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         matrix = ElementTree.SubElement(root, Firecrest.MATRIX)
  74         matrix.text = self.matrix
  75         return root
  76
  77     def set_elements(self, tree):
  78         if tree.tag != Firecrest.FIRECREST:
  79             raise ValueError('Expected "Firecrest" SubElements')
  80         xml_version = int(tree.attrib.get('version', 0))
  81         if xml_version > Firecrest.XML_VERSION:
  82             logging.warn('Firecrest XML tree is a higher version than this class')
  83         for element in list(tree):
  84             if element.tag == Firecrest.SOFTWARE_VERSION:
  85                 self.version = element.text
  86             elif element.tag == Firecrest.START:
  87                 self.start = int(element.text)
  88             elif element.tag == Firecrest.STOP:
  89                 self.stop = int(element.text)
  90             elif element.tag == Firecrest.DATE:
  91                 self.date = date.fromtimestamp(float(element.text))
  92             elif element.tag == Firecrest.USER:
  93                 self.user = element.text
  94             elif element.tag == Firecrest.MATRIX:
  95                 self.matrix = element.text
  96             else:
  97                 raise ValueError("Unrecognized tag: %s" % (element.tag,))
  98
  99 def firecrest(pathname):
 100     """
 101     Examine the directory at pathname and initalize a Firecrest object
 102     """
 103     f = Firecrest()
 104
 105     # parse firecrest directory name
 106     path, name = os.path.split(pathname)
 107     groups = name.split('_')
 108     # grab the start/stop cycle information
 109     cycle = re.match("C([0-9]+)-([0-9]+)", groups[0])
 110     f.start = int(cycle.group(1))
 111     f.stop = int(cycle.group(2))
 112     # firecrest version
 113     version = re.search(VERSION_RE, groups[1])
 114     f.version = (version.group(1))
 115     # datetime
 116     t = time.strptime(groups[2], EUROPEAN_STRPTIME)
 117     f.date = date(*t[0:3])
 118     # username
 119     f.user = groups[3]
 120
 121     bustard_pattern = os.path.join(pathname, 'Bustard*')
 122     # should I parse this deeper than just stashing the
 123     # contents of the matrix file?
 124     matrix_pathname = os.path.join(pathname, 'Matrix', 's_matrix.txt')
 125     if os.path.exists(matrix_pathname):
 126         # this is for firecrest < 1.3.2
 127         f.matrix = open(matrix_pathname, 'r').read()
 128     elif glob(bustard_pattern) > 0:
 129         f.matrix = None
 130         # there are runs here. Bustard should save the matrix.
 131     else:
 132         return None
 133
 134     return f
 135
 136 def fromxml(tree):
 137     """
 138     Initialize a Firecrest object from an element tree node
 139     """
 140     f = Firecrest()
 141     f.set_elements(tree)
 142     return f