Module Import alias identifier Import alias Import alias Import alias ImportFrom alias ImportFrom alias Import alias Assign NameStore Call AttributeLoad NameLoad attr Str Expr Str Assign NameStore Num Assign NameStore Num Assign NameStore Num Assign NameStore Num Assign NameStore Num Assign NameStore Num Assign NameStore Dict Str Str Str Str Str Str Str Str Str Str Str Str Str Str ClassDef bases body Expr Str FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign AttributeStore NameLoad attr NameLoad Assign AttributeStore NameLoad attr ListLoad Assign AttributeStore NameLoad attr ListLoad Num Assign AttributeStore NameLoad attr ListLoad Num Assign AttributeStore NameLoad attr ListLoad Str Assign AttributeStore NameLoad attr Call NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareEq Call NameLoad AttributeLoad NameLoad attr Num body Expr Call AttributeLoad AttributeLoad NameLoad attr attr Call AttributeLoad NameLoad attr orelse Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str If CompareEq NameLoad Str body Return AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body Return AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body Return AttributeLoad NameLoad attr orelse If Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad body Return SubscriptLoad AttributeLoad NameLoad attr Index NameLoad orelse Expr Call AttributeLoad NameLoad attr BinOpMod Str NameLoad Raise Call NameLoad BinOpMod Str NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str If CompareEq NameLoad Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad orelse If CompareEq NameLoad Str body Expr Call AttributeLoad AttributeLoad NameLoad attr attr NameLoad orelse If CompareEq NameLoad Str body Assign AttributeStore NameLoad attr NameLoad orelse Assign SubscriptStore AttributeLoad NameLoad attr Index NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults NameLoad body Expr Str Assign NameStore Call AttributeLoad Str attr SubscriptLoad NameLoad Index Str Assign NameStore Call NameLoad AttributeLoad NameLoad attr BinOpMult Call NameLoad AttributeLoad NameLoad attr ListLoad NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad If CompareNotEq AttributeLoad NameLoad attr Str body Assign SubscriptStore AttributeLoad NameLoad attr Index Str AttributeLoad NameLoad attr If CompareNotEq Call NameLoad AttributeLoad NameLoad attr Num body TryExcept body Assign NameStore Call AttributeLoad Str attr ListComp BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str Call NameLoad AttributeLoad NameLoad attr Str NameLoad Str NameLoad Str comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr handlers ExceptHandler body Raise Call NameLoad BinOpAdd Str NameLoad Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad If CompareNotEq AttributeLoad NameLoad attr Str body Assign SubscriptStore AttributeLoad NameLoad attr Index Str AttributeLoad NameLoad attr Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign NameStore Dict For NameStore NameLoad body If Call AttributeLoad AttributeLoad NameLoad attr attr SubscriptLoad NameLoad Index Num body If CompareNotEq SubscriptLoad AttributeLoad NameLoad attr Index SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num body Assign SubscriptStore NameLoad Index SubscriptLoad NameLoad Index Num SubscriptLoad AttributeLoad NameLoad attr Index SubscriptLoad NameLoad Index Num Delete SubscriptDel AttributeLoad NameLoad attr Index SubscriptLoad NameLoad Index Num If CompareNotEq Call NameLoad NameLoad Num body For TupleStore NameStore NameStore Call AttributeLoad NameLoad attr body Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad AttributeLoad NameLoad attr NameLoad Expr Call AttributeLoad NameLoad attr NameLoad If CompareNotEq Call NameLoad AttributeLoad NameLoad attr Num body Assign NameStore Call AttributeLoad Str attr ListComp BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd BinOpAdd Str Call NameLoad AttributeLoad NameLoad attr Str NameLoad Str NameLoad Str comprehension TupleStore NameStore NameStore Call AttributeLoad AttributeLoad NameLoad attr attr Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad decorator_list FunctionDef arguments args NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr AugAssignAdd NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str AttributeLoad NameLoad attr TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad decorator_list FunctionDef arguments args NameParam NameParam NameParam defaults body Expr Str Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Assign TupleStore AttributeStore NameLoad attr NameStore AttributeStore NameLoad attr AttributeStore NameLoad attr Call AttributeLoad NameLoad attr Assign NameStore BinOpMod Str TupleLoad SubscriptLoad NameLoad Index Str NameLoad TryExcept body Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr handlers ExceptHandler type AttributeLoad NameLoad attr name NameStore body Expr Call AttributeLoad NameLoad attr BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad Raise Call NameLoad BinOpMod Str TupleLoad SubscriptLoad AttributeLoad NameLoad attr Index Num SubscriptLoad AttributeLoad NameLoad attr Index Num NameLoad For NameStore NameLoad body Assign SubscriptStore AttributeLoad NameLoad attr Index SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num If Call AttributeLoad AttributeLoad NameLoad attr attr Str body Assign AttributeStore NameLoad attr SubscriptLoad AttributeLoad NameLoad attr Index Str Delete SubscriptDel AttributeLoad NameLoad attr Index Str orelse Assign AttributeStore NameLoad attr Str Return NameLoad decorator_list decorator_list
N/A N/A numpy np N/A cStringIO N/A MySQLdb N/A sys collections defaultdict ocpcaerror OCPCAError N/A logging N/A logger N/A N/A logging getLogger ocp N/A Classes that hold annotation metadata N/A ANNO_ANNOTATION 1 N/A ANNO_SYNAPSE 2 N/A ANNO_SEED 3 N/A ANNO_SEGMENT 4 N/A ANNO_NEURON 5 N/A ANNO_ORGANELLE 6 N/A anno_dbtables N/A annotation kvpairs synapse segment synseg organelle seed annotations kvpairs synapses segments synseg organelles seeds BatchAnnotation N/A N/A N/A Metdata common to all annotations. __init__ N/A N/A self annodb N/A N/A N/A Initialize the fields to zero or null N/A N/A self annodb annodb N/A N/A self annidList N/A N/A N/A self statusList N/A 0 N/A N/A self confidenceList N/A 0.0 N/A N/A self authorList N/A N/A N/A self kvpairs N/A defaultdict list N/A setID N/A N/A self db N/A N/A N/A if annid == 0, create a new identifier N/A N/A N/A len N/A self annidList 0 N/A N/A N/A N/A N/A self annidList append N/A N/A db nextID N/A N/A N/A N/A db setBatchID N/A self annidList N/A getField N/A N/A self field N/A N/A N/A Accessor by field name N/A N/A field status N/A N/A N/A self statusList N/A N/A N/A field confidence N/A N/A N/A self confidenceList N/A N/A N/A field author N/A N/A N/A self authorList N/A N/A N/A N/A N/A self kvpairs get field N/A N/A N/A N/A self kvpairs N/A field N/A N/A N/A N/A logger warning N/A getField: No such field %s field N/A N/A OCPCAError N/A getField: No such field %s field N/A setField N/A N/A self field value N/A N/A N/A Mutator by field name.  Then need to store the field. N/A N/A field status N/A N/A N/A N/A N/A self statusList append value N/A N/A N/A field confidence N/A N/A N/A N/A N/A self confidenceList append value N/A N/A N/A field author N/A N/A N/A self authorList value N/A N/A N/A N/A self kvpairs N/A field value N/A store N/A N/A self cursor annotype N/A ANNO_ANNOTATION N/A N/A Store the annotation to the annotations database N/A sql N/A N/A INSERT INTO {} VALUES ( %s, %s, %s, %s ) format N/A anno_dbtables N/A annotation N/A data N/A zip N/A self annidList N/A N/A len N/A self annidList N/A annotype N/A self confidenceList N/A self statusList N/A N/A N/A N/A N/A cursor executemany sql data N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error inserting annotation %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error inserting annotation: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A N/A self author N/A N/A N/A N/A self kvpairs N/A ann_author N/A self author N/A N/A N/A len N/A self kvpairs 0 N/A N/A N/A N/A kvclause N/A N/A , join N/A N/A N/A N/A N/A N/A N/A ( N/A str N/A self annid ,' k ',' v ') N/A N/A k v N/A N/A N/A self kvpairs iteritems N/A N/A N/A N/A N/A OCPCAError N/A Improperly formatted key/value csv string: kvclause N/A sql N/A INSERT INTO %s VALUES %s N/A N/A anno_dbtables N/A kvpairs kvclause N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error inserting kvpairs %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error inserting kvpairs: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A update N/A N/A self cursor N/A N/A N/A Set type and update base class. N/A N/A N/A self updateBase ANNO_ANNOTATION cursor N/A updateBase N/A N/A self annotype cursor N/A N/A N/A Update the annotation in the annotations database N/A sql N/A UPDATE %s SET type=%s, confidence=%s, status=%s WHERE annoid = %s N/A N/A anno_dbtables N/A annotation annotype N/A self confidence N/A self status N/A self annid N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error updating annotation %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error updating annotation: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A N/A self author N/A N/A N/A N/A self kvpairs N/A ann_author N/A self author N/A sql N/A SELECT * FROM %s WHERE annoid = %s N/A N/A anno_dbtables N/A kvpairs N/A self annid N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error retrieving kvpairs %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error retrieving kvpairs: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A kvresult N/A N/A cursor fetchall N/A kvupdate N/A N/A kv kvresult N/A N/A N/A N/A N/A self kvpairs has_key N/A kv N/A 1 N/A N/A N/A N/A N/A self kvpairs N/A N/A kv N/A 1 N/A kv N/A 2 N/A N/A N/A kvupdate N/A N/A kv N/A 1 N/A N/A self kvpairs N/A N/A kv N/A 1 N/A N/A N/A self kvpairs N/A N/A kv N/A 1 N/A N/A N/A len kvupdate 0 N/A N/A N/A k v N/A N/A kvupdate iteritems N/A N/A sql N/A UPDATE %s SET kv_value='%s' WHERE annoid=%s AND kv_key='%s' N/A N/A anno_dbtables N/A kvpairs v N/A self annid k N/A N/A N/A cursor execute sql N/A N/A N/A len N/A self kvpairs 0 N/A N/A kvclause N/A N/A , join N/A N/A N/A N/A N/A N/A N/A ( N/A str N/A self annid ,' k ',' v ') N/A N/A k v N/A N/A N/A self kvpairs iteritems N/A sql N/A INSERT INTO %s VALUES %s N/A N/A anno_dbtables N/A kvpairs kvclause N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error inserting annotation %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error inserting annotation: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A delete N/A N/A self cursor N/A N/A N/A Delete the annotation from the database N/A sql N/A DELETE FROM %s WHERE annoid = %s; N/A N/A anno_dbtables N/A annotation N/A self annid N/A sql N/A DELETE FROM %s WHERE annoid = %s N/A N/A anno_dbtables N/A kvpairs N/A self annid N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error deleting annotation %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error deleting annotation: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A retrieve N/A N/A self annid cursor N/A N/A N/A Retrieve the annotation by annid N/A sql N/A SELECT * FROM %s WHERE annoid = %s N/A N/A anno_dbtables N/A annotation annid N/A N/A N/A N/A N/A cursor execute sql N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error retrieving annotation %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error retrieving annotation: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A N/A self annid annotype N/A self confidence N/A self status N/A N/A cursor fetchone N/A sql N/A SELECT * FROM %s WHERE annoid = %s N/A N/A anno_dbtables N/A kvpairs annid N/A N/A N/A N/A N/A cursor execute sql N/A kvpairs N/A N/A cursor fetchall N/A N/A N/A N/A MySQLdb Error N/A e N/A N/A N/A N/A logger warning N/A Error retrieving kvpairs %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A N/A OCPCAError N/A Error retrieving kvpairs: %d: %s. sql=%s N/A N/A N/A e args N/A 0 N/A N/A e args N/A 1 sql N/A kv kvpairs N/A N/A N/A N/A self kvpairs N/A N/A kv N/A 1 N/A kv N/A 2 N/A N/A N/A N/A self kvpairs get ann_author N/A N/A N/A self author N/A N/A self kvpairs N/A ann_author N/A N/A N/A self kvpairs N/A ann_author N/A N/A N/A self author unknown N/A annotype N/A N/A