pygr/xnestedlist.py

   1 import cnestedlist
   2 from nlmsa_utils import EmptySliceError,EmptySlice
   3 import sequence
   4
   5 class NLMSAServer(cnestedlist.NLMSA):
   6     'serves NLMSA via serializable method calls for XMLRPC'
   7     xmlrpc_methods={'getSlice':0,'getInfo':0}
   8     def getSlice(self,seqID,start,stop):
   9         'perform an interval query and return results as raw ivals'
  10         try:
  11             seq=self.seqDict[seqID]
  12             nlmsa_id,ns,offset=self.seqs[seq] # GET UNION INFO FOR THIS SEQ
  13         except KeyError:
  14             return '' # failure code
  15         ival=sequence.absoluteSlice(seq,start,stop) # GET THE INTERVAL
  16         try:
  17             myslice=self[ival] # DO THE QUERY
  18         except EmptySliceError:
  19             return 'EMPTY'
  20         except KeyError:
  21             return ''  # FAILURE CODE
  22         ivals=myslice.rawIvals() # GET RAW INTERVAL DATA
  23         d={}
  24         d[nlmsa_id]=self.seqs.IDdict[str(nlmsa_id)] # SAVE INDEX INFO FOR SOURCE SEQ
  25         for v in ivals: # SAVE INDEX INFO FOR TARGET SEQS
  26             id=v[2] # target_id NLMSA_ID
  27             if not self.seqlist.is_lpo(id): # ONLY NON-LPO SEQS STORED IN THIS INDEX
  28                 d[id]=self.seqs.IDdict[str(id)]
  29         l=[(key,val) for key,val in d.items()] # XMLRPC CAN'T HANDLE int DICT, SO USE LIST
  30         return nlmsa_id,ivals,l # LIST OF ALIGNED IVALS, LIST OF (nlmsa_id,(seqID,nsID))
  31     def getInfo(self):
  32         'return list of tuples describing NLMSASequences in this NLMSA'
  33         l=[]
  34         for ns in self.seqlist:
  35             l.append((ns.id,ns.is_lpo,ns.length,ns.is_union))
  36         return l
  37
  38
  39 class NLMSAClient(cnestedlist.NLMSA):
  40     'client for accessing NLMSAServer via XMLRPC'
  41     def __init__(self,url=None,name=None,idDictClass=dict,**kwargs):
  42         cnestedlist.NLMSA.__init__(self,mode='xmlrpc',idDictClass=idDictClass,**kwargs)
  43         import coordinator
  44         self.server=coordinator.get_connection(url,name) # GET CONNECTION TO THE SERVER
  45         self.url=url
  46         self.name=name
  47         l=self.server.getInfo() # READ NS INFO TABLE
  48         for nsID,is_lpo,nsLength,is_union in l:
  49             ns=cnestedlist.NLMSASequence(self,None,None,'onDemand',is_union,nsLength) # is_lpo AUTOMATIC
  50             self.addToSeqlist(ns) # ADD THIS TO THE INDEX
  51     def close(self):
  52         pass # required interface, but nothing to do
  53     def doSlice(self,seq):
  54         'getSlice from the server, and create an NLMSASlice object from results'
  55         result=self.server.getSlice(self.seqs.getSeqID(seq),seq.start,seq.stop)
  56         if result=='':
  57             raise KeyError('this interval is not aligned!')
  58         elif result == 'EMPTY':
  59             raise EmptySliceError
  60         id,l,d=result
  61         for nlmsaID,(seqID,nsID) in d: # SAVE SEQ INFO TO INDEX
  62             self.seqs.saveSeq(seqID,nsID,0,nlmsaID)
  63         return id,l # HAND BACK THE RAW INTEGER INTERVAL DATA
  64     def __getitem__(self,k):
  65         'directly call slice without any ID lookup -- will be done server-side'
  66         try:
  67             return cnestedlist.NLMSASlice(self.seqlist[0],k.start,k.stop,-1,-1,k)
  68         except EmptySliceError:
  69             return EmptySlice(k)
  70     def __getstate__(self):
  71         return dict(url=self.url,name=self.name,seqDict=self.seqDict)
  72
  73