Beispiel #1
0
def persist(req):
    jsondata = req.REQUEST.get("data")
    initdata = json.loads(jsondata)
    logger.debug("Persisting")
    logger.debug("%s" % (initdata))
    fileutil.writeFile("test1", jsondata)

    try:
        if (initdata['_id'][:4] == 'conn'):
            con = Connection(initdata)
            con.save()
            return SmartResponse(con._id, req)
        else:
            network = Network(initdata)
            network.save()
            index(network.name, network)
            return SmartResponse(network._id, req)
    except Error as e:
        logger.error("Error saving data: %s" % traceback.format_exc())
        return SmartResponse(e, req)
Beispiel #2
0
def persist(req):
    jsondata = req.REQUEST.get("data")
    initdata = json.loads(jsondata)
    logger.debug("Persisting")    
    logger.debug( "%s" % (initdata) )
    fileutil.writeFile("test1", jsondata)
        
    try:
        if(initdata['_id'][:4] == 'conn'):
            con = Connection(initdata)
            con.save()
            return SmartResponse(con._id, req)            
        else:    
            network = Network(initdata)
            network.save()
            index(network.name, network)
            return SmartResponse(network._id, req)    
    except Error as e:
        logger.error("Error saving data: %s" %traceback.format_exc())
        return SmartResponse(e, req)
Beispiel #3
0
def importEdges(filename=None):
    """
    import edges, one pair per line 
    Edge property: - no direction, -> left to right, <- right to left
    """
    filename = filename or r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'

    # add a network
    n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
    n.name = "GBM Predicted Tumor Network"
    n.group = "predicted"
    n.owner = 'precon'
    n.save()

    col = mongo.db()['entity']
    count = 0
    now = time.time()
    ec = mongo.getCollection('edge')
    with open(filename) as f:
        content = f.read()
        for line in content.split('\n'):
            doc = {}
            line = line.strip()
            pos = line.find("///")
            if pos > 0:
                line = line[0:pos].strip()
                doc['comment'] = line[pos:]

            items = line.split("->")
            if (len(items) == 1): items = line.split("<-")
            if (len(items) == 1): items = line.split(" - ")
            if (len(items) == 1):
                error("Ignore invalid line: [%s]" % line)
                continue
            count += 1
            if (count < 8378): continue

            tmp = []
            tmp.append(items[0].lower().strip())
            tmp.append(items[1].lower().strip())
            entities = ['', '']
            print "!!! %d " % (col.find({'symbol': {'$in': tmp}}).count())
            for r in col.find({'symbol': {'$in': tmp}}):
                if (r['symbol'] == tmp[0]):
                    entities[0] = Entity(r)
                if (r['symbol'] == tmp[1]):
                    entities[1] = Entity(r)

            if (len(entities) != 2):
                raise "Invalid nodes %s, continue" % entities

            node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id})
            if not node1:
                node1 = Node({'network': n._id}, entities[0])
                node1.save()
            node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id})
            if not node2:
                node2 = Node({'network': n._id}, entities[1])
                node2.save()

            con = Connection()
            con._id = "conn_%s_%s" % (tmp[0], tmp[1])
            con.nodes = [node1._id, node2._id]
            con.entities = [entities[0]._id, entities[1]._id]
            con.type = 'predicted'
            con.network = n._id
            con.label = ""
            con.save()

            print "Saving connection %d %s" % (count, con._id)

    finish = time.time()
    print "Imported %d edges, time elpased %d seconds" % (count, finish - now)
Beispiel #4
0
	def load(self):
		
		self.columnIndexes = {}
		headers = self.rows.next()
		for i in range (len(headers)):
			col = headers[i]
			if col not in SUPPORTED_COLUMNS:
				raise Exception("Invalid column: %s. Accepted columns are: %s" %(col, SUPPORTED_COLUMNS))
			self.columnIndexes[col] = i
			
		#networks, connections, entities, nodes
		entities = {}
		nodes = {}
		networks = {}
		
		for row in self.rows:
			entityA = None
			dbid = 	self.getCol('NodeA_DBID',row )
			if dbid:
				dbid = dbid.lower()
				_id = 'enti_%s' %dbid			
				if _id not in entities: 				
					entityA = Entity()
					entityA._id = _id
					entityA.dbref = {}
					pair = dbid.split(':')							
					if(len(pair)!=2): 
						self._error("Invalid NodeA_DBID: %s" %dbid)
						continue	
					entityA.dbref[pair[0]] = pair[1]			
					entityA.group = self.getCol('NodeA_Category',row)
					#entity.label = 'Metformin'
					entityA.name = self.getCol('NodeA',row)								
					entities[_id] = entityA
				else:
					entityA=entities[_id] 			
			#Node B
			entityB = None
			dbid = 	self.getCol('NodeB_DBID',row,  False)
			if dbid:
				dbid = dbid.lower()
				_id = 'enti_%s' %dbid			
				if _id not in entities: 				
					entityB = Entity()
					entityB._id = _id
					entityB.dbref = {}
					pair = dbid.split(':')
					if(len(pair)!=2): 
						self._error("Invalid NodeB_DBID: %s" %dbid)		
						continue						
					entityB.dbref[pair[0].strip()] = pair[1].strip()			
					entityB.group = self.getCol('NodeB_Category',row)
					#entity.label = 'Metformin'
					entityB.name = self.getCol('NodeB' ,row )
					entities[_id] = entityB
				else:
					entityB = entities[_id] 
				
			edgeType = self.getCol('Edge',row,  False)
			if not edgeType: continue
			con = Connection()
			con.type = edgeType
						
			nodeA = nodes[entityA._id] if entityA._id in nodes else self.newNode(entityA)  
			nodeB = nodes[entityB._id] if entityB._id in nodes else self.newNode(entityB)
			nodes[entityA._id] = nodeA
			nodes[entityB._id] = nodeB	
			con.entities=[entityA._id, entityB._id] # this is for search
			con.nodes = [nodeA._id, nodeB._id]		
			con._nodes = [nodeA, nodeB]
			
			
			con.refs = {}
			
			edgeRefs = self.getCol('Edge_Ref',row, False)
			if edgeRefs:
				# comma separated
				pairs = edgeRefs.split(",")
				if len(pairs) == 1: pairs = edgeRefs.split("\n")
				for p in pairs:
					pair = p.split(':')
					refs = pair[1].split(';')
					if len(refs) == 1: refs = pair[1]
					con.refs[pair[0].lower().strip()] = refs
			
			
			networkName = self.getCol('Network',row) or 'DEFAULT'
			network = networks[networkName] if networkName in networks else Network()
			network.name = networkName
			network.owner='peop_precon'
			networks[networkName]  = network
			
			network._connections = network._connections or []
			network._connections.append(con)
			
			con.network = network._id
			con.owner='precon'
		#TBD, error
		return networks, self.errors
Beispiel #5
0
def parseInteractions(dom,network):
	"""
	 <interaction id="678614" imexId="IM-12113-2">
                <names>
                    <shortLabel>pf1130-pf1128-2</shortLabel>
                    <fullName>Affinity purification by hydroxy apatite chromatography</fullName>
                </names>
                <xref>
                    <primaryRef refTypeAc="MI:0356" refType="identity" id="EBI-2507294" dbAc="MI:0469" db="intact"/>
                    <secondaryRef refType="imex source" id="MI:0469" dbAc="MI:0488" db="psi-mi"/>
                    <secondaryRef refTypeAc="MI:0662" refType="imex-primary" id="IM-12113-2" dbAc="MI:0670" db="imex"/>
                </xref>
                <experimentList>
                    <experimentRef>678502</experimentRef>
                </experimentList>
                <participantList>
                    <participant id="678615">
                        <names>
                            <shortLabel>n/a</shortLabel>
                        </names>
                        <xref>
                            <primaryRef refTypeAc="MI:0356" refType="identity" id="EBI-2507299" dbAc="MI:0469" db="intact"/>
                        </xref>
                        <interactorRef>678518</interactorRef>
                        <biologicalRole>
                            <names>
                                <shortLabel>unspecified role</shortLabel>
                                <fullName>unspecified role</fullName>
                            </names>
                            <xref>
                                <primaryRef refTypeAc="MI:0356" refType="identity" id="MI:0499" dbAc="MI:0488" db="psi-mi"/>
                                <secondaryRef refTypeAc="MI:0356" refType="identity" id="EBI-77781" dbAc="MI:0469" db="intact"/>
                                <secondaryRef refTypeAc="MI:0358" refType="primary-reference" id="14755292" dbAc="MI:0446" db="pubmed"/>
                            </xref>
                        </biologicalRole>
                        <experimentalRoleList>
                            <experimentalRole>
                                <names>
                                    <shortLabel>neutral component</shortLabel>
                                    <fullName>neutral component</fullName>
                                </names>
                                <xref>
                                    <primaryRef refTypeAc="MI:0356" refType="identity" id="MI:0497" dbAc="MI:0488" db="psi-mi"/>
                                    <secondaryRef refTypeAc="MI:0356" refType="identity" id="EBI-55" dbAc="MI:0469" db="intact"/>
                                    <secondaryRef refTypeAc="MI:0358" refType="primary-reference" id="14755292" dbAc="MI:0446" db="pubmed"/>
                                </xref>
                            </experimentalRole>
                        </experimentalRoleList>
                    </participant>
	"""
	ems = dom.getElementsByTagName("interaction")	
	connections  = []
	nodeCount = 0	
	for em in ems:
		#interactions.append(interaction)		
		participants =  em.getElementsByTagName("participant")
		con_nodes = []
		for p in  participants:
			node = Node()
			node.network = network._id
			nodeCount+=1
			node._id = "node%s_%d" %(node.network[4:], nodeCount)
			node.role = getText(p, "biologicalRole", "names", "shortLabel")
			#node.refs['intact'] = p.getAttribute("id")
			setPrimaryRef(p, node)			
			ref = getText(p, 'interactorRef')
			if ref: node.refs['entity'] = ref  # temporary
			con_nodes.append(node)
		
		connection = Connection()
		connection._id = "conn_intact_%s" % em.getAttribute("id")
		connection.refs={}
		setPrimaryRef(em, connection)
		connection.type=getText( em.getElementsByTagName("interactionType")[0], 'shortLabel')		
		connection.label = getText(em,'shortLabel')
		connection.network = network._id
		
		connection.nodes = con_nodes
		connections.append(connection)
				
	network.connections = connections
Beispiel #6
0
def importEdges(filename=None):
    """
    import edges, one pair per line 
    Edge property: - no direction, -> left to right, <- right to left
    """
    filename = filename or  r'C:\work\caida\Dropbox\precon\engineering\Contents\GBM_BN-Massaged.csv'    
    
    # add a network
    n = Network.findOne({'name': "GBM Predicted Tumor Network"}) or Network()
    n.name = "GBM Predicted Tumor Network"
    n.group = "predicted"
    n.owner = 'precon'
    n.save()
     
    
    col = mongo.db()['entity']
    count = 0
    now = time.time()
    ec = mongo.getCollection('edge')
    with open(filename) as f:
        content = f.read()        
        for line in content.split('\n'):
            doc  = {}
            line = line.strip()
            pos = line.find("///")            
            if pos>0: 
                line = line[0:pos].strip()
                doc['comment'] = line[pos:]
                             
            
            items = line.split("->")
            if (len(items) == 1): items = line.split("<-")
            if (len(items) == 1): items = line.split(" - ")
            if (len(items) == 1): 
                error("Ignore invalid line: [%s]" %line)
                continue
            count+=1
            if(count<8378): continue
            
            tmp =[]
            tmp.append( items[0].lower().strip())
            tmp.append( items[1].lower().strip())
            entities = ['','']
            print "!!! %d " %( col.find({'symbol': {'$in': tmp  } }).count() )
            for r in  col.find({'symbol': {'$in': tmp  } }):
                if(r['symbol'] == tmp[0]):
                    entities[0] = Entity(r)
                if(r['symbol'] == tmp[1]):
                    entities[1] = Entity(r)
            
            if(len(entities)!=2 ):
                raise "Invalid nodes %s, continue" % entities
            
            
            node1 = Node.findOne({'network': n._id, 'entity': entities[0]._id}) 
            if not node1:
                node1 = Node({'network':n._id}, entities[0])
                node1.save()
            node2 = Node.findOne({'network': n._id, 'entity': entities[1]._id}) 
            if not node2:
                node2 = Node({'network':n._id}, entities[1])
                node2.save()
            
         
            
            con = Connection()
            con._id  = "conn_%s_%s" %(tmp[0], tmp[1])
            con.nodes = [node1._id, node2._id]
            con.entities = [ entities[0]._id, entities[1]._id ] 
            con.type = 'predicted'
            con.network = n._id
            con.label = ""
            con.save()
                        
            
            print "Saving connection %d %s" % (count, con._id) 
            
    finish = time.time()
    print "Imported %d edges, time elpased %d seconds" %(count, finish - now)
Beispiel #7
0
def parseInteractions(dom, network):
    """
	 <interaction id="678614" imexId="IM-12113-2">
                <names>
                    <shortLabel>pf1130-pf1128-2</shortLabel>
                    <fullName>Affinity purification by hydroxy apatite chromatography</fullName>
                </names>
                <xref>
                    <primaryRef refTypeAc="MI:0356" refType="identity" id="EBI-2507294" dbAc="MI:0469" db="intact"/>
                    <secondaryRef refType="imex source" id="MI:0469" dbAc="MI:0488" db="psi-mi"/>
                    <secondaryRef refTypeAc="MI:0662" refType="imex-primary" id="IM-12113-2" dbAc="MI:0670" db="imex"/>
                </xref>
                <experimentList>
                    <experimentRef>678502</experimentRef>
                </experimentList>
                <participantList>
                    <participant id="678615">
                        <names>
                            <shortLabel>n/a</shortLabel>
                        </names>
                        <xref>
                            <primaryRef refTypeAc="MI:0356" refType="identity" id="EBI-2507299" dbAc="MI:0469" db="intact"/>
                        </xref>
                        <interactorRef>678518</interactorRef>
                        <biologicalRole>
                            <names>
                                <shortLabel>unspecified role</shortLabel>
                                <fullName>unspecified role</fullName>
                            </names>
                            <xref>
                                <primaryRef refTypeAc="MI:0356" refType="identity" id="MI:0499" dbAc="MI:0488" db="psi-mi"/>
                                <secondaryRef refTypeAc="MI:0356" refType="identity" id="EBI-77781" dbAc="MI:0469" db="intact"/>
                                <secondaryRef refTypeAc="MI:0358" refType="primary-reference" id="14755292" dbAc="MI:0446" db="pubmed"/>
                            </xref>
                        </biologicalRole>
                        <experimentalRoleList>
                            <experimentalRole>
                                <names>
                                    <shortLabel>neutral component</shortLabel>
                                    <fullName>neutral component</fullName>
                                </names>
                                <xref>
                                    <primaryRef refTypeAc="MI:0356" refType="identity" id="MI:0497" dbAc="MI:0488" db="psi-mi"/>
                                    <secondaryRef refTypeAc="MI:0356" refType="identity" id="EBI-55" dbAc="MI:0469" db="intact"/>
                                    <secondaryRef refTypeAc="MI:0358" refType="primary-reference" id="14755292" dbAc="MI:0446" db="pubmed"/>
                                </xref>
                            </experimentalRole>
                        </experimentalRoleList>
                    </participant>
	"""
    ems = dom.getElementsByTagName("interaction")
    connections = []
    nodeCount = 0
    for em in ems:
        #interactions.append(interaction)
        participants = em.getElementsByTagName("participant")
        con_nodes = []
        for p in participants:
            node = Node()
            node.network = network._id
            nodeCount += 1
            node._id = "node%s_%d" % (node.network[4:], nodeCount)
            node.role = getText(p, "biologicalRole", "names", "shortLabel")
            #node.refs['intact'] = p.getAttribute("id")
            setPrimaryRef(p, node)
            ref = getText(p, 'interactorRef')
            if ref: node.refs['entity'] = ref  # temporary
            con_nodes.append(node)

        connection = Connection()
        connection._id = "conn_intact_%s" % em.getAttribute("id")
        connection.refs = {}
        setPrimaryRef(em, connection)
        connection.type = getText(
            em.getElementsByTagName("interactionType")[0], 'shortLabel')
        connection.label = getText(em, 'shortLabel')
        connection.network = network._id

        connection.nodes = con_nodes
        connections.append(connection)

    network.connections = connections