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Merge pull request #260 from TileDB-Inc/sa/sc-28015/bindings-for-delete-group
Sa/sc 28015/bindings for delete group
2 parents e396f58 + f942eef commit 6509c2d

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‎.github/scripts/install_tiledb_linux.sh‎

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set -e -x
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curl --location -o tiledb.tar.gz https://github.com/TileDB-Inc/TileDB/releases/download/2.15.0/tiledb-linux-x86_64-2.15.0-1fb59c4.tar.gz \
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curl --location -o tiledb.tar.gz https://github.com/TileDB-Inc/TileDB/releases/download/2.15.3/tiledb-linux-x86_64-2.15.3-689bea0.tar.gz \
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&& sudo tar -C /usr/local -xf tiledb.tar.gz
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sudo ldconfig /usr/local/lib

‎.github/scripts/install_tiledb_linux_debug.sh‎

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set -e -x
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.0
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.3
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cd TileDB
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mkdir build && cd build
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cmake -DSANITIZER=leak -DTILEDB_VERBOSE=OFF -DTILEDB_S3=ON -DTILEDB_SERIALIZATION=ON -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=/usr/local ..

‎.github/scripts/install_tiledb_macos.sh‎

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set -e -x
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curl --location -o tiledb.tar.gz https://github.com/TileDB-Inc/TileDB/releases/download/2.15.0/tiledb-macos-x86_64-2.15.0-1fb59c4.tar.gz \
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curl --location -o tiledb.tar.gz https://github.com/TileDB-Inc/TileDB/releases/download/2.15.3/tiledb-macos-x86_64-2.15.3-689bea0.tar.gz \
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&& sudo tar -C /usr/local -xf tiledb.tar.gz

‎.github/scripts/install_tiledb_source_linux.sh‎

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set -e -x
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.0
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.3
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cd TileDB
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mkdir build && cd build
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cmake -DTILEDB_VERBOSE=OFF -DTILEDB_S3=ON -DTILEDB_SERIALIZATION=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local ..

‎.github/scripts/install_tiledb_source_macos.sh‎

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set -e -x
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.0
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git clone https://github.com/TileDB-Inc/TileDB.git -b 2.15.3
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cd TileDB
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mkdir build && cd build
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cmake -DTILEDB_VERBOSE=OFF -DTILEDB_S3=ON -DTILEDB_SERIALIZATION=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local ..

‎group.go‎

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@@ -482,3 +482,22 @@ func (g *Group) GetIsRelativeURIByName(name string) (bool, error) {
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}
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return isRelative > 0, nil
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}
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// Delete deletes written data from an open group. The group must be opened in MODIFY_EXCLUSIVE mode,
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// otherwise the function will error out.
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// Set recursive true if all data inside the group is to be deleted.
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func (g *Group) Delete(recursive bool) error {
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curi := C.CString(g.uri)
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defer C.free(unsafe.Pointer(curi))
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var cRecursive C.uint8_t
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if recursive {
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cRecursive = 1
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}
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ret := C.tiledb_group_delete_group(g.context.tiledbContext, g.group, curi, cRecursive)
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if ret != C.TILEDB_OK {
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return fmt.Errorf("Error deleting group: %s", g.context.LastError())
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}
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return nil
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}

‎group_test.go‎

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@@ -235,6 +235,115 @@ func TestGetIsRelativeURIByName(t *testing.T) {
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require.NoError(t, group.Close())
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}
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func TestGroupDelete(t *testing.T) {
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// setup creates an hierarchy of groups and returns the
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// members URIs in the following order
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// outerGroup/
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// outerArray
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// innerGroup/
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// innerArray
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setup := func(t *testing.T) []string {
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outerGroupURI := t.TempDir()
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outerArrayURI := t.TempDir()
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innerGroupURI := t.TempDir()
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innerArrayURI := t.TempDir()
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tdbCtx, err := NewContext(nil)
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require.NoError(t, err)
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outerGroup, err := createTestGroup(tdbCtx, outerGroupURI)
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require.NoError(t, err)
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innerGroup, err := createTestGroup(tdbCtx, innerGroupURI)
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require.NoError(t, err)
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arraySchema := buildArraySchema(tdbCtx, t)
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outerArray, err := NewArray(tdbCtx, outerArrayURI)
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require.NoError(t, err)
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outerArray.Create(arraySchema)
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require.NoError(t, err)
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innerArray, err := NewArray(tdbCtx, innerArrayURI)
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require.NoError(t, err)
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innerArray.Create(arraySchema)
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require.NoError(t, err)
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require.NoError(t, innerGroup.Open(TILEDB_WRITE))
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require.NoError(t, innerGroup.AddMember(innerArray.uri, "innerArray", false))
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require.NoError(t, innerGroup.Close())
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require.NoError(t, outerGroup.Open(TILEDB_WRITE))
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require.NoError(t, outerGroup.AddMember(outerArray.uri, "outerArray", false))
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require.NoError(t, outerGroup.AddMember(innerGroup.uri, "innerGroup", false))
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require.NoError(t, outerGroup.Close())
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return []string{outerGroupURI, outerArrayURI, innerGroupURI, innerArrayURI}
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}
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// TileDB core versions 2.15.2, 2.15.3 and the upcoming 2.15.4
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// are slightly different on the files they leave behind after delete
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// To be compatible with all we check that a deleted group misses the `group.tdb` file
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// and a delete array has an empty `__schema` dir
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t.Run("recursive", func(t *testing.T) {
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uris := setup(t)
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tdbCtx, err := NewContext(nil)
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require.NoError(t, err)
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outerGroup, err := NewGroup(tdbCtx, uris[0])
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require.NoError(t, err)
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require.NoError(t, outerGroup.Open(TILEDB_MODIFY_EXCLUSIVE))
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require.NoError(t, outerGroup.Delete(true))
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tdbCfg, err := NewConfig()
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require.NoError(t, err)
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vfs, err := NewVFS(tdbCtx, tdbCfg)
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require.NoError(t, err)
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exists, err := vfs.IsFile(uris[0] + "/__tiledb_group.tdb")
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require.NoError(t, err)
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require.False(t, exists)
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exists, err = vfs.IsFile(uris[2] + "/__tiledb_group.tdb")
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require.NoError(t, err)
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require.False(t, exists)
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dirSize, err := vfs.DirSize(uris[1] + "/__schema")
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require.NoError(t, err)
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require.Equal(t, uint64(0), dirSize)
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dirSize, err = vfs.DirSize(uris[1] + "/__schema")
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require.NoError(t, err)
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require.Equal(t, uint64(0), dirSize)
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})
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t.Run("nonrecursive", func(t *testing.T) {
316+
uris := setup(t)
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tdbCtx, err := NewContext(nil)
319+
require.NoError(t, err)
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outerGroup, err := NewGroup(tdbCtx, uris[0])
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require.NoError(t, err)
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require.NoError(t, outerGroup.Open(TILEDB_MODIFY_EXCLUSIVE))
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require.NoError(t, outerGroup.Delete(false))
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tdbCfg, err := NewConfig()
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require.NoError(t, err)
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vfs, err := NewVFS(tdbCtx, tdbCfg)
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require.NoError(t, err)
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exists, err := vfs.IsFile(uris[0] + "/__tiledb_group.tdb")
332+
require.NoError(t, err)
333+
require.False(t, exists)
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exists, err = vfs.IsFile(uris[2] + "/__tiledb_group.tdb")
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require.NoError(t, err)
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require.True(t, exists)
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dirSize, err := vfs.DirSize(uris[1] + "/__schema")
339+
require.NoError(t, err)
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require.True(t, dirSize > 0)
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dirSize, err = vfs.DirSize(uris[1] + "/__schema")
342+
require.NoError(t, err)
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require.True(t, dirSize > 0)
344+
})
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}
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func memberCount(group *Group) (uint64, error) {
239348
if err := group.Open(TILEDB_READ); err != nil {
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return 0, err

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