On Jun 29, 2013, at 3:38 AM, Heejoon Chae <[email protected]> wrote:
> Hi, Suresh, > > Any updates on this? > > By the way, can you also let me know how I cloud run for-each component on > files? Actually, what I want to do is to run my script on several input > files(let's say 100 inputs), but actual input files' informations are listed > on a single file instead of getting all the input one by one. > > So, the input is single file containing all the input file informations looks > like, > > ... > http://xxx,xxx,xxx/input1.txt > http://xxx,xxx,xxx/input2.txt > http://xxx,xxx,xxx/input3.txt > … Hi Heejoon, While Chathura and Saminda help you get pass the for-each issues, let me answer this specific question. I have seen a similar requirement previously in a different project [1] as well. It should be trivial to add these kind of "convenience" nodes in workflow which can read a file and split the content and pass to for-each as an array. We can develop these nodes, but can you please spare some time and formalize this requirement. * Other than the ones you are scripting, did you come across similar bioinformatics applications or otherwise which produce such listing? Did you see and ad-hoc standards for these formats? Like what is the delimiter for each file, newline? it can be comma or space separated as well right? do you think if Airavata establishes some norm, will application writers follow them? * How do we determine the type of the parsed content? For instance, distinguishing form a URI, or a String or integer? I am sure there will be other questions, but once we agree upon such semantic issues of the content, we can add this as a feature request for next release. Suresh [1] - https://cwiki.apache.org/confluence/display/AIRAVATA/ODI > > Thanks! > Heejoon. > > > On Tue, Jun 11, 2013 at 10:26 PM, Suresh Marru <[email protected]> wrote: > Hi Heejoon, > > Normally we use for-each on files, so the way to handle that is let all the > output files go into a outputData directory and iterate over them. But I see > what you are doing here. Let me try this and get back to you within the next > day. > > Thanks for your patience, > Suresh > > On Jun 10, 2013, at 11:46 PM, Heejoon Chae <[email protected]> wrote: > >> Hi, Airavata users, >> >> Do you have any advises or experiences for my previous mail about ForEach >> component? >> I am still struggling with generating input for ForEach component in my >> script :/ >> Any comment will be helpful to me to use the component :) >> >> Thank you! >> >> ---------- Forwarded message ---------- >> From: Heejoon Chae <[email protected]> >> Date: Fri, Jun 7, 2013 at 5:44 PM >> Subject: Re: Question for Airavata For-Each component >> To: "[email protected]" <[email protected]> >> >> >> Hi, Lahir, >> >> I succeeded to use ForEach component with attaching 'Input' component in >> front of ForEach componet with comma separated value(i.e "a,b,c") as input >> like in attached figure. ForEach component works well with Input component >> with comma separate value. >> >> Now I want to mimic what Input component does within my script as in another >> figure. This is required to run ForEach on generated data not on data >> inputed from user. >> >> I tired several ways to generate a input for ForEach component in my script >> including what you suggested in previous mail, but I couldn't. Please help >> me to solve this problem. >> >> Thank you, >> Heejoon. >> >> >> On Wed, Jun 5, 2013 at 11:44 PM, Lahiru Gunathilake <[email protected]> >> wrote: >> Following script will be useful for you.. >> >> echo $@ >> echo $* >> echo $# >> for arg; do >> printf '%s\n' "$arg" >> done >> >> >> Lahir >> >> >> On Wed, Jun 5, 2013 at 9:53 AM, 채희준 <[email protected]> wrote: >> Hi Lahiru, >> >> Thank you for your answer. >> >> By the way, how to create string array in shell script, so that I can pass >> it to ForEach component? >> >> Thank you, >> Heejoon. >> >> 2013. 6. 5. 오후 10:44 Lahiru Gunathilake <[email protected]> 작성: >> >>> Hi Heejoon, >>> >>> We take string array as input but we invoke the script with each element of >>> the string array multiple times, in Foreach we don't pass whole string >>> array to the application script at once. So you really don't have to handle >>> a string array in your script. >>> >>> Lahiru >>> >>> >>> On Tue, Jun 4, 2013 at 10:06 PM, Heejoon Chae <[email protected]> >>> wrote: >>> Hi, >>> >>> I have quick question about Airavata For-Each component. >>> >>> It seems that ForEach component takes String array as an input and pass >>> them to next component one by one. >>> >>> My question is how to create string array in shell script to pass it to >>> ForEach component? >>> >>> I normally generate string result like >>> >>> echo "output=xxx" >>> >>> at the end of script and connect it as an input of next component in >>> Airavata workflow to pass the result and let next component know the input >>> is arrived. >>> >>> Thanks, >>> Heejoon. >>> >>> >>> >>> -- >>> System Analyst Programmer >>> PTI Lab >>> Indiana University >> >> >> >> -- >> System Analyst Programmer >> PTI Lab >> Indiana University >> >> >> <Screen Shot 2013-06-07 at 3.12.05 PM.png><Screen Shot 2013-06-07 at 3.11.31 >> PM.png> > >
