o Uݢgy*@sBdZddlmZddlZddlZddlZddlmZmZddl m Z m Z m Z m Z ddlmZdDd d ZeZdEddZdFddZe dddGddZe dHddZdddIddZdFddZe dddJd!d"Ze dKd$d"ZdddLd&d"Z  '  ' (dMdNd2d3ZdOd6d7Ze dPd;d<Ze dQd?d<ZdRd@d<ZdSdBdCZdS)TzHelper for functions for logging calls to subprocesses. In addition to logging, these wrappers will also (on linux) set PDEATHSIG on the child process, so that they are killed if the parent process dies. ) annotationsN)CallableSequence)IO TYPE_CHECKINGLiteraloverload ensure_strreturnCallable[[], None] | Nonecsttjdr8ddl}ddl}ddlm}||j d| d| d| |d fdd }|SdS) Nlinuxr)SIGKILLcr NonecsdS)zWhen used as the preexec_fn argument for subprocess.Popen etc,. causes the subprocess to recieve SIGKILL if the parent process terminates. N)prctlZPR_SET_PDEATHSIGlibcZsigkillzerord/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/python/tenkit/log_subprocess.py_child_preexec_set_pdeathsig%sz6__make_pdeathsig.._child_preexec_set_pdeathsig)r r) sysplatform startswithctypes ctypes.utilsignalrCDLLutil find_libraryc_intc_ulong)rrrrrr__make_pdeathsigs     r$argsSequence[str] | Sequence[bytes] list[str]cCs t|tr dd|DStd)NcSsg|]}t|qSrr ).0xrrr 7sz_str_args..zCommand must be a sequence.) isinstancer ValueError)r%rrr _str_args5s r-intcOBttjddt|d|vrt|d<tj|g|Ri|S)zSee `subprocess.check_call`.zsubprocess check_call: %s preexec_fn)logginglogINFOjoinr-child_preexec_set_pdeathsig subprocess check_callr%Zwargskwargsrrrr8<r8)encodingr<rbytescKdSNrr%r<r:rrr check_outputErAstrcKr>r?rr@rrrrANrB str | None str | bytescK@ttjddt|d|vrt|d<tj|fd|i|S)zSee `subprocess.check_output`.zsubprocess check_output: %sr0r1r<)r2r3r4r5r-r6r7rAr@rrrrAWscOr/)zSee `subprocess.call`.zsubprocess call: %sr0r1)r2r3r4r5r-r6r7callr9rrrrGbr;rGsubprocess.Popen[bytes]cKr>r?rr@rrrPopenkrBrIsubprocess.Popen[str]cKr>r?rr@rrrrItrB/subprocess.Popen[bytes] | subprocess.Popen[str]cKrF)zSee `subprocess.Popen`.subprocess Popen: %sr0r1r<)r2r3r4r5r-r6r7rIr@rrrrI}sFTcmds)Sequence[Sequence[str] | Sequence[bytes]]stdinNone | str | bytes | IO[bytes] close_inputboolstdout close_outputr3cCsnt|tsJt|dksJtdd|DsJ|r,ttjdddd|Dt|||||ddS) aRun a series of commands, piping output from each one to the next. The commands given as arguments to this method must be lists of arguments. In general, this will be much safer than using `check_call` with `shell=True` to pipe output between processes. For example, .. code-block:: python from subprocess import call filename = input("What file would you like to search?\n") # imagine the user enters `non_existent; rm -rf / #` call("cat {} | grep predicate".format(filename), shell=True) # Uh oh... While it _is_ possible to make sure the arguments in such an expression are properly quoted, there are a lot of tricky edge cases to watch out for. As compared to `pipes.Template()`, this method makes it easier to safely include commands in the pipeline which include untrusted arguments, and also offers more flexibility in terms of inputs and outputs. Args: cmds (list of list): A list of commands to execute. Must have at least one element. stdin (file or str): A filename or file object to pass as input to the first process in the pipeline. This file will be closed once the subprocess is launched. If not provided, input will not be redirected. close_input (bool): If true, close the input file after launching the first process. This value is ignored if `input_file` is not a file-like object. stdout (file or str): The name of the file to which to write the output of the final command in the pipeline. If not provided, the final process's output will not be redirected. close_output (bool): If true, close the output file after launching the final process. This value is ignored if `output_file` is not a file-like object. log (bool): If true, write the pipeline (as if it were a bash command) to the log. rcss|]}t|tVqdSr?)r+listr(cmdrrr szpipeline..rLz | css|] }dt|VqdS)r0N)r5r-rVrrrrXs input_filerQ output_filerTN) r+rUlenallr2r3r4r5 _pipeline)rMrOrQrSrTr3rrrpipelines 0 r_rZr[cCst|d||||t|dk}z%zt|dkr%t|dd|jd||dWn|W|}n|}w|rDt||ddS)NrrTrY)_get_pipeline_procr\r^rSkillwaitr7CalledProcessError)rMrZrQr[rTprocresultrrrr^s,   r^obj IO[bytes] Literal[True]cCr>r?rrfrrr_is_file_handlerjstr | bytes | intLiteral[False]cCr>r?rrirrrrjrkcCst|do t|dS)Nfilenoclose)hasattrrirrrrjs$bytes | int | str | IO[bytes] | Nonec Cs&|rt|strt|trJt|d}d}tr#|dur#t|ts#Jd}z|sTtj||tjtd}|W|rQ|rRt|rSz| WS|rP| | SSS|rjt|sjtrct|trcJt|d}d}trw|durwt|tswJzPtj|||td}|W|r|rt|rz| Wnt t jd|r| | W|r|rt|rz| WS|r| | SSS|r|rt|rz| Wwt t jd|r| | www|r|rt|rz| Ww|r| | www)zStarts a command with the given input and output. Handles all of the details around opening files and closing them if need be, even when stuff fails. rbTN)rOrSr1wbzfailed to close output file)rjrr+ropenr7rIPIPEr6rorarbr2r3r4)rWrZrQr[rTfinalrdrrrr`s            r`)r r )r%r&r r')r%r&r r.)r%r&r<rr r=)r%r&r<rCr rC)r%r&r<rDr rE)r%r&r<rr rH)r%r&r<rCr rJ)r%r&r<rDr rK)NFNFT) rMrNrOrPrQrRrSrPrTrRr3rR) rMrNrZrPrQrRr[rPrTrR)rfrgr rh)rfrlr rm)r rR) rZrqrQrRr[rqrTrRr rH)__doc__ __future__rr2r7rcollections.abcrrtypingrrrrsixr r$r6r-r8rArGrIr_r^rjr`rrrrsP             E