from datetime import datetime, date
import logging
import os
+import re
import stat
import time
LOGGER = logging.getLogger(__name__)
-class Gerald(object):
+class Alignment(object):
"""
Capture meaning out of the GERALD directory
"""
XML_VERSION = 1
- GERALD='Gerald'
RUN_PARAMETERS='RunParameters'
SUMMARY='Summary'
- def __init__(self, xml=None):
- self.pathname = None
- self.tree = None
+ def __init__(self, xml=None, pathname=None, tree=None):
+ self.pathname = pathname
+ self.tree = tree
# parse lane parameters out of the config.xml file
self.lanes = LaneSpecificRunParameters(self)
if xml is not None:
self.set_elements(xml)
+ def _get_time(self):
+ return time.mktime(self.date.timetuple())
+ time = property(_get_time, doc='return run time as seconds since epoch')
+
+ def _get_chip_attribute(self, value):
+ return self.tree.findtext('ChipWideRunParameters/%s' % (value,))
+
+ def dump(self):
+ """
+ Debugging function, report current object
+ """
+ print 'Software:'. self.__class__.__name__
+ print 'Alignment version:', self.version
+ print 'Run date:', self.date
+ print 'config.xml:', self.tree
+ self.summary.dump()
+
+ def get_elements(self):
+ if self.tree is None or self.summary is None:
+ return None
+
+ gerald = ElementTree.Element(Gerald.GERALD,
+ {'version': unicode(Gerald.XML_VERSION)})
+ gerald.append(self.tree)
+ gerald.append(self.summary.get_elements())
+ if self.eland_results:
+ gerald.append(self.eland_results.get_elements())
+ return gerald
+
+ def set_elements(self, tree):
+ if tree.tag != self.__class__.GERALD:
+ raise ValueError('expected GERALD')
+ xml_version = int(tree.attrib.get('version', 0))
+ if xml_version > Gerald.XML_VERSION:
+ LOGGER.warn('XML tree is a higher version than this class')
+ self.eland_results = ELAND()
+ for element in list(tree):
+ tag = element.tag.lower()
+ if tag == Gerald.RUN_PARAMETERS.lower():
+ self.tree = element
+ elif tag == Gerald.SUMMARY.lower():
+ self.summary = Summary(xml=element)
+ elif tag == ELAND.ELAND.lower():
+ self.eland_results = ELAND(xml=element)
+ else:
+ LOGGER.warn("Unrecognized tag %s" % (element.tag,))
+
+class Gerald(Alignment):
+ GERALD='Gerald'
+
def _get_date(self):
if self.tree is None:
return datetime.today()
return datetime.today()
date = property(_get_date)
- def _get_time(self):
- return time.mktime(self.date.timetuple())
- time = property(_get_time, doc='return run time as seconds since epoch')
-
def _get_experiment_root(self):
if self.tree is None:
return None
expt_root = os.path.normpath(self._get_experiment_root())
chip_expt_dir = self.tree.findtext('ChipWideRunParameters/EXPT_DIR')
- # hiseqs renamed the experiment dir location
- defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR')
- experiment_dir = None
- if defaults_expt_dir is not None:
- _, experiment_dir = os.path.split(defaults_expt_dir)
- elif expt_root is not None and chip_expt_dir is not None:
+ if expt_root is not None and chip_expt_dir is not None:
experiment_dir = chip_expt_dir.replace(expt_root+os.path.sep, '')
experiment_dir = experiment_dir.split(os.path.sep)[0]
ga_version = self.tree.findtext(
'ChipWideRunParameters/SOFTWARE_VERSION')
if ga_version is not None:
+ match = re.match("@.*GERALD.pl,v (?P<version>\d+(\.\d+)+)",
+ ga_version)
+ if match:
+ return match.group('version')
return ga_version
- hiseq_software_node = self.tree.find('Software')
- hiseq_version = hiseq_software_node.attrib['Version']
- return hiseq_version
-
version = property(_get_version)
- def _get_chip_attribute(self, value):
- return self.tree.findtext('ChipWideRunParameters/%s' % (value,))
+class CASAVA(Alignment):
+ GERALD='Casava'
- def dump(self):
- """
- Debugging function, report current object
- """
- print 'Gerald version:', self.version
- print 'Gerald run date:', self.date
- print 'Gerald config.xml:', self.tree
- self.summary.dump()
+ def _get_runfolder_name(self):
+ if self.tree is None:
+ return None
- def get_elements(self):
- if self.tree is None or self.summary is None:
+ # hiseqs renamed the experiment dir location
+ defaults_expt_dir = self.tree.findtext('Defaults/EXPT_DIR')
+ _, experiment_dir = os.path.split(defaults_expt_dir)
+
+ if experiment_dir is None or len(experiment_dir) == 0:
return None
+ return experiment_dir
- gerald = ElementTree.Element(Gerald.GERALD,
- {'version': unicode(Gerald.XML_VERSION)})
- gerald.append(self.tree)
- gerald.append(self.summary.get_elements())
- if self.eland_results:
- gerald.append(self.eland_results.get_elements())
- return gerald
+ runfolder_name = property(_get_runfolder_name)
- def set_elements(self, tree):
- if tree.tag != Gerald.GERALD:
- raise ValueError('exptected GERALD')
- xml_version = int(tree.attrib.get('version', 0))
- if xml_version > Gerald.XML_VERSION:
- LOGGER.warn('XML tree is a higher version than this class')
- self.eland_results = ELAND()
- for element in list(tree):
- tag = element.tag.lower()
- if tag == Gerald.RUN_PARAMETERS.lower():
- self.tree = element
- elif tag == Gerald.SUMMARY.lower():
- self.summary = Summary(xml=element)
- elif tag == ELAND.ELAND.lower():
- self.eland_results = ELAND(xml=element)
- else:
- LOGGER.warn("Unrecognized tag %s" % (element.tag,))
+ def _get_version(self):
+ if self.tree is None:
+ return None
+ hiseq_software_node = self.tree.find('Software')
+ hiseq_version = hiseq_software_node.attrib['Version']
+ return hiseq_version
+ version = property(_get_version)
class LaneParameters(object):
def gerald(pathname):
- g = Gerald()
- g.pathname = os.path.expanduser(pathname)
- path, name = os.path.split(g.pathname)
LOGGER.info("Parsing gerald config.xml")
- config_pathname = os.path.join(g.pathname, 'config.xml')
- g.tree = ElementTree.parse(config_pathname).getroot()
+ pathname = os.path.expanduser(pathname)
+ config_pathname = os.path.join(pathname, 'config.xml')
+ config_tree = ElementTree.parse(config_pathname).getroot()
# parse Summary.htm file
- summary_xml = os.path.join(g.pathname, 'Summary.xml')
- summary_htm = os.path.join(g.pathname, 'Summary.htm')
- report_summary = os.path.join(g.pathname, '..', 'Data',
+ summary_xml = os.path.join(pathname, 'Summary.xml')
+ summary_htm = os.path.join(pathname, 'Summary.htm')
+ report_summary = os.path.join(pathname, '..', 'Data',
'reports', 'Summary', )
if os.path.exists(summary_xml):
+ g = Gerald(pathname = pathname, tree=config_tree)
LOGGER.info("Parsing Summary.xml")
g.summary = SummaryGA(summary_xml)
g.eland_results = eland(g.pathname, g)
elif os.path.exists(summary_htm):
+ g = Gerald(pathname=pathname, tree=config_tree)
LOGGER.info("Parsing Summary.htm")
g.summary = SummaryGA(summary_htm)
g.eland_results = eland(g.pathname, g)
elif os.path.isdir(report_summary):
+ g = CASAVA(pathname=pathname, tree=config_tree)
LOGGER.info("Parsing %s" % (report_summary,))
g.summary = SummaryHiSeq(report_summary)
projects / htsworkflow.git / blobdiff