58f787640ea77f16c8f6d4481693a83ec9ef647b
vsmalladi
  Tue May 8 10:29:52 2012 -0700
First step in python lib reogranization. Redmine #7029.
diff --git python/lib/ucscGb/mdb.py python/lib/ucscGb/mdb.py
deleted file mode 100644
index 5c53cc5..0000000
--- python/lib/ucscGb/mdb.py
+++ /dev/null
@@ -1,182 +0,0 @@
-from ucscgenomics import ra, ordereddict, encode
-
-class MdbFile(ra.RaFile):
-    '''
-    This should be used for all files in the metaDb, since they extend RaFile
-    with useful functionality specific to metaDb ra files.
-    '''
-    
-    @property
-    def name(self):
-        return self.compositeStanza['metaObject']
-    
-    @property
-    def expVars(self):
-        '''the experimental variables used in this track'''
-        try:
-            return self._expVars
-        except AttributeError:
-            self._expVars = self.compositeStanza['expVars'].split(',')
-            return self._expVars
-    
-    @property
-    def dataType(self):
-        '''The data type of the experiment. 'None' if inconsistent.'''
-        try:
-            return self._dataType
-        except AttributeError:
-            self._dataType = None
-            for e in self.experiments.itervalues():
-                if self._dataType == None and e.dataType != None:
-                    self._dataType = e.dataType
-                elif self._dataType != e.dataType or e.dataType == None:
-                    self._dataType = None
-                    break
-            return self._dataType
-    
-    @property
-    def compositeStanza(self):
-        '''the stanza (typically first in file) describing the composite'''
-        try:
-            return self._compositeStanza
-        except AttributeError:
-            self._compositeStanza = self.filter(lambda s: s['objType'] == 'composite', lambda s: s)
-            if len(self._compositeStanza) != 1:
-                raise KeyError(self.filename)
-            else:
-                self._compositeStanza = self._compositeStanza[0]
-            return self._compositeStanza
-            
-    @property    
-    def experiments(self):
-        '''dictionary of MdbExp objects indexed by the expId'''
-        try:
-            return self._experiments
-        except AttributeError:
-            self._experiments = dict()
-            exps = self.filter(lambda s: s['objType'] != 'composite', lambda s: (s['expId'], s))
-            stanzas = dict()
-            for k, v in exps:
-                if k not in stanzas:
-                    stanzas[k] = list()
-                stanzas[k].append(v)
-            for id in stanzas.iterkeys():
-                self._experiments[id] = MdbExp(id, self, stanzas[id])
-            return self._experiments
-    
-    def __init__(self, filepath):
-        ra.RaFile.__init__(self)
-        self.read(filepath)
-        
-    def readStanza(self, stanza, key=None):
-        entry = MdbStanza(self)
-        if entry.readStanza(stanza, key) == None:
-            return None, None, None
-        val1, val2 = entry.readStanza(stanza, key)
-        return val1, val2, entry
-
-    def expIdRange(self, expIds):
-        '''
-        Takes in a list of strings, and returns a list containing the 
-        valid range of expId keys that the inputted range encompasses.
-        '''
-        ids = dict()
-        tempids = list()
-        for id in expIds:
-            if '-' in id:
-                start, end = id.split('-', 1)
-                tempids.extend(range(int(start), int(end) + 1))
-            else:
-                tempids.append(int(id))
-        for id in tempids:
-            if str(id) in self.experiments.keys():
-                ids.append(str(id))
-        return ids
-        
-class MdbStanza(ra.RaStanza):
-    
-    @property
-    def title(self):
-        '''The expVars catted together, making the title used for GEO'''
-        try:
-            return self._title
-        except AttributeError:
-            expVars = self._parent.expVars
-            if expVars[0] in self:
-                self._title = self[expVars[0]].replace('-m', '')
-            else:
-                self._title = None
-            for expVar in expVars[1:len(expVars)]:
-                if expVar in self and self[expVar] != 'None':
-                    self._title += '_' + self[expVar]
-            return self._title
-        
-    def __init__(self, parent):
-        ra.RaStanza.__init__(self)
-        self._parent = parent
-        
-    def __setitem__(self, key, value):
-        ordereddict.OrderedDict.__setitem__(self, key, value)
-        ordereddict.OrderedDict.sort(self)
-        ordereddict.OrderedDict.reorder(self, 0, 'metaObject')
-        ordereddict.OrderedDict.reorder(self, 1, 'objType')
-        
-class MdbExp(list):
-    '''
-    Describes a single experiment ID, which has a collection of its stanzas as
-    well as some additional data that should typically be consistent across all
-    the stanzas, as well as verifying that the data is in fact consistent.
-    '''
-    
-    @property
-    def name(self):
-        return self._id
-        
-    @property
-    def title(self):
-        try:
-            return self._title
-        except AttributeError:
-            self._title = None
-            for s in self.normalStanzas:
-                if self._title == None:
-                    self._title = s.title
-                elif self._title != s.title:
-                    self._title = None
-                    break
-            return self._title
-        
-    @property
-    def dataType(self):
-        '''The data type of the experiment. 'None' if inconsistent.'''
-        try:
-            return self._dataType
-        except AttributeError:
-            self._dataType = None
-            for s in self.normalStanzas:
-                if 'dataType' in s:
-                    if self._dataType == None:
-                        self._dataType = encode.dataTypes[s['dataType']]
-                    elif self._dataType.name != s['dataType']:
-                        self._dataType = None
-                        break
-            return self._dataType
-    
-    @property
-    def normalStanzas(self):
-        '''Returns the list of stanzas without revoked items'''
-        try:
-            return self._normal
-        except AttributeError:
-            self._normal = list()
-            for s in self:
-                if 'objStatus' not in s:
-                    self._normal.append(s)
-            return self._normal
-                
-    
-    def __init__(self, id, parent, stanzas):
-        list.__init__(self)
-        self.extend(stanzas)
-        self._id = id
-        self._parent = parent