from CCP4ReportParser import *
import CCP4RvapiParser
import os,shutil
import StringIO
dummy_report = '\n\nRunning Crank2\n\n'
dummy_report += '\nCRANK2 job running - no report available yet
\n\n\n'
def et(fileName=None):
parser = etree.HTMLParser()
try:
#root = etree.parse( os.path.join(rundir, "index.html"), parser=parser ).getroot()
root = etree.parse( fileName, parser=parser ).getroot()
script=root.find('body/script')
if script is not None:
script.text=script.text.replace('docURI = "";', 'docURI = "{}";'.format(os.path.dirname(fileName)+os.sep))
#root = etree.Element('iframe')
#root.set('src', fileName)
except Exception as e:
print 'Crank2 report failed with error message: {0}'.format(e)
# show logfile
if os.path.isfile(os.path.join(os.path.dirname(fileName),'log.txt')):
with open(os.path.join(os.path.dirname(fileName),'log.txt')) as f:
g = StringIO.StringIO(f.read().replace('\n','
'))
root = etree.parse( g, parser=parser ).getroot()
g.close()
else:
# the code below opens the presentation in the i2 browser. could be used as an alternative.
try:
root = etree.Element('a')
root.set('href', fileName)
root.set('style', "font-size: 130%")
root.text="Presentation not loaded. You can try to click this link to open it or use the View -> Log file option."
except Exception as e:
print 'Crank2 report failed (also returning the error message in report): {0}'.format(e)
f = StringIO.StringIO(dummy_report)
root = etree.parse( f, parser=parser ).getroot()
f.close()
return root
class crank2_report(CCP4RvapiParser.RvapiReport):
#class crank2_report(Report):
TASKNAME="crank2"
RUNNING = True
SEPARATEDATA = True
WATCHED_FILE = 'i2.xml'
def __init__(self,xmlnode=None,jobInfo={},jobStatus=None,**kw):
rundir = jobInfo['fileroot']
if os.path.isfile(os.path.join(rundir,'i2_native_present')):
#crank2_report.WATCHED_FILE = self.WATCHED_FILE ='i2.xml'
CCP4RvapiParser.RvapiReport.__init__(self,xmlnode=xmlnode,jobInfo=jobInfo,jobStatus=jobStatus,**kw)
else:
crank2_report.WATCHED_FILE = self.WATCHED_FILE = 'program.xml'
Report.__init__(self,xmlnode=xmlnode,jobInfo=jobInfo,**kw)
import functools
#if os.path.isfile(os.path.join(rundir, "index.html")):
i=0
while os.path.isdir(os.path.join(rundir, 'job_'+str(i+1))): i+=1
if os.path.isfile( os.path.join(rundir, 'job_'+str(i), "index.html") ):
html = os.path.join(rundir, 'job_'+str(i), "index.html")
else:
html = os.path.join(rundir, "index.html")
results = Container()
results.as_etree = functools.partial(et,html)
self.append( results )