[py] Adapt to annotations wrappers

bob/bio/base/script/annotate.py

@@ -2,7 +2,6 @@
 """
 import logging
 import click
-import json
 import functools
 from bob.extension.scripts.click_helper import (
     verbosity_option,
@@ -13,10 +12,6 @@ from bob.extension.scripts.click_helper import (
 from bob.pipelines import wrap, ToDaskBag
 logger = logging.getLogger(__name__)
 
-def save_annotations_to_json(data, path):
-    with open(path, "w") as f:
-        json.dump(data, f)
-
 def annotate_common_options(func):
     @click.option(
         "--annotator",
@@ -96,15 +91,14 @@ def annotate(
     log_parameters(logger)
 
     # Allows passing of Sample objects as parameters
-    annotator = wrap(["sample"], annotator)
+    annotator = wrap(["annotated_sample"], annotator)
 
     # Will save the annotations in the `data` fields to a json file
     annotator = wrap(
-        bases=["checkpoint"],
-        estimator=annotator,
-        features_dir=output_dir,
-        save_func=save_annotations_to_json,
-        extension=".json",
+        bases=["checkpoint_annotations"],
+        annotator=annotator,
+        annotations_dir=output_dir,
+        force=force,
     )
 
     # Allows reception of Dask Bags
@@ -159,6 +153,7 @@ You have to define ``samples`` in a python file (config.py) as in examples.
 )
 @click.option(
     "--samples",
+    entry_point_group="bob.bio.config",
     required=True,
     cls=ResourceOption,
     help="A list of all samples that you want to annotate.",
@@ -166,7 +161,7 @@ You have to define ``samples`` in a python file (config.py) as in examples.
 @annotate_common_options
 @verbosity_option(cls=ResourceOption)
 def annotate_samples(
-    samples, make_path, annotator, output_dir, force, dask_client, **kwargs
+    samples, annotator, output_dir, force, dask_client, **kwargs
 ):
     """Annotates a list of samples.
 
@@ -176,15 +171,14 @@ def annotate_samples(
     log_parameters(logger, ignore=("samples",))
 
     # Allows passing of Sample objects as parameters
-    annotator = wrap(["sample"], annotator)
+    annotator = wrap(["annotated_sample"], annotator)
 
     # Will save the annotations in the `data` fields to a json file
     annotator = wrap(
-        bases=["checkpoint"],
-        estimator=annotator,
-        features_dir=output_dir,
-        save_func=save_annotations_to_json,
-        extension=".json",
+        bases=["checkpoint_annotations"],
+        annotator=annotator,
+        annotations_dir=output_dir,
+        force=force,
     )
 
     # Allows reception of Dask Bags

bob/bio/base/test/dummy/samples_list.py

+from bob.bio.base.test.dummy.database import database
+
+samples = database.background_model_samples()
\ No newline at end of file

bob/bio/base/test/test_annotators.py

@@ -2,7 +2,7 @@ import tempfile
 import os
 import shutil
 from click.testing import CliRunner
-from bob.bio.base.script.annotate import annotate
+from bob.bio.base.script.annotate import annotate, annotate_samples
 from bob.bio.base.annotator import Callable, FailSafe
 from bob.db.base import read_annotation_file
 
@@ -33,6 +33,31 @@ def test_annotate():
     finally:
         shutil.rmtree(tmp_dir)
 
+def test_annotate_samples():
+
+    try:
+        tmp_dir = tempfile.mkdtemp(prefix="bobtest_")
+        runner = CliRunner()
+        result = runner.invoke(annotate_samples, args=(
+            '--samples','dummy_samples', '-a', 'dummy', '-o', tmp_dir))
+        assertion_error_message = (
+            'Command exited with this output: `{}\' \n'
+            'If the output is empty, you can run this script locally to see '
+            'what is wrong:\n'
+            'bin/bob bio annotate-samples -vvv --force --samples dummy -a dummy -o /tmp/temp_annotations'
+            ''.format(result.output))
+        assert result.exit_code == 0, assertion_error_message
+
+        # test if annotations exist
+        for dirpath, dirnames, filenames in os.walk(tmp_dir):
+            for filename in filenames:
+                path = os.path.join(dirpath, filename)
+                annot = read_annotation_file(path, 'json')
+                assert annot['topleft'] == [0, 0]
+                # size of atnt images
+                assert annot['bottomright'] == [112, 92]
+    finally:
+        shutil.rmtree(tmp_dir)
 
 def dummy_extra_key_annotator(data_batch, **kwargs):
     return [{'leye': 0, 'reye': 0, 'topleft': 0}]

setup.py

@@ -76,6 +76,7 @@ setup(
       'bob.bio.config': [
         'dummy             = bob.bio.base.test.dummy.config', # for test purposes only
         'dummy2            = bob.bio.base.test.dummy.config2', # for test purposes only
+        'dummy_samples     = bob.bio.base.test.dummy.samples_list', # for test purposes only
       ],
 
       'bob.bio.database': [