чoe7TdZddlmZddlmZddlmZddlmZdZ dZ dZ d Z d Z d Zd Zd ZdZdZdZdZdZdZdZGddZeZede deeede deeede deeede deeede deeededeeed edeed!Zd"Zd#Zd$Zd%Zed&Z d'S)(aError profile The error profile object to define different error types and handling within BIOM. The following types are registered with the associated default states empty : 'ignore' Treatment of an empty table (e.g., if Table.is_empty() is True). If a callable is provided, it implies 'call' and will set the callback function. obssize : 'raise' Treatment of a table in which the number of observation ids does not match the size of the data. sampsize : 'raise' Treatment of a table in which the number of sample ids does not match the size of the data. obsdup : 'raise' Treatment of duplicate observation IDs. sampdup : 'raise' Treatment of duplicate sample IDs. obsmdsize : 'raise' Treatment of a table in which the number of observation metadata elements differs from the size of the data. sampmdsize : 'raise' Treatment of a table in which the number of sample metadata elements differs from the size of the data. Examples -------- Use `seterr` to change how empty tables are handled: >>> from numpy import inf >>> from biom.err import seterr >>> from biom import example_table >>> make_empty_f = lambda v, i, md: v.sum() > inf >>> _ = example_table.filter(make_empty_f, inplace=False) >>> old_state = seterr(empty='raise') >>> example_table.filter(make_empty_f, inplace=False) Traceback (most recent call last): ... TableException: Empty table! >>> _ = seterr(**old_state) warn)stdout)contextmanager)TableExceptionz Empty table!z3Number of observation IDs differs from matrix size!z.Number of sample IDs differs from matrix size!zDuplicate observation IDszDuplicate sample IDs!z6Size of observation metadata differs from matrix size!z1Size of sample metadata differs from matrix size!c*|S)zCheck if t is empty)is_emptyts ]/mounts/lovelace/software/anaconda3/envs/kraken-biom/lib/python3.11/site-packages/biom/err.py_zz_test_emptyr Os ::<<cf|jdt|dkS)z3Check if the number of observations match data sizer observationaxisshapelenidsr s r _test_obssizerTs) 71:QUU U6677 77rcf|jdt|dkS)z.Check if the number of samples match data sizesamplerrr s r _test_sampsizerYs) 71:QUUU1122 22rc|jdtt|dkS)z)Check if there are duplicate observationsrrrrrsetrr s r _test_obsdupr^s1 71:SM!:!:;;<< <z&_create_error_states..vsrc"tSr,rr/msgs r r0z&_create_error_states..ws d3iircSr,r-)r/ exceptionr3s r r0z&_create_error_states..xsyy~~rNcdSr,r-r.s r r0z&_create_error_states..ysDrc2tjdzS)N )rwriter2s r r0z&_create_error_states..zsv|C$J77r)ignorerraisecallprintr-)r3callbackr5s` `r _create_error_statesr?tsM$n''''----- ( 4HH..7777  9 99rceZdZdZegdZdZdefdZdZ e dZ e j dZ d Z d Zd Zd Zd ZdS) ErrorProfilezAn error profile The error profile defines the types of errors that can be optionally handled, how those errors are handled, and performs the handling of the errors. )r;r:r<r=rc0i|_i|_i|_dSr,)_profile_state_testselfs r __init__zErrorProfile.__init__s   rNc||vrtd|z||jvrtd|zt||||j|<||j|<||j|<dS)aRegister an error type Paramters --------- errtype : str A name for the error, must be unique. msg : str An error message. state : {'raise', 'ignore', 'call', 'print', 'warn'} The default state. test : function A function to test for error. callback : function, optional A callback function for use with state 'call' exception : Exception, optional An exception to throw in state 'raises'. Raises ------ KeyError If the errtype already exists KeyError If the state is invalid zAlready registered: %szUnknown state: %sN)KeyError _valid_statesr?rCrDrE)rGerrtyper3statetestr>r5s r registerzErrorProfile.registersy6 d??3g=>> > * * *.677 7!5c8Y!O!O g$ G" 7rc||vrtd|z|j|}|j|}|j|}|||fS)aUnregister an error type Parameters ---------- errtype : str The error type to unregister Raises ------ KeyError If the error type is unknown Returns ------- dict The profile associated with the error. function The test function associated with the error. str The state at time of unregistering associated with the error Unknown error type: %s)rJrCpoprErD)rGrLproffuncrMs r unregisterzErrorProfile.unregistersk. $  3g=>> >}  ))z~~g&& ((dE""rc|jS)zReturn current staterDrFs r rMzErrorProfile.states {rcdvrfd|jD}n}|D]E\}|jvrtdz||jvrtd|z|j|<FdS)zUpdate current stateallc$g|] }|df S)rYr-).0err new_states r z&ErrorProfile.state..s#HHHS#y/0HHHrzUnknown state type: %srQN)rDitemsrKrJ)rGr] to_updaterLs ` r rMzErrorProfile.states I  HHHHDKHHHII!))I"+ - - GY 2227)CDDDdk))7'ABBB#,DK  - -rc||jvS)zCheck if an error type existsrWrGrLs r __contains__zErrorProfile.__contains__s$+%%rc|s|j}t|D]A}|j|d}||r|||cSBdS)aTest for an error Parameters ---------- item : object An item to test for error *args : list, optional Error types to check, if not provided, all known error types are checked. Examples -------- >>> from biom import example_table >>> from biom.err import __errprof >>> __errprof.test(example_table, 'empty') cdSr,r-r-rr r0z#ErrorProfile.test..s4rN)rEkeyssortedget _handle_error)rGitemargsrLrNs r rNzErrorProfile.tests$ %:??$$Dd|| 9 9G:>>'<<88DtDzz 9))'488888 9 9 9rcX|j|}|j|}|||S)zHandle an error)rDrC)rGrLrjrMprofiles r rizErrorProfile._handle_errors. G$-(wu~d###rcx||vrtd|z|j|d}||j|d<|S)a{Set a function callback Parameters ---------- errtype : str The error type to set a callback for. func : function The callback function. This function must accept a single parameter. The result of this function will be returned through the handler. Raises ------ KeyError If an unknown error type is specified. Examples -------- >>> from biom.err import __errprof >>> oldcall = __errprof.setcall('empty', lambda item: 123) >>> _ = __errprof.setcall('empty', oldcall) rQr<rJrC)rGrLrTold_calls r setcallzErrorProfile.setcall sJ0 $  3g=>> >=)&1)- gv&rcT||vrtd|z|j|dS)aLGet a function callback Parameters ---------- errtype : str The error type to get the callback for. Raises ------ KeyError If the error type is unknown. Returns ------- function The associated callback function. rQr<rorbs r getcallzErrorProfile.getcall)s5& $  3g=>> >}W%f--r)__name__ __module__ __qualname____doc__ frozensetrKrH ExceptionrOrUpropertyrMsetterrcrNrirqrsr-rr rArA}s IJJJKKM <@$########J###@X \ - -\ -&&&9996$$$ >.....rrAemptyr:)r5obssizer;sampsizeobsdupsampdup obsmdsize sampmdsizec>tjS)z'Returns the current error profile state __errprofrMcopyr-rr geterrrSs ?   ! !!rc tj}d|vrd|dit_n |t_|S)azHow table errors are handled, API based on numpy's seterr Notes ---------- all : {'ignore', 'warn', 'raise', 'call', 'print'}, optional Set treatment for all error types - ignore: Take no action when the exception occurs. - warn: Print a `RuntimeWarning` (via the Python `warnings` module). - raise: Raise a `TableException`. - call: Call a function specified using the `seterrcall` function. - print: Print a warning directly to ``stdout``. Returns ------- old_settings: dict Dictionary containing the old settings See also -------- geterr seterrcall geterrcall errstate Examples -------- >>> from numpy import inf >>> from biom.err import seterr >>> from biom import example_table >>> make_empty_f = lambda v, i, md: v.sum() > inf >>> _ = example_table.filter(make_empty_f, inplace=False) >>> old_state = seterr(empty='raise') >>> example_table.filter(make_empty_f, inplace=False) Traceback (most recent call last): ... TableException: Empty table! >>> _ = seterr(**old_state) rYrkwargs old_states r seterrrXs@T$$&&I  &-0   rcn|tvrtd|zt||S)aSet an error callback function This is similar to numpy's seterrcall, except that we define it by error type. The justification is that numpy's errors are focused specifically on floating point errors, while the types of errors we support in BIOM are more broad. Parameters ---------- errtype : str Must be a valid key in biom.__errprof func : callable A function that is called if the given error is encountered and if the current error profile indicates 'call' for the error type. Returns ------- callable or None The old error handler Raises ------ KeyError If the errtype specified is not in the error profile. rQ)rrJrq)rLrTs r seterrcallrs96i/'9:::  $///rcl|tvrtd|zt|S)aUGet the current callback function associated with an error type Parameters ---------- errtype : str Must be a valid key in the error profile Returns ------- callable The current callback function Raises ------ KeyError If the errtype specified is not in the error profile. rQ)rrJrs)rLs r geterrcallrs7&i/'9:::  )))rcXtj|g|R}t|tr||S)aCheck if there is an error, and respond appropriately Parameters ---------- table : Table The table to check errtypes : vargs of str, if not specified, defaults to all errors Errors to test Notes ----- If an error type has 'raises' as its state, the exception is raised from here to avoid cluttering the traceback. Returns ------- dependent on error state and setting )rrN isinstancery)tableerrtypesrets r errcheckrs7( . * * * *C#y!!  rc+BKtdi|}dVtdi|dS)aContext manager for error handling Using an instance of `errstate` as a context manager allows statements in that context to execute with a known error handling behavior. Upon entering the context the error handling is set with `seterr`, and upon exiting it is reset to what it was before. Please note, this text was taken near verbatim from numpy's errstate method. Parameters ---------- kwargs : {empty} Keyword arguments. The valid error types that are defined. Each keyword should have a string or callable for the particular error. Values are: {'ignore', 'warn', 'raise', 'call', 'print'} See Also -------- seterr, geterr, seterrcall, geterrcall Nr-)rrs r errstaters>,    I EEE YrN)!rwwarningsrsysr contextlibrbiom.exceptionrEMPTYOBSSIZESAMPSIZEOBSDUPSAMPDUP OBSMDSIZE SAMPMDSIZEr rrrr!r'r)r?rArrOrrrrrrr-rr rs00t%%%%%%))))))  ? ; $ ! D @  888 333 === 888 >>> >>> 999B.B.B.B.B.B.B.B.J LNN 7E8^+--- 9gw +--- :x.+--- 8VWl+--- 9gw +--- ; 7O+--- <W6F+---""" ///d000B***26r