htsworkflow/pipelines/firecrest.py

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