We are migrating informatica from windows to Unix as a result when I was running workflow in windows which consists of 10 sessions, getting succeeded.
But same workflow (code) has been migrated to unix Environment. However workflow getting failed due to NULL character in input file.
EX:
FR_3085: 513th character is a null character, which is not allowed in a text input file
Don't know where went wrong, as other 9 sessions(out of 10) getting succeeded.
You can follow 2 approaches in this case :
Replace the null character in the file using SED or any other Linux commad/method before workflow run.
User given custom properties at your session/workflow.
https://kb.informatica.com/solution/6/Pages/20698.aspx
Thanks
If you are on RHL sometimes the conversion from Window to Shell script will bring Unicode characters.
Try running dos2unix filename.txt command and then convert the file format to Unix. After doing this run the workflow.
Also you can check whether the file has Unicode or not by running cat -v filename.txt
Related
I have a RM Server running on a VM (Ubuntu) on top of my Win10 machine.
I have a process to read a .csv file and write its contents on a MySQL database on a MySQL Server which also runs on the same VM.
The problem is that the read file operator does not seem to be able to find the file.
Scenario1.
When I try as location-name in the read csv operator ../data/myFile.csv
and run the process on Server I am getting Failed to execute initialization process: Error executing process /apps/myApp/process/task_read_csv_to_db: The file 'java.io.FileNotFoundException: /root/../data/myFile.csv (No such file or directory)' does not exist.
Scenario2.
When I try as location-name in the read csv operator /apps/myApp/data/myFile.csv
and run the process on Server I am getting Failed to execute initialization process: Error executing process /apps/myApp/process/task_read_csv_to_db: The file 'java.io.FileNotFoundException: /apps/myApp/data/myFile.csv (No such file or directory)' does not exist.
What is the right filepath that I should give to the Read CSV operator?
Just to update with the answer. After David's suggestion, I resulted in storing the .csv file outside of the /rapidminer-server-home/data/repository since every remote repository seems to be depicted with an integer instead of its original name, making the use of the actual full path of the file not usable.
I would say, the issue is that depending on the location of the JobAgent that is executing your process, the relative path might be varying.
Is /apps/myApp/data/myFile.csv the correct path to the file? If not, I would suggest to use the absolute path to the file. Hope this helps.
Best,
David
I opened a file through python. So, i did a lsof on the python process. output of lsof has the following line
COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
python 15855 inaflash 3w REG 0,25 0 4150810088 /home/inaflash/he.txt
Thing is, it has 3w. which means that the file is open for writing. But, i actually opened the file as follows
a = open('he.txt','r')
I read that, w means file is open for write. Can anyone help me understand why its w instead of r
I tried the same code in Python 3 and my file is opened in read mode.
Are you sure your file is the same opened with python and same python process ?
Maybe you forgot to close the file somewhere in your code after opened it in write mode.
Edit: Also tried in Python 2, same result (read mode)
I want to open a file from within R.
I can launch the software (graphpad prism) with the following:
system2("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
I expected this to open my prism file as if I were double clicking on it or running it from cmd, but it didn't:
system2("H:/Graphs/Shell/Templates/NASH4_Standard.pzfx")
I am receiving the message:
Warning message: running command
'H:/Graphs/Shell/Templates/NASH4_Standard.pzfx' had status 127
I see that this is not an error but just a warning. Am I unintentionally "shelling" the document in the background? How would I make sure it pops up as a window?
Status 127 was addressed here, but for launching the software, not opening the document with it.
In Windows environments, you need to call a command line interpreter like CMD prompt or PowerShell. Also, any file path that has spaces needs to be enclosed in double quotes above the quotes needed in R for string literals (the case for your .exe not specific file).
With system() send entire command in one string:
system('cmd /c "H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"')
# POWER SHELL REQUIRES MORE QUOTE ESCAPING (ONLY ONE PAIR W/O SPACES)
system('powershell & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""')
With system2() use the args parameter:
# FILES
system2('cmd', args=c('/c', '"H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"'))
system2('powershell', args=c(' & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""'))
# EXECUTABLES
system2('cmd', args=c('/c', '"C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"'))
system2('powershell', args=c(' & """C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"""'))
shell.exec("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
does it work for you ?
ps. and shell.exec("MyWorkbook.xls") open file with default program
I am new to programming and mainly I am able to do some scripts within R, but for my work I need to call an external program. For this program to work on the ubuntu's terminal I have to first use setenv and then execute the program. Googling I've found the system () and Sys.setenv() functions, but unfortunately I can make it function.
This is the code that does work in the ubuntu terminal:
$ export PATH=/home/meme/bin:$PATH
$ mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp
Where the first two arguments are input files, the -o argument is the output directory and the -comp is another parameter for the program to run.
The reason that I need to do it in R despite it already works in the terminal is because I need to run the program 1000 times with 1000 different files so I want to make a for loop where the input name changes in every loop and then analyze every output in R.
I have already tried to use:
Sys.setenv(PATH="/home/meme/bin"); system(mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
and
system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
but always received:
Error: unexpected constant string in "system(mast "/home/meme/meme.txt""
or
Error: unexpected symbol in "system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt""
At this point I have run out of ideas to make this work. If this has already been answered, then my googling have just been poor and I would appreciate any links to its response.
Thank you very much for your time.
Carlos
Additional details:
I use Ubuntu 12.04 64-bits version, RStudio version 0.97.551, R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Platform: x86_64-pc-linux-gnu (64-bit).
The program I use (MAST) finds a sequence pattern in a list of letters and is part of the MEME SUIT version 4.9.1 found in http://meme.nbcr.net/meme/doc/meme-install.html and run through command line. The command-line usage for mast is:
mast <motif file> <sequence file> [options]
Construct the string you want to execute with paste and feed that to system:
for(i in 1:10){
cmd=paste("export FOO=",i," ; echo \"$FOO\" ",sep='')
system(cmd)
}
Note the use of sep='' to stop paste putting spaces in, and back-quoting quote marks in the string to preserve them.
Test before running by using print(cmd) instead of system(cmd) to make sure you are getting the right command built. Maybe do:
if(TESTING){print(cmd)}else{system(cmd)}
and set TESTING=TRUE or FALSE in R before running.
If you are going to be running more than one shell command per system call, it might be better to put them all in one shell script file and call that instead, passing parameters from R. Something like:
cmd = paste("/home/me/bin/dojob.sh ",i,i+1)
system(cmd)
and then dojob.sh is a shell script that parses the args. You'll need to learn a bit more shell scripting.
I would like to execute this DOS command under R:
iconv -f ISO-8859-1 -t UTF-8 FileName.md > FileNameNew.md
The above command creates new file after transforming from ISO to UTF.
I have tried execute this command however unsuccessfully with:
system(paste("iconv -f ISO-8859-1 -t UTF-8 FileName.md > FileNameNew.md", sep=""))
This gives me two types of errors:
Invalid argument
No such file or directory
I don't think the issue is the second since when I run the command under R it in fact executes the command as it re-reads the FileName.md, which means he found the file. I think it is just a issue with the > and hence formulation of the command in the system(paste("")) command.
When I rund this command directly under console it works.
The problem is (most likely) simply with where the R session is located. Check this by running getwd() in R and see if it is in the same place as the file. The paste part shouldn't be needed, as it is not really pasting anything (paste combines 2 strings together, while it is one string here).
Solve this by explicitly attaching input and output to those files.
If you would insist on using paste, you could use it for instance like this:
system(paste("iconv -f ISO-8859-1 -t UTF-8 ", getwd(), "/FileName.md > ",
getwd(), "/FileNameNew.md", sep=""))