htsworkflow/pipelines/firecrest.py

   1 """
   2 Extract information about the Firecrest run
   3
   4 Firecrest
   5   class holding the properties we found
   6 firecrest
   7   Firecrest factory function initalized from a directory name
   8 fromxml
   9   Firecrest factory function initalized from an xml dump from
  10   the Firecrest object.
  11 """
  12
  13 from datetime import date
  14 from glob import glob
  15 import os
  16 import re
  17 import time
  18
  19 from htsworkflow.pipelines.runfolder import \
  20    ElementTree, \
  21    VERSION_RE, \
  22    EUROPEAN_STRPTIME
  23
  24 __docformat__ = "restructuredtext en"
  25
  26 class Firecrest(object):
  27     XML_VERSION=1
  28
  29     # xml tag names
  30     FIRECREST = 'Firecrest'
  31     SOFTWARE_VERSION = 'version'
  32     START = 'FirstCycle'
  33     STOP = 'LastCycle'
  34     DATE = 'run_time'
  35     USER = 'user'
  36     MATRIX = 'matrix'
  37
  38     def __init__(self, xml=None):
  39         self.start = None
  40         self.stop = None
  41         self.version = None
  42         self.date = date.today()
  43         self.user = None
  44         self.matrix = None
  45
  46         if xml is not None:
  47             self.set_elements(xml)
  48
  49     def _get_time(self):
  50         return time.mktime(self.date.timetuple())
  51     time = property(_get_time, doc='return run time as seconds since epoch')
  52
  53     def dump(self):
  54         print "Starting cycle:", self.start
  55         print "Ending cycle:", self.stop
  56         print "Firecrest version:", self.version
  57         print "Run date:", self.date
  58         print "user:", self.user
  59
  60     def get_elements(self):
  61         attribs = {'version': str(Firecrest.XML_VERSION) }
  62         root = ElementTree.Element(Firecrest.FIRECREST, attrib=attribs)
  63         version = ElementTree.SubElement(root, Firecrest.SOFTWARE_VERSION)
  64         version.text = self.version
  65         start_cycle = ElementTree.SubElement(root, Firecrest.START)
  66         start_cycle.text = str(self.start)
  67         stop_cycle = ElementTree.SubElement(root, Firecrest.STOP)
  68         stop_cycle.text = str(self.stop)
  69         run_date = ElementTree.SubElement(root, Firecrest.DATE)
  70         run_date.text = str(self.time)
  71         user = ElementTree.SubElement(root, Firecrest.USER)
  72         user.text = self.user
  73         if self.matrix is not None:
  74             matrix = ElementTree.SubElement(root, Firecrest.MATRIX)
  75             matrix.text = self.matrix
  76         return root
  77
  78     def set_elements(self, tree):
  79         if tree.tag != Firecrest.FIRECREST:
  80             raise ValueError('Expected "Firecrest" SubElements')
  81         xml_version = int(tree.attrib.get('version', 0))
  82         if xml_version > Firecrest.XML_VERSION:
  83             logging.warn('Firecrest XML tree is a higher version than this class')
  84         for element in list(tree):
  85             if element.tag == Firecrest.SOFTWARE_VERSION:
  86                 self.version = element.text
  87             elif element.tag == Firecrest.START:
  88                 self.start = int(element.text)
  89             elif element.tag == Firecrest.STOP:
  90                 self.stop = int(element.text)
  91             elif element.tag == Firecrest.DATE:
  92                 self.date = date.fromtimestamp(float(element.text))
  93             elif element.tag == Firecrest.USER:
  94                 self.user = element.text
  95             elif element.tag == Firecrest.MATRIX:
  96                 self.matrix = element.text
  97             else:
  98                 raise ValueError("Unrecognized tag: %s" % (element.tag,))
  99
 100 def firecrest(pathname):
 101     """
 102     Examine the directory at pathname and initalize a Firecrest object
 103     """
 104     f = Firecrest()
 105
 106     # parse firecrest directory name
 107     path, name = os.path.split(pathname)
 108     groups = name.split('_')
 109     # grab the start/stop cycle information
 110     cycle = re.match("C([0-9]+)-([0-9]+)", groups[0])
 111     f.start = int(cycle.group(1))
 112     f.stop = int(cycle.group(2))
 113     # firecrest version
 114     version = re.search(VERSION_RE, groups[1])
 115     f.version = (version.group(1))
 116     # datetime
 117     t = time.strptime(groups[2], EUROPEAN_STRPTIME)
 118     f.date = date(*t[0:3])
 119     # username
 120     f.user = groups[3]
 121
 122     bustard_pattern = os.path.join(pathname, 'Bustard*')
 123     # should I parse this deeper than just stashing the
 124     # contents of the matrix file?
 125     matrix_pathname = os.path.join(pathname, 'Matrix', 's_matrix.txt')
 126     if os.path.exists(matrix_pathname):
 127         # this is for firecrest < 1.3.2
 128         f.matrix = open(matrix_pathname, 'r').read()
 129     elif glob(bustard_pattern) > 0:
 130         f.matrix = None
 131         # there are runs here. Bustard should save the matrix.
 132     else:
 133         return None
 134
 135     return f
 136
 137 def fromxml(tree):
 138     """
 139     Initialize a Firecrest object from an element tree node
 140     """
 141     f = Firecrest()
 142     f.set_elements(tree)
 143     return f