def testArrayColumnSize1(self): """ Size one arrays require special handling """ grid = self.client.sf.sharedResources() repoMap = grid.repositories() repoObj = repoMap.descriptions[0] table = grid.newTable(repoObj.id.val, "/test") assert table darr = columns.DoubleArrayColumnI('longarr', 'desc', 1) darr.values = [[0.5], [0.25]] table.initialize([darr]) table.addData([darr]) data = table.readCoordinates([0, 1]) testl = data.columns[0].values assert [0.5] == testl[0] assert [0.25] == testl[1]
def _testCreateAllColumnsAndMetadata(self): grid = self.client.sf.sharedResources() repoMap = grid.repositories() repoObj = repoMap.descriptions[0] table = grid.newTable(repoObj.id.val, "/test") assert table # Supported metadata types # https://github.com/ome/omero-py/blob/v5.5.1/src/omero/hdfstorageV2.py#L466 metadata = { 'string': rstring('a'), 'int': rint(1), 'long': rlong(1), 'double': rfloat(0.1), } fcol = columns.FileColumnI('filecol', 'file col') fcol.values = [10, 20] icol = columns.ImageColumnI('imagecol', 'image col') icol.values = [30, 40] rcol = columns.RoiColumnI('roicol', 'roi col') rcol.values = [50, 60] wcol = columns.WellColumnI('wellcol', 'well col') wcol.values = [70, 80] pcol = columns.PlateColumnI('platecol', 'plate col') pcol.values = [90, 100] bcol = columns.BoolColumnI('boolcol', 'bool col') bcol.values = [True, False] dcol = columns.DoubleColumnI('doublecol', 'double col') dcol.values = [0.25, 0.5] lcol = columns.LongColumnI('longcol', 'long col') lcol.values = [-1, -2] scol = columns.StringColumnI('stringcol', 'string col', 3) scol.values = ["abc", "de"] larr = columns.LongArrayColumnI('longarr', 'longarr col', 2) larr.values = [[-2, -1], [1, 2]] farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2) farr.values = [[-0.25, -0.5], [0.125, 0.0625]] darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2) darr.values = [[-0.25, -0.5], [0.125, 0.0625]] dscol = columns.DatasetColumnI('datasetcol', 'dataset col') dscol.values = [110, 120] mask = self.createMaskCol() cols = [ fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr, farr, darr, dscol ] table.initialize(cols) table.setAllMetadata(metadata) table.addData(cols) data = table.readCoordinates([0, 1]) testf = data.columns[0].values assert 10 == testf[0] assert 20 == testf[1] testi = data.columns[1].values assert 30 == testi[0] assert 40 == testi[1] testr = data.columns[2].values assert 50 == testr[0] assert 60 == testr[1] testw = data.columns[3].values assert 70 == testw[0] assert 80 == testw[1] testp = data.columns[4].values assert 90 == testp[0] assert 100 == testp[1] testb = data.columns[5].values assert testb[0] assert not testb[1] testd = data.columns[6].values assert 0.25 == testd[0] assert 0.5 == testd[1] testl = data.columns[7].values assert -1 == testl[0] assert -2 == testl[1] tests = data.columns[8].values assert "abc" == tests[0] assert "de" == tests[1] testm = data.columns[9] self.checkMaskCol(testm) testla = data.columns[10].values assert [-2, -1] == testla[0] assert [1, 2] == testla[1] testfa = data.columns[11].values assert [-0.25, -0.5] == testfa[0] assert [0.125, 0.0625] == testfa[1] testda = data.columns[12].values assert [-0.25, -0.5] == testda[0] assert [0.125, 0.0625] == testda[1] testds = data.columns[13].values assert 110 == testds[0] assert 120 == testds[1] ofile = table.getOriginalFile() print("Created OriginalFile:", ofile.getId().val) return table
def testCreateAllColumnsAndMetadata_5_3_4(self): """ Call this method to create the reference HDF5 table under a 5.3.4 Python 2.7 server. The OriginalFile ID of the table will be printed, and can be used to find the file under ${omero.data.dir}/Files/. Alternatively download it using ``omero download OriginalFile:FileID output.h5`` To run manually goto ``components/tools/OmeroPy``, and run: ``pytest test/integration/tablestest/test_backwards_compatibility.py\ -s -k testCreateAllColumnsAndMetadata_5_3_4`` """ grid = self.client.sf.sharedResources() repoMap = grid.repositories() repoObj = repoMap.descriptions[0] table = grid.newTable(repoObj.id.val, "/test") assert table # Supported metadata types # https://github.com/ome/omero-py/blob/v5.5.1/src/omero/hdfstorageV2.py#L466 metadata = { 'string': rstring('a'), 'int': rint(1), 'long': rlong(1), 'double': rfloat(0.1), } fcol = columns.FileColumnI('filecol', 'file col') fcol.values = [10, 20] icol = columns.ImageColumnI('imagecol', 'image col') icol.values = [30, 40] rcol = columns.RoiColumnI('roicol', 'roi col') rcol.values = [50, 60] wcol = columns.WellColumnI('wellcol', 'well col') wcol.values = [70, 80] pcol = columns.PlateColumnI('platecol', 'plate col') pcol.values = [90, 100] bcol = columns.BoolColumnI('boolcol', 'bool col') bcol.values = [True, False] dcol = columns.DoubleColumnI('doublecol', 'double col') dcol.values = [0.25, 0.5] lcol = columns.LongColumnI('longcol', 'long col') lcol.values = [-1, -2] scol = columns.StringColumnI('stringcol', 'string col', 3) scol.values = ["abc", "de"] larr = columns.LongArrayColumnI('longarr', 'longarr col', 2) larr.values = [[-2, -1], [1, 2]] farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2) farr.values = [[-0.25, -0.5], [0.125, 0.0625]] darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2) darr.values = [[-0.25, -0.5], [0.125, 0.0625]] # DatasetColumn is broken! mask = self.createMaskCol() cols = [ fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr, farr, darr ] table.initialize(cols) table.setAllMetadata(metadata) table.addData(cols) data = table.readCoordinates([0, 1]) testf = data.columns[0].values assert 10 == testf[0] assert 20 == testf[1] testi = data.columns[1].values assert 30 == testi[0] assert 40 == testi[1] testr = data.columns[2].values assert 50 == testr[0] assert 60 == testr[1] testw = data.columns[3].values assert 70 == testw[0] assert 80 == testw[1] testp = data.columns[4].values assert 90 == testp[0] assert 100 == testp[1] testb = data.columns[5].values assert testb[0] assert not testb[1] testd = data.columns[6].values assert 0.25 == testd[0] assert 0.5 == testd[1] testl = data.columns[7].values assert -1 == testl[0] assert -2 == testl[1] tests = data.columns[8].values assert "abc" == tests[0] assert "de" == tests[1] testm = data.columns[9] self.checkMaskCol(testm) testla = data.columns[10].values assert [-2, -1] == testla[0] assert [1, 2] == testla[1] testfa = data.columns[11].values assert [-0.25, -0.5] == testfa[0] assert [0.125, 0.0625] == testfa[1] testda = data.columns[12].values assert [-0.25, -0.5] == testda[0] assert [0.125, 0.0625] == testda[1] ofile = table.getOriginalFile() print("Created OriginalFile:", ofile.getId().val) table.close()
def testAllColumnsSameTable(self): """ Check all column types can coexist in the same table """ grid = self.client.sf.sharedResources() repoMap = grid.repositories() repoObj = repoMap.descriptions[0] table = grid.newTable(repoObj.id.val, "/test") assert table fcol = columns.FileColumnI('filecol', 'file col') fcol.values = [10, 20] icol = columns.ImageColumnI('imagecol', 'image col') icol.values = [30, 40] rcol = columns.RoiColumnI('roicol', 'roi col') rcol.values = [50, 60] wcol = columns.WellColumnI('wellcol', 'well col') wcol.values = [70, 80] pcol = columns.PlateColumnI('platecol', 'plate col') pcol.values = [90, 100] bcol = columns.BoolColumnI('boolcol', 'bool col') bcol.values = [True, False] dcol = columns.DoubleColumnI('doublecol', 'double col') dcol.values = [0.25, 0.5] lcol = columns.LongColumnI('longcol', 'long col') lcol.values = [-1, -2] scol = columns.StringColumnI('stringcol', 'string col', 46) scol.values = ["მიკროსკოპის პონი", "de"] mask = self.createMaskCol() larr = columns.LongArrayColumnI('longarr', 'longarr col', 2) larr.values = [[-2, -1], [1, 2]] farr = columns.FloatArrayColumnI('floatarr', 'floatarr col', 2) farr.values = [[-8.0, -4.0], [16.0, 32.0]] darr = columns.DoubleArrayColumnI('doublearr', 'doublearr col', 2) darr.values = [[-0.25, -0.5], [0.125, 0.0625]] cols = [ fcol, icol, rcol, wcol, pcol, bcol, dcol, lcol, scol, mask, larr, farr, darr ] table.initialize(cols) table.addData(cols) data = table.readCoordinates([0, 1]) testf = data.columns[0].values assert 10 == testf[0] assert 20 == testf[1] testi = data.columns[1].values assert 30 == testi[0] assert 40 == testi[1] testr = data.columns[2].values assert 50 == testr[0] assert 60 == testr[1] testw = data.columns[3].values assert 70 == testw[0] assert 80 == testw[1] testp = data.columns[4].values assert 90 == testp[0] assert 100 == testp[1] testb = data.columns[5].values assert testb[0] assert not testb[1] testd = data.columns[6].values assert 0.25 == testd[0] assert 0.5 == testd[1] testl = data.columns[7].values assert -1 == testl[0] assert -2 == testl[1] tests = data.columns[8].values assert "მიკროსკოპის პონი" == tests[0] assert "de" == tests[1] testm = data.columns[9] self.checkMaskCol(testm) testla = data.columns[10].values assert [-2, -1] == testla[0] assert [1, 2] == testla[1] testfa = data.columns[11].values assert [-8.0, -4.0] == testfa[0] assert [16.0, 32.0] == testfa[1] testda = data.columns[12].values assert [-0.25, -0.5] == testda[0] assert [0.125, 0.0625] == testda[1] ofile = table.getOriginalFile() print(("testAllColumnsSameTable", "OriginalFile:", ofile.getId().val)) # Now try an update updatel = omero.grid.LongColumn('longcol', '', [12345]) updatela = omero.grid.LongArrayColumn('longarr', '', 2, [[654, 321]]) updateData = omero.grid.Data(rowNumbers=[1], columns=[updatel, updatela]) table.update(updateData) assert table.getNumberOfRows() == 2 data2 = table.readCoordinates([0, 1]) for n in [0, 1, 2, 3, 4, 5, 6, 8, 11, 12]: assert data.columns[n].values == data2.columns[n].values self.checkMaskCol(data2.columns[9]) testl2 = data2.columns[7].values assert -1 == testl2[0] assert 12345 == testl2[1] testla2 = data2.columns[10].values assert [-2, -1] == testla2[0] assert [654, 321] == testla2[1] table.delete() table.close()