ó
ë™xTc @ sõ d d l m Z d d l Z d d l Z d d l m Z d e f d „ ƒ YZ d e f d „ ƒ YZ d e f d „ ƒ YZ d
e f d „ ƒ YZ
d e
f d
„ ƒ YZ d e f d „ ƒ YZ d e
f d „ ƒ YZ
d „ Z d e
f d „ ƒ YZ d S( iÿÿÿÿ( t divisionN( t errorst JobStatusc B s2 e Z d Z d „ Z d „ Z d „ Z d „ Z RS( s
Status class
c C s/ | | _ | | _ | | j | j g | _ d S( N( t outfilet errfilet files( t selfR R t
additional( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt __init__ s c C s† d d l } | j d k r| x? t r\ y t | j ƒ } Wn t k
rW | j d ƒ q XPq W| j ƒ j ƒ } | j ƒ n d } | S( Niÿÿÿÿi (
t timeR t Nonet Truet opent IOErrort sleept readt stript close( R R t infilet stdout( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt
get_stdout s
c C s€ d d l } | j d k rv x? t r\ y t | j ƒ } Wn t k
rW | j d ƒ q XPq W| j ƒ } | j ƒ n d } | S( Niÿÿÿÿi ( R R R
R R R
R R R ( R R R t stderr( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt
get_stderr- s
c C sL x3 | j D]( } t j j | ƒ r
t j | ƒ q
q
Wd | _ d | _ d S( N( R t ost patht existst removeR
R R ( R t fname( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt cleanupE s
( t __name__t
__module__t __doc__R R R R ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR s
t Synchronousc B s2 e Z d Z d „ Z d „ Z d „ Z d „ Z RS( s0
Determines job status for synchronous jobs
c C s2 t t | ƒ j d | d | d | ƒ | | _ d S( NR R R ( t superR R t process( R R" R R R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR T s
c C s | j j ƒ d k S( N( R" t pollR
( R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt is_finished^ s c C s | j j ƒ d S( N( R" t terminate( R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR% c s c C s’ | j ƒ s t ‚ y | j ƒ } | j ƒ } WnK t k
r{ | j j j ƒ } | j j j ƒ } t j
d | | f ‚ n X| | | j j ƒ f S( Ns Queue error:%s
%s( R$ t AssertionErrorR R R
R" R R R R t AbnormalExitErrorR# ( R R R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt resultsh s
( R R R R R$ R% R( ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR O s
t SlurmStreamc B s; e Z d Z d „ Z d „ Z d „ Z d „ Z d „ Z RS( s£
Specialized handler for Slurm, because file handles of the shell are redirected
Note that this can fill the buffers, resulting in the job never completing
c C s | | _ | | _ d S( N( R" R ( R R" R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR s c C s | j j ƒ d k S( N( R" R# R
( R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR$ … s c C s | j j ƒ d S( N( R" R% ( R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR% Š s c C sL | j ƒ s t ‚ | j j j ƒ } | j j j ƒ } | | | j j ƒ f S( N( R$ R& R" R R R R# ( R R R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR( s c C s: x3 | j D]( } t j j | ƒ r
t j | ƒ q
q
Wd S( N( R R R R R ( R R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR ˜ s ( R R R R R$ R% R( R ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR) x s t Asynchronousc B s; e Z d Z d „ Z d „ Z d „ Z e d d „ ƒ Z RS( s#
Handler for asynchronous jobs
c C sZ t t | ƒ j d | d | d | ƒ | | _ | | _ | | _ | j j d | j ƒ d S( NR R R t jobid( R! R* R R+ t pollert qdelt new_job_submitted( R R+ R, R R R R- ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR ¤ s c C s: y | j j d | j ƒ } Wn t k
r5 t } n X| S( NR+ ( R, R$ R+ t
ValueErrorR ( R t result( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR$ ³ s
c C sc y t j | j | j g ƒ } Wn2 t k
rT } t j d | j | j | f ‚ n X| j ƒ d S( Ns '%s %s': %s( t
subprocesst PopenR- R+ t OSErrorR t ExecutableErrort communicate( R R" t e( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR% ¾ s
#t .c C s | j | | | | f S( N( t SCRIPT( t clst includet
executablet scriptt cwd( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR< É s ( R R R R R$ R% t classmethodR< ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR* Ÿ s t StdStreamStrategyc B s e Z d Z d Z d „ Z RS( s*
Establishes exit code through stderr
s@ cd %s
source %s
%s 2>&1 << EOF
%s
EOF
echo exit_status $? 1>&2
c C s‡ | j ƒ } | d k rK y t d | ƒ } WqQ t j k
rG d } qQ Xn d } | d k rp d | j ƒ | f S| j ƒ d | f Sd S( Nt outputi i t ( R R
t extract_exit_code_textR t ExtractionErrorR ( R R t exit_code( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR( ß s
( R R R R8 R( ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR? Ï s t SlurmStdStreamStrategyc B s e Z d Z d Z RS( sB
Stdstream strategy specifically for Slurm (different script)
sO #!/bin/sh
cd %s
source %s
srun %s 2>&1 << EOF
%s
EOF
echo exit_status $? 1>&2
( R R R R8 ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyRE õ s t AccountingStrategyc B s e Z d Z d Z d „ Z RS( s.
Establishes exit code through accounting
s! cd %s
source %s
%s << EOF
%s
EOF
c C s¹ y1 t j d d | j g d t j d t j ƒ} Wn, t k
r_ } t j d | j | f ‚ n X| j ƒ \ } } | j ƒ r‘ t j d | ‚ n t
d | ƒ } | j ƒ | j ƒ | f S( Nt qaccts -jR R s 'qacct -j %s': %ss SGE accounting error:
%sR@ (
R1 R2 R+ t PIPER3 R R4 R5 R# R' RB R R ( R R" R6 t outt errRD ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR( s ( R R R R8 R( ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyRF s c C sm xf | j ƒ D]H } | j ƒ } t | ƒ d k r
| d d k r
t | d ƒ } | Sq
Wt j d | ‚ d S( Ni i t exit_statusi s Unexpected output: %r( t
splitlinest splitt lent intR RC ( R@ t linet tokensRD ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyRB - s "t LogfileStrategyc B s8 e Z d Z d Z d „ Z d „ Z d „ Z d „ Z RS( s:
Establishes exit code through queuing system logfile
s+ cd %s
#!/bin/sh
source %s
%s << EOF
%s
EOF
c C sH | | _ t t | ƒ j d | d | d | d | d | | j g ƒ d S( NR+ R, R R R ( t logfileR! RR R ( R R+ R, R R RS R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR I s c C sL | j d k rB t j j | j ƒ s* t ‚ t | j ƒ j ƒ } n d } | S( N( RS R
R R R R& R R ( R t stdlog( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt
get_stdlogU s
c C sÐ | j ƒ } | d k r± d d l j j } d | j ƒ } | j | ƒ } g | j d ƒ D]$ } | j j d ƒ d k rY | ^ qY } | s’ d } q· t
| d j d ƒ j ƒ } n d } | j
ƒ | j ƒ | f S( Niÿÿÿÿs %st at nt ReturnValuei t ii ( RU R
t xml.etree.ElementTreet etreet ElementTreeR t
fromstringt itert attribt getRO t findt textR R ( R RT t ETt logxmlt rootR6 t resRD ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR( a s : c C s t t | ƒ j ƒ d | _ d S( N( R! RR R R
RS ( R ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyR x s ( R R R R8 R RU R( R ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyRR : s
( t
__future__R R R1 t& libtbx.queuing_system_utils.processingR t objectR R R) R* R? RE RF RB RR ( ( ( s[ /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/libtbx/queuing_system_utils/processing/status.pyt s F)'0&&