5ie dZddlmZmZmZmZddlZddlZddlZddl Z ddl m Z m Z mZmZmZmZmZmZmZmZddlmZdZGdd eZGd d eZd d lmZmZmZd dl m!Z!mZmZd dl"m"Z"d dl#m#Z#d dl$m%Z%m&Z&m'Z'm(Z(m)Z)m*Z*m+Z+d dl,m-Z-d dl.m/Z/m0Z0d dl1m2Z2m3Z3d dl4m5Z5m6Z6d dl7m8Z8d dl9m:Z:m;Z;d dlm?Z?d dl@mAZAmBZBd dlCmDZDmEZEd dlFmGZGmHZHmIZImJZJmKZKmLZLmMZMd dlNmOZOmPZPmQZQmRZRmSZSmTZTmUZUmVZVmWZWmXZXmYZYmZZZm[Z[m\Z\m]Z]y)z The :class:`DXObject` class is the abstract base class for all remote object handlers, and its subclass :class:`DXDataObject` is the abstract base class for all remote data object handlers. )print_functionunicode_literalsdivisionabsolute_importN) DXError DXAPIError DXFileError DXSearchError DXAppletErrorDXJobFailureErrorAppErrorAppInternalErrorAppInsufficientResourceError DXCLIError) basestringct|tr|g}t|trt|dk(r t dt|tr+t j ddj|zdz|sbt|dk(r|d}n=t|dk(rdj|}nd j|d d d z|d z}t d |d|y )a :param dxid: Value to verify as a DNAnexus ID of class *expected_class* :param expected_classes: Single string or list of strings of allowed classes of the ID, e.g. "file" or ["project", "container"] :type expected_classes: string or list of strings :raises: :exc:`~dxpy.exceptions.DXError` if *dxid* is not a string or is not a valid DNAnexus ID of the expected class rzJverify_string_dxid: expected_classes should be a string or list of stringsz^(|z)-[0-9a-zA-Z]{24}$rz or z, Nz, or zInvalid ID of class z: ) isinstancerlistlenrrematchjoin)dxidexpected_classesstr_expected_classess x/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/bindings/__init__.pyverify_string_dxidr! s"J/,- & -5E1F!1Kbcc tZ ( HHTCHH%5669MMt T  A %#3A#6 ! "a '#);;/?#@ #'99-=cr-B#Cg#MP`acPd#d 6JDQRR UcDeZdZdZd dZd dZdZdZdZdZ d Z d Z y) DXObjectz3Abstract base class for all remote object handlers.Nc0d\|_|_i|_y)NNN)_dxid_proj_descselfrprojects r __init__zDXObject.__init__:s", DJ r"c n|j |jnd}|j |jnd}|r|jdvrd}nd}n|jdvrd}nd}|j|j|j j ||t||jjd }|S) Nz no ID storedzno project ID stored) containerr,appglobalworkflowz1z#zD<{module}.{classname} object at 0x{mem_loc:x}: {dxid} ({dxproj_id})>z6<{module}.{classname} object at 0x{mem_loc:x}: {dxid}>name)module classnamer dxproj_idmem_locr2) r'r(_classformat __module__ __class____name__idr)get)r+use_namerr5descs r _reprzDXObject._reprAs!ZZ3tzz"&**"8DJJ>T {{"SSJ<{{"SS]O{{$//%)^^%<%< $'0#%d8 $ v 6 8  r"c&|jdS)NT)r>r@r+s r __str__zDXObject.__str__Xszz4z((r"c"|jSNrBrCs r __repr__zDXObject.__repr__[szz|r"c|dk(r t||js|j |j|S#txYw)N __setstate__)AttributeErrorr)describe)r+attrs r __getattr__zDXObject.__getattr__^sM > !!& &zz MMO #::d# # # " "s = A ct)zU Avoid infinite recursion in __getattr__ if describe is not defined. )NotImplementedError)r+argskwargss r rKzDXObject.describels "##r"cB|t||j||_y)z :param dxid: New ID to be associated with the handler :type dxid: string Discards the currently stored ID and associates the handler with *dxid* N)r!r7r'r+rs r set_idzDXObject.set_idrs   tT[[ 1 r"c|jS)z :returns: ID of the associated object :rtype: string Returns the ID that the handler is currently associated with. )r'rCs r get_idzDXObject.get_id~szzr"r&)F) r;r9 __qualname____doc__r-r@rDrGrMrKrTrVr"r r$r$7s-=.) #$  r"r$ceZdZdZddZedZdZdZddZ dZ dd Z d Z d Z d Zd ZdZdZdZdZdZdZdZdZdZdZdZd dZdZd!dZd"dZy)# DXDataObjectaAbstract base class for all remote data object handlers. .. note:: The attribute values below are current as of the last time :meth:`~dxpy.bindings.DXDataObject.describe` was run. (Access to any of the below attributes causes :meth:`~dxpy.bindings.DXDataObject.describe` to be called if it has never been called before.) .. py:attribute:: name String giving the name of the object .. py:attribute:: folder String giving the full path to the folder containing the object .. py:attribute:: types List of strings indicating the types associated with the object .. py:attribute:: state A string containing one of the values "open", "closing", or "closed" .. py:attribute:: hidden Boolean indicating whether the object is hidden or not .. py:attribute:: links List of strings indicating object IDs that are pointed to by the object .. py:attribute:: sponsored Boolean indicating whether the object is sponsored by DNAnexus .. py:attribute:: tags List of strings indicating the tags that are assocated with the object .. py:attribute:: created Timestamp at which the object was created, in milliseconds since January 1, 1970 at midnight (UTC). .. py:attribute:: modified Timestamp at which the object was last modified, in milliseconds since January 1, 1970 at midnight (UTC). .. py:attribute:: createdBy dict containing the following keys and values: * user: the string ID of the user who created the object or launched the job that created it * job (optional): the string ID of the job that created the object, if a job created the object * executable (optional): the string ID of the app or applet that the job was running, if a job created the object Nct|ds tdtj||j ||y)Nr7zLDXDataObject is an abstract class; a subclass should be initialized instead.)hasattrrOr$r-set_idsr*s r r-zDXDataObject.__init__s<tX&%^` ` $ T7#r"chd}|Dcic]}||vs|||||}}|Dcic] }||vs|||}}d|vrtj|d<||fScc}wcc}w)N> r2tagstypesfolderhiddendetailsparentsr, propertiesr,)dxpy WORKSPACE_ID)rQcommon_creation_paramspdx_hashremaining_kwargss r _get_creation_paramsz!DXDataObject._get_creation_paramss!})/iA18N3NSYZ[S\Sh1fQi<ii28\QAE[<[AvayL\\ G #!%!2!2GI ((( j\s AAA AAc t|ds td|j|\}}|j|fi|y)a :param project: Project ID in which to create the new remote object :type project: string :param name: Name for the object :type name: string :param tags: Tags to add for the object :type tags: list of strings :param types: Types to add to the object :type types: list of strings :param hidden: Whether the object is to be hidden :type hidden: boolean :param properties: Properties given as key-value pairs of strings :type properties: dict :param details: Details to set for the object :type details: dict or list :param folder: Full path to the destination folder :type folder: string :param parents: If True, recursively create all parent folders if they are missing :type parents: boolean :rtype: :class:`DXDataObject` Creates a data object with the given fields. Only *project* is required, and only if no default project or workspace is set; the remaining arguments are optional and have default behavior as specified in the API documentation for the ``/new`` method of each data object class. r7zKDXDataObject is an abstract class; a subclass shouldbe initialized instead.N)r]rOrm_new)r+rQrkrls r newzDXDataObject.newsL<tX&%./ /%)$=$=f$E!! '.-.r"c&|j|y)aS :param dxid: Object ID or a DNAnexus link (a dict with key "$dnanexus_link"); if a project ID is provided in the DNAnexus link, it will also be used to set the project ID :type dxid: string or dict Equivalent to calling :meth:`~dxpy.bindings.DXDataObject.set_ids` with the same arguments. N)r^rSs r rTzDXDataObject.set_ids Tr"ct|rt|\}}||}|t||j||_|t j |_y|t|ddg||_yy)a7 :param dxid: Object ID or a DNAnexus link (a dict with key "$dnanexus_link"); if a project ID is provided in the DNAnexus link, it will be used as *project* unless *project* has been explictly provided :type dxid: string or dict :param project: Project ID :type project: string Discards the currently stored ID and associates the handler with *dxid*. Associates the handler with the copy of the object in *project* (if no project is explicitly specified, the default data container is used). Nr,r/) is_dxlinkget_dxlink_idsr!r7r'rgrhr()r+rr,project_from_links r r^zDXDataObject.set_idsss T?&4T&: #D#+   tT[[ 1 ?**DJ  wK(@ A DJ!r"c|jS)z :returns: Project ID of associated object :rtype: string Returns the project ID, if any, that the handler is currently associated with. )r(rCs r get_proj_idzDXDataObject.get_proj_id-szzr"c |j:tdj|jj|j |s|r|| t d|s|rt||}ni}|||d<||Dcic]}|dc}|d<|j|j|d<|j|j|fi||_ |jScc}w) a :param fields: set of fields to include in the output, for example ``{'name', 'modified'}``. The field ``id`` is always implicitly included. If ``fields`` is specified, the default fields are not included (that is, only the fields specified here, and ``id``, are included) unless ``default_fields`` is additionally set to True. :type fields: set or sequence of str :param default_fields: if True, include the default fields in addition to fields requested in ``fields``, if any; if False, only the fields specified in ``fields``, if any, are returned (defaults to False if ``fields`` is specified, True otherwise) :type default_fields: bool :param incl_properties: if true, includes the properties of the object in the output (deprecated; use ``fields={'properties'}, default_fields=True`` instead) :type incl_properties: bool :param incl_details: if true, includes the details of the object in the output (deprecated; use ``fields={'details'}, default_fields=True`` instead) :type incl_details: bool :returns: Description of the remote object :rtype: dict Return a dict with a description of the remote data object. The result includes the key-value pairs as specified in the API documentation for the ``/describe`` method of each data object class. The API defines some default set of fields that will be included (at a minimum, "id", "class", etc. should be available, and there may be additional fields that vary based on the class); the set of fields may be customized using ``fields`` and ``default_fields``. Any project-specific metadata fields (name, properties, and tags) are obtained from the copy of the object in the project associated with the handler, if possible. zZThis {handler} handler has not been initialized with a {_class} ID and cannot be described)handlerr7zQCannot specify properties or details in conjunction with fields or default_fields)rfrd defaultFieldsTfieldsr,) r'rr8r:r;r7 ValueErrordictr( _describer))r+incl_properties incl_detailsr{default_fieldsrQdescribe_input field_names r rKzDXDataObject.describe9sT :: v}}//{{~$  |&2DHbpq q l!_lSNN)2@/!OU+VJ,<+Vx( :: !(, N9 %#T^^DJJI&I zz,Ws; Cc D|j|jd|ifi|y)aI :param types: Types to add to the object :type types: list of strings :raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state Adds each of the specified types to the remote object. Takes no action for types that are already listed for the object. raN) _add_typesr'r+rarQs r add_typeszDXDataObject.add_types|s"  We$4??r"c D|j|jd|ifi|y)aQ :param types: Types to remove from the object :type types: list of strings :raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state Removes each the specified types from the remote object. Takes no action for types that the object does not currently have. raN) _remove_typesr'rs r remove_typeszDXDataObject.remove_typess$ 4::'7B6Br"c <|j|jfi|S)zb Returns the contents of the details of the object. :rtype: list or dict ) _get_detailsr'r+rQs r get_detailszDXDataObject.get_detailss !t  6v66r"c >|j|j|fi|S)a :param details: Details to set for the object :type details: dict or list :raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state Sets the details for the remote object with the specified value. If the input contains the string ``"$dnanexus_link"`` as a key in a hash, it must be the only key in the hash, and its value must be a valid ID of an existing object. ) _set_detailsr')r+rdrQs r set_detailszDXDataObject.set_detailss"!t  W???r"c B|j|jddifi|S)z :raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state Hides the remote object. rcT_set_visibilityr'rs r hidezDXDataObject.hides'$t##DJJ40@KFKKr"c B|j|jddifi|S)z :raises: :class:`~dxpy.exceptions.DXAPIError` if the object is not in the "open" state Makes the remote object visible. rcFrrs r unhidezDXDataObject.unhides'$t##DJJ50ALVLLr"c X|j|j|j|dfi|S)z :param name: New name for the object :type name: string Renames the remote object. The name is changed on the copy of the object in the project associated with the handler. )r,r2)_renamer'r()r+r2rQs r renamezDXDataObject.renames6t||DJJDJJ15)7B:@B Br"c 0|jdddi|dS)a :returns: Properties given as key-value pairs of strings :rtype: dict Returns the properties of the object. The properties are read from the copy of the object in the project associated with the handler. rTrfrYrKrs r get_propertieszDXDataObject.get_propertiess"t}}z:DXDataObject._wait_until_parts_uploaded..s&%i\_eCjnnWj&IZ&W%is"%zGReached timeout while waiting for parts of the file ({}) to be uploadedrrr) r(r~r'anyrr8rVrrr) r+rrQrrrrKr is_uploadedrrs @r _wait_until_parts_uploadedz'DXDataObject._wait_until_parts_uploadeds "dT$BC :: !(, N9 %%t~~djj.KFKH#G,hw.?LE5 "%%ich%i"ii '!Wq[gnnosozozo|}~~tQT?D JJt  FA tOG!r"r&rF)FFNN)/)iQ))r;r9rWrXr- staticmethodrmrprTr^rwrKrrrrrrrrrrrrrrrrrrrrYr"r r[r[s?B$ ) )$/L !: AF @ C7 @LM B K'>! $ 1 9&($8B $r"r[r)DXFileDXFILE_HTTP_THREADSDEFAULT_BUFFER_SIZE) DXDatabaserr)download_all_inputs)mount_all_inputs) open_dxfile new_dxfiledownload_dxfileupload_local_file upload_stringlist_subfoldersdownload_folder)download_dxdatabasefile)DXRecord new_dxrecord) DXContainer DXProject)DXJob new_dxjob) DXAnalysis) DXExecutableDXApplet)DXApp)DXGlobalWorkflow) DXWorkflownew_dxworkflow) user_infowhoami)dxlinkrsrt get_handlerrKrr)find_data_objectsfind_executions find_jobs find_analyses find_projects find_appsfind_global_workflowsfind_one_data_objectfind_one_project find_one_appresolve_data_objects find_orgsorg_find_membersorg_find_projects org_find_apps)^rX __future__rrrrrrrdxpy.apirg exceptionsrr r r r r rrrrcompatrr!objectr$r[dxfilerrr dxdatabaserrrdxfile_functionsrrrrrrrdxdatabase_functionsrdxrecordrr dxprojectrrdxjobrr dxanalysisrdxappletrrdxapprdxglobalworkflowr dxworkflowrrauthrrdxdataobject_functionsrrsrtrrKrrsearchrrrrrrrrrrrrrrrrYr"r rs" SRsssS.PvPda8aFEDLL4.KKK9,-#",.2#qqqIIIIIr"