
    5i"                         d Z ddlmZmZmZmZ ddlmZ ddlZddl	Z	ddl
Z
ddlmZ dZd Zd	 Zd
 Zd Zd Zd ZddZy)zp
Utilities used when running executables in a batch. For example, running an analysis on
a set of data samples.
    )print_functionunicode_literalsdivisionabsolute_import)defaultdictN   )err_exitzbatch IDc                     | j                         }g }d|v r|d   |d   }n7d|v r|d   |d   }n(t        dj                  | j                                     i }|D ]  }|d   ||d   <    |S )Ninputs	inputSpecz2executable {} does not have an input specificationclassname)describe	Exceptionformatget_id)
executable	exec_desc
input_specinput_key_classesarg_descs        x/home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/utils/batch_utils.py_get_types_for_inputsr   &   s    ##%IJI('x(


"
K
 
,{+
LSST^TeTeTghii @.6w.?(6*+@     c                 d   d }g }|dk(  r| }||fS |dk(  rt        |       }||fS |dk(  rt        |       }||fS |dk(  rt        |       }||fS |dk(  rt        j                  |       }||fS |dk(  r| j                  d      rC| j                  d      } t        j                  | d	   | d
         }|j                  |       ||fS | j                  d      r*t        j                  |       }|j                  |       ||fS t        dj                  |             t        dj                  |            )Nstringintbooleanfloathashfilezproject-:   r   )	object_id
project_idzfile-z8Malformed file {}, must start with 'file-' or 'project-'z class {} not currently supported)r   boolr   jsonloads
startswithsplitdxpydxlinkappendr   r   )valklassretval	ref_filess       r   _type_convert_primitiver2   ?   se   FI* 9) 
%S& 9% 
)	c" 9! 
'	s 9 
&C 9 
&>>*%))C.C[[3q6c!fEFV$ 9 ^^G$[[%FV$
 9 V]]^abcc:AA%HIIr   c                 ~   |j                  d      d   }t        |       }|dk  s| d   dk7  s| |dz
     dk7  rt        dj                  |             | d|dz
   }g }g }|j                  d      D cg c]  }|j	                          }}|D ]'  }t        ||      \  }	}
|j                  |	       ||
z  }) ||fS c c}w )	Nr"   r#   r   r   []zMalformed array {},)r*   lenr   r   stripr2   r-   )r.   r/   
inner_typelen_valval_strip_bracketsr0   r1   eelementse_with_typefiless              r   _type_convert_arrayr@   [   s    S!!$J#hG!A#GAI#,33C899Q	+FI#5#;#;C#@Aa	AHA 3AzBEk"U	 9 Bs   1B:c                     	 |j                  d      rt        | |      S t        | |      S # t        $ r t        dj	                  | |            w xY w)Nzarray:z*value={} cannot be converted into class {})r)   r@   r2   r   r   )r.   r/   s     r   _type_convertrB   l   s]    YH%&sE22 +366 YDKKCQVWXXYs   + + %Ac                 t    t        |      D ]  \  }}|| dz   k(  s|c S  t        dj                  |             )Nz IDz,Could not find a column with file IDs for {})	enumerater   r   )col_nameheader_linei	col_name2s       r   _search_column_idrI   x   sE    !+. 9E)*H BII(S
TTr   c                    g }g }d}t        ||      5 }t        j                  |t        d            }t	        |      }t        |      }d d d        t        |       }d }	i }
t        |      D ]3  \  }}|t        k(  r|}	||vr||   dv rt        ||      }||
|<   /||
|<   5 |	t        dj                  t                    t        t
              }g }|D ]Z  }t        |      D ]J  \  }}||
vr|
|   }||   }t        |j                         |      \  }}||z  }||   j                  |       L \ |D cg c]  }||	   j                          }}t         j"                  j%                  | j'                         |||g d      }t)        |t*              rd|v sJ |d   }n|}t-        |      t-        |      k7  r-t        dj                  t-        |      t-        |                  ||d	S # 1 sw Y   xY wc c}w )
Nr	)	delimiter)r!   z
array:filezCould not find column {})
batchInputcommonInputr?   instanceTypesexpandedBatchz:Mismatch in number of launch_args vs. batch_ids ({} != {}))launch_args	batch_ids)opencsvreaderstrnextlistr   rD   BATCH_IDrI   r   r   r   rB   r8   r-   r+   apiapplet_validate_batchr   
isinstancedictr7   )r   
input_jsonbatch_tsv_filerF   lines	read_modefrV   input_classesbatch_indexindex_2_columnrG   rE   idxcolumns	all_filesliner.   r/   val_w_correct_typer1   rS   expanded_argsrR   s                           r   batch_launch_argsrm      sI   KEI	ni	( AAU46lV **5M KN - 	)8xK=("&<<#Hk:C"*N3 (N1	) 299(CDD GI 9o 	9FAs&%a(H!(+E,9#))+u,M)	"IH$$%78	99 8==tk"((*=I=
 HH22:3D3D3FCJDN>GFH4KLM -&-/0/#O4#
;3y>)TK 0#i.AC 	C (#& &A V >s   7G,6G9,G6c                    |j                         }| j                         d   }|d   }|d   }g }t        |      D ]  \  }	}
||	   }dj                  ||      }||d}||d<   |j	                  d      |d   j                  |       n||d<   |r|d   dz   |z   |d<   	  | j                  |
fi |}|j                  |        |S # t        $ r t                Y w xY w)	Nr   rR   rS   z{}-{})zbatch-idz
batch-name
propertiesfolder/)
copyr   rD   r   getupdaterunr-   r   r	   )r   b_args
run_kwargsset_batch_foldersrun_args	exec_namerR   rS   
executionsrg   r_   batch_idr   ro   dxexecutions                  r   	batch_runr~      s    H##%f-I'K{#IJ$[1 ZS>~~i2 

  <<%1\"))*5%/H\"!+H!5!;h!FHX	(*..@x@Kk*%*   	J	s   $CCC)F)__doc__
__future__r   r   r   r   collectionsr   rU   r+   r'   
exceptionsr	   rZ   r   r2   r@   rB   rI   rm   r~    r   r   <module>r      sP   "
 S R # 
   !
 28"YU"E&^r   