Shell Global Standard For Temporary Pipework
Elis Riebow
$ ...; is a form of command substitution that doesn't spawn a subshell. For commands that are builtin commands, instead of having them writing their output to a pipe (for which you'd need different processes to read and write on the pipe to avoid dead-locks), ksh93 just makes them not output anything but gather what they would have been outputting in to make up the expansion. mksh uses a temporary file instead.
Is there a way to execute a multi-line shell script by piping it to the remote shell's standard input in fabric? Or must I always write it to the remote filesystem, then run it, then delete it? I like sending to stdin as it avoids the temporary file. If there's no fabric API (and it seems like there is not based on my research), presumably I can just use the ssh module directly. Basically I wish fabric.api.run was not limited to a 1-line command that gets passed to the shell as a command line argument, but instead would take a full multi-line script and write it to the remote shell's standard input.
Inside the shell command, all local and global variables, especially input and output files can be accessed via their names in the python format minilanguage.Here, input and output (and in general any list or tuple) automatically evaluate to a space-separated list of files (i.e. path/to/inputfile path/to/other/inputfile).From Snakemake 3.8.0 on, adding the special formatting instruction :q (e.g. "somecommand input:q output:q")) will let Snakemake quote each of the list or tuple elements that contains whitespace.
There are several standard resources, for total memory, disk usage, runtime, and the temporary directory of a job: mem, disk, runtime, and tmpdir.All of these resources have specific meanings understood by snakemake and are treated in varying unique ways:
The bigger question is hard. I don't think there's an easy way to do it. You'd have to build the entire pipeline into the sub-shell, eventually sending its final standard output to a file, so that you can redirect the errors to standard output.
However, if you want to CAPTURE stdout AND stderr, then I think you have to fall back on temporary files because $() will only do one at a time and it makes a subshell from which you cannot return variables.
It's always fun to start with a polemic so let me make my position quite clear: temporary files are a force for evil in the world of shell scripts and should be avoided if at all possible. If you want justification for this stance just consider the following:
Avoiding temporary files can be difficult but is not necessarily impossible. A lot of UNIX commands will read standard input (or send output to standard output) as well as to named files. Using pipes to connect such commands together will normally give the desired result without recourse to temporary files.
However, this introduces a slight overhead due to the use of cat command which introduces another pipe. I thought of a way to redirect the data from the named pipe to standard output using only exec and shell redirections and without using any other command.
This should create a new fd 3, representing the opened named pipe pipe.fifo and the data coming from the pipe should be redirected to standard output. When I run this shell script, it blocks as nothing is writing to the named pipe, as expected. However, as soon as I printf something into the named pipe from another shell, the script does not output anything and stops blocking.
When the coprocess is executed, the shell creates an array variable(see Arrays)named NAME in the context of the executing shell.The standard output of commandis connected via a pipe to a file descriptor in the executing shell,and that file descriptor is assigned to NAME[0].The standard input of commandis connected via a pipe to a file descriptor in the executing shell,and that file descriptor is assigned to NAME[1].This pipe is established before any redirections specified by thecommand (see Redirections).The file descriptors can be utilized as arguments to shell commandsand redirections using standard word expansions.Other than those created to execute command and process substitutions,the file descriptors are not available in subshells.
If parameteris null or unset, the expansion of word (or a messageto that effect if wordis not present) is written to the standard error and the shell, if itis not interactive, exits. Otherwise, the value of parameter issubstituted.
Bash performs the expansion by executing command in a subshell environmentand replacing the command substitution with the standard output of thecommand, with any trailing newlines deleted.Embedded newlines are not deleted, but they may be removed duringword splitting.The command substitution $(cat file) can bereplaced by the equivalent but faster $(< file).
This type of redirection instructs the shell to read input from thecurrent source until a line containing only word(with no trailing blanks) is seen. All ofthe lines read up to that point are then used as the standardinput (or file descriptor n if n is specified) for a command.
If this option is present, or if no arguments remain after optionprocessing, then commands are read from the standard input.This option allows the positional parameters to be setwhen invoking an interactive shell or when reading inputthrough a pipe.
shopt_option is one of the shell options accepted by theshopt builtin (see The Shopt Builtin).If shopt_option is present, -O sets the value of that option;+O unsets it. If shopt_option is not supplied, the names and values of the shelloptions accepted by shopt are printed on the standard output.If the invocation option is +O, the output is displayed in a formatthat may be reused as input.
When Bash is started in POSIX mode, as with the--posix command line option, it follows the POSIX standardfor startup files.In this mode, interactive shells expand the ENV variableand commands are read and executed from the file whose name is theexpanded value.No other startup files are read.
Bash attempts to determine when it is being run with its standard inputconnected to a network connection, as when executed bythe historical remote shell daemon, usually rshd,or the secure shell daemon sshd.If Bashdetermines it is being run non-interactively in this fashion,it reads and executes commands from /.bashrc, if thatfile exists and is readable.It will not do this if invoked as sh.The --norc option may be used to inhibit this behavior, and the--rcfile option may be used to force another file to be read, butneither rshd nor sshd generally invoke the shell with thoseoptions or allow them to be specified.
If Bash is started with the name rbash, or the--restrictedor-roption is supplied at invocation, the shell becomes restricted.A restricted shell is used toset up an environment more controlled than the standard shell.A restricted shell behaves identically to bashwith the exception that the following are disallowed or not performed:
Generate possible completion matches for word according tothe options, which may be any option accepted by thecompletebuiltin with the exception of -p and -r, and writethe matches to the standard output.When using the -F or -C options, the various shell variablesset by the programmable completion facilities, while available, will nothave useful values.
Bash implements essentially the same grammar, parameter andvariable expansion, redirection, and quoting as the Bourne Shell. Bash uses the POSIX standard as the specification ofhow these features are to be implemented. There are somedifferences between the traditional Bourne shell and Bash; thissection quickly details the differences of significance. Anumber of these differences are explained in greater depth inprevious sections.This section uses the version of sh included in SVR4.2 (thelast version of the historical Bourne shell) as the baseline reference.
Does Linux have a standard temporary directory for general use, like Windows's C:\Temp folder? If so, where is it located? I found an SO question about finding a tmp directory programmatically, but I want to set a temp location in an XML config file ahead of time.
Anyway, the standard temporary directory in a typical Linux system is /tmp. It is the equivalent of C:\Temp in the sense that it is only the default temporary directory, not universal. Even if /tmp is available, if a user (or the system) has set the TEMP environment variable, the value of that variable should be used instead.
The initial question was: Does Linux have a standard temporary directory. If so, where is it located?The tmp folder(s) are found at: File System/tmp & File System/var/tmpThe /tmp contents could be deleted - if you know which files/folders are required/not required by various apps on an "as required" basis. Unrequired files are usually those downloaded by an app to facilitate the app itself at that point only- therefore not further required after the app has performed. The /var/tmp folder should not be touched at all.
Solution: Instead of using JsonSlurper, use a shell step and return the standard out. This shell would look something like this: def JsonReturn = sh label: '', returnStdout: true, script: 'echo "$LOCAL_FILE" jq "$PARSING_QUERY"'. This will use agent resources to read the file and the $PARSING_QUERY will help parse down the file into a smaller size.
Our flowline restraint system is a safety device designed to reduce separation between lengths of temporary pipework in the event of a pressurized pipeline rupture. The system consists of just two parts: high-strength polyester restraints and steel shackles. It is designed for easy installation, leaving a cleaner finish and look.
results in the command ls -l executing ina subshell as usual, but redirects the output to a temporary namedpipe, which bash creates, names and later deletes. Therefore,cat has a valid file name to readfrom, and we see the output of ls -l, taking onemore step than usual to do so. Similarly, giving>(commands)results in Bash naming a temporary pipe, which the commands insidethe parenthesis read for input.
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