Recent IPAR xml config blocks include the runfolder name

[htsworkflow.git] / htsworkflow / pipelines / ipar.py

diff --git a/htsworkflow/pipelines/ipar.py b/htsworkflow/pipelines/ipar.py
index 9113d6f1717fd6fd2d27fe9c2bd1e848766f2b5d..8203f5e0f29fda173728e3f504522f6cd579520f 100644 (file)
--- a/htsworkflow/pipelines/ipar.py
+++ b/htsworkflow/pipelines/ipar.py
@@ -1,7 +1,7 @@
 """
 Extract information about the IPAR run
 
-IPAR 
+IPAR
     class holding the properties we found
 ipar
     IPAR factory function initalized from a directory name
@@ -12,17 +12,21 @@ fromxml
 __docformat__ = "restructuredtext en"
 
 import datetime
+from glob import glob
 import logging
 import os
 import re
 import stat
 import time
 
-from htsworkflow.pipelines.runfolder import \
+from htsworkflow.pipelines import \
    ElementTree, \
    VERSION_RE, \
    EUROPEAN_STRPTIME
 
+LOGGER = logging.getLogger(__name__)
+SOFTWARE_NAMES = ('IPAR_1.01', 'IPAR_1.3', 'Intensities')
+
 class Tiles(object):
   def __init__(self, tree):
     self.tree = tree.find("TileSelection")
@@ -67,10 +71,31 @@ class IPAR(object):
     def __init__(self, xml=None):
         self.tree = None
         self.date = datetime.datetime.today()
-       self._tiles = None
+        self._tiles = None
         if xml is not None:
             self.set_elements(xml)
 
+    def _get_runfolder_name(self):
+        """Return runfolder name"""
+        if self.tree is None:
+            raise ValueError("Can't query an empty run")
+        runfolder = self.tree.xpath('RunParameters/Runfolder')
+        return runfolder
+    runfolder_name = property(_get_runfolder)
+    
+    def _get_software(self):
+        """Return software name"""
+        if self.tree is None:
+            raise ValueError("Can't determine software name, please load a run")
+        software = self.tree.xpath('Software')
+        if len(software) == 0:
+          return None
+        elif len(software) > 1:
+            raise RuntimeError("Too many software tags, please update ipar.py")
+        else:
+            return software[0].attrib['Name']
+    software = property(_get_software)
+
     def _get_time(self):
         return time.mktime(self.date.timetuple())
     def _set_time(self, value):
@@ -81,8 +106,9 @@ class IPAR(object):
 
     def _get_cycles(self):
         if self.tree is None:
-          return None
+          raise RuntimeError("get cycles called before xml tree initalized")
         cycles = self.tree.find("Cycles")
+        assert cycles is not None
         if cycles is None:
           return None
         return cycles.attrib
@@ -159,7 +185,7 @@ class IPAR(object):
             raise ValueError('Expected "IPAR" SubElements')
         xml_version = int(tree.attrib.get('version', 0))
         if xml_version > IPAR.XML_VERSION:
-            logging.warn('IPAR XML tree is a higher version than this class')
+            LOGGER.warn('IPAR XML tree is a higher version than this class')
         for element in list(tree):
             if element.tag == IPAR.RUN:
                 self.tree = element
@@ -177,36 +203,48 @@ def load_ipar_param_tree(paramfile):
 
     tree = ElementTree.parse(paramfile).getroot()
     run = tree.find('Run')
-    if run.attrib.has_key('Name') and run.attrib['Name'].startswith("IPAR"):
+    if run.attrib.has_key('Name') and run.attrib['Name'] in SOFTWARE_NAMES:
         return run
-
-    return None
+    else:
+        LOGGER.info("No run found")
+        return None
 
 def ipar(pathname):
     """
     Examine the directory at pathname and initalize a IPAR object
     """
-    logging.info("Searching IPAR directory")
+    LOGGER.info("Searching IPAR directory %s" % (pathname,))
     i = IPAR()
+    i.pathname = pathname
 
     # parse firecrest directory name
     path, name = os.path.split(pathname)
     groups = name.split('_')
-    if groups[0] != 'IPAR':
+    if not (groups[0] == 'IPAR' or groups[0] == 'Intensities'):
       raise ValueError('ipar can only process IPAR directories')
 
+    bustard_pattern = os.path.join(pathname, 'Bustard*')
     # contents of the matrix file?
     matrix_pathname = os.path.join(pathname, 'Matrix', 's_matrix.txt')
-    if not os.path.exists(matrix_pathname):
-        return None
-    i.matrix = open(matrix_pathname, 'r').read()
+    if os.path.exists(matrix_pathname):
+        # this is IPAR_1.01
+        i.matrix = open(matrix_pathname, 'r').read()
+    elif glob(bustard_pattern) > 0:
+        i.matrix = None
+        # its still live.
 
     # look for parameter xml file
-    paramfile = os.path.join(path, '.params')
-    if os.path.exists(paramfile):
-      i.tree = load_ipar_param_tree(paramfile)
-      mtime_local = os.stat(paramfile)[stat.ST_MTIME]
-      i.time = mtime_local
+    paramfiles = [os.path.join(pathname, 'RTAConfig.xml'),
+                  os.path.join(pathname, 'config.xml'),
+                  os.path.join(path, '.params')]
+    for paramfile in paramfiles:
+        if os.path.exists(paramfile):
+            LOGGER.info("Found IPAR Config file at: %s" % ( paramfile, ))
+            i.tree = load_ipar_param_tree(paramfile)
+            mtime_local = os.stat(paramfile)[stat.ST_MTIME]
+            i.time = mtime_local
+            return i
+
     return i
 
 def fromxml(tree):
@@ -217,15 +255,15 @@ def fromxml(tree):
     f.set_elements(tree)
     return f
 
-if __name__ == "__main__":
-  i = ipar(os.path.expanduser('~/gec/081021_HWI-EAS229_0063_30HKUAAXX/Data/IPAR_1.01'))
-  x = i.get_elements()
-  j = fromxml(x)
+#if __name__ == "__main__":
+  #i = ipar(os.path.expanduser('~/gec/081021_HWI-EAS229_0063_30HKUAAXX/Data/IPAR_1.01'))
+  #x = i.get_elements()
+  #j = fromxml(x)
   #ElementTree.dump(x)
-  print j.date
-  print j.start
-  print j.stop
-  print i.tiles.keys()
-  print j.tiles.keys()
-  print j.tiles.items()
-  print j.file_list()
+  #print j.date
+  #print j.start
+  #print j.stop
+  #print i.tiles.keys()
+  #print j.tiles.keys()
+  #print j.tiles.items()
+  #print j.file_list()