From 72bc1ea55adb4d93dea6b6262bf1f80bd5bd7b69 Mon Sep 17 00:00:00 2001
From: Frank Greguska <89428916+frankinspace@users.noreply.github.com>
Date: Tue, 20 Aug 2024 14:46:19 -0700
Subject: [PATCH] Converted harmony adapter to operate on STAC catalog (#27)

---
 .github/workflows/build-pipeline.yml          |   2 +-
 CHANGELOG.md                                  |   2 +
 net2cog/netcdf_convert_harmony.py             | 141 +++---
 poetry.lock                                   | 401 ++++++++++--------
 pyproject.toml                                |   6 +-
 .../test_service_invoke.input.json            |  11 +-
 6 files changed, 320 insertions(+), 243 deletions(-)

diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml
index 3eb9022..535b15f 100644
--- a/.github/workflows/build-pipeline.yml
+++ b/.github/workflows/build-pipeline.yml
@@ -162,7 +162,7 @@ jobs:
             -Dsonar.tests=tests/
             -Dsonar.projectName=${{ github.repository }}
             -Dsonar.projectVersion=${{ env.software_version }}
-            -Dsonar.python.version=3.9,3.10
+            -Dsonar.python.version=3.10,3.11
       - name: Run Snyk as a blocking step
         uses: snyk/actions/python-3.10@master
         env:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 53d0952..398a284 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Changed
+- [issues/25](https://github.com/podaac/net2cog/issues/25): Converted harmony adapter to operate on STAC catalog
 
 ## [0.3.0]
 ### Changed
diff --git a/net2cog/netcdf_convert_harmony.py b/net2cog/netcdf_convert_harmony.py
index d5028fb..c98aac1 100644
--- a/net2cog/netcdf_convert_harmony.py
+++ b/net2cog/netcdf_convert_harmony.py
@@ -9,10 +9,16 @@
 Implementation of harmony-service-lib that invokes the netcdf converter.
 """
 import argparse
+import json
 import os
 import pathlib
+import shutil
+import tempfile
 
 import harmony
+import pystac
+from harmony.exceptions import HarmonyException
+from pystac import Asset
 
 from net2cog import netcdf_convert
 
@@ -29,66 +35,91 @@ def __init__(self, message):
         super().__init__(message)
 
         self.data_dir = os.getenv(DATA_DIRECTORY_ENV, '/home/dockeruser/data')
-        self.job_data_dir = os.path.join(self.data_dir, message.requestId)
+        pathlib.Path(self.data_dir).mkdir(parents=True, exist_ok=True)
+
         # Create temp directory
-        pathlib.Path(self.job_data_dir).mkdir(parents=True, exist_ok=True)
+        self.job_data_dir = tempfile.mkdtemp(prefix=message.requestId, dir=self.data_dir)
 
-    def invoke(self):
-        """Run the service on the message contained in `self.message`.
-        Fetches data, runs the service, puts the result in a file,
-        calls back to Harmony, and cleans up after itself.
+    def process_item(self, item: pystac.Item, source: harmony.message.Source) -> pystac.Item:
         """
+        Performs net2cog on input STAC Item's data, returning
+        an output STAC item
+
+        Parameters
+        ----------
+        item : pystac.Item
+            the item that should be coggified
+        source : harmony.message.Source
+            the input source defining the item
+
+        Returns
+        -------
+        pystac.Item
+            a STAC item describing the output
+        """
+        result = item.clone()
+        result.assets = {}
+        output_dir = self.job_data_dir
 
-        logger = self.logger
-        message = self.message
-
-        logger.info("Received message %s", message)
-
+        self.logger.info('Input item %s', json.dumps(item.to_dict()))
         try:
-            # Limit to the first granule.  See note in method documentation
-            granules = message.granules
-            if message.isSynchronous:
-                granules = granules[:1]
-
-            for i, granule in enumerate(granules):
-                self.download_granules([granule])
-
-                self.logger.info('local_filename = %s', granule.local_filename)
-                directory_name = os.path.splitext(os.path.basename(granule.local_filename))[0]
-                output_file_directory = os.path.join(self.job_data_dir,
-                                                     f'converted_{directory_name}')
-                output_filename = pathlib.Path(f'{output_file_directory}').joinpath(os.path.basename(granule.name))
-                self.logger.debug('output: %s', output_filename)
-
-                # Run the netcdf converter for the complete netcdf granule
-                cogs_generated = netcdf_convert.netcdf_converter(
-                    granule.local_filename, output_filename
-                )
-                current_progress = int(100 * i / len(granules))
-                next_progress = int(100 * (i + 1) / len(granules))
-                for cog in cogs_generated:
-                    if message.isSynchronous:
-                        self.completed_with_local_file(
-                            cog,
-                            remote_filename=os.path.basename(cog),
-                            mime="tiff"
-                        )
-                    else:
-                        self.async_add_local_file_partial_result(
-                            cog,
-                            remote_filename=os.path.basename(cog),
-                            title=granule.id,
-                            progress=current_progress if cog != cogs_generated[-1] else next_progress,
-                            mime="tiff"
-                        )
-            if not message.isSynchronous:
-                self.async_completed_successfully()
-
-        except Exception as ex:  # pylint: disable=W0703
-            logger.exception(ex)
-            self.completed_with_error('An unexpected error occurred')
+            # Get the data file
+            asset = next(v for k, v in item.assets.items() if 'data' in (v.roles or []))
+            self.logger.info('Downloading %s to %s', asset.href, output_dir)
+            input_filename = harmony.adapter.util.download(asset.href,
+                                                           output_dir,
+                                                           logger=self.logger,
+                                                           access_token=self.message.accessToken,
+                                                           cfg=self.config)
+
+            # Generate output filename
+            output_filename, output_file_ext = os.path.splitext(
+                harmony.adapter.util.generate_output_filename(input_filename, ext='tif'))
+            output_filename = f'{output_filename}_converted{output_file_ext}'
+
+            # Determine variables that need processing
+            self.logger.info('Generating COG(s) for %s output will be saved to %s', input_filename, output_filename)
+            var_list = source.process('variables')
+            if not isinstance(var_list, list):
+                var_list = [var_list]
+            if len(var_list) > 1:
+                raise HarmonyException(
+                    'net2cog harmony adapter currently only supports processing one variable at a time. '
+                    'Please specify a single variable in your Harmony request.')
+            var_list = list(map(lambda var: var.name, var_list))
+            self.logger.info('Processing variables %s', var_list)
+
+            # Run the netcdf converter for the complete netcdf granule
+            cog_generated = next(iter(netcdf_convert.netcdf_converter(pathlib.Path(input_filename),
+                                                                      pathlib.Path(output_dir).joinpath(
+                                                                          output_filename),
+                                                                      var_list=var_list)), [])
+
+            # Stage the output file with a conventional filename
+            self.logger.info('Generated COG %s', cog_generated)
+            staged_filename = os.path.basename(cog_generated)
+            url = harmony.adapter.util.stage(cog_generated,
+                                             staged_filename,
+                                             pystac.MediaType.COG,
+                                             location=self.message.stagingLocation,
+                                             logger=self.logger,
+                                             cfg=self.config)
+            self.logger.info('Staged %s to %s', cog_generated, url)
+
+            # Update the STAC record
+            result.assets['visual'] = Asset(url, title=staged_filename, media_type=pystac.MediaType.COG,
+                                            roles=['visual'])
+
+            # Return the STAC record
+            self.logger.info('Processed item %s', json.dumps(result.to_dict()))
+            return result
+        except Exception as uncaught_exception:
+            raise HarmonyException(str(f'Uncaught error in net2cog. '
+                                       f'Notify net2cog service provider. '
+                                       f'Message: {uncaught_exception}')) from uncaught_exception
         finally:
-            self.cleanup()
+            # Clean up any intermediate resources
+            shutil.rmtree(self.job_data_dir)
 
 
 def main():
@@ -100,7 +131,7 @@ def main():
     None
 
     """
-    parser = argparse.ArgumentParser(prog='podaac-netcdf-converter',
+    parser = argparse.ArgumentParser(prog='net2cog_harmony',
                                      description='Run the netcdf converter service')
     harmony.setup_cli(parser)
     args = parser.parse_args()
diff --git a/poetry.lock b/poetry.lock
index 8ec7706..fdc0a0f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -58,32 +58,32 @@ wrapt = [
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
+    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
-version = "2.15.0"
+version = "2.16.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
+    {file = "babel-2.16.0-py3-none-any.whl", hash = "sha256:368b5b98b37c06b7daf6696391c3240c938b37767d4584413e8438c5c435fa8b"},
+    {file = "babel-2.16.0.tar.gz", hash = "sha256:d1f3554ca26605fe173f3de0c65f750f5a42f924499bf134de6423582298e316"},
 ]
 
 [package.extras]
@@ -91,17 +91,17 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "boto3"
-version = "1.34.148"
+version = "1.34.159"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.34.148-py3-none-any.whl", hash = "sha256:d63d36e5a34533ba69188d56f96da132730d5e9932c4e11c02d79319cd1afcec"},
-    {file = "boto3-1.34.148.tar.gz", hash = "sha256:2058397f0a92c301e3116e9e65fbbc70ea49270c250882d65043d19b7c6e2d17"},
+    {file = "boto3-1.34.159-py3-none-any.whl", hash = "sha256:21120d23cc37c0e80dc4f64434bc5664d2a5645dcd9bf8a8fa97ed5c82164ca0"},
+    {file = "boto3-1.34.159.tar.gz", hash = "sha256:ffe7bbb88ba81b5d54bc8fa0cfb2f3b7fe63a6cffa0f9207df2ef5c22a1c0587"},
 ]
 
 [package.dependencies]
-botocore = ">=1.34.148,<1.35.0"
+botocore = ">=1.34.159,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -110,13 +110,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.148"
+version = "1.34.159"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.34.148-py3-none-any.whl", hash = "sha256:9e09428b0bc4d0c1cf5e368dd6ab18eabf6047304060f8b5dd8391677cfe00e6"},
-    {file = "botocore-1.34.148.tar.gz", hash = "sha256:258dd95570b43db9fa21cce5426eabaea5867e3a61224157650448b5019d1bbd"},
+    {file = "botocore-1.34.159-py3-none-any.whl", hash = "sha256:7633062491457419a49f5860c014251ae85689f78266a3ce020c2c8688a76b97"},
+    {file = "botocore-1.34.159.tar.gz", hash = "sha256:dc28806eb21e3c8d690c422530dff8b4b242ac033cbe98f160a9d37796c09cb1"},
 ]
 
 [package.dependencies]
@@ -125,7 +125,7 @@ python-dateutil = ">=2.1,<3.0.0"
 urllib3 = {version = ">=1.25.4,<2.2.0 || >2.2.0,<3", markers = "python_version >= \"3.10\""}
 
 [package.extras]
-crt = ["awscrt (==0.20.11)"]
+crt = ["awscrt (==0.21.2)"]
 
 [[package]]
 name = "certifi"
@@ -140,63 +140,78 @@ files = [
 
 [[package]]
 name = "cffi"
-version = "1.16.0"
+version = "1.17.0"
 description = "Foreign Function Interface for Python calling C code."
 optional = true
 python-versions = ">=3.8"
 files = [
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-    {file = "cffi-1.16.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:ac0f5edd2360eea2f1daa9e26a41db02dd4b0451b48f7c318e217ee092a213e9"},
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 [package.dependencies]
@@ -407,63 +422,83 @@ files = [
 
 [[package]]
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+version = "7.6.1"
 description = "Code coverage measurement for Python"
 optional = false
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 [package.dependencies]
@@ -765,13 +800,13 @@ files = [
 
 [[package]]
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-version = "5.3.0"
+version = "5.3.1"
 description = "Construct and use map tile grids (a.k.a TileMatrixSet / TMS)."
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
@@ -780,43 +815,43 @@ pydantic = ">=2.0,<3.0"
 pyproj = ">=3.1,<4.0"
 
 [package.extras]
-dev = ["pre-commit"]
+dev = ["bump-my-version", "pre-commit"]
 docs = ["mkdocs", "mkdocs-material", "pygments"]
 rasterio = ["rasterio (>=1.2.1)"]
 test = ["mercantile", "pytest", "pytest-cov", "rasterio (>=1.2.1)"]
 
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -1499,13 +1534,13 @@ crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"]
 
 [[package]]
 name = "setuptools"
-version = "71.1.0"
+version = "72.1.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-71.1.0-py3-none-any.whl", hash = "sha256:33874fdc59b3188304b2e7c80d9029097ea31627180896fb549c578ceb8a0855"},
-    {file = "setuptools-71.1.0.tar.gz", hash = "sha256:032d42ee9fb536e33087fb66cac5f840eb9391ed05637b3f2a76a7c8fb477936"},
+    {file = "setuptools-72.1.0-py3-none-any.whl", hash = "sha256:5a03e1860cf56bb6ef48ce186b0e557fdba433237481a9a625176c2831be15d1"},
+    {file = "setuptools-72.1.0.tar.gz", hash = "sha256:8d243eff56d095e5817f796ede6ae32941278f542e0f941867cc05ae52b162ec"},
 ]
 
 [package.extras]
@@ -1590,49 +1625,49 @@ test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.8"
+version = "2.0.0"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_applehelp-1.0.8-py3-none-any.whl", hash = "sha256:cb61eb0ec1b61f349e5cc36b2028e9e7ca765be05e49641c97241274753067b4"},
-    {file = "sphinxcontrib_applehelp-1.0.8.tar.gz", hash = "sha256:c40a4f96f3776c4393d933412053962fac2b84f4c99a7982ba42e09576a70619"},
+    {file = "sphinxcontrib_applehelp-2.0.0-py3-none-any.whl", hash = "sha256:4cd3f0ec4ac5dd9c17ec65e9ab272c9b867ea77425228e68ecf08d6b28ddbdb5"},
+    {file = "sphinxcontrib_applehelp-2.0.0.tar.gz", hash = "sha256:2f29ef331735ce958efa4734873f084941970894c6090408b079c61b2e1c06d1"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.6"
+version = "2.0.0"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_devhelp-1.0.6-py3-none-any.whl", hash = "sha256:6485d09629944511c893fa11355bda18b742b83a2b181f9a009f7e500595c90f"},
-    {file = "sphinxcontrib_devhelp-1.0.6.tar.gz", hash = "sha256:9893fd3f90506bc4b97bdb977ceb8fbd823989f4316b28c3841ec128544372d3"},
+    {file = "sphinxcontrib_devhelp-2.0.0-py3-none-any.whl", hash = "sha256:aefb8b83854e4b0998877524d1029fd3e6879210422ee3780459e28a1f03a8a2"},
+    {file = "sphinxcontrib_devhelp-2.0.0.tar.gz", hash = "sha256:411f5d96d445d1d73bb5d52133377b4248ec79db5c793ce7dbe59e074b4dd1ad"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.6"
+version = "2.1.0"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_htmlhelp-2.0.6-py3-none-any.whl", hash = "sha256:1b9af5a2671a61410a868fce050cab7ca393c218e6205cbc7f590136f207395c"},
-    {file = "sphinxcontrib_htmlhelp-2.0.6.tar.gz", hash = "sha256:c6597da06185f0e3b4dc952777a04200611ef563882e0c244d27a15ee22afa73"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0-py3-none-any.whl", hash = "sha256:166759820b47002d22914d64a075ce08f4c46818e17cfc9470a9786b759b19f8"},
+    {file = "sphinxcontrib_htmlhelp-2.1.0.tar.gz", hash = "sha256:c9e2916ace8aad64cc13a0d233ee22317f2b9025b9cf3295249fa985cc7082e9"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
@@ -1652,33 +1687,33 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
-version = "1.0.8"
+version = "2.0.0"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_qthelp-1.0.8-py3-none-any.whl", hash = "sha256:323d6acc4189af76dfe94edd2a27d458902319b60fcca2aeef3b2180c106a75f"},
-    {file = "sphinxcontrib_qthelp-1.0.8.tar.gz", hash = "sha256:db3f8fa10789c7a8e76d173c23364bdf0ebcd9449969a9e6a3dd31b8b7469f03"},
+    {file = "sphinxcontrib_qthelp-2.0.0-py3-none-any.whl", hash = "sha256:b18a828cdba941ccd6ee8445dbe72ffa3ef8cbe7505d8cd1fa0d42d3f2d5f3eb"},
+    {file = "sphinxcontrib_qthelp-2.0.0.tar.gz", hash = "sha256:4fe7d0ac8fc171045be623aba3e2a8f613f8682731f9153bb2e40ece16b9bbab"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
-version = "1.1.10"
+version = "2.0.0"
 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "sphinxcontrib_serializinghtml-1.1.10-py3-none-any.whl", hash = "sha256:326369b8df80a7d2d8d7f99aa5ac577f51ea51556ed974e7716cfd4fca3f6cb7"},
-    {file = "sphinxcontrib_serializinghtml-1.1.10.tar.gz", hash = "sha256:93f3f5dc458b91b192fe10c397e324f262cf163d79f3282c158e8436a2c4511f"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl", hash = "sha256:6e2cb0eef194e10c27ec0023bfeb25badbbb5868244cf5bc5bdc04e4464bf331"},
+    {file = "sphinxcontrib_serializinghtml-2.0.0.tar.gz", hash = "sha256:e9d912827f872c029017a53f0ef2180b327c3f7fd23c87229f7a8e8b70031d4d"},
 ]
 
 [package.extras]
-lint = ["docutils-stubs", "flake8", "mypy"]
+lint = ["mypy", "ruff (==0.5.5)", "types-docutils"]
 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
@@ -1823,13 +1858,13 @@ files = [
 
 [[package]]
 name = "xarray"
-version = "2024.6.0"
+version = "2024.7.0"
 description = "N-D labeled arrays and datasets in Python"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "xarray-2024.6.0-py3-none-any.whl", hash = "sha256:721a7394e8ec3d592b2d8ebe21eed074ac077dc1bb1bd777ce00e41700b4866c"},
-    {file = "xarray-2024.6.0.tar.gz", hash = "sha256:0b91e0bc4dc0296947947640fe31ec6e867ce258d2f7cbc10bedf4a6d68340c7"},
+    {file = "xarray-2024.7.0-py3-none-any.whl", hash = "sha256:1b0fd51ec408474aa1f4a355d75c00cc1c02bd425d97b2c2e551fd21810e7f64"},
+    {file = "xarray-2024.7.0.tar.gz", hash = "sha256:4cae512d121a8522d41e66d942fb06c526bc1fd32c2c181d5fe62fe65b671638"},
 ]
 
 [package.dependencies]
@@ -1851,4 +1886,4 @@ harmony = ["harmony-service-lib"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.10,<4.0"
-content-hash = "e76670fbfec14267dd53bbbc004c945cf708f2e5d9a9ffbcacacb248356145b2"
+content-hash = "161a76b2c499c39fc7442a582053b5d0c191c376362b26c6edbb68902dc54fa8"
diff --git a/pyproject.toml b/pyproject.toml
index 138903a..21d6408 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ python = ">=3.10,<4.0"
 boto3 = "^1.28.3"
 requests = "^2.31.0"
 netcdf4 = "^1.6.4"
-xarray = "^2024.6.0"
+xarray = "^2024.7.0"
 rio-cogeo = "^5.3.3"
 rasterio = "^1.3.8"
 rioxarray = "^0.17.0"
@@ -39,6 +39,10 @@ harmony = ["harmony-service-lib"]
 [tool.poetry.scripts]
 net2cog_harmony = 'net2cog.netcdf_convert_harmony:main'
 
+[tool.coverage.run]
+source = ['net2cog']
+relative_files = true
+
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
diff --git a/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json b/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json
index 7fe6fbb..1172cbb 100644
--- a/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json
+++ b/tests/data/test_netcdf_convert_harmony/test_service_invoke.input.json
@@ -13,15 +13,20 @@
       "variables": [
         {
           "id": "V0001-EXAMPLE",
-          "name": "ExampleVar",
-          "fullPath": "example/group/path/ExampleVar"
+          "name": "sss_smap",
+          "fullPath": "sss_smap"
         }
       ],
       "granules": [
         {
           "id": "RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0",
           "name": "Example2",
-          "url": "file:///home/tests/data/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc"
+          "url": "file:///home/tests/data/RSS_smap_SSS_L3_8day_running_2020_005_FNL_v04.0.nc",
+          "temporal": {
+            "start": "2001-01-01T01:01:01Z",
+            "end": "2002-02-02T02:02:02Z"
+          },
+          "bbox": [-1, -2, 3, 4]
         }
       ]
     }