diff --git a/.github/workflows/.release-created.yml b/.github/workflows/.release-created.yml new file mode 100644 index 0000000..94067e0 --- /dev/null +++ b/.github/workflows/.release-created.yml @@ -0,0 +1,63 @@ + +name: Release Branch Created + +# Run whenever a ref is created https://docs.github.com/en/actions/reference/events-that-trigger-workflows#create +on: + create + +jobs: + # First job in the workflow builds and verifies the software artifacts + bump: + name: Bump minor version on develop + # The type of runner that the job will run on + runs-on: ubuntu-latest + # Only run if ref created was a release branch + if: + ${{ startsWith(github.ref, 'refs/heads/release/') }} + steps: + # Checks-out the develop branch + - uses: actions/checkout@v2 + with: + ref: 'refs/heads/develop' + - uses: actions/setup-python@v2 + with: + python-version: 3.9 + - name: Install Poetry + uses: abatilo/actions-poetry@v2.0.0 + with: + poetry-version: 1.3.2 + - name: Bump minor version + env: + COMMIT_VERSION: ${{ github.ref }} + run: | + + # only update the develop branch if were making #.#.0 release + # Get the branch name from the GITHUB_REF environment variable + branch_name=${GITHUB_REF#refs/heads/} + + # Extract the last number in the branch name using a regular expression + if [[ $branch_name =~ /([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then + + first_number=${BASH_REMATCH[1]} + middle_number=${BASH_REMATCH[2]} + last_number=${BASH_REMATCH[3]} + + # Increment the middle number by 1 + incremented_middle_number=$((middle_number + 1)) + + # Check if the last number is '0' + if [ "$last_number" == "0" ]; then + + update_version=$first_number.$incremented_middle_number.$last_number-alpha.1 + + poetry version $update_version + echo "software_version=$update_version" >> $GITHUB_ENV + + git config --global user.name 'podaac-tig bot' + git config --global user.email 'podaac-tig@noreply.github.com' + git commit -am "/version ${{ env.software_version }}" + git push + + fi + + fi \ No newline at end of file diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 46e0e66..f7c6aab 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -184,9 +184,9 @@ jobs: # These are gradle-specific steps for installing the application - name: Install Software run: | - pip install setuptools -U \ - pip install pylint \ - pip install pytest \ + pip install setuptools -U + pip install pylint + pip install pytest poetry install @@ -240,9 +240,8 @@ jobs: # This is where tests go - name: Run Poetry Tests run: | - poetry run pylint podaac \ - poetry run flake8 podaac \ - poetry run pytest --help \ + poetry run pylint podaac + poetry run flake8 podaac poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=html -m "not aws and not integration" tests/ # poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=xml:build/reports/coverage.xml -m "not aws and not integration" tests/ @@ -298,7 +297,7 @@ jobs: - name: Upload Release Artifacts uses: ncipollo/release-action@v1.12.0 with: - tag: ${{ env.the_version }} + tag: ${{ env.new_version }} artifacts: "*.zip" token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.pylintrc b/.pylintrc index 14b4157..162a480 100644 --- a/.pylintrc +++ b/.pylintrc @@ -60,17 +60,7 @@ confidence= # --enable=similarities". If you want to run only the classes checker, but have # no Warning level messages displayed, use "--disable=all --enable=classes # --disable=W". -disable=print-statement, - parameter-unpacking, - unpacking-in-except, - old-raise-syntax, - backtick, - long-suffix, - old-ne-operator, - old-octal-literal, - import-star-module-level, - non-ascii-bytes-literal, - raw-checker-failed, +disable=raw-checker-failed, bad-inline-option, locally-disabled, file-ignored, @@ -78,67 +68,6 @@ disable=print-statement, useless-suppression, deprecated-pragma, use-symbolic-message-instead, - apply-builtin, - basestring-builtin, - buffer-builtin, - cmp-builtin, - coerce-builtin, - execfile-builtin, - file-builtin, - long-builtin, - raw_input-builtin, - reduce-builtin, - standarderror-builtin, - unicode-builtin, - xrange-builtin, - coerce-method, - delslice-method, - getslice-method, - setslice-method, - no-absolute-import, - old-division, - dict-iter-method, - dict-view-method, - next-method-called, - metaclass-assignment, - indexing-exception, - raising-string, - reload-builtin, - oct-method, - hex-method, - nonzero-method, - cmp-method, - input-builtin, - round-builtin, - intern-builtin, - unichr-builtin, - map-builtin-not-iterating, - zip-builtin-not-iterating, - range-builtin-not-iterating, - filter-builtin-not-iterating, - using-cmp-argument, - eq-without-hash, - div-method, - idiv-method, - rdiv-method, - exception-message-attribute, - invalid-str-codec, - sys-max-int, - bad-python3-import, - deprecated-string-function, - deprecated-str-translate-call, - deprecated-itertools-function, - deprecated-types-field, - next-method-defined, - dict-items-not-iterating, - dict-keys-not-iterating, - dict-values-not-iterating, - deprecated-operator-function, - deprecated-urllib-function, - xreadlines-attribute, - deprecated-sys-function, - exception-escape, - comprehension-escape, too-many-arguments, too-many-locals # Enable the message, report, category or checker with the given id(s). You can @@ -331,8 +260,8 @@ max-module-lines=1000 # separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. # `trailing-comma` allows a space between comma and closing bracket: (a, ). # `empty-line` allows space-only lines. -no-space-check=trailing-comma, - dict-separator +#no-space-check=trailing-comma, +# dict-separator # Allow the body of a class to be on the same line as the declaration if body # contains single statement. @@ -567,7 +496,7 @@ min-public-methods=2 # Exceptions that will emit a warning when being caught. Defaults to # "BaseException, Exception". -overgeneral-exceptions=BaseException, - Exception +#overgeneral-exceptions=BaseException, +# Exception disable=consider-using-f-string, W1514, R0402, R1730 diff --git a/CHANGELOG.md b/CHANGELOG.md index 43cacf8..a33a940 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Security +## [0.6.0] + +### Added +- ** Issue-2 ** + - Add lambda to clean up cma messages with descriptions + - Add in variable description for images generated +### Changed +### Deprecated +### Removed +### Fixed +### Security + +## [0.5.0] + +### Added +- **PODAAC-5277** + - Update tig to handle multipe lon and lats for different groups + - Update some python libraries for snyk and cma python +- **PODAAC-5541** + - Replace spaces " " with "_" to handle group names with spaces + - Fixes collection AQUARIUS_L2_SSS_V5 +### Changed +### Deprecated +### Removed +### Fixed +### Security + ## [0.4.0] ### Added diff --git a/podaac/lambda_handler/clean_lambda_handler.py b/podaac/lambda_handler/clean_lambda_handler.py new file mode 100644 index 0000000..1f56b43 --- /dev/null +++ b/podaac/lambda_handler/clean_lambda_handler.py @@ -0,0 +1,68 @@ +"""lambda function used for image generation in aws lambda with cumulus""" + +import logging +import os +from cumulus_logger import CumulusLogger +from cumulus_process import Process + +cumulus_logger = CumulusLogger('tig_lambda_message_cleaner') + + +class CMACleaner(Process): + """ + A class to help clean up the CMA message after running tig. + """ + + def __init__(self, *args, **kwargs): + + super().__init__(*args, **kwargs) + self.logger = cumulus_logger + + def process(self): + """Main process to generate images for granules + + Returns + ---------- + dict + Payload that is returned to the cma which is a dictionary with list of granules + """ + + granules = self.input['granules'] + + for granule in granules: + for file in granule['files']: + if 'description' in file: + del file['description'] + + return self.input + + +def handler(event, context): + """handler that gets called by aws lambda + + Parameters + ---------- + event: dictionary + event from a lambda call + context: dictionary + context from a lambda call + + Returns + ---------- + string + A CMA json message + """ + + # pylint: disable=duplicate-code + levels = { + 'critical': logging.CRITICAL, + 'error': logging.ERROR, + 'warn': logging.WARNING, + 'warning': logging.WARNING, + 'info': logging.INFO, + 'debug': logging.DEBUG + } + logging_level = os.environ.get('LOGGING_LEVEL', 'info') + cumulus_logger.logger.level = levels.get(logging_level, 'info') + cumulus_logger.setMetadata(event, context) + return CMACleaner.cumulus_handler(event, context=context) diff --git a/podaac/lambda_handler/lambda_handler.py b/podaac/lambda_handler/lambda_handler.py index 654cbd6..e596b7a 100644 --- a/podaac/lambda_handler/lambda_handler.py +++ b/podaac/lambda_handler/lambda_handler.py @@ -198,7 +198,7 @@ def download_palette_files(self, config): if palette not in palettes: palettes.append(palette) palette_url = "{}/{}.json".format(palette_base_url, palette) - response = requests.get(palette_url) + response = requests.get(palette_url, timeout=60) palette_full_path = "{}/{}.json".format(self.path, palette) with open(palette_full_path, 'wb') as file_: file_.write(response.content) @@ -217,7 +217,7 @@ def get_config(self): if config_url: file_url = "{}/{}.cfg".format(config_url, config_name) - response = requests.get(file_url) + response = requests.get(file_url, timeout=60) cfg_file_full_path = "{}/{}.cfg".format(self.path, config_name) with open(cfg_file_full_path, 'wb') as file_: file_.write(response.content) @@ -226,7 +226,7 @@ def get_config(self): config_s3 = 's3://{}.cfg'.format(os.path.join(config_bucket, config_dir, config_name)) cfg_file_full_path = self.download_file_from_s3(config_s3, self.path) else: - raise Exception('Environment variable to get configuration files were not set') + raise ValueError('Environment variable to get configuration files were not set') return cfg_file_full_path @@ -257,7 +257,7 @@ def process(self): return self.input - def generate_file_dictionary(self, file_, image_file, output_file_basename, collection_files, buckets): + def generate_file_dictionary(self, file_, image_file, output_file_basename, collection_files, buckets, variable, group): """function to generate an information for an image for cumulus Parameters @@ -272,6 +272,10 @@ def generate_file_dictionary(self, file_, image_file, output_file_basename, coll collection list of files on how to handle each file type buckets: dict dictionary of buckets + variable: string + variable used to generate image file + group: string + group the variable belong to could be none Returns ---------- @@ -279,6 +283,10 @@ def generate_file_dictionary(self, file_, image_file, output_file_basename, coll dictionary data of an image uploaded to s3 """ + description = variable + if group is not None: + description = f'{group}/{variable}' + try: prefix = os.path.dirname(file_['key']) upload_file_dict = { @@ -286,7 +294,8 @@ def generate_file_dictionary(self, file_, image_file, output_file_basename, coll "fileName": output_file_basename, "bucket": self.get_bucket(output_file_basename, collection_files, buckets)['name'], "size": os.path.getsize(image_file), - "type": self.get_file_type(output_file_basename, collection_files) + "type": self.get_file_type(output_file_basename, collection_files), + "description": description } s3_link = f's3://{upload_file_dict["bucket"]}/{upload_file_dict["key"]}' @@ -340,12 +349,12 @@ def image_generate(self, file_, config_file, palette_dir, granule_id): with open(config_file) as config_f: read_config = json.load(config_f) - variables = read_config.get('imgVariables', []) + variables_config = read_config.get('imgVariables', []) parent_connections = [] processes = [] - var_list = [variables[:len(variables)//2], variables[len(variables)//2:]] + var_list = [variables_config[:len(variables_config)//2], variables_config[len(variables_config)//2:]] for variables in var_list: if variables: @@ -366,10 +375,13 @@ def image_generate(self, file_, config_file, palette_dir, granule_id): for parent_connection in parent_connections: image_list += parent_connection.recv()[0] - for image_file in image_list: + for image_dict in image_list: try: + image_file = image_dict.get('image_file') + variable = image_dict.get('variable') + group = image_dict.get('group') output_file_basename = os.path.basename(image_file) - upload_file_dict = self.generate_file_dictionary(file_, image_file, output_file_basename, collection_files, buckets) + upload_file_dict = self.generate_file_dictionary(file_, image_file, output_file_basename, collection_files, buckets, variable, group) uploaded_files.append(upload_file_dict) except Exception as ex: self.logger.error("Error uploading image from s3: {}".format(ex), exc_info=True) diff --git a/podaac/tig/tig.py b/podaac/tig/tig.py index 9e9a495..4aacf13 100644 --- a/podaac/tig/tig.py +++ b/podaac/tig/tig.py @@ -103,7 +103,7 @@ def get_lon_lat_grids(self): lon_grid, lat_grid = np.meshgrid(exact_lons, exact_lats) return(lon_grid, lat_grid) - def get_lon_lat(self): + def get_lon_lat(self, param_group=None): """ Function to get the longitude masked array and latatiude masked array @@ -114,6 +114,9 @@ def get_lon_lat(self): group, _, lon_var = self.config['lonVar'].rpartition('/') _, _, lat_var = self.config['latVar'].rpartition('/') + + if param_group: + group = param_group local_dataset = xr.open_dataset(self.input_file, group=group, decode_times=False) lon_array = local_dataset[lon_var].to_masked_array() @@ -147,6 +150,8 @@ def generate_images(self, image_format='png', nearest=False, world_file=False, g Fill in values from the nearest grid cell to match pixel resolution world_file : bool Output an Esri world file for each image that can be used by GIS tools + granule_id : string + The granule_id of the granule file Returns ------- list @@ -154,6 +159,34 @@ def generate_images(self, image_format='png', nearest=False, world_file=False, g """ self.logger.info("\nProcessing %s", self.input_file) + output_images = [] + if self.config.get('multi_lon_lat'): + for group in self.config.get('multi_groups'): + output_images += self.generate_images_group(image_format, nearest, world_file, granule_id, group=group) + else: + output_images = self.generate_images_group(image_format, nearest, world_file, granule_id, group=None) + return output_images + + def generate_images_group(self, image_format='png', nearest=False, world_file=False, granule_id="", group=None): + """ + Generates images for each configured variable in a NetCDF file. + Parameters + ---------- + image_format : string + Any output image formatted supported by matplotlib + nearest : bool + Fill in values from the nearest grid cell to match pixel resolution + world_file : bool + Output an Esri world file for each image that can be used by GIS tools + granule_id : string + The granule_id of the granule file + param_group : string + The group name in which the dataset file will be open with + Returns + ------- + list + List of dictionary with image_file location, variable and group + """ # Only use alpha channel with PNGs if image_format == 'png': @@ -162,7 +195,7 @@ def generate_images(self, image_format='png', nearest=False, world_file=False, g self.logger.debug("No alpha channel") alpha = False - lon_array, lat_array = self.get_lon_lat() + lon_array, lat_array = self.get_lon_lat(param_group=group) # Get Bounds of the dataset eastern = lon_array.max() @@ -200,9 +233,10 @@ def generate_images(self, image_format='png', nearest=False, world_file=False, g image_format, nearest, world_file, - granule_id) + granule_id, + group) if output_image_file is not None: - output_images.append(output_image_file) + output_images.append({'image_file': output_image_file, 'variable': var['id'], 'group': group}) self.logger.info("Finished processing variables") return output_images @@ -215,7 +249,8 @@ def process_variable(self, image_format='png', nearest=False, world_file=False, - granule_id=""): + granule_id="", + param_group=None): """ Processes an invidual variable to generate an image Parameters @@ -234,6 +269,10 @@ def process_variable(self, Fill in values from the nearest grid cell to match pixel resolution world_file : bool Output an Esri world file for each image that can be used by GIS tools + granule_id : string + The granule_id of the granule file + param_group : string + The group name in which the dataset file will be open with Returns ------- list @@ -245,6 +284,8 @@ def process_variable(self, self.logger.info('variable: %s', config_variable) group, _, variable = config_variable.rpartition('/') + if param_group: + group = param_group local_dataset = xr.open_dataset(self.input_file, group=group, decode_times=False) # Get variable array and fill value @@ -256,7 +297,7 @@ def process_variable(self, # if no fill value get fill value from configuration if defined fill_value = var.get('fill_value') if fill_value is None: - raise Exception(f'There is no fill value for variable {variable}') from KeyError + raise KeyError(f'There is no fill value for variable {variable}') from KeyError local_dataset.close() # Get palette info @@ -264,7 +305,7 @@ def process_variable(self, colormap = load_json_palette(self.palette_dir, var['palette'], alpha) # Set the output location - group_string = group.strip('/').replace('/', '.') + group_string = group.strip('/').replace('/', '.').replace(" ", "_") file_name = '.'.join(x for x in [granule_id, group_string, variable, image_format] if x) output_location = "{}/{}".format(self.output_dir, file_name) if not os.path.exists(self.output_dir): @@ -477,7 +518,11 @@ def load_json_palette(palette_dir, palette_name, alpha): for y in palette['Palette']['values']['value']] cmap = col.ListedColormap(colors, palette_name) - cm.register_cmap(cmap=cmap) + try: + cm.register_cmap(cmap=cmap) + except ValueError: + # palette register via other images + pass return cm.get_cmap(palette_name) diff --git a/poetry.lock b/poetry.lock index 54c655f..9486f0f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,145 +1,448 @@ +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. + [[package]] name = "alabaster" -version = "0.7.12" +version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false -python-versions = "*" +python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] [[package]] name = "astroid" -version = "2.11.2" +version = "2.15.6" description = "An 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aws_lambda_function.tig_cleaner_task.arn +} diff --git a/terraform/tig_lambda.tf b/terraform/tig_lambda.tf index 338ad10..2b9d936 100644 --- a/terraform/tig_lambda.tf +++ b/terraform/tig_lambda.tf @@ -42,3 +42,38 @@ resource "aws_cloudwatch_log_group" "tig_task" { retention_in_days = var.task_logs_retention_in_days tags = merge(var.tags, { Project = var.prefix }) } + + +resource "aws_lambda_function" "tig_cleaner_task" { + function_name = "${local.lambda_resources_name}-lambda-cleaner" + image_uri = var.image + role = var.role + timeout = var.timeout + memory_size = var.memory_size + package_type = "Image" + + image_config { + command = ["podaac.lambda_handler.clean_lambda_handler.handler"] + entry_point = var.entry_point + working_directory = var.working_directory + } + + environment { + variables = { + CMR_ENVIRONMENT = var.cmr_environment + stackName = var.prefix + CONFIG_BUCKET = var.config_bucket + CONFIG_DIR = var.config_dir + LOGGING_LEVEL = var.log_level + CONFIG_URL = var.config_url + PALETTE_URL = var.palette_url + } + } + + vpc_config { + subnet_ids = var.subnet_ids + security_group_ids = var.security_group_ids + } + + tags = merge(var.tags, { Project = var.prefix }) +} \ No newline at end of file diff --git a/tests/images/SWOT_GPR_2PTP003_005_20111115_030538_20111115_035643.nc/data_01.ku.ssha.png b/tests/images/SWOT_GPR_2PTP003_005_20111115_030538_20111115_035643.nc/data_01.ku.ssha.png index d36f862..0dcadbe 100644 Binary files a/tests/images/SWOT_GPR_2PTP003_005_20111115_030538_20111115_035643.nc/data_01.ku.ssha.png and b/tests/images/SWOT_GPR_2PTP003_005_20111115_030538_20111115_035643.nc/data_01.ku.ssha.png differ diff --git a/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_density.png b/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_density.png index 14938f0..5dfad6e 100644 Binary files a/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_density.png and b/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_density.png differ diff --git a/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_temperature.png b/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_temperature.png index 9ac5a80..300ec4c 100644 Binary files a/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_temperature.png and b/tests/images/cyg.ddmi.s20201031-000000-e20201031-235959.l2.surface-flux-cdr.a10.d10.nc/air_temperature.png differ diff --git a/tests/input.txt b/tests/input.txt index ac6276e..490a6e4 100644 --- a/tests/input.txt +++ b/tests/input.txt @@ -56,7 +56,15 @@ "fileName": "test_granule.nc", "key": "test_folder/test_granule.nc", "type":"data" + }, + { + "bucket": "test-prefix-protected-test", + "fileName": "test_granule.nc", + "key": "test_folder/test_granule.nc", + "type": "data", + "description": "test_var" } + ] } ] diff --git a/tests/test_lambda_handler.py b/tests/test_lambda_handler.py index 48b81dc..8a52b35 100644 --- a/tests/test_lambda_handler.py +++ b/tests/test_lambda_handler.py @@ -51,6 +51,10 @@ "type": { "description": "Type of file (e.g. data, metadata, browse)", "type": "string" + }, + "description": { + "description": "variable values", + "type": "string" } } } diff --git a/tests/test_lambda_handler_cleaner.py b/tests/test_lambda_handler_cleaner.py new file mode 100644 index 0000000..0fa8cad --- /dev/null +++ b/tests/test_lambda_handler_cleaner.py @@ -0,0 +1,16 @@ +import json +import os +from podaac.lambda_handler import clean_lambda_handler + +def test_get_bucket(): + """Test get_bucket function to get the correct bucket for a file""" + + dir_path = os.path.dirname(os.path.realpath(__file__)) + input_file = dir_path + '/input.txt' + + with open(input_file) as json_event: + event = json.load(json_event) + output = clean_lambda_handler.handler(event, {}) + + for file in output['payload']['granules'][0]['files']: + assert 'description' not in file \ No newline at end of file