From b9675696ac757badedead6f54a5c91a469f2d5ab Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 07:18:50 +0100
Subject: [PATCH 01/13] Add additional asserts for readCoordinate tests

---
 test/unit/tablestest/test_hdfstorage.py | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index 9ffa71916..7b9c874c8 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -129,20 +129,39 @@ def testModifyRow(self):
         self.append(hdf, {"a": 1, "b": 2, "c": 3})
         self.append(hdf, {"a": 5, "b": 6, "c": 7})
         data = hdf.readCoordinates(hdf._stamp, [0, 1], self.current)
+        assert 1 == data.columns[0].values[0]
+        assert 5 == data.columns[0].values[1]
+        assert 2 == data.columns[1].values[0]
+        assert 6 == data.columns[1].values[1]
+        assert 3 == data.columns[2].values[0]
+        assert 7 == data.columns[2].values[1]
+
         data.columns[0].values[0] = 100
         data.columns[0].values[1] = 200
         data.columns[1].values[0] = 300
         data.columns[1].values[1] = 400
         hdf.update(hdf._stamp, data)
         hdf.readCoordinates(hdf._stamp, [0, 1], self.current)
+        assert 100 == data.columns[0].values[0]
+        assert 200 == data.columns[0].values[1]
+        assert 300 == data.columns[1].values[0]
+        assert 400 == data.columns[1].values[1]
+        assert 3 == data.columns[2].values[0]
+        assert 7 == data.columns[2].values[1]
         hdf.cleanup()
 
     def testReadTicket1951(self):
         hdf = HdfStorage(self.hdfpath(), self.lock)
         self.init(hdf, True)
         self.append(hdf, {"a": 1, "b": 2, "c": 3})
-        hdf.readCoordinates(hdf._stamp, [0], self.current)
-        hdf.read(hdf._stamp, [0, 1, 2], 0, 1, self.current)
+        data = hdf.readCoordinates(hdf._stamp, [0], self.current)
+        assert 1 == data.columns[0].values[0]
+        assert 2 == data.columns[1].values[0]
+        assert 3 == data.columns[2].values[0]
+        data = hdf.read(hdf._stamp, [0, 1, 2], 0, 1, self.current)
+        assert 1 == data.columns[0].values[0]
+        assert 2 == data.columns[1].values[0]
+        assert 3 == data.columns[2].values[0]
         hdf.cleanup()
 
     def testSorting(self):  # Probably shouldn't work

From 6ed7978bbac7635c0433d8acd5904da4f3e1e356 Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 07:19:20 +0100
Subject: [PATCH 02/13] Do not mark testMaskColumn as broken

---
 test/unit/tablestest/test_hdfstorage.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index 7b9c874c8..ebad9c125 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -326,7 +326,6 @@ def testStringColWhereUnicode(self):
     #
     # ROIs
     #
-    @pytest.mark.broken
     def testMaskColumn(self):
         hdf = HdfStorage(self.hdfpath(), self.lock)
         mask = omero.columns.MaskColumnI('mask', 'desc', None)

From 9b25c6918f993772f11fabefe3ba80fcf1f8929f Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 07:22:09 +0100
Subject: [PATCH 03/13] Call table.read on MaskColumn

---
 test/unit/tablestest/test_hdfstorage.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index ebad9c125..b097c558e 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -358,6 +358,8 @@ def testMaskColumn(self):
         assert 6 == test.w[1]
         assert 7 == test.h[1]
         assert [0 == 1, 2, 3, 4], test.bytes[1]
+
+        data = hdf.read(hdf._stamp, [0], 0, 1, self.current)
         hdf.cleanup()
 
 

From fe8b863a1a168c79e16336f328dc569fb37e58e2 Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 08:46:18 +0100
Subject: [PATCH 04/13] table.read(): use getsize() API rather than values

---
 src/omero/hdfstorageV2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/omero/hdfstorageV2.py b/src/omero/hdfstorageV2.py
index b5c0a13ac..1cd705d90 100644
--- a/src/omero/hdfstorageV2.py
+++ b/src/omero/hdfstorageV2.py
@@ -593,7 +593,7 @@ def _rowstocols(self, rows, colNumbers, cols):
             col.fromrows(rows)
             rv.append(col)
             if not l:
-                l = len(col.values)
+                l = col.getsize()
         return rv, l
 
     @stamped

From 179e736d896a2ed694d4736ce1968ae3c7eef379 Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 08:55:45 +0100
Subject: [PATCH 05/13] Fix bytes assert

---
 test/unit/tablestest/test_hdfstorage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index b097c558e..fb808464a 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -357,7 +357,7 @@ def testMaskColumn(self):
         assert 5 == test.y[1]
         assert 6 == test.w[1]
         assert 7 == test.h[1]
-        assert [0 == 1, 2, 3, 4], test.bytes[1]
+        assert [0, 1, 2, 3, 4] == test.bytes[1]
 
         data = hdf.read(hdf._stamp, [0], 0, 1, self.current)
         hdf.cleanup()

From 938086ef416fd3f5d7e860d47efcea0672e9b193 Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 09:48:29 +0100
Subject: [PATCH 06/13] Add tests for table.read() output

---
 test/unit/tablestest/test_hdfstorage.py | 58 +++++++++++++++++--------
 1 file changed, 40 insertions(+), 18 deletions(-)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index fb808464a..a461d000d 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -129,6 +129,7 @@ def testModifyRow(self):
         self.append(hdf, {"a": 1, "b": 2, "c": 3})
         self.append(hdf, {"a": 5, "b": 6, "c": 7})
         data = hdf.readCoordinates(hdf._stamp, [0, 1], self.current)
+        assert len(data.columns) == 3
         assert 1 == data.columns[0].values[0]
         assert 5 == data.columns[0].values[1]
         assert 2 == data.columns[1].values[0]
@@ -142,6 +143,7 @@ def testModifyRow(self):
         data.columns[1].values[1] = 400
         hdf.update(hdf._stamp, data)
         hdf.readCoordinates(hdf._stamp, [0, 1], self.current)
+        assert len(data.columns) == 3
         assert 100 == data.columns[0].values[0]
         assert 200 == data.columns[0].values[1]
         assert 300 == data.columns[1].values[0]
@@ -276,9 +278,18 @@ def testStringCol(self):
         # Unicode conditions don't work on Python 3
         # Fetching should still work though
         r1 = hdf.readCoordinates(time.time(), [1], self.current)
+        assert len(r1.columns) == 1
+        assert len(r1.columns[0].values) == 1
         assert r1.columns[0].size == bytesize
         assert r1.columns[0].values[0] == "მიკროსკოპის პონი"
 
+        r2 = hdf.read(time.time(), [0], 0, 2, self.current)
+        assert len(r2.columns) == 1
+        assert len(r2.columns[0].values) == 2
+        assert r2.columns[0].size == bytesize
+        assert r2.columns[0].values[0] == "foo"
+        assert r2.columns[0].values[1] == "მიკროსკოპის პონი"
+
         # Doesn't work yet.
         hdf.cleanup()
 
@@ -340,26 +351,37 @@ def testMaskColumn(self):
         mask.bytes = [[0], [0, 1, 2, 3, 4]]
         hdf.append([mask])
         data = hdf.readCoordinates(hdf._stamp, [0, 1], self.current)
-        test = data.columns[0]
-        assert 1 == test.imageId[0]
-        assert 2 == test.theZ[0]
-        assert 3 == test.theT[0]
-        assert 4 == test.x[0]
-        assert 5 == test.y[0]
-        assert 6 == test.w[0]
-        assert 7 == test.h[0]
-        assert [0] == test.bytes[0]
-
-        assert 2 == test.imageId[1]
-        assert 2 == test.theZ[1]
-        assert 3 == test.theT[1]
-        assert 4 == test.x[1]
-        assert 5 == test.y[1]
-        assert 6 == test.w[1]
-        assert 7 == test.h[1]
-        assert [0, 1, 2, 3, 4] == test.bytes[1]
+        assert len(data.columns) == 1
+        assert len(data.columns[0].imageId) == 2
+        assert 1 == data.columns[0].imageId[0]
+        assert 2 == data.columns[0].theZ[0]
+        assert 3 == data.columns[0].theT[0]
+        assert 4 == data.columns[0].x[0]
+        assert 5 == data.columns[0].y[0]
+        assert 6 == data.columns[0].w[0]
+        assert 7 == data.columns[0].h[0]
+        assert [0] == data.columns[0].bytes[0]
+
+        assert 2 == data.columns[0].imageId[1]
+        assert 2 == data.columns[0].theZ[1]
+        assert 3 == data.columns[0].theT[1]
+        assert 4 == data.columns[0].x[1]
+        assert 5 == data.columns[0].y[1]
+        assert 6 == data.columns[0].w[1]
+        assert 7 == data.columns[0].h[1]
+        assert [0, 1, 2, 3, 4] == data.columns[0].bytes[1]
 
         data = hdf.read(hdf._stamp, [0], 0, 1, self.current)
+        assert len(data.columns) == 1
+        assert len(data.columns[0].imageId) == 1
+        assert 1 == data.columns[0].imageId[0]
+        assert 2 == data.columns[0].theZ[0]
+        assert 3 == data.columns[0].theT[0]
+        assert 4 == data.columns[0].x[0]
+        assert 5 == data.columns[0].y[0]
+        assert 6 == data.columns[0].w[0]
+        assert 7 == data.columns[0].h[0]
+        assert [0] == data.columns[0].bytes[0]
         hdf.cleanup()
 
 

From 6c27eae0c859c2b6087264a4d5e76408ac0a813e Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 10:55:07 +0100
Subject: [PATCH 07/13] Update hdfv2storage.read to use column.read() API

---
 src/omero/hdfstorageV2.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/src/omero/hdfstorageV2.py b/src/omero/hdfstorageV2.py
index 1cd705d90..36ddaa7cd 100644
--- a/src/omero/hdfstorageV2.py
+++ b/src/omero/hdfstorageV2.py
@@ -576,11 +576,12 @@ def readCoordinates(self, stamp, rowNumbers, current):
     def read(self, stamp, colNumbers, start, stop, current):
         self.__initcheck()
         self.__sizecheck(colNumbers, None)
-        cols = self.cols(None, current)
+        all_cols = self.cols(None, current)
+        cols = [all_cols[i] for i in colNumbers]
 
-        rows = self._getrows(start, stop)
-        rv, l = self._rowstocols(rows, colNumbers, cols)
-        return self._as_data(rv, list(range(start, start + l)))
+        for col in cols:
+            col.read(self.__mea, start, stop)
+        return self._as_data(cols, range(stop - start + 1))
 
     def _getrows(self, start, stop):
         return self.__mea.read(start, stop)

From 146d65d34a889c6af9d6ae97b3d5b8306c86656b Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Thu, 27 May 2021 12:58:17 +0100
Subject: [PATCH 08/13] Add unit test covering different read arguments

---
 test/unit/tablestest/test_hdfstorage.py | 46 +++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index a461d000d..7aadf8155 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -334,6 +334,52 @@ def testStringColWhereUnicode(self):
         # Doesn't work yet.
         hdf.cleanup()
 
+    def testRead(self):
+        hdf = HdfStorage(self.hdfpath(), self.lock)
+        cols = [
+            omero.columns.LongColumnI('a'),
+            omero.columns.LongColumnI('b'),
+            omero.columns.LongColumnI('c')]
+        hdf.initialize(cols)
+        cols[0].values = [1, 2, 3]
+        cols[1].values = [4, 5, 6]
+        cols[2].values = [7, 8, 9]
+        hdf.append(cols)
+
+        data = hdf.read(time.time(), [0, 1, 2], 0, 2, self.current)
+        assert len(data.columns) == 3
+        assert len(data.columns[0].values) == 2
+        assert data.columns[0].name == 'a'
+        assert data.columns[0].values[0] == 1
+        assert data.columns[0].values[1] == 2
+        assert data.columns[1].name == 'b'
+        assert data.columns[1].values[0] == 4
+        assert data.columns[1].values[1] == 5
+        assert data.columns[2].name == 'c'
+        assert data.columns[2].values[0] == 7
+        assert data.columns[2].values[1] == 8
+
+        data = hdf.read(time.time(), [0, 2], 1, 3, self.current)
+        assert len(data.columns) == 2
+        assert len(data.columns[0].values) == 2
+        assert data.columns[0].name == 'a'
+        assert data.columns[0].values[0] == 2
+        assert data.columns[0].values[1] == 3
+        assert data.columns[1].name == 'c'
+        assert data.columns[1].values[0] == 8
+        assert data.columns[1].values[1] == 9
+
+        data = hdf.read(time.time(), [1], 1, 2, self.current)
+        assert len(data.columns) == 1
+        assert len(data.columns[0].values) == 1
+        assert data.columns[0].name == 'b'
+        assert data.columns[0].values[0] == 5
+
+        data = hdf.read(time.time(), [0, 1, 2], 1, 1, self.current)
+        assert len(data.columns) == 3
+        assert len(data.columns[0].values) == 0
+        hdf.cleanup()
+
     #
     # ROIs
     #

From b3199f97786fb855737e78cd058ff0f6aed07bff Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Fri, 28 May 2021 14:26:36 +0100
Subject: [PATCH 09/13] Expand unit test to covering table.read(start, stop)
 with None values

---
 test/unit/tablestest/test_hdfstorage.py | 30 +++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index 7aadf8155..f33190a48 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -375,11 +375,41 @@ def testRead(self):
         assert data.columns[0].name == 'b'
         assert data.columns[0].values[0] == 5
 
+        # (start=1, stop=1) should return no rows
         data = hdf.read(time.time(), [0, 1, 2], 1, 1, self.current)
         assert len(data.columns) == 3
         assert len(data.columns[0].values) == 0
         hdf.cleanup()
 
+        # (start=None, stop=None) should return all rows
+        data = hdf.read(time.time(), [0, 1, 2], None, None, self.current)
+        assert len(data.columns) == 3
+        assert len(data.columns[0].values) == 3
+        assert data.columns[0].name == 'a'
+        assert data.columns[0].values[0] == 1
+        assert data.columns[0].values[1] == 2
+        assert data.columns[0].values[2] == 3
+        assert data.columns[1].name == 'b'
+        assert data.columns[1].values[0] == 4
+        assert data.columns[1].values[1] == 5
+        assert data.columns[1].values[2] == 6
+        assert data.columns[2].name == 'c'
+        assert data.columns[2].values[0] == 7
+        assert data.columns[2].values[1] == 8
+        assert data.columns[2].values[2] == 9
+
+        # (start=0, stop=None) should return one rows
+        data = hdf.read(time.time(), [0, 1, 2], 1, None, self.current)
+        assert len(data.columns) == 3
+        assert len(data.columns[0].values) == 1
+        assert data.columns[0].name == 'a'
+        assert data.columns[0].values[0] == 2
+        assert data.columns[1].name == 'b'
+        assert data.columns[1].values[0] == 5
+        assert data.columns[2].name == 'c'
+        assert data.columns[2].values[0] == 8
+        hdf.cleanup()
+
     #
     # ROIs
     #

From 25cb4964bd790a0331bd3654727a7bcca959523b Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Fri, 28 May 2021 14:30:09 +0100
Subject: [PATCH 10/13] Fix row numbers returned by HDFStorage.read()

---
 src/omero/hdfstorageV2.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/omero/hdfstorageV2.py b/src/omero/hdfstorageV2.py
index 36ddaa7cd..a821036af 100644
--- a/src/omero/hdfstorageV2.py
+++ b/src/omero/hdfstorageV2.py
@@ -581,7 +581,14 @@ def read(self, stamp, colNumbers, start, stop, current):
 
         for col in cols:
             col.read(self.__mea, start, stop)
-        return self._as_data(cols, range(stop - start + 1))
+        if start is not None and stop is not None:
+            rowNumbers = list(range(start, stop))
+        elif start is not None and stop is None:
+            rowNumbers =  list(range(start, start + 1))
+        elif start is None and stop is None:
+            rowNumbers = list(range(self.__length()))
+
+        return self._as_data(cols, rowNumbers)
 
     def _getrows(self, start, stop):
         return self.__mea.read(start, stop)

From e37d12f2af445fd4f0954c9b9774fb26688b26da Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Fri, 28 May 2021 14:33:09 +0100
Subject: [PATCH 11/13] Also test rowNumbers output

---
 test/unit/tablestest/test_hdfstorage.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index f33190a48..9140aaf49 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -358,6 +358,7 @@ def testRead(self):
         assert data.columns[2].name == 'c'
         assert data.columns[2].values[0] == 7
         assert data.columns[2].values[1] == 8
+        assert data.rowNumbers == [0, 1]
 
         data = hdf.read(time.time(), [0, 2], 1, 3, self.current)
         assert len(data.columns) == 2
@@ -368,18 +369,20 @@ def testRead(self):
         assert data.columns[1].name == 'c'
         assert data.columns[1].values[0] == 8
         assert data.columns[1].values[1] == 9
+        assert data.rowNumbers == [1, 2]
 
         data = hdf.read(time.time(), [1], 1, 2, self.current)
         assert len(data.columns) == 1
         assert len(data.columns[0].values) == 1
         assert data.columns[0].name == 'b'
         assert data.columns[0].values[0] == 5
+        assert data.rowNumbers == [1]
 
         # (start=1, stop=1) should return no rows
         data = hdf.read(time.time(), [0, 1, 2], 1, 1, self.current)
         assert len(data.columns) == 3
         assert len(data.columns[0].values) == 0
-        hdf.cleanup()
+        assert data.rowNumbers == []
 
         # (start=None, stop=None) should return all rows
         data = hdf.read(time.time(), [0, 1, 2], None, None, self.current)
@@ -397,6 +400,7 @@ def testRead(self):
         assert data.columns[2].values[0] == 7
         assert data.columns[2].values[1] == 8
         assert data.columns[2].values[2] == 9
+        assert data.rowNumbers == [1, 2, 3]
 
         # (start=0, stop=None) should return one rows
         data = hdf.read(time.time(), [0, 1, 2], 1, None, self.current)
@@ -408,6 +412,7 @@ def testRead(self):
         assert data.columns[1].values[0] == 5
         assert data.columns[2].name == 'c'
         assert data.columns[2].values[0] == 8
+        assert data.rowNumbers == [1]
         hdf.cleanup()
 
     #

From 2147ffc68b49019bd571fbe0792aaf4a6e95aa0d Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Fri, 28 May 2021 14:35:55 +0100
Subject: [PATCH 12/13] Fix rowNumbers when stop=None and update tests
 accordingly

---
 src/omero/hdfstorageV2.py               |  2 +-
 test/unit/tablestest/test_hdfstorage.py | 25 +++++++++++++------------
 2 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/omero/hdfstorageV2.py b/src/omero/hdfstorageV2.py
index a821036af..c45fbac58 100644
--- a/src/omero/hdfstorageV2.py
+++ b/src/omero/hdfstorageV2.py
@@ -584,7 +584,7 @@ def read(self, stamp, colNumbers, start, stop, current):
         if start is not None and stop is not None:
             rowNumbers = list(range(start, stop))
         elif start is not None and stop is None:
-            rowNumbers =  list(range(start, start + 1))
+            rowNumbers =  list(range(start, self.__length()))
         elif start is None and stop is None:
             rowNumbers = list(range(self.__length()))
 
diff --git a/test/unit/tablestest/test_hdfstorage.py b/test/unit/tablestest/test_hdfstorage.py
index 9140aaf49..d3ffaa5a8 100755
--- a/test/unit/tablestest/test_hdfstorage.py
+++ b/test/unit/tablestest/test_hdfstorage.py
@@ -371,6 +371,7 @@ def testRead(self):
         assert data.columns[1].values[1] == 9
         assert data.rowNumbers == [1, 2]
 
+        # Reads row 1
         data = hdf.read(time.time(), [1], 1, 2, self.current)
         assert len(data.columns) == 1
         assert len(data.columns[0].values) == 1
@@ -378,13 +379,13 @@ def testRead(self):
         assert data.columns[0].values[0] == 5
         assert data.rowNumbers == [1]
 
-        # (start=1, stop=1) should return no rows
+       # Reads no row
         data = hdf.read(time.time(), [0, 1, 2], 1, 1, self.current)
         assert len(data.columns) == 3
         assert len(data.columns[0].values) == 0
         assert data.rowNumbers == []
 
-        # (start=None, stop=None) should return all rows
+        # Read all rows
         data = hdf.read(time.time(), [0, 1, 2], None, None, self.current)
         assert len(data.columns) == 3
         assert len(data.columns[0].values) == 3
@@ -400,19 +401,19 @@ def testRead(self):
         assert data.columns[2].values[0] == 7
         assert data.columns[2].values[1] == 8
         assert data.columns[2].values[2] == 9
-        assert data.rowNumbers == [1, 2, 3]
+        assert data.rowNumbers == [0, 1, 2]
 
-        # (start=0, stop=None) should return one rows
-        data = hdf.read(time.time(), [0, 1, 2], 1, None, self.current)
-        assert len(data.columns) == 3
-        assert len(data.columns[0].values) == 1
+        # Read from row 1 until the end of the table
+        data = hdf.read(time.time(), [0, 2], 1, None, self.current)
+        assert len(data.columns) == 2
+        assert len(data.columns[0].values) == 2
         assert data.columns[0].name == 'a'
         assert data.columns[0].values[0] == 2
-        assert data.columns[1].name == 'b'
-        assert data.columns[1].values[0] == 5
-        assert data.columns[2].name == 'c'
-        assert data.columns[2].values[0] == 8
-        assert data.rowNumbers == [1]
+        assert data.columns[0].values[1] == 3
+        assert data.columns[1].name == 'c'
+        assert data.columns[1].values[0] == 8
+        assert data.columns[1].values[1] == 9
+        assert data.rowNumbers == [1, 2]
         hdf.cleanup()
 
     #

From 981113537f3841389b7056724bf9b2a67a21ee2b Mon Sep 17 00:00:00 2001
From: Sebastien Besson <seb.besson@gmail.com>
Date: Fri, 28 May 2021 20:41:57 +0100
Subject: [PATCH 13/13] Remove obsolete internal API

---
 src/omero/hdfstorageV2.py | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/src/omero/hdfstorageV2.py b/src/omero/hdfstorageV2.py
index c45fbac58..58201b09b 100644
--- a/src/omero/hdfstorageV2.py
+++ b/src/omero/hdfstorageV2.py
@@ -590,20 +590,6 @@ def read(self, stamp, colNumbers, start, stop, current):
 
         return self._as_data(cols, rowNumbers)
 
-    def _getrows(self, start, stop):
-        return self.__mea.read(start, stop)
-
-    def _rowstocols(self, rows, colNumbers, cols):
-        l = 0
-        rv = []
-        for i in colNumbers:
-            col = cols[i]
-            col.fromrows(rows)
-            rv.append(col)
-            if not l:
-                l = col.getsize()
-        return rv, l
-
     @stamped
     def slice(self, stamp, colNumbers, rowNumbers, current):
         self.__initcheck()