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From: Sebastien M. <Seb...@un...> - 2008-03-28 10:50:16
|
> So, is there a way to do a kind of 'cd path/' and then to run > applications with infiles and outfiles from the current directory. > > > Before it starts an external application, Soaplab2 changes its working > directory (making a 'cd') into the job directory (which is a directory > .../SANDBOX/[job-name]/ > > Martin Nevertheless, service report file shows the full path -in=/opt/tomcat/temp/_R_/SANDBOX/[embnet.tmpred]-47cb20aa.118f4f77748.-7fff/i_infile So, external applications use full paths or relative paths ? -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-28 10:45:36
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> So, is there a way to do a kind of 'cd path/' and then to run > applications with infiles and outfiles from the current directory. > Before it starts an external application, Soaplab2 changes its working directory (making a 'cd') into the job directory (which is a directory .../SANDBOX/[job-name]/ Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 10:37:09
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> Hi Martin, > >> One other option would be to write an input data adaptor class >> in Java >> that should implement the interface >> org.soaplab.services.adaptor.DataAdaptor. >> >> I am afraid that it may not be true. The adaptors are in charge when >> data arrives from a user and before the Soaplab service processes >> them. But Sebastien's problem occurs when Soaplab calls an external, >> command-line, application. In that moment all input data are already >> "adapted" (if there was any adaptor for them) and they sit in a >> Soaplab's internal file whose name is passed to the external >> application. And here the name is the problem - not the data inside >> the file. > > I was looking at the InputManyFiles adaptor (for some EMBASSY > applications which expects directory name rather than list of file > names), given some input objects it returns a string with the list of > input file names. It seems Soaplab should not make problem if this > adaptor returns a string without these special characters. > > Meantime, I noticed the following method in echo.acd. > > # comment: 'method foreachs (str, " ", "-&&# $str")' > > I don't know much about the substitution support in Soaplab. Is it > possible to use the existing substitution support for this problem? > > Mahmut I made several tests and it is clearly a problem from my application. The path works fine in interactive mode but not in command line ! So, is there a way to do a kind of 'cd path/' and then to run applications with infiles and outfiles from the current directory. -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-28 10:06:13
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> One other option would be to write an input data adaptor class in Java > that should implement the interface > org.soaplab.services.adaptor.DataAdaptor. I am afraid that it may not be true. The adaptors are in charge when data arrives from a user and before the Soaplab service processes them. But Sebastien's problem occurs when Soaplab calls an external, command-line, application. In that moment all input data are already "adapted" (if there was any adaptor for them) and they sit in a Soaplab's internal file whose name is passed to the external application. And here the name is the problem - not the data inside the file. Cheers, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2008-03-28 10:05:39
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Hi Martin, > One other option would be to write an input data adaptor class > in Java > that should implement the interface > org.soaplab.services.adaptor.DataAdaptor. > > I am afraid that it may not be true. The adaptors are in charge when > data arrives from a user and before the Soaplab service processes > them. But Sebastien's problem occurs when Soaplab calls an external, > command-line, application. In that moment all input data are already > "adapted" (if there was any adaptor for them) and they sit in a > Soaplab's internal file whose name is passed to the external > application. And here the name is the problem - not the data inside > the file. I was looking at the InputManyFiles adaptor (for some EMBASSY applications which expects directory name rather than list of file names), given some input objects it returns a string with the list of input file names. It seems Soaplab should not make problem if this adaptor returns a string without these special characters. Meantime, I noticed the following method in echo.acd. # comment: 'method foreachs (str, " ", "-&&# $str")' I don't know much about the substitution support in Soaplab. Is it possible to use the existing substitution support for this problem? Mahmut |
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From: Mahmut U. <ul...@eb...> - 2008-03-28 09:50:11
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> you need to write a script that will warp it - and this script will > read the file name given to it by Soaplab, will copy the file to a > temporary directory and will pass a new name to your application > itself (together with the other parameters gotten from the Soaplab > service). One other option would be to write an input data adaptor class in Java that should implement the interface org.soaplab.services.adaptor.DataAdaptor. However, for your case writing a wrapper seems to be a more practical solution. Mahmut |
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From: Martin S. <mar...@gm...> - 2008-03-28 08:38:07
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> No, my application is the Soaplab service. If you application is the one called by a Soaplab service, then it gets data without using any shell. Therefore, it is, indeed, your application that is not able to use a parameter that has special characters. I have just tried to rename > > /opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]4a976779.118f46927cf.-7ffe/ No, you cannot rename it: this file name (and the file itself) is created every time a Soaplab service is called. You do not have access to a file to rename it in the right time. You need to look into your application how it parses and uses parameters. If you cannot do it (because it's too old or not well readable etc.) you need to write a script that will warp it - and this script will read the file name given to it by Soaplab, will copy the fiole to a temporary directory and will pass a new name to your application itself (together with the other parameters gotten from the Soaplab service). Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 08:28:03
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> I use bash and it is my application which seems to be the real problem. > It cannot read the file from this path even if special characters are > escaped. > > > Just please confirm that I understand it correctly: Your application is > a client that sends data to a Soaplab service, right? > > Martin No, my application is the Soaplab service. Here is the output I get: sequence file not found Runtime error 2 at $08062B7E $08062B7E $080638B6 $08066193 $0804BCD7 $0804C192 $0804809F I have just tried to rename /opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]4a976779.118f46927cf.-7ffe/ to /opt/tomcat/temp/_R_/SANDBOX/protein_2d_structure.tmpred_4a976779.118f46927cf.7ffe/ and now -in=/opt/tomcat/temp/_R_/SANDBOX/protein_2d_structure.tmpred_4a976779.118f46927cf.7ffe/i_infile works -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-28 08:22:01
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> I use bash and it is my application which seems to be the real problem. > It cannot read the file from this path even if special characters are > escaped. Just please confirm that I understand it correctly: Your application is a client that sends data to a Soaplab service, right? Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 08:17:26
|
> It's my application which cannot read the file with this path. > It doesn't read it in command line, except if I use a path without > special characters ( [ ] - ) > > > Okay, I understand, but your application is running on your machine, it > is a Soaplab's client. Once this client application sends a filename to > a Soplab's service, things should be fine (first, because there is no > shell involved on the Soaplab side, and second, because it work fine for > other Soaplab services, as shown in the example in my previous email). > > > Something like template: "-in=\"$$\"" > or template: "-in='$$'" > but it failed. > > > Again, we are now talking about a client application, so it has nothing > to do with ACD files - therefore using different templates cannot hep here. > > What can help is to deal with your shell. If you use bash, it does not > have problems with [ and ], only if you use tcsh you need to escape (or > quote) these characters. What shell are you using? > > Martin I know it is not the ACD syntax but the shell which is involved because I have the same problem in command line with these paths. I use bash and it is my application which seems to be the real problem. It cannot read the file from this path even if special characters are escaped. It is an old application (mid 90's) and I wonder if ACD syntax could protect path for my application. -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-28 08:09:06
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> It's my application which cannot read the file with this path. > It doesn't read it in command line, except if I use a path without > special characters ( [ ] - ) Okay, I understand, but your application is running on your machine, it is a Soaplab's client. Once this client application sends a filename to a Soplab's service, things should be fine (first, because there is no shell involved on the Soaplab side, and second, because it work fine for other Soaplab services, as shown in the example in my previous email). > Something like template: "-in=\"$$\"" > or template: "-in='$$'" > but it failed. > Again, we are now talking about a client application, so it has nothing to do with ACD files - therefore using different templates cannot hep here. What can help is to deal with your shell. If you use bash, it does not have problems with [ and ], only if you use tcsh you need to escape (or quote) these characters. What shell are you using? Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 07:58:11
|
> I have (now) a problem with an old application which doesn't seem to > accept path provided by SoapLab2 for input file: > -in=/opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/i_infile > > > I have tried myself, and I cannot reproduce the error here. > > Could you checks if the path mentioned in your example is a path of the > SANDBOX of your current Soaplab2? Because Soaplab2 refuses to take local > (local on the server side) files unless they are in its SANDBOX > directory. What is the full error message you are getting (something > like "Refusing to resolve the reference...")? The file is exactly where mentioned by the path. It is readable and has the proper syntax. It's my application which cannot read the file with this path. It doesn't read it in command line, except if I use a path without special characters ( [ ] - ), or if I change path to /opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/ and run -in=./i_infile So, I am looking for a way to protect the path, or to avoid special characters inside it. Something like template: "-in=\"$$\"" or template: "-in='$$'" but it failed. > Could you try to run a testing service (which comes with Soaplab2) - > using as an input an existing file in your SANDBOX (the example below is > just from my machine): > > build/run/run-cmdline-client -protocol local -name testing.files -w -r > input_url > /home/senger/soaplab2/_R_/SANDBOX/\[classic.helloworld\]-24c8efb0.117ea7cd13f.-8000/o_output Other services, like EMBOSS services with infile, work fine. > This calls works fine on my machine, how about on yours? > > Thanks, > Martin -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 07:49:31
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> You mean that template is deprecated ? > > > No, it is not, only sometimes ways are possible (this is from the > historical reasons). As the parameter attribute, one can use either: > > template: "blah-blah-blah" > > or > > comment: "method blah-blah-blah" > > And as the application attribute,one can use only: > > comment: "method blah-blah-blah" > > [Here are the historical reasons: The EMBOSS developers were very kind > and they included few new attribute names into EMBOSS parser of the ACD > files. One of them was the 'template' attribute - but it was included > only in the parameter attributes, not in the application attribute. > That's why we still need to use the general 'comment' in the application > part. Why is it important to have it recognized by the EMBOSS parser > when Soaplab2 does not use this parser? Well, it is not important but it > can be handy if you have EMBOSS installed and you wish to check the > syntax of your ACD file using the EMBOSS programs.] > > Cheers, > Martin Thanks again ! -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Sebastien M. <Seb...@un...> - 2008-03-28 07:48:52
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> Hi, Hi, > Sorry for my delayed answer (different time zone). > > > I try to find the right way to create boolean parameters (I mean > parameter name without parameter value) in ACD format. > But they don't appear in the report file when I run the service. > > > I have put an answer into Soaplab2's FAQ page (but it will take > sometimes before it appears there). But simply: the default values are > not sent to the service unless you explicitly ask for it by "comment: > defaults". Therefore, try to add such line in both of your examples. > > Martin Mahmut told me the same, right, thing. I think I mixed up my mind between acdtable output and soaplab specific ACD syntax. Thanks -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-28 01:12:10
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> I have (now) a problem with an old application which doesn't seem to > accept path provided by SoapLab2 for input file: > > -in=/opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/i_infile > I have tried myself, and I cannot reproduce the error here. Could you checks if the path mentioned in your example is a path of the SANDBOX of your current Soaplab2? Because Soaplab2 refuses to take local (local on the server side) files unless they are in its SANDBOX directory. What is the full error message you are getting (something like "Refusing to resolve the reference...")? Could you try to run a testing service (which comes with Soaplab2) - using as an input an existing file in your SANDBOX (the example below is just from my machine): build/run/run-cmdline-client -protocol local -name testing.files -w -r input_url /home/senger/soaplab2/_R_/SANDBOX/\[classic.helloworld\]- 24c8efb0.117ea7cd13f.-8000/o_output This calls works fine on my machine, how about on yours? Thanks, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Martin S. <mar...@gm...> - 2008-03-28 00:41:13
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> You mean that template is deprecated ? > No, it is not, only sometimes ways are possible (this is from the historical reasons). As the parameter attribute, one can use either: template: "blah-blah-blah" or comment: "method blah-blah-blah" And as the application attribute,one can use only: comment: "method blah-blah-blah" [Here are the historical reasons: The EMBOSS developers were very kind and they included few new attribute names into EMBOSS parser of the ACD files. One of them was the 'template' attribute - but it was included only in the parameter attributes, not in the application attribute. That's why we still need to use the general 'comment' in the application part. Why is it important to have it recognized by the EMBOSS parser when Soaplab2 does not use this parser? Well, it is not important but it can be handy if you have EMBOSS installed and you wish to check the syntax of your ACD file using the EMBOSS programs.] Cheers, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Martin S. <mar...@gm...> - 2008-03-28 00:31:08
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Hi, Sorry for my delayed answer (different time zone). I try to find the right way to create boolean parameters (I mean > parameter name without parameter value) in ACD format. > But they don't appear in the report file when I run the service. > I have put an answer into Soaplab2's FAQ page (but it will take sometimes before it appears there). But simply: the default values are not sent to the service unless you explicitly ask for it by "comment: defaults". Therefore, try to add such line in both of your examples. Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Martin S. <mar...@gm...> - 2008-03-27 14:34:21
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> Do you have any idea how to deal with this ? If the file is in the SANDBOX it should be fine. I have just looked into the code and it seems to confirm what I have just said but obviously it does not work that way (otherwise you would not have this error). Again, I need to run some tests on this - which I will do the first thing in (my) morning. We had this issues before (it was for EMBOSS jobs) and I remember that we have decided to allow (by setting a property) to overwrite this SANDBOX location - but I have never implemented it. I may do it now when looking into it. I will let you know asap. Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Sebastien M. <Seb...@un...> - 2008-03-27 14:19:01
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Hi, I have (now) a problem with an old application which doesn't seem to accept path provided by SoapLab2 for input file: -in=/opt/tomcat/temp/_R_/SANDBOX/[protein_2d_structure.tmpred]3bd3a626.118f08a1fec.-7ffe/i_infile Do you have any idea how to deal with this ? I have tried this syntax to protect the path but without result: template: "-in=\"$$\"" Thanks -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Martin S. <mar...@gm...> - 2008-03-27 13:43:59
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I think Mahmut already replied to your questions, but I will make a new look into Soaplab2 as soon as I boot my linux machine (which will be tomorrow my time - which is about 10 hours from now) and I will check again the answers. I may even put your questions into FAQ if you do not mind. Cheers, Martin -- Martin Senger email: mar...@gm...,m.s...@cg... skype: martinsenger |
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From: Mahmut U. <ul...@eb...> - 2008-03-27 13:39:18
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> You mean that template is deprecated ? I was wrong. I replied by just looking at the example ACD files but without reading the relevant documentation. http://soaplab.sourceforge.net/soaplab2/MetadataGuide.html Sorry, Mahmut |
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From: Sebastien M. <Seb...@un...> - 2008-03-27 13:31:07
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> Hi Sebastien, > >> what is exactly the difference between comment-"method ...." and >> template: ""? > > I just made a quick search on my EMBOSS and Soaplab2 directories and > could not find any example where the "template:" option is used. It > seems that it was supported by Soaplab-1 and but is not supported in > Soaplab-2. Martin should know. > > Regards, > Mahmut You mean that template is deprecated ? I use it because comment: "tagsepar = =" seems to involve that '-' is removed at the beginning of <parameter-name> Thus, for me, template: "-&&=$$" keeps '-' at the beginning of <parameter-name> and add '=' (here) between <parameter-name> and <parameter-value> -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Mahmut U. <ul...@eb...> - 2008-03-27 13:20:44
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Hi Sebastien, > what is exactly the difference between comment-"method ...." and > template: ""? I just made a quick search on my EMBOSS and Soaplab2 directories and could not find any example where the "template:" option is used. It seems that it was supported by Soaplab-1 and but is not supported in Soaplab-2. Martin should know. Regards, Mahmut |
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From: Sebastien M. <Seb...@un...> - 2008-03-27 13:10:40
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> Hi Sebastien, Hi Mahmut, >> I try to find the right way to create boolean parameters (I mean >> parameter name without parameter value) in ACD format. >> But they don't appear in the report file when I run the service. >> >> >> I have two different cases: >> >> -html parameter which can be present or not, depending on user choice. >> -def parameter which must be always present >> >> >> Here is my ACD code: >> boolean: html [ >> additional: "Y" >> default: "true" >> prompt: "Output format" >> information: "Output format, html or not " >> outputmodifier: "Y" >> ] >> >> boolean: def [ >> default: "true" >> comment: "display false" >> information: "The 'def' parameter" >> ] >> >> Do you have any ideas why these parameters are not added on command line >> when the application is running ? > > I think you need to use the comment-"method ...." and the > comment-"defaults" options as in the following examples. > > boolean: html [ > additional: "Y" > default: "true" > prompt: "Output format" > information: "Output format, html or not " > outputmodifier: "Y" > comment: "method -html" > ] > > boolean: def [ > default: "true" > comment: "defaults" > comment: "display false" > information: "The 'def' parameter" > comment: "method -def" > ] > > Regards, > Mahmut Thanks. Now I can get what I expected for. I thought that comment-"method ...." was reserved for application main section. But what is exactly the difference between comment-"method ...." and template: ""? Thanks again -- Sébastien Moretti SIB, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4056/4221 |
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From: Mahmut U. <ul...@eb...> - 2008-03-27 12:02:41
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Hi Sebastien,
> I try to find the right way to create boolean parameters (I mean
> parameter name without parameter value) in ACD format.
> But they don't appear in the report file when I run the service.
>
>
> I have two different cases:
>
> -html parameter which can be present or not, depending on user choice.
> -def parameter which must be always present
>
>
> Here is my ACD code:
> boolean: html [
> additional: "Y"
> default: "true"
> prompt: "Output format"
> information: "Output format, html or not "
> outputmodifier: "Y"
> ]
>
> boolean: def [
> default: "true"
> comment: "display false"
> information: "The 'def' parameter"
> ]
>
> Do you have any ideas why these parameters are not added on command line
> when the application is running ?
I think you need to use the comment-"method ...." and the
comment-"defaults" options as in the following examples.
boolean: html [
additional: "Y"
default: "true"
prompt: "Output format"
information: "Output format, html or not "
outputmodifier: "Y"
comment: "method -html"
]
boolean: def [
default: "true"
comment: "defaults"
comment: "display false"
information: "The 'def' parameter"
comment: "method -def"
]
Regards,
Mahmut
|
