all. I had some questions about the Perl module HTTP::Cookies. The example on CPAN is like below:
$cookie_jar = HTTP::Cookies->new( file => '$ENV{\'HOME\'}/lwp_cookies.dat', autosave => 1);
The lwp_cookies.dat file is used to save cookie data on my local machine as I understand. On my machine, '$ENV{\'HOME\'}' is an empty path. The script runs good, even after execution I can't find any file named "lwp_cookies.dat" on my machine. I changed '$ENV{\'HOME\'}' to '$ENV{\'TMP\'}', which is a path really exists after I verified by Perl print. Still I can't find the "lwp_cookies.dat" in my TEMP folder. My first question is how the HTTP::Cookies is working with the "lwp_cookies.dat" file.
On the other hand, on one of my systems(all're Windows system as mentioned here), the same code produce error message below:
Can't open $ENV{'HOME'}/lwp_cookies.dat: No such file or directory
So it's strange to me. On my good system, even file or path not exists, the script runs well, which I suppose the file is created on some temp memory instead; on bad system, the code example doesn't work at all.
If you want the $ENV{'HOME'} variable to interpolate into the string, you need double quotes; single quotes don't interpolate variables:
`file => "$ENV{'HOME'}/lwp_cookies.dat",`
Related
I am configuring Blast+ on my mac (os sierra) and am having trouble configuring my nr and nt databases that I also downloaded locally. I am trying to follow NCBI's instructions here, and am getting hung up on the Configuration and Example Execution steps.
They say to change my .bash_profile so that it says:
export PATH=$PATH:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/ncbi-blast-2.6.0+/bin
That works fine, and they say configure a path for BLASTDB "similarly" but to the file where my DB will be, so I have done this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/nt.00
which specifies the exact folder that I got when I unzipped the nt tar file from their FTP. With this path, if I run the command...
blastn -query test_query.fa -db nt.00 -task blastn -outfmt "7 qseqid sseqid evalue bitscore" -max_target_seqs 5
then it runs successfully and I get results, but I am worried that these are only being checked against the nt.00 section of the entire nt.00 database file, especially because if I run my test_query.fa sequence on the Web Blast, I get different results.
Also, their instructions say that the path only needs to point to the folder that contains the whole database folder nt.00, from the tar I unzipped--and not the specific nt.00 itself--, which in my case would just be "blastdb/" (As opposed to "blastdb/nt.00/" which then contains nt.00.nhd, nt.00.nal, etc.). That makes sense because when I am working I want to be able to blastn on the nt database but also blastp on the nr one, etc. by changing the -db flag on my command, and there shouldn't be a problem with having them all in this folder, right? But if I must specify the path for BLASTDB with the nt.00 DB added to the end, how could I ever use nr.00 in the same folder (blastdb/)? Essentially, I want to do as the instructions say, and just have this:
export BLASTDB=$BLASTDB:$HOME/Documents/Luke/Research/Pedulla\ 17-18/blast/blastdb/
And then depending on what database I want to use I could just say so after the -db flag on my command. But when I make the path like that above, it gives me this error:
BLAST Database error: No alias or index file found for nucleotide database [nt] in search path [/Users/LJStout::/Users/LJStout/Documents/Luke/Research/Pedulla 17-18/blast/blastdb:]
I have tried running that same blastn command from above and swapping out "nt" for "nt.00", and have tried these commands with the path for BLASTDB ending in both "blastdb/" and "blastdb/nt" and of course "blastdb/nt.00" which is the only one that runs without errors.
Here's an example of another thread I read where the OP is worried about his executions not checking the entire nt.00 folder, this was different than my problem however.
Thanks for you help!
This whole problem came down to having the nt.00 & nr.00 files, the original folders that result from unzipping their respective .tar.gz's, in the same parent folder when it should be that their contents are in the same parent folder. I simply deleted the folders they came in and copied the contents over to my new, singular parent. I was kind of mislead by the instructions, it was a simple mistake. Now, I have one folder, blastdb/ that contains all of the contents of every database I plan on using, including nt,nr, and refseq.
Hallo everyone once again,
I did various searches but couldn't gind a suitable/applicable answer to the simple problem below:
On pgAdminIII (Windows 7 64-bit) I am running the following command using SQL editor:
COPY public.Raw20120113 FROM 'D:\my\path\to\Raw CSV Data\13_01_2012.csv';
I tried many different variations for the path name and verified the path, but I keep getting:
ERROR: could not open file "D:\my\path\to\Raw CSV Data\13_01_2012.csv" for reading: No such file or directory
Any suggestions why this happens?
Thank you all in advance
Petros
UPDATE!!
After some tests I came to the following conclusion: The reason I am getting this error is that the path includes some Greek characters. So, while Windows uses codepage 1253, the console is using 727 and this whole thing is causing the confusion. So, some questions arise, you may answer them if you like or prompt me to other questions?
1) How can I permanently change the codepageof the console?
2) How can I define the codepage is SQL editor?
Thank you again, and sorry if the place to post the question was inappropriate!
Try DIR "D:\my\path\to\Raw CSV Data\13_01_2012.csv" from command line and see if it works - just to ensure that you got the directory, file name, extension etc correct.
The problem is that COPY command runs on server so it takes the path to the file from the server's scope.
To use local file to import you need to use \COPY command. This takes local path to the file into account and loads it correctly.
I am having a configuration INI file to store all configuration required for my script to run. I have a Logger.PM which uses Log4Perl, and ConfigReader.PM which reads the INI file and stores the value in global variable. My Start.PL is the entry point where i call the methods from Logger and configreader.
What I do currently
In Start.PL I hardcoded the INI file path
In Logger.Pm I harcoded the directory name where log files should be stored
What I want
I want the INI file path as configurable
I want the log folder path to be taken from the INI file
I could do this by following
Pass the INI file path as a parameter to the start.pl
Read the INI file and get the folder path from INI file
What I could face is that
I cannot use the Logger.PM in ConfigReader (partially) since the
folder name required for logger is part of INI file
I want to log every step of my script (for logging/debugging purpose in case of failure. )
I can use print but this will write to console and to capture i need to use >>log.txt. Then i will be forced to maintain 2 logs for my application which is not what I wanted
Anyone have a good solution for this scenario?
You can pass INI file path in command line using Getopt::Long, and command line switches for istance:
Start.pl --ini=/path/to/INI_file
Here is a code sample to show what changes are needed in Start.pl, in order to have switches:
#!/usr/bin/env perl
use v5.12;
use strict;
use Getopt::Long;
# That little tiny 's' after 'ini=' is for string
GetOptions ( 'ini=s' => \my $ini_file );
say $ini_file;
After this change, you can read all options from your INI file, including log folder path ( are you already using a module to manage INI files like Config::IniFiles? ).
There is something still unclear in your question about print: although one of my master said that print with a pair of square brackets is the best debugger in the world, why use print when you have set up Log::Log4perl?
When you say that Logger.PL can't be used in ConfigReader, are you referring to the log object?
In SQL I'm using xp_cmdShell to run FTP commands. I have no problem getting the list of files or copying files to the local server, but I want to compare copied file size to the original to make sure the get has been successful.
Any ideas on how to compare file sizes?
From a command prompt you can use the DOS File Compare command (fc). In your case you probably want to do a binary compare (there is no file size compare). I binary compare should work in your case.
Most DOS commands will return some code that let s you know the status.
http://www.computerhope.com/fchlp.htm
EDIT
Sorry, I read your question and realized you want to compare it against a file on the ftp server. I think this is a moot point since if ftp reports a successful file transfer there is no reason to compare (unless your source of comparison for not the ftp site). Does that make sense?
What you could do it use the FTP command ls command.
ftp> ls <filename>
where ftp> is the ftp prompt and not part of the command. This command gives you the file size in bytes. Then you need to use the dos command for the local file. Here is a StackOverflow question (and answer) about that.
Windows command for file size only?
On all my Windows servers, except for one machine, when I execute the following code to allocate a temporary files folder:
use CGI;
my $tmpfile = new CGITempFile(1);
print "tmpfile='", $tmpfile->as_string(), "'\n";
The variable $tmpfile is assigned the value '.\CGItemp1' and this is what I want. But on one of my servers it's incorrectly set to C:\temp\CGItemp1.
All the servers are running Windows 2003 Standard Edition, IIS6 and ActivePerl 5.8.8.822 (upgrading to later version of Perl not an option). The result is always the same when running a script from the command line or in IIS as a CGI script (where scriptmap .pl = c:\perl\bin\perl.exe "%s" %s).
How I can fix this Perl installation and force it to return '.\CGItemp1' by default?
I've even copied the whole Perl folder from one of the working servers to this machine but no joy.
#Hometoast:
I checked the 'TMP' and 'TEMP' environment variables and also $ENV{TMP} and $ENV{TEMP} and they're identical.
From command line they point to the user profile directory, for example:
C:\DOCUME~1\[USERNAME]\LOCALS~1\Temp\1
When run under IIS as a CGI script they both point to:
c:\windows\temp
In registry key HKEY_USERS/.DEFAULT/Environment, both servers have:
%USERPROFILE%\Local Settings\Temp
The ActiveState implementation of CGITempFile() is clearly using an alternative mechanism to determine how it should generate the temporary folder.
#Ranguard:
The real problem is with the CGI.pm module and attachment handling. Whenever a file is uploaded to the site CGI.pm needs to store it somewhere temporary. To do this CGITempFile() is called within CGI.pm to allocate a temporary folder. So unfortunately I can't use File::Temp. Thanks anyway.
#Chris:
That helped a bunch. I did have a quick scan through the CGI.pm source earlier but your suggestion made me go back and look at it more studiously to understand the underlying algorithm. I got things working, but the oddest thing is that there was originally no c:\temp folder on the server.
To obtain a temporary fix I created a c:\temp folder and set the relevant permissions for the website's anonymous user account. But because this is a shared box I couldn't leave things that way, even though the temp files were being deleted. To cut a long story short, I renamed the c:\temp folder to something different and magically the correct '.\' folder path was being returned. I also noticed that the customer had enabled FrontPage extensions on the site, which removes write access for the anonymous user account on the website folders, so this permission needed re-applying. I'm still at a loss as to why at the start of this issue CGITempFile() was returning c:\temp, even though that folder didn't exist, and why it magically started working again.
The name of the temporary directory is held in $CGITempFile::TMPDIRECTORY and initialised in the find_tempdir function in CGI.pm.
The algorithm for choosing the temporary directory is described in the CGI.pm documentation (search for -private_tempfiles).
IIUC, if a C:\Temp folder exists on the server, CGI.pm will use it. If none of the directories checked in find_tempdir exist, then the current directory "." is used.
I hope this helps.
Not the direct answer to your question, but have you tried using File::Temp?
It is specifically designed to work on any OS.
If you're running this script as you, check the %TEMP% environment variable to see if if it differs.
If IIS is executing, check the values in registry for TMP and TEMP under
HKEY_USERS/.DEFAULT/Environment