Merge pull request #135 from nasa/feature/issue1-28-increase-test-cov…

…erage Feature/issue 128 increase test coverage
nasa · Jun 27, 2024 · 39698ec · 39698ec
2 parents 96e5cc2 + f5e9d46
commit 39698ec
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Showing 18 changed files with 670 additions and 102 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,7 +20,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.4.2'
+    rev: 'v0.4.10'
     hooks:
       - id: ruff
         args: [ "--fix" ]

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [issue #127](https://github.com/nasa/batchee/issues/127): Group dependabot updates into fewer PRs
 - [issue #129](https://github.com/nasa/batchee/issues/129): Add autoupdate schedule for pre-commit
 ### Changed
+- [issue #128](https://github.com/nasa/batchee/issues/128): Increase continuous integration/unit test coverage
 ### Deprecated
 ### Removed
 ### Fixed

diff --git a/batcher/harmony/service_adapter.py b/batcher/harmony/service_adapter.py
@@ -125,7 +125,7 @@ def process_catalog(self, catalog: pystac.Catalog) -> list[pystac.Catalog]:
                         _get_output_date_range([item]),
                     )
                     output_item.add_asset(
-                        f"data_{idx}",
+                        "data",
                         Asset(
                             _get_item_url(item),
                             title=_get_item_url(item),

diff --git a/batcher/tempo_filename_parser.py b/batcher/tempo_filename_parser.py
@@ -28,7 +28,6 @@
 import logging
 import re
 from argparse import ArgumentParser
-from pathlib import Path
 
 default_logger = logging.getLogger(__name__)
 
@@ -99,7 +98,7 @@ def main() -> list[list[str]]:
     if args.verbose:
         logging.basicConfig(level=logging.DEBUG)
 
-    input_filenames = [str(Path(f).resolve()) for f in args.file_names]
+    input_filenames = args.file_names
 
     batch_indices = get_batch_indices(input_filenames)
     unique_category_indices: list[int] = sorted(set(batch_indices), key=batch_indices.index)

diff --git a/poetry.lock b/poetry.lock
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -0,0 +1,23 @@
+from pathlib import Path
+
+import pytest
+
+
+def pytest_addoption(parser):
+    """Sets up optional argument to keep temporary testing directory."""
+    parser.addoption(
+        "--keep-tmp",
+        action="store_true",
+        help="Keep temporary directory after testing. Useful for debugging.",
+    )
+
+
+@pytest.fixture(scope="class")
+def pass_options(request):
+    """Adds optional argument to a test class."""
+    request.cls.KEEP_TMP = request.config.getoption("--keep-tmp")
+
+
+@pytest.fixture(scope="function", autouse=True)
+def temp_output_dir(tmpdir_factory) -> Path:
+    return Path(tmpdir_factory.mktemp("tmp-"))
diff --git a/tests/data/harmony/message.json b/tests/data/harmony/message.json
@@ -0,0 +1,16 @@
+{
+    "sources": [{
+        "collection": "C1234088182-EEDTEST"
+    }],
+    "format": {
+        "mime": "application/x-netcdf4"
+    },
+    "subset": {},
+    "requestId": "00001111-2222-3333-4444-555566667777",
+    "user": "jdoe",
+    "client": "harmony-example",
+    "isSynchronous": false,
+    "stagingLocation": "s3://example-bucket/public/some-org/some-service/some-uuid/",
+    "callback": "http://localhost/some-path",
+    "version": "0.10.0"
+}
diff --git a/tests/data/harmony/source/catalog.json b/tests/data/harmony/source/catalog.json
@@ -0,0 +1,48 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59",
+  "links": [
+    {
+      "rel": "harmony_source",
+      "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S012G01.json",
+      "type": "application/json",
+      "title": "granule_S012G01"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S012G02.json",
+      "type": "application/json",
+      "title": "granule_S012G02"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S013G01.json",
+      "type": "application/json",
+      "title": "granule_S013G01"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S013G02.json",
+      "type": "application/json",
+      "title": "granule_S013G02"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S014G01.json",
+      "type": "application/json",
+      "title": "granule_S014G01"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S014G02.json",
+      "type": "application/json",
+      "title": "granule_S014G02"
+    }
+  ],
+  "description": "CMR Granules for C1234088182-EEDTEST batch 1"
+}
diff --git a/tests/data/harmony/source/catalog0.json b/tests/data/harmony/source/catalog0.json
@@ -0,0 +1,36 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59",
+  "links": [
+    {
+      "rel": "harmony_source",
+      "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S012G01.json",
+      "type": "application/json",
+      "title": "granule_S012G01"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S012G02.json",
+      "type": "application/json",
+      "title": "granule_S012G02"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S013G01.json",
+      "type": "application/json",
+      "title": "granule_S013G01"
+    },
+    {
+      "rel": "next",
+      "href": "tests/data/harmony/source/catalog1.json",
+      "type": "application/json",
+      "title": "Next page"
+    }
+  ],
+  "description": "CMR Granules for C1234088182-EEDTEST batch 1"
+}
diff --git a/tests/data/harmony/source/catalog1.json b/tests/data/harmony/source/catalog1.json
@@ -0,0 +1,36 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "cfc32383-cfd1-4e43-8d5f-55f539b6fa59",
+  "links": [
+    {
+      "rel": "harmony_source",
+      "href": "https://cmr.uat.earthdata.nasa.gov/search/concepts/C1234088182-EEDTEST"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S013G02.json",
+      "type": "application/json",
+      "title": "granule_S013G02"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S014G01.json",
+      "type": "application/json",
+      "title": "granule_S014G01"
+    },
+    {
+      "rel": "item",
+      "href": "./granule_S014G02.json",
+      "type": "application/json",
+      "title": "granule_S014G02"
+    },
+    {
+      "rel": "prev",
+      "href": "tests/data/harmony/source/catalog0.json",
+      "type": "application/json",
+      "title": "Previous page"
+    }
+  ],
+  "description": "CMR Granules for C1234088182-EEDTEST batch 2"
+}
diff --git a/tests/data/harmony/source/granule_S012G01.json b/tests/data/harmony/source/granule_S012G01.json
@@ -0,0 +1,49 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "51d02b24-d00e-4640-9887-05f98f6b96d8",
+  "type": "Feature",
+  "links": [],
+  "properties": {
+    "start_datetime": "2020-01-02T00:00:00.000Z",
+    "end_datetime": "2020-01-02T23:59:59.000Z"
+  },
+  "bbox": [1, 3, 1, 3],
+  "geometry": {
+    "type": "Polygon",
+    "coordinates": [
+      [
+        [
+          -179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          89.95
+        ],
+        [
+          179.95,
+          89.95
+        ],
+        [
+          179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          -89.95
+        ]
+      ]
+    ]
+  },
+  "assets": {
+    "data": {
+      "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120101Z_S012G01.nc",
+      "title": "TEMPO_NO2_L2_V03_20240601T120101Z_S012G01.nc",
+      "type": "application/x-netcdf4",
+      "roles": [
+        "data"
+      ]
+    }
+  }
+}
diff --git a/tests/data/harmony/source/granule_S012G02.json b/tests/data/harmony/source/granule_S012G02.json
@@ -0,0 +1,49 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "21eb7dc5-7a9d-4374-9a88-12451ba653ef",
+  "type": "Feature",
+  "links": [],
+  "properties": {
+    "start_datetime": "2020-01-03T00:00:00.000Z",
+    "end_datetime": "2020-01-03T23:59:59.000Z"
+  },
+  "bbox": [-1, -3, -1, -3],
+  "geometry": {
+    "type": "Polygon",
+    "coordinates": [
+      [
+        [
+          -179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          89.95
+        ],
+        [
+          179.95,
+          89.95
+        ],
+        [
+          179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          -89.95
+        ]
+      ]
+    ]
+  },
+  "assets": {
+    "data": {
+      "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120107Z_S012G02.nc",
+      "title": "TEMPO_NO2_L2_V03_20240601T120107Z_S012G02.nc",
+      "type": "application/x-netcdf4",
+      "roles": [
+        "data"
+      ]
+    }
+  }
+}
diff --git a/tests/data/harmony/source/granule_S013G01.json b/tests/data/harmony/source/granule_S013G01.json
@@ -0,0 +1,49 @@
+{
+  "stac_version": "1.0.0-beta.2",
+  "stac_extensions": [],
+  "id": "dc07a25a-54bd-4389-97b6-c1d68cf0d586",
+  "type": "Feature",
+  "links": [],
+  "properties": {
+    "start_datetime": "2020-01-05T00:00:00.000Z",
+    "end_datetime": "2020-01-05T23:59:59.000Z"
+  },
+  "bbox": [-4, -2, -4, 2],
+  "geometry": {
+    "type": "Polygon",
+    "coordinates": [
+      [
+        [
+          -179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          89.95
+        ],
+        [
+          179.95,
+          89.95
+        ],
+        [
+          179.95,
+          -89.95
+        ],
+        [
+          -179.95,
+          -89.95
+        ]
+      ]
+    ]
+  },
+  "assets": {
+    "data": {
+      "href": "file://tests/data/harmony/granules/TEMPO_NO2_L2_V03_20240601T120202Z_S013G01.nc",
+      "title": "TEMPO_NO2_L2_V03_20240601T120202Z_S013G01.nc",
+      "type": "application/x-netcdf4",
+      "roles": [
+        "data"
+      ]
+    }
+  }
+}