I am in the process of using the GenABEL package of R studio to convert the output of the Affymetrix Genotyping Console into a .tfam file. This is my code thus far:
rm(list = ls())
setwd("C:/U/Is/GD/Affymetrix")
library("GenABEL", lib.loc="C:/PROGRA~1/R/R-211~1.1-X/library")
read.table("Genotyping_results.txt", fill = TRUE)
convert.snp.affymetrix(dir = "C:/U/Is/GD/Affymetrix", map = "Genotyping_results.txt" , outfile ="Genotyping_results.tfam")
I am getting the following error:
"Error in system(command, intern = T) : 'ls' not found".
I have a limited understanding of programming and am finding it difficult to understand what is wrong or how I can solve it.
Any help would be greatly appreciated
You mentioned in the comments that you're using Windows. ls is not a command on your OS.
ls is a command in Linux and in R.
There are many ways to add that command to Windows, like Cygwin.
Related
I have a simple beam pipeline, as follows:
with beam.Pipeline() as pipeline:
output = (
pipeline
| 'Read CSV' >> beam.io.ReadFromText('raw_files/myfile.csv',
skip_header_lines=True)
| 'Split strings' >> beam.Map(lambda x: x.split(','))
| 'Convert records to dictionary' >> beam.Map(to_json)
| beam.io.WriteToBigQuery(project='gcp_project_id',
dataset='datasetID',
table='tableID',
create_disposition=bigquery.CreateDisposition.CREATE_NEVER,
write_disposition=bigquery.WriteDisposition.WRITE_APPEND
)
)
However upon runnning I get a typeError, stating the following:
line 2147, in __init__
self.table_reference = bigquery_tools.parse_table_reference(if isinstance(table,
TableReference):
TypeError: isinstance() arg 2 must be a type or tuple of types
I have tried defining a TableReference object and passing it to the WriteToBigQuery class but still facing the same issue. Am I missing something here? I've been stuck at this step for what feels like forever and I don't know what to do. Any help is appreciated!
This probably occurred since you installed Apache Beam without the GCP modules. Please make sure to do following (in a virtual environment).
pip install apache-beam[gcp]
It's a weird error though so feel free to file a Github issue against the Apache Beam project.
Im trying to get param from SSHOperator into Xcom and get it in python.
def decision_function(**context):
ti = context['ti']
output_ssh= ti.xcom_pull(task_ids='ssh_task')
print('ssh output is: {}'.format(output_ssh))
ls = SSHOperator(
task_id="ssh_task",
command= "ls",
ssh_hook = sshHook,
dag = mydag)
get_xcom = PythonOperator(
task_id='test',
python_callable=decision_function,
provide_context=True,
dag=mydag
ls >> get_xcom
I get the wrong result in the xcom_pull:
ssh output is: MTcySyBhaXJmbG93CTIuMUcgQXV0b0hpdHVtX05ld
Every thing is work fine with BashOperator but when I try to use the SSH, it not working currect.
I also try to change in the config the enable_xcom_pickling param, but still not working.
airflow: 2.1.4
linux
thank you.
The value of Xcom may be b64encoded depending on the value of enable_xcom_pickling as you can see in the source code
The issue you are facing has been discussed in PR which suggested to change functionality to be like other operators but the PR was not merged and you can see the reasons for it in the code review comments.
if you wish you can create custom version of the operator without the enable_xcom_pickling condition:
class MySSHOperator(SSHOperator):
def execute(self, context=None) -> Union[bytes, str]:
result: Union[bytes, str]
if self.command is None:
raise AirflowException("SSH operator error: SSH command not specified. Aborting.")
# Forcing get_pty to True if the command begins with "sudo".
self.get_pty = self.command.startswith('sudo') or self.get_pty
try:
with self.get_ssh_client() as ssh_client:
result = self.run_ssh_client_command(ssh_client, self.command)
except Exception as e:
raise AirflowException(f"SSH operator error: {str(e)}")
return result.decode('utf-8')
Got a project with Apache FOP, have to make a server based application which will use Apache FOP and pick XML+XSLT files, convert it to XSL:FO and then output an PDF file.
Everything works fine until it comes to XSL:FO=>PDF, Im getting a error in my console which tells me:
"could not connect to java server at line 15"
I'm a newbie programmer, and this might be a simple task to complete but I just can't figure it out how to run this bloody java server ... so my code might be working. Any help would be great. (FYI Im working on Windows)
Here is the Perl Code:
use XML::LibXSLT;
use XML::LibXML;
use XML::ApacheFOP;
my $parser = XML::LibXML->new();
my $xslt = XML::LibXSLT->new();
my $source = $parser->parse_file('books.xml');
my $style_doc = $parser->parse_file('books.xsl');
my $stylesheet = $xslt->parse_stylesheet($style_doc);
my $results = $stylesheet->transform($source);
my $Fop = XML::ApacheFOP->new();
$Fop->fop( xml => "books.xml", xsl => "books.xsl", outfile => "temp.pdf" )
or die "cannot create pdf: " . $Fop->errstr;
Would be glad to get some help.
Cheers.
You need to run JavaServer by this command
/path/to/java -classpath \
/path/to/JavaServer.jar\
:/usr/local/xml-fop/build/fop-0.20.5-RFC3066-patched.jar\
:/usr/local/xml-fop/lib/avalon-framework-cvs-20020806.jar\
:/usr/local/xml-fop/lib/batik.jar\
:/usr/local/xml-fop/lib/xalan-2.4.1.jar\
:/usr/local/xml-fop/lib/xercesImpl-2.2.1.jar \
com.zzo.javaserver.JavaServer
This works for me but with fop 0.20 with fop-0.20.5-RFC3066-patched.jar
I want to run the following command from vb.net code. When I put it in process.start(" ")
it returns syntax error. Please advise
>E:\UnInstall\SQLServer\SQLServerExpress2008\SQLEXPR_x64_ENU.exe / SQ/SAPWD="testpwd123"/security=SQL/BROWSERSVCSTARTUPTYPE="Enabled"/TCPENABLED="1"/NPENABLED="0"/INDICATEPROGRESS="True"/INSTANCENAME="CBEInstance"/IACCEPTSQLSERVERLICENSETERMS="True"
You specify the file to run with Process.StartInfo.Filename, and the command line arguments with Process.StartInfo.Arguments.
Dim DosRun As Process = New Process
DosRun.StartInfo.FileName = "E:\UnInstall\SQLServer\SQLServerExpress2008\SQLEXPR_x64_ENU.exe"
DosRun.StartInfo.Arguments = String.Format("SQ/SAPWD=testpwd123/security=SQL/BROWSERSVCSTARTUPTYPE=Enabled/TCPENABLED=1/NPENABLED=0/INDICATEPROGRESS=True/INSTANCENAME=CBEInstance/IACCEPTSQLSERVERLICENSETERMS=True")
DosRun.Start()
I'm trying to run dos commands within vb.net program and capture output. I have the following code:
Dim CMDServer As Diagnostics.ProcessStartInfo
Dim CMDReply As Diagnostics.Process
CMDServer = New Diagnostics.ProcessStartInfo
CMDServer.FileName = "cmd.exe"
CMDServer.UseShellExecute = False
CMDServer.RedirectStandardOutput = True
CMDServer.CreateNoWindow = True
CMDServer.Arguments = "/C " + command
CMDReply = Process.Start(CMDServer)
Dim Reply As String = CMDReply.StandardOutput.ReadToEnd()
The code runs successfully if command is a valid dos command, and I get the output in Reply. If the command have no output ( eg: cd\ ) Reply is null. The problem is Reply is null even when the command is invalid. How to capture errors like "command is not recognized as an internal or external command...", "The system cannot find the path specified.." etc.. Please help me. Thanks..
Error messages come in a different output stream called StandardError. Just use a StreamReader or read it directly. Of course, the RedirectStandardError-Property of your ProcessStartInfo instance must be set to True.
Also, there is a ExitCode-Property which returns the ExitCode of the program after it has finished. 0 means 'successful'. Other error codes can be found in the MSDN Documentation. Here is a list of the common exit codes. For example, 2 means The system cannot find the file specified..
Errors are probably output on CMDReply.StandardError, not CMDReply.StandardOutput; try reading it, too. (And set CMDServer.RedirectStandardError to True as well.)