table.insert supports blobs

datajoint/table.py

@@ -84,7 +84,7 @@ def iter_insert(self, iter, **kwargs):
         """
         Inserts an entire batch of entries. Additional keyword arguments are passed it insert.
 
-        :param iter: Must be an iterator that generates a sequence of valid arguments for insert. 
+        :param iter: Must be an iterator that generates a sequence of valid arguments for insert.
         """
         for row in iter:
             self.insert(row, **kwargs)
@@ -113,15 +113,23 @@ def insert(self, tup, ignore_errors=False, replace=False):  # TODO: in progress
         """
 
         if isinstance(tup, tuple) or isinstance(tup, list) or isinstance(tup, np.ndarray):
-            value_list = ','.join([repr(q) for q in tup])
+            value_list = ','.join([repr(val) if not name in self.heading.blobs else '%s'
+                                    for name, val in zip(self.heading.names, tup)])
+            args = tuple(pack(val) for name, val in zip(self.heading.names, tup) if name in self.heading.blobs)
             attribute_list = '`' + '`,`'.join(self.heading.names[0:len(tup)]) + '`'
+
         elif isinstance(tup, dict):
-            value_list = ','.join([repr(tup[q])
-                                   for q in self.heading.names if q in tup])
-            attribute_list = '`' + '`,`'.join([q for q in self.heading.names if q in tup]) + '`'
+            value_list = ','.join([repr(tup[name]) if not name in self.heading.blobs else '%s'
+                                    for name in self.heading.names if name in tup])
+            args = tuple(pack(tup[name]) for name in self.heading.names
+                                if (name in tup and name in self.heading.blobs) )
+            attribute_list = '`' + '`,`'.join([name for name in self.heading.names if name in tup]) + '`'
         elif isinstance(tup, np.void):
-            value_list = ','.join([repr(tup[q])
-                                   for q in self.heading.names if q in tup.dtype.fields])
+            value_list = ','.join([repr(tup[name]) if not name in self.heading.blobs else '%s'
+                                    for name in self.heading.names if name in tup.dtype.fields])
+
+            args = tuple(pack(tup[name]) for name in self.heading.names
+                                if (name in tup.dtype.fields and name in self.heading.blobs) )
             attribute_list = '`' + '`,`'.join([q for q in self.heading.names if q in tup.dtype.fields]) + '`'
         else:
             raise DataJointError('Datatype %s cannot be inserted' % type(tup))
@@ -133,9 +141,8 @@ def insert(self, tup, ignore_errors=False, replace=False):  # TODO: in progress
             sql = 'INSERT'
         sql += " INTO %s (%s) VALUES (%s)" % (self.full_table_name,
                                               attribute_list, value_list)
-
         logger.info(sql)
-        self.conn.query(sql)
+        self.conn.query(sql, args=args)
 
     def delete(self):  # TODO: (issues #14 and #15)
         pass

tests/schemata/schema1/test4.py

@@ -0,0 +1,17 @@
+"""
+Test 1 Schema definition - fully bound and has connection object
+"""
+__author__ = 'fabee'
+
+import datajoint as dj
+
+
+class Matrix(dj.Base):
+    definition = """
+    test4.Matrix (manual)        # Some numpy array
+
+    matrix_id       : int       # unique matrix id
+    ---
+    data                        :  longblob   #  data
+    comment                     :  varchar(1000) # comment
+    """

tests/test_blob.py

@@ -0,0 +1,10 @@
+__author__ = 'fabee'
+import numpy as np
+from datajoint.blob import pack, unpack
+from numpy.testing import assert_array_equal
+
+
+def test_pack():
+    x = np.random.randn(10, 10)
+
+    assert_array_equal(x, unpack(pack(x)), "Arrays do not match!")

tests/test_table.py

@@ -1,13 +1,13 @@
 __author__ = 'fabee'
 
-from .schemata.schema1 import test1
+from .schemata.schema1 import test1, test4
 
 from . import BASE_CONN, CONN_INFO, PREFIX, cleanup
 from datajoint.connection import Connection
 from nose.tools import assert_raises, assert_equal, assert_regexp_matches, assert_false, assert_true, assert_list_equal
 from datajoint import DataJointError
 import numpy as np
-
+from numpy.testing import assert_array_equal
 
 def setup():
     """
@@ -34,8 +34,11 @@ def setup(self):
         cleanup()  # drop all databases with PREFIX
         self.conn = Connection(**CONN_INFO)
         test1.conn = self.conn
+        test4.conn = self.conn
         self.conn.bind(test1.__name__, PREFIX + '_test1')
+        self.conn.bind(test4.__name__, PREFIX + '_test4')
         self.relvar = test1.Subjects()
+        self.relvar_blob = test4.Matrix()
 
     def teardown(self):
         cleanup()
@@ -47,6 +50,13 @@ def test_tuple_insert(self):
         testt2 = tuple((self.relvar & 'subject_id = 1').fetch()[0])
         assert_equal(testt2, testt, "Inserted and fetched tuple do not match!")
 
+    def test_list_insert(self):
+        "Test whether tuple insert works"
+        testt = [1, 'Peter', 'mouse']
+        self.relvar.insert(testt)
+        testt2 = list((self.relvar & 'subject_id = 1').fetch()[0])
+        assert_equal(testt2, testt, "Inserted and fetched tuple do not match!")
+
     def test_record_insert(self):
         "Test whether record insert works"
         tmp = np.array([(2, 'Klara', 'monkey')],
@@ -104,4 +114,11 @@ def test_iter_insert(self):
         delivered = self.relvar.fetch()
 
         for e,d in zip(expected, delivered):
-            assert_equal(tuple(e), tuple(d),'Inserted and fetched records do not match')
+            assert_equal(tuple(e), tuple(d),'Inserted and fetched records do not match')
+
+    def test_blob_insert(self):
+        x = np.random.randn(10)
+        t = (0, x, 'this is a random image')
+        self.relvar_blob.insert(t)
+        x2 = self.relvar_blob.fetch()[0][1]
+        assert_array_equal(x,x2, 'inserted blob does not match')