5i|ZddlmZddlZddlZddlZddlmZddlmZdZ dZ dZ d dZ y) )print_functionN)file_load_utils)err_exitcg}|D]_}i}|d}|j|d<|d|d<|d}dtjj|z|d<|j |ad|i}t d t ||S) Nhandlerproj_id src_file_idfile_id trg_fname/parentFileszFile mount manifest:) get_proj_idospathdirnameappendprint)to_mount files_listfile_rec file_entry file_handler file_namefiles_manifests /home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/bindings/mount_all_inputs.py_build_mount_manifestrsJ&  * , 8 8 : 9 ( 7 9[) "RWW__Y%?? 8*%&z*N ! . cd}tjdjtjD].}tjj ||}||s,|cSy)Nctjj|xr$tj|tjSN)rrisfileaccessX_OK)fpaths ris_exez_which..is_exe(s)ww~~e$B5"'')BBrPATH)renvironsplitpathseprjoin)programr&rexe_files r_whichr.'sWC 6"((477<<g. ( O rctjtjd\}}i}d}|D]<}||vr||}||dz|d|||dz|d|||dz|d|>|S) z~ Create a dict of values for the mounted files. This is similar to the variables created when running a bash app. Nc||vr|||<yyr!)keyvaluedict_s radd_if_no_collisionz-_gen_helper_dict..add_if_no_collision<s e E#J r_pathr_namebasename_prefixprefix)ranalyze_bash_varsget_input_json_file)filtered_inputsfile_key_descs_ignoreflattened_dictr5input_input_var_dicts r_gen_helper_dictrC1s .??++-t5NGN"Z  ' '/FW,nV.DnUFW,nZ.H.YFY.x0H.Y Z rctdtjd}tjj |d}tjj |d}t d}| t dtjd|g tj}tj|\}}} |rtj||}g} |jD]} | j!| t#| } t%|d 5}t'j(| |dddtj|d g}td t+|zt+t-tjddg}t+t-tjddg}|d|d|||g}|rddg|ddttj|tdtj.d|ddgt1|}|S#t$r#d j} | d z } t| wxYw#1swYxYw)a :param exclude: List of input variables that should not be mounted. :type exclude: Array of strings :returns: dict of lists of strings where each key is the input variable and each list element is the full path to the file that has been mounted. :param verbose: Start dxfuse with '-verbose 2' logging :type verbose: boolean This function mounts all files that were supplied as inputs to the app. By convention, if an input parameter "FOO" has value {"$dnanexus_link": "file-xxxx"} and filename INPUT.TXT, then the linked file will be mounted into the path: $HOME/in/FOO/INPUT.TXT If an input is an array of files, then all files will be placed into numbered subdirectories under a parent directory named for the input. For example, if the input key is FOO, and the inputs are {A, B, C}.vcf then, the directory structure will be: $HOME/in/FOO/0/A.vcf 1/B.vcf 2/C.vcf Zero padding is used to ensure argument order. For example, if there are 12 input files {A, B, C, D, E, F, G, H, I, J, K, L}.txt, the directory structure will be: $HOME/in/FOO/00/A.vcf ... 11/L.vcf This allows using shell globbing (FOO/*/*.vcf) to get all the files in the input order and prevents issues with files which have the same filename.zMounting inputs...HOMEinzmount-manifest.jsondxfuseNz&dxfuse is not installed on this systemmkdirz0Error: Could not find the input json file: {0}. zE This function should only be called from within a running job.wz-versionzUsing dxfuse version idz-uz-gz-uidz-gidz-verbose2zDone mounting inputs.findz-name*)rrr(rr+r.r subprocess check_outputrr<get_job_input_filenamesIOErrorformat filter_dictvaluesextendropenjsondumpstrintcallrC)excludeverbosehome_dir mount_dirmount_manifest_file dxfuse_cmdjob_input_filedirsinputsrestmsgr ival_listrmfiledxfuse_versionuidgidcmd helper_varss rmount_all_inputsroKsR zz&!H Xt,I'',,x1FG!J9:Wi01(<<>,DD^Tfd ,,VW=H]]_#  "#+84N !3 ')5 .%() ,,j*-EFN !C$7 78 c*))4,78 9C c*))4,78 9C vsFCrss."& &$ 4Yr