Repository: opendatacube/datacube-core

Issue:
Incomplete Ingestion Runs
### Expected behaviour
When running `ingest` on a large job, it should output *all* of the expected tiles.

### Actual behaviour
Ingest completes up to the `--queue-size` number of tiles.

### Environment information

* Which ``datacube --version`` are you using?
1.6.1
* What datacube deployment/enviornment are you running against?
DEA NCI. Anywhere.


Discussion:
Broke here: 0afd9e8769995e5a491b2282f9e27b0487807120
https://github.com/opendatacube/datacube-core/pull/515
Can you please have a look at this @santoshamohan, Kirill has pointed out exactly where the breakage happened.

Thanks
Sure Damien, I will have a look at it.

Resolving patch:
diff --git a/datacube/scripts/ingest.py b/datacube/scripts/ingest.py
--- a/datacube/scripts/ingest.py
+++ b/datacube/scripts/ingest.py
@@ -302,30 +302,34 @@ def submit_task(task):
 
     pending = []
 
+    # Count of storage unit/s creation successful/failed
+    nc_successful = nc_failed = 0
+
     # Count of storage unit/s indexed successfully or failed to index
     index_successful = index_failed = 0
 
-    # Count of storage unit/s failed during file creation
-    f_failed = 0
-
     tasks = iter(tasks)
-    pending += [submit_task(task) for task in itertools.islice(tasks, max(0, queue_size - len(pending)))]
-    total = pending
-    while pending:
-        completed, failed, pending = executor.get_ready(pending)
+
+    while True:
+        pending += [submit_task(task) for task in itertools.islice(tasks, queue_size)]
+        if len(pending) == 0:
+            break
+
+        nc_completed, failed, pending = executor.get_ready(pending)
+        nc_successful += len(nc_completed)
 
         for future in failed:
             try:
                 executor.result(future)
             except Exception as err:  # pylint: disable=broad-except
-                _LOG.exception('Failed to create storage unit file (Exception: %s) ', str(err))
-                f_failed += 1
-
-        _LOG.info('Storage unit file creation status (completed: %s, failed: %s, pending: %s)',
-                  (len(total) - len(pending) - f_failed),
-                  f_failed,
-                  len(pending))
-        if not completed:
+                _LOG.exception('Failed to create storage unit file (Exception: %s) ', str(err), exc_info=True)
+                nc_failed += 1
+
+        _LOG.info('Storage unit file creation status (Created_Count: %s, Failed_Count: %s)',
+                  nc_successful,
+                  nc_failed)
+
+        if not nc_completed:
             time.sleep(1)
             continue
 
@@ -333,13 +337,13 @@ def submit_task(task):
             # TODO: ideally we wouldn't block here indefinitely
             # maybe limit gather to 50-100 results and put the rest into a index backlog
             # this will also keep the queue full
-            results = executor.results(completed)
+            results = executor.results(nc_completed)
             index_successful += _index_datasets(index, results)
         except Exception as err:  # pylint: disable=broad-except
-            _LOG.exception('Failed to index storage unit file (Exception: %s)', str(err))
+            _LOG.exception('Failed to index storage unit file (Exception: %s)', str(err), exc_info=True)
             index_failed += 1
 
-        _LOG.info('Storage unit files indexed (successful: %s, failed: %s)', index_successful, index_failed)
+        _LOG.info('Storage unit files indexed (Successful: %s, Failed: %s)', index_successful, index_failed)
 
     return index_successful, index_failed
 
@@ -388,8 +392,8 @@ def ingest_cmd(index,
                save_tasks,
                load_tasks,
                dry_run,
-               executor,
-               allow_product_changes):
+               allow_product_changes,
+               executor):
     # pylint: disable=too-many-locals
 
     if config_file:
diff --git a/datacube/ui/task_app.py b/datacube/ui/task_app.py
--- a/datacube/ui/task_app.py
+++ b/datacube/ui/task_app.py
@@ -73,7 +73,7 @@ def save_tasks(config, tasks, taskfile):
         os.remove(taskfile)
         return 0
     else:
-        _LOG.info('Saved config and %d tasks to %s', i, taskfile)
+        _LOG.info('Saved config and %d tasks to %s', i - 1, taskfile)
     return i - 1
 
 


Test patch:
diff --git a/integration_tests/test_double_ingestion.py b/integration_tests/test_double_ingestion.py
--- a/integration_tests/test_double_ingestion.py
+++ b/integration_tests/test_double_ingestion.py
@@ -1,11 +1,14 @@
 from pathlib import Path
 
 import pytest
-from hypothesis import given
-from hypothesis.strategies import lists
+import netCDF4
 
-from integration_tests.data_utils import scene_datasets, write_test_scene_to_disk
 from integration_tests.utils import prepare_test_ingestion_configuration
+from integration_tests.test_full_ingestion import (check_open_with_api, check_data_with_api,
+                                                   ensure_datasets_are_indexed, check_data_shape,
+                                                   check_grid_mapping, check_cf_compliance, check_attributes,
+                                                   check_dataset_metadata_in_storage_unit,
+                                                   check_open_with_xarray)
 
 PROJECT_ROOT = Path(__file__).parents[1]
 
@@ -15,8 +18,7 @@
 @pytest.mark.parametrize('datacube_env_name', ('datacube',), indirect=True)
 @pytest.mark.usefixtures('default_metadata_type',
                          'indexed_ls5_scene_products')
-@given(scenes=lists(scene_datasets(), min_size=2, max_size=2))
-def test_double_ingestion(clirunner, index, tmpdir, ingest_configs, scenes):
+def test_double_ingestion(clirunner, index, tmpdir, ingest_configs, example_ls5_dataset_paths):
     """
     Test for the case where ingestor does not need to create a new product,
     but should re-use an existing target product.
@@ -24,11 +26,54 @@ def test_double_ingestion(clirunner, index, tmpdir, ingest_configs, scenes):
     """
     # Make a test ingestor configuration
     config = INGESTER_CONFIGS / ingest_configs['ls5_nbar_albers']
-    config_path, config = prepare_test_ingestion_configuration(
-        tmpdir, None, config, mode='fast_ingest')
-
-    for ls5_dataset in scenes:
-        # Write and ingest each dataset in turn
-        dataset_file = write_test_scene_to_disk(ls5_dataset, tmpdir)
-        clirunner(['dataset', 'add', str(dataset_file)])
-        clirunner(['ingest', '--config-file', str(config_path)])
+    config_path, config = prepare_test_ingestion_configuration(tmpdir, None,
+                                                               config, mode='fast_ingest')
+
+    def index_dataset(path):
+        return clirunner(['dataset', 'add', str(path)])
+
+    def ingest_products():
+        valid_uuids = []
+        for uuid, ls5_dataset_path in example_ls5_dataset_paths.items():
+            valid_uuids.append(uuid)
+            index_dataset(ls5_dataset_path)
+
+        # Ensure that datasets are actually indexed
+        ensure_datasets_are_indexed(index, valid_uuids)
+
+        # Ingest them
+        clirunner([
+            'ingest',
+            '--config-file',
+            str(config_path)
+        ])
+
+        # Validate that the ingestion is working as expected
+        datasets = index.datasets.search_eager(product='ls5_nbar_albers')
+        assert len(datasets) > 0
+        assert datasets[0].managed
+
+        check_open_with_api(index, len(valid_uuids))
+        check_data_with_api(index, len(valid_uuids))
+
+        # NetCDF specific checks, based on the saved NetCDF file
+        ds_path = str(datasets[0].local_path)
+        with netCDF4.Dataset(ds_path) as nco:
+            check_data_shape(nco)
+            check_grid_mapping(nco)
+            check_cf_compliance(nco)
+            check_dataset_metadata_in_storage_unit(nco, example_ls5_dataset_paths)
+            check_attributes(nco, config['global_attributes'])
+
+            name = config['measurements'][0]['name']
+            check_attributes(nco[name], config['measurements'][0]['attrs'])
+        check_open_with_xarray(ds_path)
+
+    # Create and Index some example scene datasets
+    ingest_products()
+
+    ######################
+    #  Double Ingestion  #
+    ######################
+    # Create and Index some more scene datasets
+    ingest_products()
diff --git a/integration_tests/test_full_ingestion.py b/integration_tests/test_full_ingestion.py
--- a/integration_tests/test_full_ingestion.py
+++ b/integration_tests/test_full_ingestion.py
@@ -37,6 +37,7 @@
 COMPLIANCE_CHECKER_NORMAL_LIMIT = 2
 
 
+@pytest.mark.timeout(20)
 @pytest.mark.parametrize('datacube_env_name', ('datacube',), indirect=True)
 @pytest.mark.usefixtures('default_metadata_type',
                          'indexed_ls5_scene_products')
@@ -122,6 +123,64 @@ def test_s3_full_ingestion(clirunner, index, tmpdir, example_ls5_dataset_paths,
     check_data_with_api(index, len(valid_uuids))
 
 
+@pytest.mark.timeout(20)
+@pytest.mark.parametrize('datacube_env_name', ('datacube',), indirect=True)
+@pytest.mark.usefixtures('default_metadata_type',
+                         'indexed_ls5_scene_products')
+def test_process_all_ingest_jobs(clirunner, index, tmpdir, example_ls5_dataset_paths, ingest_configs):
+    """
+    Test for the case where ingestor processes upto `--queue-size` number of tasks and not all the available scenes
+    """
+    # Make a test ingestor configuration
+    config = INGESTER_CONFIGS / ingest_configs['ls5_nbar_albers']
+    config_path, config = prepare_test_ingestion_configuration(tmpdir, None,
+                                                               config, mode='fast_ingest')
+
+    def index_dataset(path):
+        return clirunner(['dataset', 'add', str(path)])
+
+    # Number of scenes generated is 3 (as per NUM_TIME_SLICES const from conftest.py)
+    # Set the queue size to process 2 tiles
+    queue_size = 2
+    valid_uuids = []
+    for uuid, ls5_dataset_path in example_ls5_dataset_paths.items():
+        valid_uuids.append(uuid)
+        index_dataset(ls5_dataset_path)
+
+    # Ensure that datasets are actually indexed
+    ensure_datasets_are_indexed(index, valid_uuids)
+
+    # Ingest all scenes (Though the queue size is 2, all 3 tiles will be ingested)
+    clirunner([
+        'ingest',
+        '--config-file',
+        str(config_path),
+        '--queue-size',
+        queue_size,
+        '--allow-product-changes',
+    ])
+
+    # Validate that the ingestion is working as expected
+    datasets = index.datasets.search_eager(product='ls5_nbar_albers')
+    assert len(datasets) > 0
+    assert datasets[0].managed
+
+    check_open_with_api(index, len(valid_uuids))
+
+    # NetCDF specific checks, based on the saved NetCDF file
+    ds_path = str(datasets[0].local_path)
+    with netCDF4.Dataset(ds_path) as nco:
+        check_data_shape(nco)
+        check_grid_mapping(nco)
+        check_cf_compliance(nco)
+        check_dataset_metadata_in_storage_unit(nco, example_ls5_dataset_paths)
+        check_attributes(nco, config['global_attributes'])
+
+        name = config['measurements'][0]['name']
+        check_attributes(nco[name], config['measurements'][0]['attrs'])
+    check_open_with_xarray(ds_path)
+
+
 def ensure_datasets_are_indexed(index, valid_uuids):
     datasets = index.datasets.search_eager(product='ls5_nbar_scene')
     assert len(datasets) == len(valid_uuids)