5i4pdZddlmZmZmZmZddlZddlmZm Z m Z m Z ddl m Z ddlmZGd d ee Zy) z4 DXGlobalWorkflow Handler ++++++++++++++++++++++++ )print_functionunicode_literalsdivisionabsolute_importN)DXObject DXAnalysis DXExecutableverify_string_dxid)DXError) basestringc|eZdZdZdZddZddZdZdZddZ dZ dd Z dd Z d Z dd Zdd ZdZfdZxZS)DXGlobalWorkflowz0 Remote global workflow object handler. globalworkflowcztj||||j|||i|_i|_y)N)dxidnamealias)r__init__set_id_workflows_by_region_workflow_desc_by_regionselfrrrs /home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/bindings/dxglobalworkflow.pyrzDXGlobalWorkflow.__init__*s?$  t/ KKTEK :%'!(*%c:d|_d|_d|_|-|| tdt ||j ||_y|U||_t |tstd||&t |tstd|||_yd|_yy)aj :param dxid: Global workflow ID :type dxid: string :param name: Global workflow name :type name: string :param alias: Global workflow version or tag :type alias: string :raises: :exc:`~dxpy.exceptions.DXError` if *dxid* and some other input are both given or if neither *dxid* nor *name* are given Discards the currently stored ID and associates the handler with the requested parameters. Note that if *dxid* is given, the other fields should not be given, and if *name* is given, *alias* has default value "default". Nz9Did not expect name or alias to be given if dxid is givenz+Global workflow name needs to be a string: z,Global workflow alias needs to be a string: default)_dxid_name_aliasr r _class isinstancerrs rrzDXGlobalWorkflow.set_id4s     5#4YZZ tT[[ 1DJ  DJdJ/QUWXX !%4!V["]^^# ' rcp|j |jSd|jzdz|jzS)z :returns: Object ID of associated global workflow :rtype: string Returns the object ID of the global workflow that the handler is currently associated with. globalworkflow-/)r r!r")rs rget_idzDXGlobalWorkflow.get_idWs5 :: !:: $tzz1C7$++E Erc i}dD]6}||vr%t|jjd|d||||<||=8d|vr |d|d<|d=tjj |fi|}|j |dy) a, .. note:: It is highly recommended that `dx build --create-global-workflow `_ be used instead for global workflow creation. Creates a workflow in the global space with the given parameters by using the specified workflow(s) in regionalOptions as a base. The workflow is available only to its developers until :meth:`publish()` is called, and is not run until :meth:`run()` is called. )versionrregionalOptionsz: Keyword argument z is requiredbill_tobillToid)rN)r __class____name__dxpyapiglobal_workflow_newr)rkwargsdx_hashfieldresps rnewzDXGlobalWorkflow.newds; EF"t~~G^G^`efgg#E]GENu     &y 1GH y!xx++G>v> d $rc <i}|r||d<|j=tjj|jfd|i||_|jStjjd|j zf|j |d||_|jS)aX :param fields: Hash where the keys are field names that should be returned, and values should be set to True (default is that all fields are returned) :type fields: dict :returns: Description of the remote global workflow object :rtype: dict Returns a dict with a description of the workflow. fields input_paramsr&rr;)r r1r2global_workflow_describe_descr!r")rr:r4describe_inputs rdescribezDXGlobalWorkflow.describes '-N8 $ :: !::4::mTbmflmDJ zz::;Ltzz;YbaealalHVbZ`bDJzzrc |j*tjj|jfi|Stjjd|jzfd|j i|S)z Publishes the global workflow, so all users can find it and use it on the platform. The current user must be a developer of the workflow. r&r)r r1r2global_workflow_publishr!r")rr4s rpublishzDXGlobalWorkflow.publishs] :: !8833DJJI&I I88334E 4RpZ^ZeZepiop prc||jdddk(sJ| td||jvr|j|S|s|j}||dj vr)tdj |j ||d|d}tj|}|j}||_|S)aN :param region: region name :type region: string :param describe_output: description of a global workflow :type describe_output: dict :returns: object description of a workflow :rtype: : dict Returns an object description of an underlying workflow from a given region. classrGDXGlobalWorkflow: region must be provided to get an underlying workflowr+DDXGlobalWorkflow: the global workflow {} is not enabled in region {}workflow) getr rr@keysformatr(r1 DXWorkflow)rregiondescribe_outputunderlying_workflow_id dxworkflowdxworkflow_descs rdescribe_underlying_workflowz-DXGlobalWorkflow.describe_underlying_workflows&/*=*=gr*JN^*^_^ >Y[ [ T22 2008 8"mmoO ):;@@B B`gg v'( ("11B!CF!KJ!W__%;< $--/(7%rc||jddk(sJ| td||jvr|j|S|s|j}||dj vr)tdj |j ||d|d}tj||_ tj|S)am :param region: region name :type region: string :param describe_output: description of a global workflow :type describe_output: dict :returns: object handler of a workflow :rtype: :class:`~dxpy.bindings.dxworkflow.DXWorkflow` Returns an object handler of an underlying workflow from a given region. rErrGr+rHrI) rJr rr@rKrLr(r1rMr)rrNrOrPs rget_underlying_workflowz(DXGlobalWorkflow.get_underlying_workflows&/*=*=g*FJZ*Z[Z >Y[ [ T.. .,,V4 4"mmoO ):;@@B B`gg v'( ("11B!CF!KJ!W(,8N(O%566rcz||jddk(sJ|j||}dD] }||||< |S)a :param region: region name :type region: string :param describe_output: description of a global workflow :type describe_output: dict :returns: object description of the global workflow :rtype: : dict Appends stages, inputs, outputs and other workflow-specific metadata to a global workflow describe output. Note: global workflow description does not contain functional metadata (stages, IO), since this data is region-specific (due to applets and bound inputs) and so reside only in region-specific underlying workflows. We add them to global_workflow_desc so that it can be used for a workflow or a global workflow rErrO)inputsoutputs inputSpec outputSpecstages)rJrS)rrOrNunderlying_workflow_descr6s rappend_underlying_workflow_descz0DXGlobalWorkflow.append_underlying_workflow_descsf&/*=*=g*FJZ*Z[Z#'#D#DVUd$E$f O EE%=e%DOE " ErcJ|j||}|j|S)NrW)rU_get_input_name)r input_strrNrOrQs rr`z DXGlobalWorkflow._get_input_names(11&/1Z )))44rc tjj|dddiid}|j|}|j|fd|i|S)z Checks the region in which the global workflow is run and returns the input associated with the underlying workflow from that region. r:rNT)r;project)r1r2project_describerU_get_run_input)rworkflow_inputrcr4rNrQs rrezDXGlobalWorkflow._get_run_inputsc **79AHdCS8T+VV^`11&9 (z((SSFSSrc |j8ttjj|jfd|i|dSttjjd|j zf|j |d|dS)Nr;r.r&r<)r r r1r2global_workflow_runr!r")r run_inputr4s r _run_implzDXGlobalWorkflow._run_impl s :: !dhh::4::hT]haghimno odhh::;Ltzz;YEaealalHQE=CEEIKL Lrc2tt| |g|i|S)a :param workflow_input: Dictionary of the workflow's input arguments; see below for more details :type workflow_input: dict :param instance_type: Instance type on which all stages' jobs will be run, or a dict mapping function names to instance types. These may be overridden on a per-stage basis if stage_instance_types is specified. :type instance_type: string or dict :param stage_instance_types: A dict mapping stage IDs, names, or indices to either a string (representing an instance type to be used for all functions in that stage), or a dict mapping function names to instance types. :type stage_instance_types: dict :param stage_folders: A dict mapping stage IDs, names, indices, and/or the string "*" to folder values to be used for the stages' output folders (use "*" as the default for all unnamed stages) :type stage_folders: dict :param rerun_stages: A list of stage IDs, names, indices, and/or the string "*" to indicate which stages should be run even if there are cached executions available :type rerun_stages: list of strings :returns: Object handler of the newly created analysis :rtype: :class:`~dxpy.bindings.dxanalysis.DXAnalysis` Run the workflow. See :meth:`dxpy.bindings.dxapplet.DXExecutable.run` for additional args. When providing input for the workflow, keys should be of one of the following forms: * "N.name" where *N* is the stage number, and *name* is the name of the input, e.g. "0.reads" if the first stage takes in an input called "reads" * "stagename.name" where *stagename* is the stage name, and *name* is the name of the input within the stage * "stageID.name" where *stageID* is the stage ID, and *name* is the name of the input within the stage * "name" where *name* is the name of a workflow level input (defined in inputs) or the name that has been exported for the workflow (this name will appear as a key in the "inputSpec" of this workflow's description if it has been exported for this purpose) )superrrun)rrfargsr4r/s rrmzDXGlobalWorkflow.runs#H%t0Q$Q&QQr)NNN)N)NN)r0 __module__ __qualname____doc__r#rrr(r8r@rCrSrUr^r`rerjrm __classcell__)r/s@rrr#s^F+!(F F%<, q D7@.5 TL$R$Rrr)rq __future__rrrrr1rFrr r r exceptionsr compatrrrrrws4" SR DD TRxTRr