5iW!ddlZddlZddlZddlZddlmZddlZddlZddlmZddl m Z m Z ddl m Z mZmZmZmZmZmZddlmZddlmZddlmZej4d Z dd Z dd Zdd Zy)N)glob)partial)get_nextflow_dxappget_nextflow_src)get_template_dir write_exec write_dxappget_importer_name create_readme get_nested get_allowed_extra_fields_mapping) parse_obj)try_call)resolve_existing_pathzUploads a DNAnexus App.) descriptionc d} | xsi} tj} d} | | } || d<|df|df|df|df|ttdf|ttdfd}|j D]\}\}}|s |r||n|| |<|rt t |d\} } }| tjd tjt j| | | d |zd }|std|j|jdtj|j!dd idd\}}|std|z|Stt#j$t'||S)a :param repository: URL to a Git repository :type repository: string :param tag: tag of a given Git repository. If it is not provided, the default branch is used. :type tag: string :param cache_docker: Pull a remote docker image and store it on the platform :type cache_docker: bool :param docker_secrets: Dx file id with the private docker registry credentials :type docker_secrets: string :param nextflow_pipeline_params: Custom Nextflow pipeline parameters :type nextflow_pipeline_params: string :param profile: Custom Nextflow profile, for more information visit https://www.nextflow.io/docs/latest/config.html#config-profiles :type profile: string :param brief: Level of verbosity :type brief: boolean :returns: ID of the created applet Runs the Nextflow Pipeline Importer app, which creates a Nextflow applet from a given Git repository. cftDcic]\}}t||x}||c}}Scc}}w)zq :param args: extra args from command input :returns: overridable fields from extra_args )r r )argsarg_path target_keyvals /home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/nextflow/nextflow_builder.pyparse_extra_argsz1build_pipeline_with_npi..parse_extra_args6sB)I(J $*!$11> O   s-Nrepository_urlfile)klass)repository_tagconfig_profile cache_dockernextflow_pipeline_paramsdocker_secretsgithub_credentialsfolder)expectedzCan't create an applet without specifying a destination project; please use the -d/--destination flag to explicitly specify a project)namezNextflow build of %sT) app_inputprojectr#r%detachzStarted builder job )intervaloutput)fields output_appletzCreated Nextflow pipeline %s)id)dxpy WORKSPACE_IDrritemsrrparsererrorDXAppr runprintget_id wait_on_doneget_dxlink_idsdescribejsondumpsdict) repositorytagrr!r profile git_credsbrief destination extra_argsrbuild_project_id build_folder input_hash input_updateskey raw_value transform_nf_builder_job applet_ids rbuild_pipeline_with_npirOs@  !rJ((L!*-J#-J +"D/%t,%=t$D)79F+KL(')6*JK M(5':':'<O# #i 6?i 2YJsOO,45JKbj,k),  T UZZ%6%89== \lEQCY]gChqu>wN  .*?*?*ACD+&&~'>'>xQUFV'>'WX`'abq'rsLIq  , :;  djj+,- c$tjj|sJttjj |ds"t j jd|ztjd}ttjj |d}t||||||}t|||}tjt|d t!||t#||t%|||S) az :param resources_dir: Directory with all resources needed for the Nextflow pipeline. Usually directory with user's Nextflow files. :type resources_dir: str or Path :param profile: Custom Nextflow profile. More profiles can be provided by using comma separated string (without whitespaces). :type profile: str :param region: The region in which the applet will be built. :type region: str :param cache_docker: Perform pipeline analysis and cache the detected docker images on the platform :type cache_docker: boolean :param nextflow_pipeline_params: Custom Nextflow pipeline parameters :type nextflow_pipeline_params: string :returns: Path to the created dxapp_dir :rtype: Path Creates files necessary for creating an applet on the Platform, such as dxapp.json and a source file. These files are created in '.dx.nextflow' directory. z*.nfzRDirectory %s does not contain Nextflow file (*.nf): not a valid Nextflow directoryz .dx.nextflow)prefixznextflow_schema.json) schema_file) custom_inputs resources_dirregionr@rr )rTr@rUT) dirs_exist_ok)ospathexistsrjoinr/ app_builderAppBuilderExceptiontempfilemkdtempprepare_custom_inputsrrshutilcopytreerr rr ) rUr@rVrr dxapp_dirrT dxapp_content exec_contents rprepare_nextflowrfhs. 77>>- (( (  ]F3 422 `cp pr r  7I)bggll=Rh6ijM&##!!9 M$-`mnL OO$& F =)y,'-+ rPcdd}g}tjj|s|St|d5}t j |}ddddvrdnd|vrdni}|j |jD]Y\}}|j dg}|j dijD]\} } i} | | d<| d| d <d | vr$d j| j d d | d <d| vr(| j d d | j dd z| d <| j dd| d<|| j d| j d| d<d| d<| |vr6dj| j d d | d <|j| dj| j d d | d <|jd|  \|S#1swYxYw)a$ :param schema_file: path to nextflow_schema.json file :type schema_file: str or Path :returns: list of custom inputs defined with DNAnexus datatype :rtype: list Creates custom input list from nextflow_schema.json that will be added in dxapp.json inputSpec field Ncdddddd}dddd}|dk(r ||vr||S||vr||Std j|) Nstringintfloatbooleanhash)riintegernumberrlobjectr)z file-pathzdirectory-pathrYz$type {} is not supported by DNAnexus) Exceptionformat)nf_type nf_formattypes str_typess r get_dx_typez*prepare_custom_inputs..get_dx_typeso    & h 9 #9Y' '  > !>EEgNOOrPr definitionsz$defsrequired propertiesr%titledefaultzDefault value:{} help help_texthiddenFtyperrclassToptionalz(Nextflow pipeline optional) {}z(Nextflow pipeline required) {}r)N) rXrYrZopenr;loadgetr1rrappendinsert) rSrwinputsfhschemadefs_keyd_keyd_schemarequired_inputs property_keypropertydx_inputs rr`r`sP&F 77>>+ & k3 22 - 7}SYHYW_aH!::h/557+x",,z26&.ll<&D&J&J&L + "L(H+HV  ( 0HW H$#7#>#>x||IWY?Z#[ h&#+<<#;hll;XZ>[#[ !)h!>HX  +HLL,@(,,xBX YHW #'HZ ?2#D#K#KHLLY_acLd#e  h'#D#K#KHLLY_acLd#e  a*! ++( M/s GG() NNFNr~r~NFNN)Fr~)z./nextflow_schema.json)rXr/r;argparserrar^ functoolsr dxpy.nextflow.nextflow_templatesrrdxpy.nextflow.nextflow_utilsrrr r r r r dxpy.cli.exec_iordxpy.clirdxpy.utils.resolverrArgumentParserr2rOrfr`rPrrs  Sggg&5 ! -F G !#Ol!# +\8rP