$dZddlmZddlmZddlmZddlZddlmZddlm Z ddlm Z dd lm Z dd lm Z ddlm Zdd lmZddlm Zdd lmZdd lmZddlmZddlmZddlmZddlZdZdZdZ ddZ!ddZ"ddZ#dZ$dZ%dZ&dZ'dZ(dZ)y)z,Common helper methods for Genomics commands.)absolute_import)division)unicode_literalsN) DecodeError)encoding) exceptions) extra_types)transfer)apis)log) properties)yaml)resource_printer)fileszgs://cT|Dcgc]}tj|c}Scc}w)zConverts a list of strings to the API JsonValue equivalent. Args: values: the string values to be converted Returns: An equivalent list of JsonValue strings  string_value)r JsonValuevaluesvs 4lib/googlecloudsdk/api_lib/genomics/genomics_util.pyInfoValuesToAPIr+s(:@ @A+  Q / @@ @s%c@|Dcgc]}|jc}Scc}w)zConverts a list of strings to an API JsonValue equivalent. Args: values: the list of JsonValue strings to be converted Returns: An equivalent list of strings rrs rInfoValuesFromAPIr6s #) )&Q!..& )) )scRtj|g|tjy)zPrints the given resource.) resources print_formatoutN)rPrintr r)resourcers r PrettyPrintr"As  ''c.tjd|SNgenomics) core_apisGetClientInstanceversions rGetGenomicsClientr+I  $ $Z 99r#c.tjd|Sr%)r'GetMessagesModuler)s rGetGenomicsMessagesr/Mr,r#cjtjjjj dS)NT)required)r VALUEScoreprojectGetr#r GetProjectIdr7Qs(      ' ' + +T + ::r#c,|jtS)N) startswith GCS_PREFIX)paths r IsGcsPathr<Us  $$r#c t|rtjd}|jt |\}}t j dd}|j||} tjj|jd}|jj||~|j}t+j,|} | s$t!j"d j%| t/j0|t3j4| } | S#tj$r=} t!j"d j%|t'j(| d } ~ wwxYw#t6t8t2j:f$rj t/j<|| } Y| S#t6t>f$r=} t!j"d j%|t'j(| d } ~ wwxYwwxYw) aReads a YAML or JSON object of type message from path (local or GCS). Args: path: A local or GCS path to an object specification in YAML or JSON format. message: The message type to be parsed from the file. client: The storage_v1 client to use. Returns: Object of type message, if successful. Raises: files.Error, genomics_exceptions.GenomicsInputFileError F)deletestoragev1)bucketobjectT) overwrite)downloadz-Unable to read remote file [{0}] due to [{1}]NzEmpty file [{0}]zGPipeline file [{0}] is not properly formatted YAML or JSON due to [{1}]) r<tempfileNamedTemporaryFileclose_SplitBucketAndObjectr'r.StorageObjectsGetRequestr DownloadFromFilenameobjectsr5apitools_exceptions HttpErrorgenomics_exceptionsGenomicsInputFileErrorformatsix text_typerReadFileContentsrPyValueToMessagerload ValueErrorAttributeErrorYAMLParseError JsonToMessager) r;messageclienttfrAobjstorage_messages get_requestrDein_textresults rGetFileAsMessagereYst_  $ $E 2BHHJ'-KFC 229dC";;c<#K'""++BGGt+Dh nnx8  77D  " "4 ('   4 4!!$' )) 9  & &w '0B CF -1  ( ('  6 6 9 @ @CMM!$ & ''' nd&9&9 :99%%gw7f -  $9 6 6 cmmA&67 9999sC*A D&;)E9&E698E11E69HF11G=8G88G==Hcg}||Sttj|D]\}}|j||| |S)N)keyvalue)sortedrS iteritemsappend)argdictr\rdkrs r!ArgDictToAdditionalPropertiesListrnsG & _ MS]]7+,da MM'aq)*- -r#c|ttdjdjdd}t|dk7r$t j dj ||S)zHSplit a GCS path into bucket & object tokens, or raise BadFileException.N/z.[{0}] is not a valid Google Cloud Storage path)lenr:stripsplitcalliope_exceptionsBadFileExceptionrR)gcs_pathtokenss rrHrHs_ C O$ % + +C 0 6 6sA >&[A  . .8??I KK -r#c z|sydjdg|Dcgc]}dj||gc}zScc}w)aDReturns the comma separated list of field names referenced by the command. Args: referenced_fields: A list of field names referenced by the format and filter expressions. prefix: The referenced field name resource prefix. Returns: The comma separated list of field names referenced by the command. N, nextPageToken.)join)referenced_fieldsprefixfields rGetQueryFieldsrsL   ?#:KL:K388VUO,:KLM NNLs8 )json)r@)*__doc__ __future__rrrrE#apitools.base.protorpclite.messagesrapitools.base.pyrrrNr r googlecloudsdk.api_lib.genomicsrPgooglecloudsdk.api_lib.utilr r'googlecloudsdk.calliopervgooglecloudsdk.corer r rgooglecloudsdk.core.resourcergooglecloudsdk.core.utilrrSr:rrr"r+r/r7r<rernrHrr6r#rrs 3&';%>(%M9E#*$9*  A*::;%2jNr#