b20b5da970264162002689608d4f412a7f640c30
wong
  Tue Dec 13 12:11:28 2011 -0800
corrected an error in morgan's modification
diff --git python/lib/ucscgenomics/ra.py python/lib/ucscgenomics/ra.py
index f8e44ba..d0f087f 100644
--- python/lib/ucscgenomics/ra.py
+++ python/lib/ucscgenomics/ra.py
@@ -1,487 +1,488 @@
 import sys
 import re
 from ucscgenomics.ordereddict import OrderedDict
 import collections
 
 class RaFile(OrderedDict):
     '''
     Stores a Ra file in a set of entries, one for each stanza in the file.
 
     To make a RaFile, it is usually easiest to just pass it's path:
         rafile = ra.RaFile('kent/src/hg/.../wgEncodeSomeRaFile.ra')
 
     The data is read in and organized as a collection of stanzas. Ra files
     store the stanza by it's name, so to access a specific stanza, say:
         somestanza = rafile['wgEncodeSomeStanzaName']
 
     Once you have a stanza, you may want specific data about that stanza.
     Stanzas are, as ra files, organized as a collection of terms. Therefore
     to get the description of the stanza, we can say:
         somedescription = somestanza['description']
 
     You can also access a stanza's name from the stanza itself, since by the
     nature of ra files, the first key is it's name. Therefore for most ra
     files the following holds true:
         somestanza.name = somestanza['metaObject'] = 'wgEncodeSomeStanzaName'
 
     Although the above is useful if you want one thing, it's usually more
     helpful to be able to loop and query on the stanza. To add a term named
     'foobar' to every stanza in a ra file:
         for stanza in rafile.values():
             stanza['foobar'] = 'some value'
 
     Note that I iterated over values. It can also be useful to iterate over
     a stanza's keys:
         for key in rafile.keys():
             print key
 
     Note that ra files are order preserving. Added entries are appended to the
     end of the file. This allows you to print out a ra file easily:
         print rafile
 
     Most of the time you don't want to do something with all stanzas though,
     instead you want to filter them. The included filter method allows you to
     specify two functions (or lambda expressions). The first is the 'where'
     predicate, which must take in one stanza, and return true/false depending
     on whether you want to take that stanza. The second is the 'select'
     predicate, which takes in the stanza, and returns some subset or superset
     of the stanza as a list. Using filter is preferable to for loops where
     there are no side effects, or to filter data before iterating over it as
     opposed to using if statements in the loop. To get all stanzas with one
     experiment ID for instance, we would do something like this:
         stanzas = rafile.filter(lambda s: s['expId'] == '123', lambda s: s)
 
     Note that you don't have to ensure 'expId' is in the stanza, it will
     silently fail. Let's look at another example, say you want to find all
     stanza's with an geoSampleAccession that are also fastq's
         submittedfastqs = rafile.filter(
             lambda s: 'geoSampleAccession' in s and s['fileName'].endswith('.fastq'),
             lambda s: s)
 
     We don't always have to just return the stanza in the second parameter
     however. If we wanted to, for each stanza, return the file associated
     with that stanza, we could easily do that as well. This would return a
     simple list of the string filenames in a ra file:
         files = rafile.filter(lambda s: 1, lambda s: s['fileName'])
 
     Note that once again, we don't have to ensure 'fileName' exists. Also note
     that lambda s: 1 means always return true. Lambda expressions are always
     preferable to functions unless the expression would need to be reused
     multiple times. It is also best to reduce the set of stanzas as much as
     possible before operating over them.
 
     Filtering allows you to eliminate a lot of code.
     '''
 
-    def __init__(self, filePath=None):
+    def __init__(self, filePath=None, key=None):
         OrderedDict.__init__(self)
         if filePath != None:
-            self.read(filePath)
+            self.read(filePath, key)
 
     def read(self, filePath, key=None):
         '''
         Reads an rafile stanza by stanza, and internalizes it.
         '''
 
         file = open(filePath, 'r')
 
         #entry = None
         stanza = list()
         keyValue = ''
 
         reading = 1
         
         while reading:
             line = file.readline()
             if line == '':
                 reading = 0
         
             line = line.strip()
-
             if len(stanza) == 0 and (line.startswith('#') or (line == '' and reading)):
                 OrderedDict.append(self, line)
                 continue
 
             if line != '':
                 stanza.append(line)
             elif len(stanza) > 0:
                 if keyValue == '':
                     keyValue, name, entry = self.readStanza(stanza, key)
                 else:
                     testKey, name, entry = self.readStanza(stanza, key)
                     if entry != None and keyValue != testKey:
                         raise KeyError('Inconsistent Key ' + testKey)
 
                 if entry != None:
                     if name != None or key == None:
                         if name in self:
                             raise KeyError('Duplicate Key ' + name)
                         self[name] = entry
 
                 stanza = list()
 
         file.close()
 
 
     def readStanza(self, stanza, key=None):
         entry = RaStanza()
+        if entry.readStanza(stanza, key) == None:
+            return None, None, None
         val1, val2 = entry.readStanza(stanza, key)
         return val1, val2, entry
 
 
     def iter(self):
         pass
 
 
     def iterkeys(self):
         for item in self._OrderedDict__ordering:
             if not(item.startswith('#') or item == ''):
                 yield item
 
 
     def itervalues(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield self[item]
 
 
     def iteritems(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield item, self[item]
             else:
                 yield [item]
 
 
     def append(self, item):
         OrderedDict.append(self, item)
 
 
     def filter(self, where, select):
         '''
         select useful data from matching criteria
 
         where: the conditional function that must be met. Where takes one
         argument, the stanza and should return true or false
         select: the data to return. Takes in stanza, should return whatever
         to be added to the list for that stanza.
 
         For each stanza, if where(stanza) holds, it will add select(stanza)
         to the list of returned entities. Also forces silent failure of key
         errors, so you don't have to check that a value is or is not in the stanza.
         '''
 
         ret = list()
         for stanza in self.itervalues():
             try:
                 if where(stanza):
                     ret.append(select(stanza))
             except KeyError:
                 continue
         return ret
 
     def filter2(self, where):
         '''
         select useful data from matching criteria
         Filter2 returns a Ra dictionary. Easier to use but more memory intensive.
 
         where: the conditional function that must be met. Where takes one
         argument, the stanza and should return true or false
         select: the data to return. Takes in stanza, should return whatever
         to be added to the list for that stanza.
 
         For each stanza, if where(stanza) holds, it will add select(stanza)
         to the list of returned entities. Also forces silent failure of key
         errors, so you don't have to check that a value is or is not in the stanza.
         '''
         ret = RaFile()
         for stanza in self.itervalues():
             try:
                 if where(stanza):
                         ret[stanza.name] = stanza
             except KeyError:
                 continue
         return ret
 
     def summaryDiff(self,other):
         '''
         Input:
             RaFile object being compared.
         Output: RaFile with differences.
 
         Returns ***partial*** stanzas of ***anything*** different
         from the self dictionary compared to the other dictionary.
         For versatility, it only returns stanzas from the self Ra file. In other
         words, it returns the self dictionary lines that are either not present
         in or different from the other dictionary.
 
         To obtain full set of differences, run summaryDiff twice
         ra1 = this.summaryDiff(that)
         and
         ra2 = that.summaryDiff(this)
         '''
         this = RaFile()
         RetThis = RaFile()
         for stanza in self.itervalues():
             if stanza.name not in other.keys():
                 RetThis[stanza.name] = stanza
             else:
                 if stanza.difference(other[stanza.name]):
                     RetThis[stanza.name] = stanza.difference(other[stanza.name])
         return RetThis
 
     def changeSummary(self, otherRa):
         '''
         Input:
             Two RaFile objects
         Output:
             Dictionary showing differences between stanzas, list of added and dropeed stanzas
         '''
         retDict = collections.defaultdict(list)
         dropList = set(self.iterkeys()) - set(otherRa.iterkeys())
         addList = set(otherRa.iterkeys()) - set(self.iterkeys())
         common = set(self.iterkeys()) & set(otherRa.iterkeys())
 
         p = re.compile('^\s*#')
         for stanza in common:
             if p.match(stanza):
                 continue
             for key in self[stanza]:
                 if p.match(key):
                     continue
                 if key in otherRa[stanza]:
                     if self[stanza][key] != otherRa[stanza][key]:
                         retDict[stanza].append("Changed %s from  %s -> %s" %(key, self[stanza][key], otherRa[stanza][key]))
                 else:
                     retDict[stanza].append("Added %s -> %s" %(key, self[stanza][key]))
             for key in otherRa[stanza]:
                 if p.match(key):
                     continue
                 if key not in self[stanza]:
                     retDict[stanza].append("Dropped %s -> %s" %(key, otherRa[stanza][key]))
         return retDict, dropList, addList
 
     def diffFilter(self, select, other):
         '''
         Input:
             Lambda function of desired comparison term
             RaFile object being compared.
         Output: RaFile with differences.
 
         Filter returns ***full*** stanzas of a ***select function*** from
         the self dictionary compared to the other dictionary. For
         versatility, it only returns stanzas from the self Ra file. In other
         words, it only returns self dictionary stanzas with the function term
         that are either not found in or different from the other
         dictionary.
 
         To obtain full set of differences, run diffFilter twice
         ra1 = this.diffFilter(select function, that)
         and
         ra2 = that.diffFilter(select function, this)
         '''
         this = RaFile()
         RetThis = RaFile()
         thisSelectDict = dict()
         thatSelectDict = dict()
         #Build 2 dict of stanzas to later compare line-by-line
         for stanza in self.itervalues():
             try:
                 if select(stanza):
                     this[stanza.name] = stanza #'this' only records stanzas of the self dict
                     thisSelectDict[stanza.name] = select(stanza)
             except KeyError:
                 continue
         for stanza in other.itervalues():
             #Exact code as filter2 but kept for clarity.
             try:
                 if select(stanza):
                     thatSelectDict[stanza.name] = select(stanza)
             except KeyError:
                 continue
         #Compare this and that dict
         for stanza in this.itervalues():
             if stanza.name not in thatSelectDict:
                 RetThis[stanza.name] = stanza
             elif thisSelectDict[stanza.name] != thatSelectDict[stanza.name]:
                 RetThis[stanza.name] = stanza
         return RetThis
 
     def updateDiffFilter(self, term, other):
         '''
         Replicates updateMetadata.
         Input:
             Term
             Other raFile
 
         Output:
             Merged RaFile
                 Stanzas found in 'self' and 'other' that have the 'Term' in 'other'
                 are overwritten (or inserted if not found) into 'self'. Final merged
                 dictionary is returned.
         '''
         ret = self
         common = set(self.iterkeys()) & set(self.iterkeys())
         for stanza in common:
             if term not in self[stanza] and term not in other[stanza]:
                 continue
             if term in self[stanza] and term not in other[stanza]:
                     del ret[stanza][term]
                     continue
 
             if term in other[stanza]:
                 #Remake stanza to keep order of terms
                 tempStanza = RaStanza()
                 tempStanza._name = stanza
                 try:
                     tempStanza['metaObject'] = self[stanza]['metaObject']
                     tempStanza['objType'] = self[stanza]['objType']
                     termList = self[stanza].keys()
                     termList.remove('metaObject')
                     termList.remove('objType')
                 except KeyError:
                     termList = self[stanza].keys()
                 if term not in termList:
                     termList.append(term)
                 for t in sorted(termList, key=str.lower):
                     if t == term:
                         if t not in self[stanza]:
                             tempStanza[t] = other[stanza][t]
                         elif self[stanza][t] != other[stanza][t]:
                             tempStanza[t] = other[stanza][t]
                         else:
                             tempStanza[t] = self[stanza][t]
                     else:
                         tempStanza[t] = self[stanza][t]
                 ret[stanza] = tempStanza
 
         return ret
 
     def __str__(self):
         str = ''
         for item in self.iteritems():
             if len(item) == 1:
                 str += item[0].__str__() + '\n'
             else:
                 str += item[1].__str__() + '\n'
         return str #.rsplit('\n', 1)[0]
 
 
 class RaStanza(OrderedDict):
     '''
     Holds an individual entry in the RaFile.
     '''
 
     def __init__(self):
         self._name = ''
         self._nametype = ''
         OrderedDict.__init__(self)
 
     @property
     def name(self):
         return self._name
 
 
     def readStanza(self, stanza, key=None):
         '''
         Populates this entry from a single stanza
         '''
 
         for line in stanza:
             self.readLine(line)
 
         return self.readName(stanza, key)
 
 
     def readName(self, stanza, key=None):
         '''
         Extracts the Stanza's name from the value of the first line of the
         stanza.
         '''
         
         if key == None:
             line = stanza[0]
         else:
             line = None
             for s in stanza:
                 if s.split(' ', 1)[0] == key:
                     line = s
                     break
             if line == None:
                 return None
         
         if len(line.split(' ', 1)) != 2:
             raise ValueError()
 
         names = map(str.strip, line.split(' ', 1))
         self._nametype = names[0]
         self._name = names[1]
         return names
 
     def readLine(self, line):
         '''
         Reads a single line from the stanza, extracting the key-value pair
         '''
 
         if line.startswith('#') or line == '':
             OrderedDict.append(self, line)
         else:
             raKey = line.split(' ', 1)[0]
             raVal = ''
             if (len(line.split(' ', 1)) == 2):
                 raVal = line.split(' ', 1)[1]
             #if raKey in self:
                 #raise KeyError(raKey + ' already exists')
             self[raKey] = raVal
 
     def difference(self, other):
         '''
         Complement function to summaryDiff.
         Takes in self and a comparison Stanza.
         Returns new stanza with terms from 'self' that are different from 'other'
         Like the summaryDiff, to get the other terms, this needs to be run
         again with self and other switched.
         '''
         retRa = RaStanza()
         retRa._name = self.name
         for key in other.keys():
             try:
                 if other[key] != self[key] and not key.startswith('#'):
                     retRa[key] = self[key]
             except KeyError:
                 continue
                 #maybe add empty keys
         return retRa
 
     def iterkeys(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield item
 
 
     def itervalues(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield self[item]
 
 
     def iteritems(self):
         for item in self._OrderedDict__ordering:
             if not (item.startswith('#') or item == ''):
                 yield item, self[item]
 
 
     def iter(self):
         iterkeys(self)
 
         
     def __str__(self):
         str = ''
         for key in self:
             if key.startswith('#'):
                 str += key + '\n'
             else:
                 str += key + ' ' + self[key] + '\n'
 
         return str