3 dp@sddlZddlmZddlmZmZmZmZmZm Z m Z m Z ddl m Z ejeddd Zejedejd ee d ejd d e e ddddZejedejdee d ejd dddddejddddddejddddddejddedd d!d"Zejedejd#ee d d$d%Zejedejd&e d'e d(ejd)ed'd*ejd+ddd,dejd-d.ddd/dejd0d1Zejedd2d3Zejd4d5Zejedejdd6edd7d8ejd9d:e de d;d<ejd=d>ede d?d<ejd@dAdedBdCejdDdEdedFdCejdGdHedId ejdJdKeddLdMejdNdOdddPdejdQdRedSd ejdTdUedVd dWdXZdS)YN)list_interfaces)CONTEXT_SETTINGSUNKNOWN_OPTIONSExistingDirPathExistingFilePathUnexistingFilePathRegularExpression PythonModulecheck_not_none) __version__)Zcontext_settingscCsdS)Nrrr4/tmp/pip-build-7vycvbft/nipype/nipype/scripts/cli.pyclisrlogdir)typecallbackz-rz--regexz4Regular expression to be searched in each traceback.)rrhelpcCshddlm}xV||D]J\}}|j|rtjdt|tj|tjdt|tj|qWdS)zSearch for tracebacks content. Search for traceback inside a folder of nipype crash log files that match a given regular expression. Examples: nipypecli search nipype/wd/log -r '.*subject123.*' r)iter_tracebacks-N) crash_filesrsearchclickecholen)rregexrfiletracerrrrs   r crashfilez--rerunTzRerun crashed node.)Zis_flag flag_valuerz-dz--debugz)Enable Python debugger when re-executing.z-iz --ipydebugz*Enable IPython debugger when re-executing.z-wz--dirz#Directory where to run the node in.)rrcCsXddlm}|rdn|}|dkrFddl}ddlm}|jdddd |_|||||dS) zDisplay Nipype crash files. For certain crash files, one can rerun a failed node in a temp directory. Examples: nipypecli crash crashfile.pklz nipypecli crash crashfile.pklz -r -i r)display_crash_fileZipythonrN)ultratbVerboseLinux)modeZ color_schemeZcall_pdb)rr!sysZ IPython.corer"Z FormattedTB excepthook)rZrerundebugZipydebugdirr!r&r"rrrcrash7s   r* pklz_filecCs,ddlm}ddlm}||}||dS)z^Print the content of Nipype node .pklz file. Examples: nipypecli show node.pklz r)pprintr )loadpklN)r,Zutils.filemanipr-)r+r,r-Zpkl_datarrrshowcs  r.moduleF)rrequiredr interface)rr0z--listz6List the available Interfaces inside the given module.z-hz--helpzShow help message and exit.cCs.ddl}ddlm}ddlm}t|}|s@tj|jj |n|rH|sR|r| rt |} tjdx| D]} tjdj | qjWn|o|r*d j |} d j |j |j|g|j} |j| | d } t||}|| |} |jsz&y | jWntd YnXWd| jXn| j|jd }|||dS)zRun a Nipype Interface. Examples: nipypecli run nipype.interfaces.nipy --list nipypecli run nipype.interfaces.nipy ComputeMask --help rNr)add_args_optionsr ) run_instancezAvailable Interfaces:z {}zRun {} ) descriptionprogzKAn error ocurred when trying to print the fullcommand help, printing usage.)args)argparseutilsr2Zutils.nipype_cmdr3boolrrcommandZget_helprformatjoinZ command_path__name__r7ArgumentParsergetattr print_helpprint print_usage parse_args)ctxr/r1listrr8r2r3Z module_givenZ iface_namesZif_namer5r6Z iface_parsernoder7rrrrunrs4          rHcCstjtdS)z Print current version of Nipype.N)rrr rrrrversionsrIcCsdS)z*Export nipype interfaces to other formats.NrrrrrconvertsrJz --interfacez'Name of the Nipype interface to export.)rr0rz-mz--modulez&Module where the interface is defined.)rr0rrz-oz--outputz>JSON file name where the Boutiques descriptor will be written.z-cz--container-imagez8Name of the container image where the tool is installed.)r0rrz-pz--container-typez0Type of container image (Docker or Singularity).z-xz--container-indexzJOptional index where the image is available (e.g. http://index.docker.io).z-gz--ignore-inputsz:List of interface inputs to not include in the descriptor.)rmultiplerz-vz --verbosezPrint information messages.z-az--authorz-Author of the tool (required for publishing).z-tz--tagszRJSON string containing tags to include in the descriptor,e.g. "{"key1": "value1"}"c Cs,ddlm} | ||||||d|||| dS)zkNipype to Boutiques exporter. See Boutiques specification at https://github.com/boutiques/schema. r)generate_boutiques_descriptorTN)Znipype.utils.nipype2boutiquesrL) r/r1Zcontainer_imageZcontainer_typeoutputZcontainer_indexverboseauthorZ ignore_inputstagsrLrrr boutiquessQ rQ)rinstancerr9rrrrrr r r r grouprr;Zargumentoptionrr*r.strZ pass_contextrHrIrJrQrrrrs (      4