just starting to use Perl here. I previously have successfully used backticks to capture system command output in Perl, such as:
my #sysOut = `cleartool checkout -nc \"$file\"`; # works fine!
but I have run into some trouble, and even after looking around for some time I didn't find the solution to this problem. I am trying to write a Perl script to check in a list of checked out files (#allfiles) using cleartool, except if any are identical to their predecessor, then un-checkout them.
The way I am (...failing at!) detecting whether they are identical or not is to get the output from the check in attempt, see if it matches /error.*identical/i, and then if so uncheckout the file. However, for some reason the output seems to bypassing the array I am passing it into.
See code which generates this problem:
foreach my $file (#allfiles){
chomp( my #checkInErr = `cleartool checkin -nc \"$file\"`);
foreach my $err (#checkInErr) { # if no error, checkin done
if ($err =~ m/error.*identical/i) { # if there is error:
print $err;
print "No change detected: unchecking out.\n"; # uncheckout same version
system "cleartool uncheckout -rm -cact \"$file\"";
}
}
}
Here is my command line output (as if I had just used a system() call):
cleartool: Error: Unable to check in "a5TI.txt".
cleartool: Error: By default, won't create version with data identical to predecessor.
cleartool: Error: Unable to check in "a6cm.txt".
cleartool: Error: By default, won't create version with data identical to predecessor.
cleartool: Error: Unable to check in "a6FT.txt".
cleartool: Error: By default, won't create version with data identical to predecessor.
cleartool: Error: Unable to check in "a6pm.txt".
cleartool: Error: By default, won't create version with data identical to predecessor.
cleartool: Error: Unable to check in "a6TI.txt".
cleartool: Error: By default, won't create version with data identical to predecessor.
SOLUTION: check std error stream as well when grabbing output (in retrospect this makes sense as I was trying to parse error messages... oh well)
my #checkInErr = `cleartool checkin -nc \"$file\" 2>&1`;
It's possible the error output from cleartool is not coming out on Standard Output (stdout). With any luck, it's coming out on Standard Error (stderr). If so, this should work:
system "cleartool uncheckout -rm -cact \"$file\" 2>&1";
Related
In my loop, I run a dbt command and save the output to a .yml file. The following command works and generates a schema in my .yml file accurately:
for file in models/l30_mart/*.sql; do
table=$(basename "$file" .sql)
dbt run-operation generate_model_yaml --args "{\"model_name\": \"$table\"}" > test.yml
done
However, in the example above, I am saving the test.yml file in the root directory. When I try to save the file in another path for example models/l30_mart/test.yml like this, it doesn't work:
for file in models/l30_mart/*.sql; do
table=$(basename "$file" .sql)
dbt run-operation generate_model_yaml --args "{\"model_name\": \"$table\"}" > models/l30_mart/test.yml
done
In this case, when I open the test.ymlfile, I see this:
12:06:42 Running with dbt=1.0.1
12:06:43 Encountered an error:
Compilation Error
The schema file at models/l30_mart/test.yml is invalid because no version is specified. Please consult the documentation for more information on schema.yml syntax:
https://docs.getdbt.com/docs/schemayml-files
What am I missing out on?
If I try something like this to save different files with the extracted tablename variable as the filename, it also doesn't work:
for file in models/l30_mart/*.sql; do
table=$(basename "$file" .sql)
dbt run-operation generate_model_yaml --args "{\"model_name\": \"$table\"}" > models/l30_mart/$table.yml
done
In this case, the files either have this output:
20:39:44 Running with dbt=1.0.1
20:39:45 Encountered an error:
Compilation Error
The schema file at models/l30_mart/**firsttable.yml** is invalid because no version is specified. Please consult the documentation for more information on schema.yml syntax:
https://docs.getdbt.com/docs/schemayml-files
or this (eg in the secondtablename.yml file):
20:39:48 Running with dbt=1.0.1
20:39:49 Encountered an error:
Parsing Error
Error reading dbt_4flow: l30_mart/firstablename.yml - Runtime Error
Syntax error near line 2
------------------------------
1 | 20:39:44 Running with dbt=1.0.1
2 | 20:39:45 Encountered an error:
3 | Compilation Error
4 | The schema file at models/l30_mart/firsttablename.yml is invalid because no version is specified. Please consult the documentation for more information on schema.yml syntax:
5 |
Raw Error:
------------------------------
mapping values are not allowed in this context
in "<unicode string>", line 2, column 31
Note that the secondtablename.yml mentions the firsttablename.yml.
I don't know dbt but the explanation that seems likely is that dbt for some reason parses all *.yml files in that target directory when you call it. Since the shell opens the pipe to the *.yml file before calling dbt, the file already exists (but initially empty) when dbt is called. Since dbt expects the file to contain a version, you get an error.
To check whether this assessment is correct, write into a temporary file:
for file in models/l30_mart/*.sql; do
target_file=$(mktemp)
table=$(basename "$file" .sql)
dbt run-operation generate_model_yaml --args "{\"model_name\": \"$table\"}" > $target_file
mv $target_file models/l30_mart/test.yml
done
(Be aware of mktemp shenanigans if you're using macOS)
Edit: Since dbt seems to be affected by the files existing, you can also try to generate all files and move them into the correct directory afterwards:
target_dir=$(mktemp -d)
for file in models/l30_mart/*.sql; do
table=$(basename "$file" .sql)
dbt run-operation generate_model_yaml --args "{\"model_name\": \"$table\"}" > $target_dir/$table.yml
done
mv $target_dir/*.yml models/l30_mart/
rmdir $target_dir
I am relatively new to the world of coding, so I am having trouble resolving an issue when running TranslocWrapper.pl tutorial_metadata.txt preprocess/ results/ --threads 2. I am trying to run the HTGTS Pipeline according to this GitHub project. This is the full error:
. Library Genome Chr Start End Strand
1 RAG1A_SRep2 hg19 chr11 36594878 36595030 -
Metadata error: chr must be valid at /home/micah/transloc_pipeline/bin/TranslocWrapper.pl line 285.
main::check_validity_of_metadata('HASH(0x2903ac8)') called at /home/micah/transloc_pipeline/bin/TranslocWrapper.pl line 248
main::read_in_meta_file() called at /home/micah/transloc_pipeline/bin/TranslocWrapper.pl line 90
I have already double-checked the successful installation of the Software Dependencies, so everything should be all good, but I am having trouble interpreting the "Metadata error: chr must be valid at ..." line. If it helps, these are the specific lines that are being called in the error:
TranslocWrapper.pl line 285:
croak "Metadata error: chr must be valid" unless grep { $_ eq $expt->{chr} } #chrlist;
TranslocWrapper.pl line 248:
check_validity_of_metadata($expt);
TranslocWrapper.pl line 90:
read_in_meta_file;
Thanks in advance for the help!
So the error is saying that one of the sequence characters in the metadata file is not present in the sequence's assembly file.
Given that this is the provided example you should assume that the data is correct and your invocation is faulty.
Have you done the TranslocPreprocess.pl preprocessing steps?
If you have try looking at the first line of the metadata file, identify the assembly entry. Ensure that the assembly file exists and that it contains the required sequence.
One common problem with this kind of code is the case of the filenames. The examples are designed to be run in Linux where filename case matters. Windows likes to pretend that case doesn't matter, this can cause problems. If you are running this code from Microsoft Windows or extracted any of the archives from within Windows this is a likely cause of the error.
I am trying to configure the environment for OpenDDS, but I could not run the configure script. Would really appreciate much, if there are any insight from you guys. =D
So basically, after I download the OpenDDS-3.12.zip from here. I have extracted to a folder and tried to run the configure file with this command in VS command prompt (VS2017)
configure --compiler=gcc
Next, the "ACE+TAO-2.2a_with_latest_patches_NO_makefiles" is downloaded and I extract the zip file to the root folder.
Then it shows this message.
ACE_ROOT/ace/config.h exists, skipping configuration of ACE+TAO
Use of uninitialized value $mpctype in string eq at configure line 1103.
Use of uninitialized value $mpctype in concatenation (.) or string at configure line 1257.
Use of uninitialized value $mpctype in string eq at configure line 1266.
Running MPC to generate project files.
MPC_ROOT was set to C:\src\OpenDDS-DDS-3.12.2\ACE_wrappers\MPC.
Using .../OpenDDS-DDS-
3.12.2/ACE_wrappers/bin/MakeProjectCreator/config/MPC.cfg
ERROR: Invalid type: C:\src\OpenDDS-DDS-3.12.2\DDS_TAOv2_all.mwc
mwc.pl v4.1.28
...
/*lots of explanation of each file here*
*then followed by*/
...
ERROR: Error from MPC, stopped at configure line 1270.
I have both Visual Studio 2017 and Perl 5.22 installed as well, I am not sure whether if this is a compiler issue or any other issue. The following is the configure script that printed the error above.
## line 1268 -- 1270 ##
if (!$opts{'dry-run'}) {
if (system("perl \"$ENV{'ACE_ROOT'}/bin/mwc.pl\" $mwcargs") != 0) {
die "ERROR: Error from MPC, stopped";
}
}
$mpctype is defined here:
my $mpctype = ($slash eq '/' ||
($cross_compile && $buildEnv->{'build'} eq 'target'))
? 'gnuace' : $opts{'compiler_version'};
It seems to be looking at $opts{'compiler_version'}, which is apparently empty. %opts is defined here:
my %opts = %{parseArgs()};
so it looks like you should define the compiler_version in the command line or define the target platform. It's probably better if you check out the INSTALL options thoroughly
VS2017 doesn't install c++ compiler by default.
Modify VS 2017 and select c++ compiler and install if VS 2017 already install.
configure (without --compiler=gcc flag)
I had a similar question. Being a newbie, I started with the getting started with java and windows on https://opendds.org/quickstart/GettingStartedWindows.html .
Step 5, "configure (To enable Java support, use configure --java)" didn't work in a visual studio command window despite
having set JAVA_HOME. I had sent ACE_ROOT, DDS_ROOT, TAO_ROOT and MPC_ROOT though the tutorial didn't specify based on trying to debug this problem.
When using the "--compiler" option I get errors similar to the ones in this thread. Was there any resolution just to get the"
"off-the-shelf" tutorial working. Using Windows 10.
D:\data\OpenDDS-3.13.3>configure --java --compiler="C:\Program Files\Java\jdk1.8.0_221\bin"
ACE_ROOT/ace/config.h exists, skipping configuration of ACE+TAO
Use of uninitialized value $mpctype in string eq at configure line 1482.
Use of uninitialized value $mpctype in concatenation (.) or string at configure line
1646.
Use of uninitialized value $mpctype in string eq at configure line 1655.
Running MPC to generate project files.
MPC_ROOT was set to D:\data\OpenDDS-3.13.3\ACE_WRAPPERS\MPC.
Using .../OpenDDS-3.13.3/ACE_WRAPPERS/bin/MakeProjectCreator/config/MPC.cfg
ERROR: Invalid type: D:\data\OpenDDS-3.13.3\DDS_TAOv2_all.mwc
mwc.pl v4.1.44
...
ERROR: Error from MPC, stopped at configure line 1659.
I am using unoconv to convert an ods spreadsheet to a csv file.
Here is the command:
unoconv -vvv --doctype=spreadsheet --format=csv --output= ~/Dropbox
/mariners_site/textFiles/expenses.csv ~/Dropbox/Aldeburgh/expenses
/expenses.ods
It saves the output file in the same directory as the source file, not in the specified directory. The error message is:
Output file: /home/richard/Dropbox/mariners_site/textFiles/expenses.csv
unoconv: UnoException during export phase:
Unable to store document to file:///home/richard/Dropbox/mariners_site
/textFiles/expenses.csv (ErrCode 19468)
I'm sure that this worked initially, but it has since stopped.
I have checked for permissions and they are identical for both directories.
I translated ErrCode 19468 for you and it boils down to meaning ERRCODE_SFX_DOCUMENTREADONLY.
You can find more information about the specific meaning of LibreOffice ErrCode numbers from the unoconv documentation at: https://github.com/dagwieers/unoconv/blob/master/doc/errcode.adoc
The clue here is that you have a whitespace-character between --output= and the filename (--output= ~/Dropbox
/mariners_site/textFiles/expenses.csv) and because of that unoconv gets an empty output value (which means the current directory) and is given 2 files. And that explains why you get this specific error IMO
I was testing the functionality of PDF::Tk by installing in cpan module and installed the pdftk binary file and the path to variable and tried running source code.
source code:
use PDF::Tk;
my $doc = PDF::Tk->new( pdftk => '/apps/free/pdftk/' );
$doc->call_pdftk( 'input.pdf', 'outPDF.pdf', 'cat', '1-14' );
getting error as below:
pdftk input.pdf cat 1-14 releasenote.pdf failed: -1 at
/usr/lib/perl5/site_perl/5.10.0/PDF/Tk.pm line 73.
please guide me in resolving it.
Seems you are passing the wrong argument to the constructor of PDF::Tk. Have a look here.
You're supposed to pass a hash, with the key pdftk, and this should be the path of the executable, not a directory. As you can see here, this will be executed via system, so of course, executing a directory does not work.
To clarify, you should be using:
my $doc=PDF::Tk->new(pdftk => '/path/to/pdftk/executable');
If your pdftk executable is /usr/bin/pdftk, then you do not have to pass it at all as this is the default.
for testing the encryption function (by default 128 bit encryption) , i created a pdf file 'apps.pdf' with password protected 'abcd' as password.
source code 1:
use PDF::Tk;
my $doc=PDF::Tk->new(pdftk=>'/apps/free/pdftk/1.44/bin/pdftk');
$doc->call_pdftk('apps.pdf', '1.128.pdf', 'owner_pw', 'abcd');
getting error:
Error: Unexpected command-line data:
owner_pw
where we were expecting an input PDF filename,
operation (e.g. "cat") or "input_pw". Exiting.
Errors encountered. No output created.
Done. Input errors, so no output created.
pdftk apps.pdf owner_pw abcd 1.128.pdf failed: 256 at /usr/lib/perl5/site_perl/5.10.0/PDF/Tk.pm line 73.
note: created a new pdf 'apps.pdf' with Document Open Password as 'abcd' and permission Password as 'abcd123'.
Please let me know how to resolve it.