Back porting Diane's firecrest.py from the trunk to v0.1.x branch

diff --git a/gaworkflow/pipeline/firecrest.py b/gaworkflow/pipeline/firecrest.py
new file mode 100644 (file)
index 0000000..dd06aec
--- /dev/null
+++ b/gaworkflow/pipeline/firecrest.py
@@ -0,0 +1,127 @@
+"""
+Extract information about the Firecrest run
+
+Firecrest - class holding the properties we found
+firecrest - Firecrest factory function initalized from a directory name
+fromxml - Firecrest factory function initalized from an xml dump from
+          the Firecrest object.
+"""
+
+from datetime import date
+import os
+import re
+import time
+
+from gaworkflow.pipeline.runfolder import \
+   ElementTree, \
+   VERSION_RE, \
+   EUROPEAN_STRPTIME
+
+class Firecrest(object):
+    XML_VERSION=1
+
+    # xml tag names
+    FIRECREST = 'Firecrest'
+    SOFTWARE_VERSION = 'version'
+    START = 'FirstCycle'
+    STOP = 'LastCycle'
+    DATE = 'run_time'
+    USER = 'user'
+    MATRIX = 'matrix'
+
+    def __init__(self, xml=None):
+        self.start = None
+        self.stop = None
+        self.version = None
+        self.date = date.today()
+        self.user = None
+        self.matrix = None
+
+        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 dump(self):
+        print "Starting cycle:", self.start
+        print "Ending cycle:", self.stop
+        print "Firecrest version:", self.version
+        print "Run date:", self.date
+        print "user:", self.user
+
+    def get_elements(self):
+        attribs = {'version': str(Firecrest.XML_VERSION) }
+        root = ElementTree.Element(Firecrest.FIRECREST, attrib=attribs)
+        version = ElementTree.SubElement(root, Firecrest.SOFTWARE_VERSION)
+        version.text = self.version
+        start_cycle = ElementTree.SubElement(root, Firecrest.START)
+        start_cycle.text = str(self.start)
+        stop_cycle = ElementTree.SubElement(root, Firecrest.STOP)
+        stop_cycle.text = str(self.stop)
+        run_date = ElementTree.SubElement(root, Firecrest.DATE)
+        run_date.text = str(self.time)
+        user = ElementTree.SubElement(root, Firecrest.USER)
+        user.text = self.user
+        matrix = ElementTree.SubElement(root, Firecrest.MATRIX)
+        matrix.text = self.matrix
+        return root
+
+    def set_elements(self, tree):
+        if tree.tag != Firecrest.FIRECREST:
+            raise ValueError('Expected "Firecrest" SubElements')
+        xml_version = int(tree.attrib.get('version', 0))
+        if xml_version > Firecrest.XML_VERSION:
+            logging.warn('Firecrest XML tree is a higher version than this class')
+        for element in list(tree):
+            if element.tag == Firecrest.SOFTWARE_VERSION:
+                self.version = element.text
+            elif element.tag == Firecrest.START:
+                self.start = int(element.text)
+            elif element.tag == Firecrest.STOP:
+                self.stop = int(element.text)
+            elif element.tag == Firecrest.DATE:
+                self.date = date.fromtimestamp(float(element.text))
+            elif element.tag == Firecrest.USER:
+                self.user = element.text
+            elif element.tag == Firecrest.MATRIX:
+                self.matrix = element.text
+            else:
+                raise ValueError("Unrecognized tag: %s" % (element.tag,))
+
+def firecrest(pathname):
+    """
+    Examine the directory at pathname and initalize a Firecrest object
+    """
+    f = Firecrest()
+
+    # parse firecrest directory name
+    path, name = os.path.split(pathname)
+    groups = name.split('_')
+    # grab the start/stop cycle information
+    cycle = re.match("C([0-9]+)-([0-9]+)", groups[0])
+    f.start = int(cycle.group(1))
+    f.stop = int(cycle.group(2))
+    # firecrest version
+    version = re.search(VERSION_RE, groups[1])
+    f.version = (version.group(1))
+    # datetime
+    t = time.strptime(groups[2], EUROPEAN_STRPTIME)
+    f.date = date(*t[0:3])
+    # username
+    f.user = groups[3]
+
+    # should I parse this deeper than just stashing the 
+    # contents of the matrix file?
+    matrix_pathname = os.path.join(pathname, 'Matrix', 's_matrix.txt')
+    f.matrix = open(matrix_pathname, 'r').read()
+    return f
+
+def fromxml(tree):
+    """
+    Initialize a Firecrest object from an element tree node
+    """
+    f = Firecrest()
+    f.set_elements(tree)
+    return f