5i6SddlmZmZddlZddlZddlZddlZddlZddlm Z ddl Z ddl m Z m Z mZmZmZmZmZmZmZmZmZmZmZmZmZmZddlmZmZmZm Z m!Z!ddl"m#Z#ddl$m%Z%ddl&m'Z' ddl(Z(e(jRejTd Z+d Z,d Z-d Z.d Z/ej`dZ1e1jedde1jedde1jedgddde1jeddde1jgZ4e4jjCejljoe4jjse1jqde4jjzdZ9e:d k(re9yy#YxYw)!)print_functionunicode_literalsN) OrderedDict) print_introget_name get_version get_metadata Completerget_ordinal_strprompt_for_var prompt_for_yn use_completer get_languagelanguage_options get_pattern get_timeoutfill_in_name_and_vercleancreate_files_from_templates)fillBOLD UNDERLINE DNANEXUS_LOGOENDC)APP_CATEGORIES)InstanceTypesCompleter) format_tablez^[a-zA-Z_][0-9a-zA-Z_]*$z aws:us-east-1z azure:westuszoci:us-ashburn-1z1.0.0zCreate a source code directory for a DNAnexus app. You will be prompted for various metadata for the app as well as for its input and output specifications.) descriptionz --json-filez4Use the metadata and IO spec found in the given file)helpz --languagez Programming language of your appz --template)basic parallelizedscatter-process-gatherr zExecution pattern of your app)choicesdefaultrnamezName of your app?)rnargszFile not found: c $ g}tttjt tjd5}t j |j}ttjxs|jd}||d<t|jd}||d<ddd tjdntttj} tj|t't\}}t}t)}||d<|xs||d <|xs||d <t|d <||d<t+gd }t+d dg} t-dt-t/dzt1zt-dd} g} d} | rg|d<t-t#d t-dt3t5|ddz} t7| dzd}|dk(rn|| vrt-t#dVt8j;|st-t#d| j=|t7dd}t?|| st-dt-dd} t7d}||j@vrnt-t#d/t?tCd}d}|r|dvrtCd }|rw |d!k(r%t?| t7d"d dg#}t?n|d$k(rt7d"d}n t7d"} |d!k(r|d k(}n!|d%k(r tE|}n|d&k(r tG|}nd}t)}||d<|dk7r||d(<||d)<||d*<|||d+<|d,k(s|d-k(rd.g|d/<d|d0<|dj=|t-dt-t/d1zt1zt-dd}g}|r^g|d2<t-t#d3 t-dt3t5|d2dz} t7| d4zd}|dk(rn||vrt-t#d5Vt8j;|st-t#d|j=|t7dd}t?|| st-d6t-d7d} t7d}||j@vrnt-t#d/t?t)}||d<|dk7r||d(<||d)<|d,k(s|d-k(rd.g|d/<d|d0<|d2j=|Dg}g}g}g}g}d|vrX|dD]P}|jd*xrd+|v}|d)d,k(r|r|n|} n|d)d-k(r|r|n|} nd} | =| j=|dRd2|vr|d2Dcgc]}|d)d,k(s |d}}t-dt-t/d8zt1zt)i|d9<|d9jId:itK|d9d:jd.\}!}"|d9d:jId.i|d9d:d.jI|"|!t-dt-t/d;zt1ztjLtjLn tO}#tP|#jS}$|$|d9d<<tjTjWtjTjYtZj\d=d>tP|#j_}%tjTjatjTjW|%tjbs4t-t#d?tjbzd@zte|%}&ntjb}&tjTjW|%|&}%t tjTjW|%dAd5}'tg|'j}(t j |(})|)d9D]}*|)d9|*|d9|*< ddd|#tjLk(r|&tjbk(r t-dBt-dt-t/dCt-t#dDt/dEzdFzt-dt-t#tidGdHztCdIdr>|jIdJid.g|dJdK<t-t#dLtidMzdNzt-dt-t#tidOdPztCdQdrL|jIdJidR|dJdS<t-t#dTtidUzdVztidWzdXzt-dt-t/dYt-dt-t/dZt-tktljnjqtstljnjqd[jt\t-t/d]t-tktljvjqtstljvjqd[jt\t-t/d^t-tktljxjqtstljxjqd[jt\t-t#t/d_d`zdazt/dbzdczt?tmt7ddtljzj|tstlj~e}+t},|+tljvjvrt},n&|+tljxjvrt},t)i|df<t)i|df|,<|df|,jIdgi|df|,dgjId.i|+|df|,dgd.dh<di|d9dj<dk|d9dl<dm|d9d<t-dt-t/dnztzt/zdozt1zt tjTjWdAdp5}-|-j!tt j|dqrdzddd|j=tjTjW|dAt-dt-t#dsd|vrd2|vsdtndzt-dduD]f}. tjtjTjW||.|j=tjTjW||.dhdxg}/|&dyk(rgdz}/n |&d{k(rgd|}/|t|%||#||||||&d}|/~ z }t-dt|D]}0t-d|0t-dt#dj|zdzt-t#dt/zdzt1zdzy#1swYDxYw#tjj!t#ddzdztj$dY xYw#tjj!t#d|zdztj$dYxYw#t-d'|zYnxYw cc}w#1swYGxYw#1swY[xYw#tjj!dv|dw|.tj$dY5xYw)z} Entry point for dx-app-wizard. Note that this function is not meant to be used as a subroutine in your program. Nrr%)r$versionzUnable to create a directory for %s, please check that it is a valid app name and the working directory exists and is writable. titlesummarydxapi)intfloatstringbooleanhashz array:intz array:floatz array:stringz array:booleanrecordfileappletz array:record array:filez array:applettruefalsezInput SpecificationTF inputSpeczYou will now be prompted for each input parameter to your app. Each parameter should have a unique name that uses only the underscore "_" and alphanumeric characters, and does not start with a number.z input name ( to finish)) allow_emptyzLError: Cannot use the same input parameter name twice. Please choose again.zError: Parameter names may use only underscore "_", ASCII letters, and digits; and may not start with a digit. Please choose again.z$Label (optional human-readable name)z=Your input parameter must be of one of the following classes:zapplet array:file array:record file int array:applet array:float array:string float record array:boolean array:int boolean hash string z(Choose a class ( twice for choices)z,Not a recognized class; please choose again.zThis is an optional parameter)r0r1r2r3z"A default value should be providedr3z Default value)r#r2r0r1z.Not a valid default value for the given class labelclassoptionalr$r6r8*patternsrzOutput Specification outputSpeczYou will now be prompted for each output parameter of your app. Each parameter should have a unique name that uses only the underscore "_" and alphanumeric characters, and does not start with a number.z output name ( to finish)zMError: Cannot use the same output parameter name twice. Please choose again.z>Your output parameter must be of one of the following classes:zapplet array:file array:record file int array:applet array:float array:string float record array:boolean array:int boolean hash stringzTimeout PolicyrunSpec timeoutPolicyzTemplate Options interpreter templating templateszThe execution pattern "z1" is not available for your programming language.z dxapp.jsonz3All template options are supplied in the arguments.zAccess PermissionszIf you request these extra permissions for your app, users will see this fact when launching your app, and certain other restrictions will apply. For more information, see zAhttps://documentation.dnanexus.com/developer/apps/app-permissions.zAccess to the Internetz) (other than accessing the DNAnexus API).z*Will this app need access to the Internet?accessnetworkzRApp has full access to the Internet. To narrow access to specific sites, edit the zaccess.networkz. field of dxapp.json once we generate the app.z#Direct access to the parent projectzv. This is not needed if your app specifies outputs, which will be copied into the project after it's done running.z0Will this app need access to the parent project? CONTRIBUTEprojectzzApp has CONTRIBUTE access to the parent project. To change the access level or request access to other projects, edit the zaccess.projectz and zaccess.allProjectsz/ fields of dxapp.json once we generate the app.zSystem RequirementszCommon AWS instance types:r) column_nameszCommon Azure instance types:zCommon OCI instance types:zDefault instance type:zE The instance type you select here will apply to all entry points in z%your app unless you override it. See zPhttps://documentation.dnanexus.com/developer/api/running-analyses/instance-typesz for more information.z$Choose an instance type for your app)r$r#regionalOptionssystemRequirements instanceTypeUbuntu distributionz24.04release0z*** Generating z App Template... ***w)indentzYour app specification has been written to the dxapp.json file. You can specify more app options by editing this file directly (see https://documentation.dnanexus.com/developer for complete documentation).z Note that without an input and output specification, your app can only be built as an APPLET on the system. To publish it to the DNAnexus community, you must first specify your inputs and outputs. )srctest resourceszUnable to create subdirectory /mainr!)r]process postprocessr")r]scattermapr^r_z.)r entry_pointszCreated files: zApp directory created! See https://documentation.dnanexus.com/developer for tutorials on how to modify these files, or run "dx build {n}" or "dx build --create-app {n}" while logged in with dx.)nzoRunning the DNAnexus build utility will create an executable on the DNAnexus platform. Any files found in the r[zj directory will be uploaded so that they will be present in the root directory when the executable is run.)Jr API_VERSIONargs json_fileopenjsonloadsreadrr%getrosmkdirsysstderrwriterexitr rr printrrr lenr IO_NAME_PATTERNmatchappendrr#r r0r1 setdefaultrlanguagerrget_interpreterpathjoindirnamedxpy__file__get_pathisdirtemplaterrrrraws_preferred_instance_typesvalueslist_fieldsazure_preferred_instance_typesoci_preferred_instance_typesdefault_instance_typeNameinstance_typesDEFAULT_REGION_AWSkeysDEFAULT_REGION_AZUREDEFAULT_REGION_OCIrrdumpsrsortedformat)1kwargsmanifestrgapp_jsonr%r*r-r.class_completerbool_completer input_spec input_namesprinted_classesordinal input_name input_label input_classr@ default_valparameter_json output_spec output_names output_name output_label output_classrequired_file_input_namesoptional_file_input_namesrequired_file_array_input_namesoptional_file_array_input_namesfile_output_namesparammay_be_missing param_listtimeout timeout_unitsryrF template_dirpatterntemplate_app_json_file file_texttemplate_app_jsonkey instance_type target_region prog_filesubdirrbfilenames1 |/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/scripts/dx_app_wizard.pyr]r];s H  ~~! $..# & *)zz).."23HDII$Ef1EFD#HV !(,,y*ABG")HY   *  HHXf% & *  HHTN &k2w-=!MT%o'% $%ST#FG#45 b  df,,tv56 b    $&H[ ! $cd eb )#h{.C*Dq*HI+G6W,Weij #,$mno&,,Z8$ fgh"":.,-SUWX o.&YZ'+O"01["\K"o&=&==d#QRS ()HI"  /T T"/0T"UK""*i7 -n =.<=NY_ahXi.j -!,!8.<=N\`.a .<=N.O  f#.)#;3>&3HK%0E%925k2BK%0G%;27 2DK %'+ "-)3v&"$.9N7+*5w'-5z**0;N9-&(K<,G25N:.)+v&%,,^<_b b  df--67 b   %'H\ " $de fb )#h|.D*E*IJ,W7Y-Ygkl "$,.$nop&,,[9$ fgh##K0-.TVXY o.&Z[FG'+O#12\#]L#'>'>>d#QRS "-)4v&2%.:N7+*6w' 6)\\-I25N:.)+v&&--n=Y\!# "&(#&(#hk* 1E"YYz2My7MNW~':H6Ng w</@NK)4HY &77<< > k[klt[u[~[~\ABL 77==lDMMB C d,t}}?CFF GHGQVWHb)(49% d/1:;K1LMOVWYbcwYxyDEF G "I $$ %& "I $+ ,- ,-JJQQS$()?)\)\)c)c)e$fgh$i$q$q st $- ./ ,-LLSSU$()?)^)^)e)e)g$hij$k$s$s uv $+ ,- ,-JJQQS$()?)\)\)c)c)e$fgh$i$q$q st $t,-0ww67fghkCC DE(*+"#I+A+W+W+\+\+/0F0U0U+VXM'M.MMRRTT, 0MMRRT T* "-b/H 1A} A~~,6 rsh&:  # wwwwwKJ.70 HMMO"**78$%'  .M NM(^_L'IJLOY`8:F!33? >>bggnnT^^&D LL#dnn45M^  zFI  s ,E//E3