a44e3254174152b2d4b3f241d1935654cd139181
vsmalladi
  Tue May 8 10:11:21 2012 -0700
Renamed library from ucscgenomics to ucscGb. Redmine #7029.
diff --git python/lib/ucscGb/mdb.py python/lib/ucscGb/mdb.py
new file mode 100644
index 0000000..5c53cc5
--- /dev/null
+++ python/lib/ucscGb/mdb.py
@@ -0,0 +1,182 @@
+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