htsworkflow/pipelines/gerald.py

   1 """
   2 Provide access to information stored in the GERALD directory.
   3 """
   4 from datetime import datetime, date
   5 import logging
   6 import os
   7 import time
   8
   9 from htsworkflow.pipelines.summary import Summary
  10 from htsworkflow.pipelines.eland import eland, ELAND
  11
  12 from htsworkflow.pipelines.runfolder import \
  13    ElementTree, \
  14    EUROPEAN_STRPTIME, \
  15    LANES_PER_FLOWCELL, \
  16    VERSION_RE
  17 from htsworkflow.util.ethelp import indent, flatten
  18
  19 class Gerald(object):
  20     """
  21     Capture meaning out of the GERALD directory
  22     """
  23     XML_VERSION = 1
  24     GERALD='Gerald'
  25     RUN_PARAMETERS='RunParameters'
  26     SUMMARY='Summary'
  27
  28     class LaneParameters(object):
  29         """
  30         Make it easy to access elements of LaneSpecificRunParameters from python
  31         """
  32         def __init__(self, gerald, lane_id):
  33             self._gerald = gerald
  34             self._lane_id = lane_id
  35
  36         def __get_attribute(self, xml_tag):
  37             subtree = self._gerald.tree.find('LaneSpecificRunParameters')
  38             container = subtree.find(xml_tag)
  39             if container is None:
  40                 return None
  41             if len(container.getchildren()) > LANES_PER_FLOWCELL:
  42                 raise RuntimeError('GERALD config.xml file changed')
  43             lanes = [x.tag.split('_')[1] for x in container.getchildren()]
  44             index = lanes.index(self._lane_id)
  45             element = container[index]
  46             return element.text
  47         def _get_analysis(self):
  48             return self.__get_attribute('ANALYSIS')
  49         analysis = property(_get_analysis)
  50
  51         def _get_eland_genome(self):
  52             genome = self.__get_attribute('ELAND_GENOME')
  53             # default to the chipwide parameters if there isn't an
  54             # entry in the lane specific paramaters
  55             if genome is None:
  56                 subtree = self._gerald.tree.find('ChipWideRunParameters')
  57                 container = subtree.find('ELAND_GENOME')
  58                 genome = container.text
  59             return genome
  60         eland_genome = property(_get_eland_genome)
  61
  62         def _get_read_length(self):
  63             return self.__get_attribute('READ_LENGTH')
  64         read_length = property(_get_read_length)
  65
  66         def _get_use_bases(self):
  67             return self.__get_attribute('USE_BASES')
  68         use_bases = property(_get_use_bases)
  69
  70     class LaneSpecificRunParameters(object):
  71         """
  72         Provide access to LaneSpecificRunParameters
  73         """
  74         def __init__(self, gerald):
  75             self._gerald = gerald
  76             self._lane = None
  77
  78         def _initalize_lanes(self):
  79             """
  80             build dictionary of LaneParameters
  81             """
  82             self._lanes = {}
  83             tree = self._gerald.tree
  84             analysis = tree.find('LaneSpecificRunParameters/ANALYSIS')
  85             # according to the pipeline specs I think their fields
  86             # are sampleName_laneID, with sampleName defaulting to s
  87             # since laneIDs are constant lets just try using
  88             # those consistently.
  89             for element in analysis:
  90                 sample, lane_id = element.tag.split('_')
  91                 self._lanes[lane_id] = Gerald.LaneParameters(self._gerald, lane_id)
  92
  93         def __getitem__(self, key):
  94             if self._lane is None:
  95                 self._initalize_lanes()
  96             return self._lanes[key]
  97         def keys(self):
  98             if self._lane is None:
  99                 self._initalize_lanes()
 100             return self._lanes.keys()
 101         def values(self):
 102             if self._lane is None:
 103                 self._initalize_lanes()
 104             return self._lanes.values()
 105         def items(self):
 106             if self._lane is None:
 107                 self._initalize_lanes()
 108             return self._lanes.items()
 109         def __len__(self):
 110             if self._lane is None:
 111                 self._initalize_lanes()
 112             return len(self._lanes)
 113
 114     def __init__(self, xml=None):
 115         self.pathname = None
 116         self.tree = None
 117
 118         # parse lane parameters out of the config.xml file
 119         self.lanes = Gerald.LaneSpecificRunParameters(self)
 120
 121         self.summary = None
 122         self.eland_results = None
 123
 124         if xml is not None:
 125             self.set_elements(xml)
 126
 127     def _get_date(self):
 128         if self.tree is None:
 129             return datetime.today()
 130         timestamp = self.tree.findtext('ChipWideRunParameters/TIME_STAMP')
 131         epochstamp = time.mktime(time.strptime(timestamp, '%c'))
 132         return datetime.fromtimestamp(epochstamp)
 133     date = property(_get_date)
 134
 135     def _get_time(self):
 136         return time.mktime(self.date.timetuple())
 137     time = property(_get_time, doc='return run time as seconds since epoch')
 138
 139     def _get_version(self):
 140         if self.tree is None:
 141             return None
 142         return self.tree.findtext('ChipWideRunParameters/SOFTWARE_VERSION')
 143     version = property(_get_version)
 144
 145     def dump(self):
 146         """
 147         Debugging function, report current object
 148         """
 149         print 'Gerald version:', self.version
 150         print 'Gerald run date:', self.date
 151         print 'Gerald config.xml:', self.tree
 152         self.summary.dump()
 153
 154     def get_elements(self):
 155         if self.tree is None or self.summary is None:
 156             return None
 157
 158         gerald = ElementTree.Element(Gerald.GERALD,
 159                                      {'version': unicode(Gerald.XML_VERSION)})
 160         gerald.append(self.tree)
 161         gerald.append(self.summary.get_elements())
 162         if self.eland_results:
 163             gerald.append(self.eland_results.get_elements())
 164         return gerald
 165
 166     def set_elements(self, tree):
 167         if tree.tag !=  Gerald.GERALD:
 168             raise ValueError('exptected GERALD')
 169         xml_version = int(tree.attrib.get('version', 0))
 170         if xml_version > Gerald.XML_VERSION:
 171             logging.warn('XML tree is a higher version than this class')
 172         for element in list(tree):
 173             tag = element.tag.lower()
 174             if tag == Gerald.RUN_PARAMETERS.lower():
 175                 self.tree = element
 176             elif tag == Gerald.SUMMARY.lower():
 177                 self.summary = Summary(xml=element)
 178             elif tag == ELAND.ELAND.lower():
 179                 self.eland_results = ELAND(xml=element)
 180             else:
 181                 logging.warn("Unrecognized tag %s" % (element.tag,))
 182
 183
 184 def gerald(pathname):
 185     g = Gerald()
 186     g.pathname = pathname
 187     path, name = os.path.split(pathname)
 188     logging.info("Parsing gerald config.xml")
 189     config_pathname = os.path.join(pathname, 'config.xml')
 190     g.tree = ElementTree.parse(config_pathname).getroot()
 191
 192     # parse Summary.htm file
 193     logging.info("Parsing Summary.htm")
 194     summary_pathname = os.path.join(pathname, 'Summary.htm')
 195     g.summary = Summary(summary_pathname)
 196     # parse eland files
 197     g.eland_results = eland(g.pathname, g)
 198     return g
 199
 200 if __name__ == "__main__":
 201   # quick test code
 202   import sys
 203   g = gerald(sys.argv[1])
 204   #ElementTree.dump(g.get_elements())