From 3d7e1a699ebc0512052af59401b9cfb47c52f3d8 Mon Sep 17 00:00:00 2001 From: James Wood Date: Fri, 11 Oct 2024 15:20:59 -0700 Subject: [PATCH 1/6] add granule list --- podaac/hitide_backfill_tool/args.py | 1 + podaac/hitide_backfill_tool/cli.py | 46 +- podaac/hitide_backfill_tool/cmr/search.py | 59 ++ .../cnm_message_writer.py | 1 - poetry.lock | 946 +++++++++--------- pyproject.toml | 2 +- 6 files changed, 558 insertions(+), 497 deletions(-) diff --git a/podaac/hitide_backfill_tool/args.py b/podaac/hitide_backfill_tool/args.py index 5c324a9..3c04b9c 100644 --- a/podaac/hitide_backfill_tool/args.py +++ b/podaac/hitide_backfill_tool/args.py @@ -41,6 +41,7 @@ def create_parser(): parser.add_argument("--provider") parser.add_argument("-sd", "--start-date") parser.add_argument("-ed", "--end-date") + parser.add_argument("--granule-list-file", default=None) parser.add_argument("--page-size", type=int) parser.add_argument("--page-limit", type=int) parser.add_argument("--edl-token") diff --git a/podaac/hitide_backfill_tool/cli.py b/podaac/hitide_backfill_tool/cli.py index 97027e4..8dadec8 100644 --- a/podaac/hitide_backfill_tool/cli.py +++ b/podaac/hitide_backfill_tool/cli.py @@ -11,6 +11,7 @@ import json from datetime import datetime, timezone import requests +import traceback from podaac.hitide_backfill_tool.cmr.search import GranuleSearch from podaac.hitide_backfill_tool.cmr.cmr_granule import CmrGranule @@ -127,7 +128,7 @@ class Backfiller: # pylint: disable=too-many-instance-attributes,too-many-arguments def __init__(self, search, message_writer, message_senders, granule_options, logger, - message_limit, cli_execution_id, s3, collection): + message_limit, cli_execution_id, s3, collection, granule_list_file): # pylint: disable=C0103 # dependencies @@ -140,6 +141,8 @@ def __init__(self, search, message_writer, message_senders, granule_options, log self.cli_execution_id = cli_execution_id self.s3 = s3 self.collection = collection + self.granule_list_file = granule_list_file + self.granule_list = None # statistics self.granules_analyzed = 0 @@ -178,28 +181,43 @@ def __init__(self, search, message_writer, message_senders, granule_options, log destination_message.append('nowhere') self.destination_message = f"Messages being sent to {', '.join(destination_message)}" + if self.granule_list_file: + self.read_granule_list_file() + # for thread-safe operations self.lock = Lock() + def read_granule_list_file(self): + """read the self.granule_list_file and store the granule list in self.granule_list""" + + with open(self.granule_list_file, 'r') as file: + self.granule_list = [line.strip() for line in file] + + def process_granules(self): """Loop through granules (in parallel) from granule-search and call the process_one_granule() method.""" - while self.search.get_next_page(): - print("Processing granules...", end='', flush=True) + if self.granule_list: + print('Processing granules from granule list file...', end='', flush=True) + granules = self.search.get_granules_from_list(self.granule_list) + with ThreadPoolExecutor() as executor: - executor.map(self.process_one_granule, self.search.granules()) + executor.map(self.process_one_granule, granules) print("done.") - if self.message_limit_reached(): - self.logger.info("\n**** Message limit reached ****") - return - self.log_stats() + else: + while self.search.get_next_page(): + print("Processing granules...", end='', flush=True) + with ThreadPoolExecutor() as executor: + executor.map(self.process_one_granule, self.search.granules()) + print("done.") + if self.message_limit_reached(): + self.logger.info("\n**** Message limit reached ****") + return + self.log_stats() def print_monthly_results_table(self): """Function to print out monthly stats""" - if not self.message_senders: - print("** NOTE: When in preview mode, the messages sent count may not be accurate since it's only simulating sending messages. ** \n") - print("Monthly Counts Summary:\n") header = f"{'Date':<10} {'Granules':<10} {'Need Image':<12} {'Need Footprint':<16} {'Both FP & BBox':<16} {'Need DMRPP':<12}" @@ -274,6 +292,7 @@ def process_one_granule(self, umm_granule): self.granules_analyzed += 1 except Exception as exc: self.logger.error(f"Error: {str(exc)}\n") + traceback.print_exc() def update_image(self, granule): """Create and send messages for one granule's image update.""" @@ -420,6 +439,9 @@ def log_stats(self): f"-- {self.destination_message} --\n" "==============================================================\n" ) + if not self.message_senders: + print("** NOTE: When in preview mode, the messages sent count may not be accurate since it's only simulating sending messages. ** \n") + if len(self.concept_ids_needing_image) > 0: self.logger.info(f"Granule IDs needing images (showing first 100):\n" f" {self.concept_ids_needing_image[:100]}\n" @@ -483,7 +505,7 @@ def main(args=None): # setup backfiller backfiller = Backfiller(search, message_writer, message_senders, - granule_options, logger, args.message_limit, args.cli_execution_id, s3, collection) + granule_options, logger, args.message_limit, args.cli_execution_id, s3, collection, args.granule_list_file) # Check forge configurations before running backfill backfiller.get_forge_tig_configuration() diff --git a/podaac/hitide_backfill_tool/cmr/search.py b/podaac/hitide_backfill_tool/cmr/search.py index de5fd18..dadfa2a 100644 --- a/podaac/hitide_backfill_tool/cmr/search.py +++ b/podaac/hitide_backfill_tool/cmr/search.py @@ -3,6 +3,7 @@ import ast import json import logging +import re from requests import Session from requests.exceptions import RequestException from requests.adapters import HTTPAdapter @@ -192,6 +193,64 @@ def pages_loaded(self): """Return the total number of granule search pages that have been loaded up to this point""" return self._pages_loaded + def get_one_granule(self, granule_name): + """Request a single granule from CMR using granule_name""" + + url = (f"{self._base_url}/search/granules.umm_json?") + + # Regex for granule concept id + pattern = r"^G\d{10}-" + url += (f"concept_id={granule_name}" if re.match(pattern, granule_name) else + f"provider={self._provider}&short_name={self._collection_short_name}&readable_granule_name={granule_name}") + + headers = {} + if self._edl_token: + headers["Authorization"] = f"Bearer {self._edl_token}" + elif self._launchpad_token: + headers["Authorization"] = self._launchpad_token + + body = {} + try: + response = self.session.get(url, headers=headers) + response.raise_for_status() + + body = json.loads(response.text) + except RequestException as exc: + self._logger.error(f"Error requesting CMR: {exc}") + except json.JSONDecodeError as exc: + self._logger.error(f"Error decoding CMR JSON response: {exc}") + + # Error message if there is a problem + if response.status_code >= 400 or body.get("hits") is None or body.get("items") is None or len(body.get("items")) == 0: + granule_message = f"Granule not found: {granule_name}" + self._logger.error( + f"\nCMR problem:\n" + f"url: {url}\n" + f"----------\n" + f"http_code: {response.status_code}\n" + f"body: {response.text}\n" + f"----------\n" + f"{granule_message}\n" + ) + raise Exception("CMR error") + + return body["items"][0] + + + def get_granules_from_list(self, granule_list): + """Iterate through granule_list and get cmr for each item and return a list of umm granule json""" + + granules = [] + + for granule_name in granule_list: + try: + granule = self.get_one_granule(granule_name) + granules.append(granule) + except Exception: + pass + + return granules + # # Helpers # diff --git a/podaac/hitide_backfill_tool/cnm_message_writer.py b/podaac/hitide_backfill_tool/cnm_message_writer.py index 30aa101..2f0944f 100644 --- a/podaac/hitide_backfill_tool/cnm_message_writer.py +++ b/podaac/hitide_backfill_tool/cnm_message_writer.py @@ -89,5 +89,4 @@ def write(self, granule, needs_footprint, needs_image, needs_dmrpp, skip_cmr_ope "username": self.user } - print(message["payload"]) return json.dumps(message) diff --git a/poetry.lock b/poetry.lock index e4be6d7..f7a33a8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,13 +2,13 @@ [[package]] name = "astroid" -version = "3.2.4" +version = "3.3.5" description = "An abstract syntax tree for Python with inference support." optional = false -python-versions = ">=3.8.0" +python-versions = ">=3.9.0" files = [ - {file = "astroid-3.2.4-py3-none-any.whl", hash = "sha256:413658a61eeca6202a59231abb473f932038fbcbf1666587f66d482083413a25"}, - {file = "astroid-3.2.4.tar.gz", hash = "sha256:0e14202810b30da1b735827f78f5157be2bbd4a7a59b7707ca0bfc2fb4c0063a"}, + {file = "astroid-3.3.5-py3-none-any.whl", hash = "sha256:a9d1c946ada25098d790e079ba2a1b112157278f3fb7e718ae6a9252f5835dc8"}, + {file = "astroid-3.3.5.tar.gz", hash = "sha256:5cfc40ae9f68311075d27ef68a4841bdc5cc7f6cf86671b49f00607d30188e2d"}, ] [package.dependencies] @@ -16,17 +16,17 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} [[package]] name = "boto3" -version = "1.35.13" +version = "1.35.39" description = "The AWS SDK for Python" optional = false python-versions = ">=3.8" files = [ - 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15 insertions(+), 12 deletions(-) diff --git a/podaac/hitide_backfill_tool/cmr/search.py b/podaac/hitide_backfill_tool/cmr/search.py index dadfa2a..57d2fdb 100644 --- a/podaac/hitide_backfill_tool/cmr/search.py +++ b/podaac/hitide_backfill_tool/cmr/search.py @@ -1,5 +1,6 @@ """Search for CMR granules""" +from concurrent.futures import ThreadPoolExecutor import ast import json import logging @@ -194,9 +195,9 @@ def pages_loaded(self): return self._pages_loaded def get_one_granule(self, granule_name): - """Request a single granule from CMR using granule_name""" + """Request a single granule from CMR using granule_name or concept_id""" - url = (f"{self._base_url}/search/granules.umm_json?") + url = f"{self._base_url}/search/granules.umm_json?" # Regex for granule concept id pattern = r"^G\d{10}-" @@ -235,22 +236,24 @@ def get_one_granule(self, granule_name): raise Exception("CMR error") return body["items"][0] - def get_granules_from_list(self, granule_list): - """Iterate through granule_list and get cmr for each item and return a list of umm granule json""" - - granules = [] - - for granule_name in granule_list: + """Iterate through granule_list, get cmr for each item in parallel, and return a list of umm granule json""" + + def safe_get_granule(granule_name): + """Safely get one granule, catching exceptions""" try: - granule = self.get_one_granule(granule_name) - granules.append(granule) + return self.get_one_granule(granule_name) except Exception: - pass + return None - return granules + with ThreadPoolExecutor() as executor: + granules = list(executor.map(lambda granule_name: + safe_get_granule(granule_name), granule_list)) + # Filter out any None values due to exceptions + return [granule for granule in granules if granule is not None] + # # Helpers # From 5e7e3c6d6df00dc38a7cc1f8efa8885f4e7bb20a Mon Sep 17 00:00:00 2001 From: James Wood Date: Mon, 14 Oct 2024 10:30:04 -0700 Subject: [PATCH 3/6] fixes for pylint8 and flake8 --- podaac/hitide_backfill_tool/cli.py | 10 ++++------ podaac/hitide_backfill_tool/cmr/cmr_granule.py | 2 +- podaac/hitide_backfill_tool/cmr/search.py | 14 ++++++++------ podaac/hitide_backfill_tool/cnm_message_writer.py | 2 +- podaac/hitide_backfill_tool/config_creator.py | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/podaac/hitide_backfill_tool/cli.py b/podaac/hitide_backfill_tool/cli.py index 8dadec8..d419bc9 100644 --- a/podaac/hitide_backfill_tool/cli.py +++ b/podaac/hitide_backfill_tool/cli.py @@ -10,8 +10,8 @@ import copy import json from datetime import datetime, timezone -import requests import traceback +import requests from podaac.hitide_backfill_tool.cmr.search import GranuleSearch from podaac.hitide_backfill_tool.cmr.cmr_granule import CmrGranule @@ -124,8 +124,7 @@ class Backfiller: # Disable broad-except since many types of error indicate the absense # of data when attempting access (e.g. TypeError, IndexError, KeyError, ...) # pylint: disable=broad-except - - # pylint: disable=too-many-instance-attributes,too-many-arguments + # pylint: disable=too-many-instance-attributes,too-many-arguments,too-many-positional-arguments def __init__(self, search, message_writer, message_senders, granule_options, logger, message_limit, cli_execution_id, s3, collection, granule_list_file): @@ -190,10 +189,9 @@ def __init__(self, search, message_writer, message_senders, granule_options, log def read_granule_list_file(self): """read the self.granule_list_file and store the granule list in self.granule_list""" - with open(self.granule_list_file, 'r') as file: + with open(self.granule_list_file, 'r', encoding='utf-8') as file: self.granule_list = [line.strip() for line in file] - def process_granules(self): """Loop through granules (in parallel) from granule-search and call the process_one_granule() method.""" @@ -202,7 +200,7 @@ def process_granules(self): granules = self.search.get_granules_from_list(self.granule_list) with ThreadPoolExecutor() as executor: - executor.map(self.process_one_granule, granules) + executor.map(self.process_one_granule, granules) print("done.") else: while self.search.get_next_page(): diff --git a/podaac/hitide_backfill_tool/cmr/cmr_granule.py b/podaac/hitide_backfill_tool/cmr/cmr_granule.py index 141a7e2..dba7f82 100644 --- a/podaac/hitide_backfill_tool/cmr/cmr_granule.py +++ b/podaac/hitide_backfill_tool/cmr/cmr_granule.py @@ -11,7 +11,7 @@ class CmrGranule: # of data when attempting access (e.g. TypeError, IndexError, KeyError, ...) # pylint: disable=broad-except - # pylint: disable=too-many-instance-attributes + # pylint: disable=too-many-instance-attributes,too-many-positional-arguments # pylint: disable-next=too-many-arguments def __init__(self, umm_granule, diff --git a/podaac/hitide_backfill_tool/cmr/search.py b/podaac/hitide_backfill_tool/cmr/search.py index 57d2fdb..aff8ea3 100644 --- a/podaac/hitide_backfill_tool/cmr/search.py +++ b/podaac/hitide_backfill_tool/cmr/search.py @@ -1,5 +1,7 @@ """Search for CMR granules""" +# pylint: disable=line-too-long + from concurrent.futures import ThreadPoolExecutor import ast import json @@ -15,7 +17,7 @@ class GranuleSearch: """Searches for CMR granules, with paging""" - # pylint: disable=too-many-instance-attributes,too-many-arguments,too-many-locals + # pylint: disable=too-many-instance-attributes,too-many-arguments,too-many-locals,too-many-positional-arguments def __init__(self, base_url, @@ -198,7 +200,7 @@ def get_one_granule(self, granule_name): """Request a single granule from CMR using granule_name or concept_id""" url = f"{self._base_url}/search/granules.umm_json?" - + # Regex for granule concept id pattern = r"^G\d{10}-" url += (f"concept_id={granule_name}" if re.match(pattern, granule_name) else @@ -239,7 +241,8 @@ def get_one_granule(self, granule_name): def get_granules_from_list(self, granule_list): """Iterate through granule_list, get cmr for each item in parallel, and return a list of umm granule json""" - + + # pylint: disable=broad-except def safe_get_granule(granule_name): """Safely get one granule, catching exceptions""" try: @@ -248,12 +251,11 @@ def safe_get_granule(granule_name): return None with ThreadPoolExecutor() as executor: - granules = list(executor.map(lambda granule_name: - safe_get_granule(granule_name), granule_list)) + granules = list(executor.map(safe_get_granule, granule_list)) # Filter out any None values due to exceptions return [granule for granule in granules if granule is not None] - + # # Helpers # diff --git a/podaac/hitide_backfill_tool/cnm_message_writer.py b/podaac/hitide_backfill_tool/cnm_message_writer.py index 2f0944f..bbebb4e 100644 --- a/podaac/hitide_backfill_tool/cnm_message_writer.py +++ b/podaac/hitide_backfill_tool/cnm_message_writer.py @@ -6,7 +6,7 @@ class CnmMessageWriter: """Creates a Cumulus CNM message from granule.""" - # pylint: disable=too-many-instance-attributes,too-many-arguments + # pylint: disable=too-many-instance-attributes,too-many-arguments,too-many-positional-arguments def __init__(self, message_config, diff --git a/podaac/hitide_backfill_tool/config_creator.py b/podaac/hitide_backfill_tool/config_creator.py index c4978c1..5b73f11 100644 --- a/podaac/hitide_backfill_tool/config_creator.py +++ b/podaac/hitide_backfill_tool/config_creator.py @@ -99,7 +99,7 @@ def create_defaults(env): "aws_profile": "ngap-services-sit" } - raise f"create_defaults({env}) - env must be ops | uat | sit" + raise Exception(f"create_defaults({env}) - env must be ops | uat | sit") def create_config(args=None): From 20039a69276e96b81be8bab2633ea3355941a7ff Mon Sep 17 00:00:00 2001 From: James Wood Date: Mon, 14 Oct 2024 14:14:25 -0700 Subject: [PATCH 4/6] cleanup --- podaac/hitide_backfill_tool/cli.py | 15 +++++++++++++-- podaac/hitide_backfill_tool/cmr/search.py | 2 +- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/podaac/hitide_backfill_tool/cli.py b/podaac/hitide_backfill_tool/cli.py index d419bc9..bf0989b 100644 --- a/podaac/hitide_backfill_tool/cli.py +++ b/podaac/hitide_backfill_tool/cli.py @@ -187,7 +187,18 @@ def __init__(self, search, message_writer, message_senders, granule_options, log self.lock = Lock() def read_granule_list_file(self): - """read the self.granule_list_file and store the granule list in self.granule_list""" + """Read the granule_list_file and store contents in array granule_list + The items in the list are one granule per line: + Can be either a GranuleUR or a granlue concept ID, and all items must the same type. + Example: + 20240702060501-JPL-L2P_GHRSST-SSTskin-MODIS_A-D-v02.0-fv01.0 + 20240702083501-JPL-L2P_GHRSST-SSTskin-MODIS_A-N-v02.0-fv01.0 + 20240702174000-JPL-L2P_GHRSST-SSTskin-MODIS_A-D-v02.0-fv01.0 + OR + G3141860732-POCLOUD + G3142056458-POCLOUD + G3142846484-POCLOUD + """ with open(self.granule_list_file, 'r', encoding='utf-8') as file: self.granule_list = [line.strip() for line in file] @@ -197,7 +208,7 @@ def process_granules(self): if self.granule_list: print('Processing granules from granule list file...', end='', flush=True) - granules = self.search.get_granules_from_list(self.granule_list) + granules = self.search.get_granules_in_list(self.granule_list) with ThreadPoolExecutor() as executor: executor.map(self.process_one_granule, granules) diff --git a/podaac/hitide_backfill_tool/cmr/search.py b/podaac/hitide_backfill_tool/cmr/search.py index aff8ea3..3481bc8 100644 --- a/podaac/hitide_backfill_tool/cmr/search.py +++ b/podaac/hitide_backfill_tool/cmr/search.py @@ -239,7 +239,7 @@ def get_one_granule(self, granule_name): return body["items"][0] - def get_granules_from_list(self, granule_list): + def get_granules_in_list(self, granule_list): """Iterate through granule_list, get cmr for each item in parallel, and return a list of umm granule json""" # pylint: disable=broad-except From 58b2017ef934a33744ed58f87d8ee442abad3886 Mon Sep 17 00:00:00 2001 From: James Wood Date: Mon, 14 Oct 2024 14:45:43 -0700 Subject: [PATCH 5/6] added changelog updated args help --- CHANGELOG.md | 3 +++ podaac/hitide_backfill_tool/args.py | 3 ++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 866722b..4d3fbff 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added +- Added a new input argument *granule-list-file* to input a specific list of granules to process, + and ignore start-date, end-date, cycles, etc + - List can be a list of GranuleURs or granule concept-IDs ### Deprecated ### Removed ### Fixed diff --git a/podaac/hitide_backfill_tool/args.py b/podaac/hitide_backfill_tool/args.py index 3c04b9c..ecc1b60 100644 --- a/podaac/hitide_backfill_tool/args.py +++ b/podaac/hitide_backfill_tool/args.py @@ -41,13 +41,14 @@ def create_parser(): parser.add_argument("--provider") parser.add_argument("-sd", "--start-date") parser.add_argument("-ed", "--end-date") - parser.add_argument("--granule-list-file", default=None) parser.add_argument("--page-size", type=int) parser.add_argument("--page-limit", type=int) parser.add_argument("--edl-token") parser.add_argument("--launchpad-token") parser.add_argument("--cmr-search-after") + parser.add_argument("--granule-list-file", help='Process only this list of granuleURs or concept-IDs, and ignore start-date, end-date, cycles, etc.', default=None) + parser.add_argument("-g", "--geometry", dest="geometries", action="append", default=None) parser.add_argument("--footprint", choices=["on", "off", "force"]) From 4df806abf74541f990ad0121e2dbcf4a5a8d0ea3 Mon Sep 17 00:00:00 2001 From: James Wood Date: Mon, 14 Oct 2024 14:55:34 -0700 Subject: [PATCH 6/6] fix linting --- podaac/hitide_backfill_tool/args.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/podaac/hitide_backfill_tool/args.py b/podaac/hitide_backfill_tool/args.py index ecc1b60..39cd964 100644 --- a/podaac/hitide_backfill_tool/args.py +++ b/podaac/hitide_backfill_tool/args.py @@ -47,7 +47,12 @@ def create_parser(): parser.add_argument("--launchpad-token") parser.add_argument("--cmr-search-after") - parser.add_argument("--granule-list-file", help='Process only this list of granuleURs or concept-IDs, and ignore start-date, end-date, cycles, etc.', default=None) + parser.add_argument( + "--granule-list-file", + help=("Process only this list of granuleURs or concept-IDs, and ignore start-date, " + "end-date, cycles, etc."), + default=None + ) parser.add_argument("-g", "--geometry", dest="geometries", action="append", default=None)