.0, 0.0, 0.0, 15.0, 0.0, 0.0, 0.0, 0.0, 1.0, 6.0, 0.0, 0.0, 0.2174, 45.0, 23.0, 0.0, 312.342, 1.0, 18.3403, 6.8571, 2.922, 43.3222, 1.9692, 17.9281, 14.8864, 3.0417, 12.0, 11.0, 9.4223, 5.5908, 139.0, 0.0, 0.0, 0.0589, 0.3885, 0.0, 0.0, 0.0361, 0.1994, 2.2082, 0.2033, 1.5001, 0.4448, 1.146, 0.1006, 0.5297, 0.1384, 16.5436, 10.2857, 9.6801, 8.2726, 7.2839, 4.9582, 2.6106, 1.7283, 12.5276, 7.5207, 6.2826, 5.0096, 3.672, 2.3118, 1.1798, 0.7019, 6.2715, 11.9929, 16.8764, 2.8822, 4.3564, 5.1734, 920.0, 43.0, 9.8365, 6.0074, 330.0, 10.0, 45.0, 3.0, 1.1974, -0.6576, 0.0027, -0.0407, 0.146, 27.1688, 27.3805, 43.6461, 56.8724, 63.7556, 27.7198, 47.6482, 1737.9365, 41.6886, 12.023, 2004.6114, 44.7729, 12.6089, 4320.3114, 65.7291, 16.2869, 2.071, 1.9596, 3264.7591, 3129.1874, 832.4512, 1.0433, 3.9219, 3.759, 6.4, 12.6475, 0.9721, 1.4198, 2.0378, 10.8917, 0.0989, 0.142, 0.4315, 0.3879, 0.4619, 14.3494, 40.5529, 86.4153, 0.3193, 1.2813, 28.0, 7.0, 4.0, 5.0, 1.0, 0.0, 0.0, 3.0, 0.0, 0.0, 0.0, 0.0, 0.0, 97.8635, 1.6469, 129.92, 2.0061, 452.0649, 1189.1524, 40.2413, 152.5738, -401.344, -43.4179, 299.4911, 1590.4964, 83.6593, 0.7477, 1.9667, 0.0666, 0.2523, -0.6638, -0.0718, 273.336, 719.0076, 24.3315, 92.2521, -242.6682, -26.2522, 0.1085, 0.1504, 0.0205, 4.747, 354.1158, 250.523, 0.5857, 0.4143, 0.306, 0.0
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