def initFromDatabase(self, identifier, connection):
""" method for initialising labResourceList from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "labResourceList", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "labResourceList",
self.databaseFields['obid'])
# for this object type we need to get the members of the list
sql = "select labresourceob from labresourcelistmembershiplink where labresourcelist = %s " % self.databaseFields[
'obid']
#print "executing " + sql
obCursor = connection.cursor()
obCursor.execute(sql)
obFieldValues = obCursor.fetchall()
self.databaseFields.update(
{'labresources': [item[0] for item in obFieldValues]})
obCursor.close()
self.obState.update({
'ERROR': 0,
'NEW': 0,
'DB_PENDING': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising bioLibraryOb from database """
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "bioLibraryOb", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "bioLibraryOb", self.databaseFields['obid'])
def initFromDatabase(self, identifier, connection):
""" method for initialising sequencealignmentfact from database """
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "sequenceAlignmentFact", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "sequenceAlignmentFact", self.databaseFields['obid'])
def initFromDatabase(self, identifier, connection):
""" method for initialising geneticob from database """
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "bioSequenceFeatureFact", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "bioSequenceFeatureFact", self.databaseFields['obid'])
def initFromDatabase(self, identifier, connection):
""" method for initialising geneticob from database """
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "bioSequenceOb", connection)
# now get the complete object
# self.databaseFields = getObjectRecord(connection, "bioSequenceOb", self.databaseFields['obid'])
# replace this with a method that handles large sequences
sql = """
select
obid ,
obtypeid ,
xreflsid ,
createddate ,
createdby ,
lastupdateddate ,
lastupdatedby ,
checkedout ,
checkedoutby ,
checkoutdate ,
obkeywords ,
statuscode ,
sequencename ,
sequencetype ,
sequencedescription,
sequencetopology ,
seqlength ,
sequenceurl ,
seqcomment ,
gi ,
fnindex_accession ,
fnindex_id
from biosequenceob where obid = %(obid)s
"""%self.databaseFields
obCursor = connection.cursor()
obCursor.execute(sql)
obFieldValues = obCursor.fetchone()
if obCursor.rowcount != 1:
raise brdfException, "getObjectRecord : unable to find one unique object using " + sql
fieldNames = [item[0] for item in obCursor.description]
self.databaseFields = dict(zip(fieldNames,obFieldValues))
# if the sequence is not too long then get that as well
if self.databaseFields['seqlength'] > self.MAX_INLINE_SEQUENCE_LENGTH:
self.databaseFields["seqstring"] = "( ** only sequences of length less than %s are displayed inline in this panel - click View | asFasta or View | asGenbank to view sequence ** )"%self.MAX_INLINE_SEQUENCE_LENGTH
else:
sql = """select seqstring from biosequenceob where obid = %(obid)s"""%self.databaseFields
obCursor = connection.cursor()
obCursor.execute(sql)
obFieldValues = obCursor.fetchone()
self.databaseFields["seqstring"] = obFieldValues[0]
obCursor.close()
# get any column alises that have been defined
if self.columnAliases == None:
self.columnAliases = getColumnAliases(connection, "bioSequenceOb")
def initFromDatabase(self, identifier, connection):
""" method for initialising workFlowStageOb from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "workFlowStageOb", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "workFlowStageOb",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising an object from database"""
# initialise base fields from ob table
ob.initFromDatabase(self, identifier, "batchOb", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "batchOb",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising an object from database - arg can be an integer obid, or a string importProcedureName"""
# initialise base fields from ob table
ob.initFromDatabase(self, identifier, "bioSubjectOb", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "bioSubjectOb",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising microarraySpotFact from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "microarraySpotFact", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "microarraySpotFact",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'MESSAGE': "initialised from database OK"
})
# obtain display procedures that are linked to the parent study object , and have the virtual flag set
sql = """
select
df.invocation,
df.functioncomment,
dp.xreflsid,
dp.procedurename,
ds.datasourcename,
ds.physicalsourceuri,
ds.datasourcetype,
df.voptypeid
from
(displayfunction df join displayprocedureob dp on
df.displayprocedureob = dp.obid) left outer join
datasourceob ds on ds.obid = df.datasourceob
where
df.ob = %(labresourceob)s and
df.voptypeid is not null
"""
labresourcemodulelogger.info(
'executing SQL to retrieve virtual dynamic display functions : %s'
% str(sql % self.databaseFields))
displayCursor = connection.cursor()
displayCursor.execute(sql, self.databaseFields)
self.virtualDisplayFunctions = displayCursor.fetchall()
labresourcemodulelogger.info(str(self.virtualDisplayFunctions))
if displayCursor.rowcount > 0:
self.obState.update({
'VIRTUAL_DYNAMIC_DISPLAYS':
displayCursor.rowcount,
'MESSAGE':
"virtual dynamic displays initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising namedListMembershipLink from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "namedListMembershipLink",
connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection,
"namedListMembershipLink",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'DB_PENDING': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self, identifier, connection):
""" method for initialising geneExpressionExperimentSeriesFact from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier,
"geneExpressionExperimentSeriesFact", connection)
# now get the complete object
self.databaseFields = getObjectRecord(
connection, "geneExpressionExperimentSeriesFact",
self.databaseFields['obid'])
self.obState.update({
'ERROR': 0,
'NEW': 0,
'DB_PENDING': 0,
'MESSAGE': "initialised from database OK"
})
def initFromDatabase(self,
identifier,
connection,
startAtItem=0,
maxItems=15,
asSet=True):
""" method for initialising predicateLink from database"""
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "predicateLink", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "predicateLink",
self.databaseFields['obid'])
self.obState.update({
'NEW': 0,
'DB_PENDING': 0,
'MESSAGE': "init from database OK"
})
def initFromDatabase(self,
identifier,
connection,
startAtItem=0,
maxItems=15,
asSet=True):
""" method for initialising list from database,
The asSet option causes the list to prune identical obids after loading - i.e. so that it ends
up being a set (no duplcates) rather than a list. This is
mainly as a workaround for the lack of adequate array support in the current postgres
database - in version 8.0.3 we can easily and efficiently ensure that we do not insert duplicate
obids into a list, however this code does not work in 7.4.3 - the array assignments execute without
error , however the code using these assignments does not produce expected results. Once the db is upgraded , then
code like this can be used in the search function :
create function testarray(integer) returns integer as '
declare
intarg alias for $1;
intarray int[];
result int;
begin
intarray[0] := 2;
intarray[1] := 4;
intarray[2] := 6;
intarray[3] := 8;
if not intarg = ANY(intarray) then
result = intarg;
else
result = 0;
end if;
return result;
END;
' LANGUAGE plpgsql;
(note that it is assumed we can't use naive SQL to avoid duplicate entries .....insert into .... and not in ....
due to the potential performance problems this would cause.
"""
self.chunkSize = maxItems
# first init base class - this will get obid
ob.initFromDatabase(self, identifier, "obList", connection)
# now get the complete object
self.databaseFields = getObjectRecord(connection, "obList",
self.databaseFields['obid'])
# for this object type we need to get the members of the list. We get the obid and listorder for
# up to maxItems members of the list, in the order specified by listOrder.
#sql = "select l.ob,l.listorder,o.xreflsid from ob o,listmembershiplink l where l.oblist = %s and l.listorder >= %s and o.obid = l.ob order by listorder" % (self.databaseFields['obid'],maxItems)
if not asSet:
sql = """
select
l.ob,
l.listorder,
l.obxreflsid,
l.membershipcomment
from
listmembershiplink l
where
l.oblist = %s and
l.listorder >= %s
order by listorder""" % (self.databaseFields['obid'],
startAtItem)
else:
sql = """
select
l.ob,
l.listorder,
l.obxreflsid,
l.membershipcomment
from
listmembershiplink l
where
l.oblist = %s
order by listorder""" % (self.databaseFields['obid'])
listmodulelogger.info("list executing %s" % sql)
obCursor = connection.cursor()
obCursor.execute(sql)
if not asSet:
obFieldValues = obCursor.fetchall()
self.databaseFields.update({
'alllistitems': [(item[0], item[1], item[2], item[3])
for item in obFieldValues]
})
#obFieldValues = obCursor.fetchmany(maxItems)
self.databaseFields.update({
'listitems': [(item[0], item[1], item[2], item[3])
for item in obFieldValues[0:maxItems]]
})
self.obState.update({'LIST_MODE': 'LIST'})
else:
# if we are to make a set , then do so. A problem is that we do not know the size of the
# set (as a set rather than as a list) - but this is needed by the user interface to
# figure out how many pages to display - so need to get wholelist
listmodulelogger.info("creating a set ")
setDict = {}
row = obCursor.fetchone()
listmodulelogger.info("row count = %d" % obCursor.rowcount)
listmodulelogger.info("fetched %s" % str(row))
self.databaseFields['alllistitems'] = []
# update 5/2012 - psycopg driver leaves rowcount set to
# 1 when fetching past the last record :-(
#while obCursor.rowcount == 1
while obCursor.rowcount >= 1 and row != None:
item = tuple(row)
self.databaseFields['alllistitems'].append(item)
setDict[item[0]] = (item[1], item[2], item[3])
row = obCursor.fetchone()
# sort the set by list order and get a chunk, starting from startAtItem
listmodulelogger.info(
"sorting and selecting bookmarks > %s chunk size %s" %
(startAtItem, maxItems))
setKeys = setDict.keys()
setKeys.sort(lambda x, y: setDict[x][0] - setDict[y][0])
chunkDict = {}
for i in range(0, len(setDict)):
#listmodulelogger.info("checking %s"%str(setDict[setKeys[i]]))
if (int(setDict[setKeys[i]][0]) >=
int(startAtItem)) and (len(chunkDict) < maxItems):
#listmodulelogger.info("selecting %s"%str(setDict[setKeys[i]]))
chunkDict[setKeys[i]] = setDict[setKeys[i]]
#listmodulelogger.info(str(chunkDict))
self.databaseFields.update({
'listitems':
[(key, chunkDict[key][0], chunkDict[key][1], chunkDict[key][2])
for key in chunkDict.keys()],
'currentmembership':
len(setDict)
})
self.obState.update({'LIST_MODE': 'SET'})
obCursor.close()
self.obState.update({
'ERROR': 0,
'NEW': 0,
'MESSAGE': "initialised from database OK"
})
