From 19b9c70fd95cfb6d7d0c1d8062cd080224865290 Mon Sep 17 00:00:00 2001 From: sliu008 <69875423+sliu008@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:26:12 -0800 Subject: [PATCH 001/124] Feature/update add collection test (#94) * update add collection test to get the url for json history * update changelog --- CHANGELOG.md | 1 + add_collection_test.py | 38 ++++++++++++-------------------------- 2 files changed, 13 insertions(+), 26 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5c880a25..7d387a08 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update notebook test to use python code directly instead of using jupyter notebook - Updated python libraries - Update history json to have url in history + - Update add collection test to use url in json history ### Deprecated ### Removed ### Fixed diff --git a/add_collection_test.py b/add_collection_test.py index cd960de1..d0a029bf 100644 --- a/add_collection_test.py +++ b/add_collection_test.py @@ -6,6 +6,7 @@ import numpy as np import netCDF4 as nc import requests +import json from harmony import BBox, Client, Collection, Request, Environment import argparse from utils import FileHandler @@ -142,7 +143,10 @@ def verify_variables(merged_group, origin_group, subset_index, both_merged): unittest.TestCase().assertTrue(np.array_equal(merged_data, origin_data, equal_nan=True)) -def verify_groups(merged_group, origin_group, subset_index, both_merged=False): +def verify_groups(merged_group, origin_group, subset_index, file=None, both_merged=False): + if file: + print("verifying groups ....." + file) + verify_dims(merged_group, origin_group, both_merged) verify_attrs(merged_group, origin_group, both_merged) verify_variables(merged_group, origin_group, subset_index, both_merged) @@ -150,7 +154,7 @@ def verify_groups(merged_group, origin_group, subset_index, both_merged=False): for child_group in origin_group.groups: merged_subgroup = merged_group[child_group] origin_subgroup = origin_group[child_group] - verify_groups(merged_subgroup, origin_subgroup, subset_index, both_merged) + verify_groups(merged_subgroup, origin_subgroup, subset_index, both_merged=both_merged) # GET TOKEN FROM CMR @@ -173,7 +177,7 @@ def download_file(url, local_path, headers): with open(local_path, 'wb') as file: for chunk in response.iter_content(chunk_size=8192): file.write(chunk) - print("Original File downloaded successfully.") + print("Original File downloaded successfully. " + local_path) else: print(f"Failed to download the file. Status code: {response.status_code}") @@ -233,34 +237,16 @@ def test(collection_id, venue): } original_files = merge_dataset.variables['subset_files'] + history_json = json.loads(merge_dataset.history_json) assert len(original_files) == max_results - for file in original_files: - - # if the file name end in an alphabet so we know there is some extension - if file[-1].isalpha(): - file_name = file.rsplit(".", 1)[0] - else: - file_name = file - - print(file_name) - cmr_query = f"{cmr_base_url}{file_name}&collection_concept_id={collection_id}" - print(cmr_query) - - response = requests.get(cmr_query, headers=headers) - - result = response.json() - links = result.get('items')[0].get('umm').get('RelatedUrls') - for link in links: - if link.get('Type') == 'GET DATA': - data_url = link.get('URL') - parsed_url = urlparse(data_url) - local_file_name = os.path.basename(parsed_url.path) - download_file(data_url, local_file_name, headers) + for url in history_json[0].get("derived_from"): + local_file_name = os.path.basename(url) + download_file(url, local_file_name, headers) for i, file in enumerate(original_files): origin_dataset = nc.Dataset(file) - verify_groups(merge_dataset, origin_dataset, i) + verify_groups(merge_dataset, origin_dataset, i, file=file) def run(): From efa2115f8684f826e9f398f29fafa2277e3b2f6d Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 6 Nov 2023 18:30:36 +0000 Subject: [PATCH 002/124] /version 0.7.0a24 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dd4f2afb..1ed6d770 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.7.0a23" +version = "0.7.0a24" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From f63db117181d2fc78ebed43a888215a804d60f30 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Mon, 6 Nov 2023 19:30:41 +0000 Subject: [PATCH 003/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 5f124ae7..b48cdfc0 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -80,3 +80,4 @@ C1238621102-POCLOUD C1240739713-POCLOUD C1243175554-POCLOUD C1245295750-POCLOUD +C1256783381-POCLOUD From 461995ba5acc738eeb3936bae318fd3e894b8e94 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Mon, 6 Nov 2023 19:45:38 +0000 Subject: [PATCH 004/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index b48cdfc0..f4077048 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -81,3 +81,4 @@ C1240739713-POCLOUD C1243175554-POCLOUD C1245295750-POCLOUD C1256783381-POCLOUD +C1259115177-POCLOUD From 50190f59495bf485b65993861d0bad9cf19ce402 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Mon, 6 Nov 2023 20:15:51 +0000 Subject: [PATCH 005/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index f4077048..fe527cf8 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -82,3 +82,4 @@ C1243175554-POCLOUD C1245295750-POCLOUD C1256783381-POCLOUD C1259115177-POCLOUD +C1256783388-POCLOUD From bd6bcdae5bcb770042b486c9bc6f1a38f550ca2a Mon Sep 17 00:00:00 2001 From: sliu008 <69875423+sliu008@users.noreply.github.com> Date: Mon, 6 Nov 2023 14:43:43 -0800 Subject: [PATCH 006/124] Feature/update add collection test (#95) * update add collection test to get the url for json history * update changelog * update test to test for nan --- add_collection_test.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/add_collection_test.py b/add_collection_test.py index d0a029bf..a3bc1db4 100644 --- a/add_collection_test.py +++ b/add_collection_test.py @@ -136,11 +136,15 @@ def verify_variables(merged_group, origin_group, subset_index, both_merged): merged_data = np.resize(merged_var[subset_index], origin_var.shape) origin_data = origin_var + equal_nan = True + if merged_data.dtype.kind == 'S': + equal_nan = False + # verify variable data if isinstance(origin_data, str): unittest.TestCase().assertEqual(merged_data, origin_data) else: - unittest.TestCase().assertTrue(np.array_equal(merged_data, origin_data, equal_nan=True)) + unittest.TestCase().assertTrue(np.array_equal(merged_data, origin_data, equal_nan=equal_nan)) def verify_groups(merged_group, origin_group, subset_index, file=None, both_merged=False): @@ -221,6 +225,7 @@ def test(collection_id, venue): print('\nDone downloading.') filename = file_names[0] + # Handle time dimension and variables dropping merge_dataset = nc.Dataset(filename, 'r') From 7fff1af1f8247cce944a2c4547e98180b2c55c27 Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 6 Nov 2023 22:47:16 +0000 Subject: [PATCH 007/124] /version 0.7.0a25 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 1ed6d770..10ab2cc4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.7.0a24" +version = "0.7.0a25" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 0f77a7dd5f84914f678d7008e6ffc9ef136168ff Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 7 Nov 2023 00:07:47 +0000 Subject: [PATCH 008/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index fe527cf8..cc4089bc 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -83,3 +83,4 @@ C1245295750-POCLOUD C1256783381-POCLOUD C1259115177-POCLOUD C1256783388-POCLOUD +C1259115167-POCLOUD From 8230bf381c31db6e767ff5798720a8c9528f5dd2 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 7 Nov 2023 00:19:16 +0000 Subject: [PATCH 009/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index cc4089bc..d7f7ffe0 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -84,3 +84,4 @@ C1256783381-POCLOUD C1259115177-POCLOUD C1256783388-POCLOUD C1259115167-POCLOUD +C1259115178-POCLOUD From 885c385b3924bd24c3acba37ba577cfc511dec85 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 7 Nov 2023 00:30:39 +0000 Subject: [PATCH 010/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index d7f7ffe0..107bbc4a 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -85,3 +85,4 @@ C1259115177-POCLOUD C1256783388-POCLOUD C1259115167-POCLOUD C1259115178-POCLOUD +C1256783382-POCLOUD From 820ffdd651796efc221d091e433d51bc2fc8cb35 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 7 Nov 2023 00:45:38 +0000 Subject: [PATCH 011/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 107bbc4a..92a644f1 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -86,3 +86,4 @@ C1256783388-POCLOUD C1259115167-POCLOUD C1259115178-POCLOUD C1256783382-POCLOUD +C1259115166-POCLOUD From 8c4618e6403089d697264117e2641d47b7a547ce Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 10 Nov 2023 22:08:55 +0000 Subject: [PATCH 012/124] /version 0.8.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 5863034b..c624d195 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.8.0a0" +version = "0.8.0a1" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From a66474e8fd9c1385005542acc0a522ea3b813f16 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 17:16:09 +0000 Subject: [PATCH 013/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 0d8b7c33..5ce264d0 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -70,3 +70,4 @@ C2274919541-POCLOUD C2205620319-POCLOUD C2183155461-POCLOUD C2208421887-POCLOUD +C2628595723-POCLOUD From 6df14eccea27d3bb94e8327406d4b19baa27cd1a Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 17:30:37 +0000 Subject: [PATCH 014/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 5ce264d0..cf72d63a 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -71,3 +71,4 @@ C2205620319-POCLOUD C2183155461-POCLOUD C2208421887-POCLOUD C2628595723-POCLOUD +C2746966926-POCLOUD From e517fe0a07eff8799a2c56232a7c19049e8d0b3b Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 17:46:02 +0000 Subject: [PATCH 015/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index cf72d63a..145eb17e 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -72,3 +72,4 @@ C2183155461-POCLOUD C2208421887-POCLOUD C2628595723-POCLOUD C2746966926-POCLOUD +C2628600898-POCLOUD From b6f6d5a2aafbc424b09370789781b2219324bcd1 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 18:04:44 +0000 Subject: [PATCH 016/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 145eb17e..6a5e7631 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -73,3 +73,4 @@ C2208421887-POCLOUD C2628595723-POCLOUD C2746966926-POCLOUD C2628600898-POCLOUD +C2746966928-POCLOUD From 60fbb6bd04503f50bf29bc56e9603cccac5420a7 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 18:16:30 +0000 Subject: [PATCH 017/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 6a5e7631..1f0879ca 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -74,3 +74,4 @@ C2628595723-POCLOUD C2746966926-POCLOUD C2628600898-POCLOUD C2746966928-POCLOUD +C2746966927-POCLOUD From 7ef82631166e053cac6b77362644de0e8988f511 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 18:31:57 +0000 Subject: [PATCH 018/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 1f0879ca..c77a6326 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -75,3 +75,4 @@ C2746966926-POCLOUD C2628600898-POCLOUD C2746966928-POCLOUD C2746966927-POCLOUD +C2754895884-POCLOUD From a85bb0880bd18a23e9feb77c2a5a05d5deb175c3 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 18:45:36 +0000 Subject: [PATCH 019/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index c77a6326..6ab4b2c2 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -76,3 +76,4 @@ C2628600898-POCLOUD C2746966928-POCLOUD C2746966927-POCLOUD C2754895884-POCLOUD +C2746966657-POCLOUD From c166f5a9d44069139506ed2e1b538ba0a3faa4de Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 15 Nov 2023 19:01:05 +0000 Subject: [PATCH 020/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 6ab4b2c2..db0da1b1 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -77,3 +77,4 @@ C2746966928-POCLOUD C2746966927-POCLOUD C2754895884-POCLOUD C2746966657-POCLOUD +C2628598809-POCLOUD From 361119bce07363b2036e206b286b284147d15d91 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 01:16:34 +0000 Subject: [PATCH 021/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 92a644f1..b2ea6bf9 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -87,3 +87,4 @@ C1259115167-POCLOUD C1259115178-POCLOUD C1256783382-POCLOUD C1259115166-POCLOUD +C1261072655-POCLOUD From 7e7f56485f23882c1487e33d1f7b054a1ef85bf1 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 01:16:35 +0000 Subject: [PATCH 022/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index db0da1b1..cd29647a 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -78,3 +78,4 @@ C2746966927-POCLOUD C2754895884-POCLOUD C2746966657-POCLOUD C2628598809-POCLOUD +C2799465529-POCLOUD From 32126588eae691b3c7616f15f60e426d8e2f3897 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 01:30:41 +0000 Subject: [PATCH 023/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index b2ea6bf9..5aa9d37f 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -88,3 +88,4 @@ C1259115178-POCLOUD C1256783382-POCLOUD C1259115166-POCLOUD C1261072655-POCLOUD +C1261072658-POCLOUD From 1440a5c0c7564a3a78b933a995e749431ca2f248 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 01:45:34 +0000 Subject: [PATCH 024/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index cd29647a..b9ece565 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -79,3 +79,4 @@ C2754895884-POCLOUD C2746966657-POCLOUD C2628598809-POCLOUD C2799465529-POCLOUD +C2799465526-POCLOUD From 861a8ce19083a449ef3dc98f4d1f913eb9985cfa Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 02:01:15 +0000 Subject: [PATCH 025/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 5aa9d37f..6b2ddab2 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -89,3 +89,4 @@ C1256783382-POCLOUD C1259115166-POCLOUD C1261072655-POCLOUD C1261072658-POCLOUD +C1261072648-POCLOUD From 5f0405fddddbab1268f7df4eb36d0628af810bce Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 02:01:16 +0000 Subject: [PATCH 026/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index b9ece565..ac8d9be9 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -80,3 +80,4 @@ C2746966657-POCLOUD C2628598809-POCLOUD C2799465529-POCLOUD C2799465526-POCLOUD +C2799465507-POCLOUD From 4e0a6e3ecf4d3adffea6bf389e70b61d3c89e510 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 03:00:46 +0000 Subject: [PATCH 027/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index ac8d9be9..39638538 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -81,3 +81,4 @@ C2628598809-POCLOUD C2799465529-POCLOUD C2799465526-POCLOUD C2799465507-POCLOUD +C2799465497-POCLOUD From ca0e397fe503499f06322ab29a9b7a6f6cfadbd9 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 03:30:26 +0000 Subject: [PATCH 028/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 39638538..673372d8 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -82,3 +82,4 @@ C2799465529-POCLOUD C2799465526-POCLOUD C2799465507-POCLOUD C2799465497-POCLOUD +C2799465538-POCLOUD From ccb3d6ce9d56625c8bfb92e58f1d963fdb4748d8 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 04:15:35 +0000 Subject: [PATCH 029/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 673372d8..7952cae3 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -83,3 +83,4 @@ C2799465526-POCLOUD C2799465507-POCLOUD C2799465497-POCLOUD C2799465538-POCLOUD +C2799465544-POCLOUD From 6e5bcaa23a4d4e5c79ba4b8427371690e62a97b5 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 04:30:54 +0000 Subject: [PATCH 030/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 6b2ddab2..fc352351 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -90,3 +90,4 @@ C1259115166-POCLOUD C1261072655-POCLOUD C1261072658-POCLOUD C1261072648-POCLOUD +C1261072646-POCLOUD From 5cd88cad6642682580ea0e15f949a3afb1aed372 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 04:46:03 +0000 Subject: [PATCH 031/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index fc352351..cc090fad 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -91,3 +91,4 @@ C1261072655-POCLOUD C1261072658-POCLOUD C1261072648-POCLOUD C1261072646-POCLOUD +C1261072656-POCLOUD From ad91fe7408403d12e3877cc981fec43b1c3c8745 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 04:46:04 +0000 Subject: [PATCH 032/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 7952cae3..3b1cdc50 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -84,3 +84,4 @@ C2799465507-POCLOUD C2799465497-POCLOUD C2799465538-POCLOUD C2799465544-POCLOUD +C2799465542-POCLOUD From 74d05e07cecd85282a2c631316892d69e29d0f78 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 05:01:15 +0000 Subject: [PATCH 033/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index cc090fad..6885ce05 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -92,3 +92,4 @@ C1261072658-POCLOUD C1261072648-POCLOUD C1261072646-POCLOUD C1261072656-POCLOUD +C1261072645-POCLOUD From 2a29cc9f0e8e66516eca505974e88c37951ffeb0 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 05:01:15 +0000 Subject: [PATCH 034/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 3b1cdc50..ae6456c5 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -85,3 +85,4 @@ C2799465497-POCLOUD C2799465538-POCLOUD C2799465544-POCLOUD C2799465542-POCLOUD +C2799465428-POCLOUD From ae0c8829aa6705efbdb8c8d3df33ce58e7eea0ee Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 05:30:21 +0000 Subject: [PATCH 035/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 6885ce05..1ca91d3b 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -93,3 +93,4 @@ C1261072648-POCLOUD C1261072646-POCLOUD C1261072656-POCLOUD C1261072645-POCLOUD +C1261072659-POCLOUD From b937944b6b250d76acc8df10df52a8a6f3145f44 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 6 Dec 2023 05:45:34 +0000 Subject: [PATCH 036/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 1ca91d3b..5fc5963d 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -94,3 +94,4 @@ C1261072646-POCLOUD C1261072656-POCLOUD C1261072645-POCLOUD C1261072659-POCLOUD +C1261072654-POCLOUD From 2bc73bb1a9883e9161ef4090c29bac0b58146f0f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 16 Jan 2024 09:33:54 -0800 Subject: [PATCH 037/124] Bump jinja2 from 3.1.2 to 3.1.3 (#99) Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.2...3.1.3) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 108 ++++++++-------------------------------------------- 1 file changed, 16 insertions(+), 92 deletions(-) diff --git a/poetry.lock b/poetry.lock index 364ec580..9eeb2f8c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,10 +1,9 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. [[package]] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -16,7 +15,6 @@ files = [ name = "ansiwrap" version = "0.8.4" description = "textwrap, but savvy to ANSI colors and styles" -category = "dev" optional = false python-versions = "*" files = [ @@ -31,7 +29,6 @@ textwrap3 = ">=0.9.2" name = "astroid" version = "2.15.8" description = "An abstract syntax tree for Python with inference support." -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -51,7 +48,6 @@ wrapt = [ name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -70,7 +66,6 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.13.1" description = "Internationalization utilities" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -88,7 +83,6 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] name = "boto3" version = "1.28.73" description = "The AWS SDK for Python" -category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -108,7 +102,6 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] name = "botocore" version = "1.31.73" description = "Low-level, data-driven core of boto 3." -category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -131,7 +124,6 @@ crt = ["awscrt (==0.16.26)"] name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -143,7 +135,6 @@ files = [ name = "cffi" version = "1.16.0" description = "Foreign Function Interface for Python calling C code." -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -208,7 +199,6 @@ pycparser = "*" name = "cftime" version = "1.6.2" description = "Time-handling functionality from netcdf4-python" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -242,7 +232,6 @@ numpy = ">1.13.3" name = "cftime" version = "1.6.3" description = "Time-handling functionality from netcdf4-python" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -276,7 +265,6 @@ numpy = {version = ">1.13.3", markers = "python_version < \"3.12.0.rc1\""} name = "charset-normalizer" version = "3.3.1" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." -category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -376,7 +364,6 @@ files = [ name = "click" version = "8.1.7" description = "Composable command line interface toolkit" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -391,7 +378,6 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -403,7 +389,6 @@ files = [ name = "coverage" version = "7.3.2" description = "Code coverage measurement for Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -471,7 +456,6 @@ toml = ["tomli"] name = "deprecation" version = "2.1.0" description = "A library to handle automated deprecations" -category = "main" optional = false python-versions = "*" files = [ @@ -486,7 +470,6 @@ packaging = "*" name = "dill" version = "0.3.7" description = "serialize all of Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -501,7 +484,6 @@ graph = ["objgraph (>=1.7.2)"] name = "docutils" version = "0.17.1" description = "Docutils -- Python Documentation Utilities" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" files = [ @@ -513,7 +495,6 @@ files = [ name = "entrypoints" version = "0.4" description = "Discover and load entry points from installed packages." -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -525,7 +506,6 @@ files = [ name = "exceptiongroup" version = "1.1.3" description = "Backport of PEP 654 (exception groups)" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -540,7 +520,6 @@ test = ["pytest (>=6)"] name = "fastjsonschema" version = "2.18.1" description = "Fastest Python implementation of JSON schema" -category = "dev" optional = false python-versions = "*" files = [ @@ -555,7 +534,6 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc name = "flake8" version = "6.1.0" description = "the modular source code checker: pep8 pyflakes and co" -category = "dev" optional = false python-versions = ">=3.8.1" files = [ @@ -572,7 +550,6 @@ pyflakes = ">=3.1.0,<3.2.0" name = "harmony-service-lib" version = "1.0.23" description = "A library for Python-based Harmony services to parse incoming messages, fetch data, stage data, and call back to Harmony" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -593,7 +570,6 @@ urllib3 = ">=1.26.9,<1.27.0" name = "idna" version = "3.4" description = "Internationalized Domain Names in Applications (IDNA)" -category = "main" optional = false python-versions = ">=3.5" files = [ @@ -605,7 +581,6 @@ files = [ name = "imagesize" version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" -category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -617,7 +592,6 @@ files = [ name = "importlib-metadata" version = "6.8.0" description = "Read metadata from Python packages" -category = "main" optional = false python-versions = ">=3.8" files = [ @@ -637,7 +611,6 @@ testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs name = "iniconfig" version = "2.0.0" description = "brain-dead simple config-ini parsing" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -649,7 +622,6 @@ files = [ name = "isort" version = "5.12.0" description = "A Python utility / library to sort Python imports." -category = "dev" optional = false python-versions = ">=3.8.0" files = [ @@ -665,14 +637,13 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jinja2" -version = "3.1.2" +version = "3.1.3" description = "A very fast and expressive template engine." -category = "dev" optional = false python-versions = ">=3.7" files = [ - 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Formerly nbconvert's ExecutePreprocessor." -category = "dev" optional = false python-versions = ">=3.8.0" files = [ @@ -907,7 +879,7 @@ files = [ [package.dependencies] jupyter-client = ">=6.1.12" -jupyter-core = ">=4.12,<5.0.0 || >=5.1.0" +jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0" nbformat = ">=5.1" traitlets = ">=5.4" @@ -920,7 +892,6 @@ test = ["flaky", "ipykernel (>=6.19.3)", "ipython", "ipywidgets", "nbconvert (>= name = "nbformat" version = "5.9.2" description = "The Jupyter Notebook format" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -942,7 +913,6 @@ test = ["pep440", "pre-commit", "pytest", "testpath"] name = "netcdf4" version = "1.6.5" description = "Provides an object-oriented python interface to the netCDF version 4 library" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -987,7 +957,6 @@ tests = ["Cython", "packaging", "pytest"] name = "numpy" version = "1.25.2" description = "Fundamental package for array computing in Python" -category = "main" optional = false python-versions = ">=3.9" files = [ @@ -1022,7 +991,6 @@ files = [ name = "packaging" version = "23.2" description = "Core utilities for Python packages" -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1034,7 +1002,6 @@ files = [ name = "papermill" version = "2.4.0" description = "Parametrize and run Jupyter and nteract Notebooks" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1068,7 +1035,6 @@ test = ["attrs (>=17.4.0)", "azure-datalake-store (>=0.0.30)", "azure-storage-bl name = "platformdirs" version = "3.11.0" description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1084,7 +1050,6 @@ test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-co name = "pluggy" version = "1.3.0" description = "plugin and hook calling mechanisms for python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1100,7 +1065,6 @@ testing = ["pytest", "pytest-benchmark"] name = "pycodestyle" version = "2.11.1" description = "Python style guide checker" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1112,7 +1076,6 @@ files = [ name = "pycparser" version = "2.21" description = "C parser in Python" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -1124,7 +1087,6 @@ files = [ name = "pyflakes" version = "3.1.0" description = "passive checker of Python programs" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1136,7 +1098,6 @@ files = [ name = "pygments" version = "2.16.1" description = "Pygments is a syntax highlighting package written in Python." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1151,7 +1112,6 @@ plugins = ["importlib-metadata"] name = "pylint" version = "2.17.7" description = "python code static checker" -category = "dev" optional = false python-versions = ">=3.7.2" files = [ @@ -1181,7 +1141,6 @@ testutils = ["gitpython (>3)"] name = "pynacl" version = "1.5.0" description = "Python binding to the Networking and Cryptography (NaCl) library" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1208,7 +1167,6 @@ tests = ["hypothesis (>=3.27.0)", "pytest (>=3.2.1,!=3.3.0)"] name = "pystac" version = "0.5.6" description = "Python library for working with Spatiotemporal Asset Catalog (STAC)." -category = "main" optional = false python-versions = "*" files = [ @@ -1226,7 +1184,6 @@ validation = ["jsonschema (==3.2.0)"] name = "pytest" version = "7.4.3" description = "pytest: simple powerful testing with Python" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1249,7 +1206,6 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no name = "pytest-cov" version = "4.1.0" description = "Pytest plugin for measuring coverage." -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1268,7 +1224,6 @@ testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtuale name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" files = [ @@ -1283,7 +1238,6 @@ six = ">=1.5" name = "python-json-logger" version = "2.0.7" description = "A python library adding a json log formatter" -category = "main" optional = false python-versions = ">=3.6" files = [ @@ -1295,7 +1249,6 @@ files = [ name = "pywin32" version = "306" description = "Python for Window Extensions" -category = "dev" optional = false python-versions = "*" files = [ @@ -1319,7 +1272,6 @@ files = [ name = "pyyaml" version = "6.0.1" description = "YAML parser and emitter for Python" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1379,7 +1331,6 @@ files = [ name = "pyzmq" version = "25.1.1" description = "Python bindings for 0MQ" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1485,7 +1436,6 @@ cffi = {version = "*", markers = "implementation_name == \"pypy\""} name = "referencing" version = "0.30.2" description = "JSON Referencing + Python" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1501,7 +1451,6 @@ rpds-py = ">=0.7.0" name = "requests" version = "2.31.0" description = "Python HTTP for Humans." -category = "main" optional = false python-versions = ">=3.7" files = [ @@ -1523,7 +1472,6 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"] name = "rpds-py" version = "0.10.6" description = "Python bindings to Rust's persistent data structures (rpds)" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1632,7 +1580,6 @@ files = [ name = "s3transfer" version = "0.7.0" description = "An Amazon S3 Transfer Manager" -category = "main" optional = false python-versions = ">= 3.7" files = [ @@ -1650,7 +1597,6 @@ crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"] name = "setuptools" version = "66.1.1" description = "Easily download, build, install, upgrade, and uninstall Python packages" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1667,7 +1613,6 @@ testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs ( name = "six" version = "1.16.0" description = "Python 2 and 3 compatibility utilities" -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*" files = [ @@ -1679,7 +1624,6 @@ files = [ name = "snowballstemmer" version = "2.2.0" description = "This package provides 29 stemmers for 28 languages generated from Snowball algorithms." -category = "dev" optional = false python-versions = "*" files = [ @@ -1691,7 +1635,6 @@ files = [ name = "sphinx" version = "4.5.0" description = "Python documentation generator" -category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -1727,7 +1670,6 @@ test = ["cython", "html5lib", "pytest", "pytest-cov", "typed-ast"] name = "sphinx-rtd-theme" version = "1.3.0" description = "Read the Docs theme for Sphinx" -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ @@ -1747,7 +1689,6 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"] name = "sphinxcontrib-applehelp" version = "1.0.4" description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1763,7 +1704,6 @@ test = ["pytest"] name = "sphinxcontrib-devhelp" version = "1.0.2" description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1779,7 +1719,6 @@ test = ["pytest"] name = "sphinxcontrib-htmlhelp" version = "2.0.1" description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1795,7 +1734,6 @@ test = ["html5lib", "pytest"] name = "sphinxcontrib-jquery" version = "4.1" description = "Extension to include jQuery on newer Sphinx releases" -category = "dev" optional = false python-versions = ">=2.7" files = [ @@ -1810,7 +1748,6 @@ Sphinx = ">=1.8" name = "sphinxcontrib-jsmath" version = "1.0.1" description = "A sphinx extension which renders display math in HTML via JavaScript" -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1825,7 +1762,6 @@ test = ["flake8", "mypy", "pytest"] name = "sphinxcontrib-qthelp" version = "1.0.3" description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1841,7 +1777,6 @@ test = ["pytest"] name = "sphinxcontrib-serializinghtml" version = "1.1.5" description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)." -category = "dev" optional = false python-versions = ">=3.5" files = [ @@ -1857,7 +1792,6 @@ test = ["pytest"] name = "tenacity" version = "8.2.3" description = "Retry code until it succeeds" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1872,7 +1806,6 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"] name = "textwrap3" version = "0.9.2" description = "textwrap from Python 3.6 backport (plus a few tweaks)" -category = "dev" optional = false python-versions = "*" files = [ @@ -1884,7 +1817,6 @@ files = [ name = "tomli" version = "2.0.1" description = "A lil' TOML parser" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1896,7 +1828,6 @@ files = [ name = "tomlkit" version = "0.12.1" description = "Style preserving TOML library" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1908,7 +1839,6 @@ files = [ name = "tornado" version = "6.3.3" description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed." -category = "dev" optional = false python-versions = ">= 3.8" files = [ @@ -1929,7 +1859,6 @@ files = [ name = "tqdm" version = "4.66.1" description = "Fast, Extensible Progress Meter" -category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -1950,7 +1879,6 @@ telegram = ["requests"] name = "traitlets" version = "5.12.0" description = "Traitlets Python configuration system" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1966,7 +1894,6 @@ test = ["argcomplete (>=3.0.3)", "mypy (>=1.6.0)", "pre-commit", "pytest (>=7.0, name = "typing-extensions" version = "4.8.0" description = "Backported and Experimental Type Hints for Python 3.8+" -category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -1978,7 +1905,6 @@ files = [ name = "urllib3" version = "1.26.18" description = "HTTP library with thread-safe connection pooling, file post, and more." -category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" files = [ @@ -1995,7 +1921,6 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] name = "wrapt" version = "1.15.0" description = "Module for decorators, wrappers and monkey patching." -category = "dev" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -2080,7 +2005,6 @@ files = [ name = "zipp" version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" -category = "main" optional = false python-versions = ">=3.8" files = [ From e7fbcce0ccfa6d2ee016fff246280fc1e430ce4f Mon Sep 17 00:00:00 2001 From: James Wood Date: Tue, 16 Jan 2024 11:18:23 -0800 Subject: [PATCH 038/124] Using cmr-umm-updater default branch (develop) --- .github/workflows/add-collection-test.yml | 2 +- .github/workflows/build-pipeline.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/add-collection-test.yml b/.github/workflows/add-collection-test.yml index a156eb6b..9cd69436 100644 --- a/.github/workflows/add-collection-test.yml +++ b/.github/workflows/add-collection-test.yml @@ -46,7 +46,7 @@ jobs: pip3 install netCDF4 pip3 install git+https://github.com/nasa/harmony-py.git pip3 install git+https://github.com/podaac/cmr-umm-updater.git - pip3 install git+https://github.com/podaac/cmr-association-diff.git@6193079a14e36f4c9526aa426015c2b6be41f0e2 + pip3 install git+https://github.com/podaac/cmr-association-diff.git pip3 install python-dateutil --upgrade - name: Run CMR Association diff scripts run: | diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 5994d5ce..13c193e5 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -141,7 +141,7 @@ jobs: git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}" git push origin "${{ env.software_version }}" - name: Publish UMM-S with new version - uses: podaac/cmr-umm-updater@feature/umm_version + uses: podaac/cmr-umm-updater if: | github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/release') @@ -160,7 +160,7 @@ jobs: LAUNCHPAD_TOKEN_UAT: ${{secrets.LAUNCHPAD_TOKEN_UAT}} LAUNCHPAD_TOKEN_OPS: ${{secrets.LAUNCHPAD_TOKEN_OPS}} - name: Publish L2ss Concise Chain UMM-S with new version - uses: podaac/cmr-umm-updater@feature/umm_version + uses: podaac/cmr-umm-updater if: | github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/release') From 67d63a44b3652d8f8e9f27c300aa5c93b845a2d2 Mon Sep 17 00:00:00 2001 From: James Wood Date: Tue, 16 Jan 2024 11:21:01 -0800 Subject: [PATCH 039/124] use develop --- .github/workflows/build-pipeline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 13c193e5..bfe739fb 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -141,7 +141,7 @@ jobs: git tag -a "${{ env.software_version }}" -m "Version ${{ env.software_version }}" git push origin "${{ env.software_version }}" - name: Publish UMM-S with new version - uses: podaac/cmr-umm-updater + uses: podaac/cmr-umm-updater@develop if: | github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/release') @@ -160,7 +160,7 @@ jobs: LAUNCHPAD_TOKEN_UAT: ${{secrets.LAUNCHPAD_TOKEN_UAT}} LAUNCHPAD_TOKEN_OPS: ${{secrets.LAUNCHPAD_TOKEN_OPS}} - name: Publish L2ss Concise Chain UMM-S with new version - uses: podaac/cmr-umm-updater + uses: podaac/cmr-umm-updater@develop if: | github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/heads/release') From 6336fc5d49c7ed6c255d1e572e303902bf7d6422 Mon Sep 17 00:00:00 2001 From: concise bot Date: Tue, 16 Jan 2024 19:24:07 +0000 Subject: [PATCH 040/124] /version 0.8.0a2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c624d195..95adfc53 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.8.0a1" +version = "0.8.0a2" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 35c8c3c0febae3296e8c90e7ca155195ba3a218d Mon Sep 17 00:00:00 2001 From: Frank Greguska <89428916+frankinspace@users.noreply.github.com> Date: Fri, 19 Jan 2024 11:03:57 -0800 Subject: [PATCH 041/124] Update CONTRIBUTING.md --- CONTRIBUTING.md | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index a0245d33..d81412c1 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -77,14 +77,6 @@ If any performance improvements are being made, include graphs and charts. - `feature/issue-#` - Work for enhancements and new features should be done in a branch with this naming convention - The issue number should match the associated Github issue number -- `bugfix/issue-#` - - Work for bug fixes should be done in a branch with this naming convention - - The issue number should match the associated Github issue number -- `hotfix/issue-#` or `hotfix/short-fix-description` - - Rare/special case to address a special anomaly. - - The issue number should match the associated Github issue number, - unless no such issue exists. If not, use a short description of the - issue e.g. `hotfix/fix-request-url` ### Changelog @@ -200,4 +192,4 @@ All functions should contain a docstring, though short or trivial function may contain a 1-line docstring. If adding a new module, ensure it has been added to [index.rst](docs/index.rst) -for inclusion in auto-generated Sphinx docs. \ No newline at end of file +for inclusion in auto-generated Sphinx docs. From f9ac10c2374a07c2c43dd2afeb8a0ece6c67a0e3 Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 19 Jan 2024 19:06:40 +0000 Subject: [PATCH 042/124] /version 0.8.0a3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 95adfc53..94297702 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.8.0a2" +version = "0.8.0a3" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 6d5207267dc460f00a7a795895a64f171b915247 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 22:00:51 +0000 Subject: [PATCH 043/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 5fc5963d..8e8006b7 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -95,3 +95,4 @@ C1261072656-POCLOUD C1261072645-POCLOUD C1261072659-POCLOUD C1261072654-POCLOUD +C1254854453-LARC_CLOUD From 3c106cb3c8627d0429c64cde63ba0242c602c9f0 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 22:15:45 +0000 Subject: [PATCH 044/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 8e8006b7..31f14710 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -96,3 +96,4 @@ C1261072645-POCLOUD C1261072659-POCLOUD C1261072654-POCLOUD C1254854453-LARC_CLOUD +C1254855648-LARC_CLOUD From a99f0908a3363016f1403c30abb1af1d9f0eda23 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 22:30:47 +0000 Subject: [PATCH 045/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 31f14710..e1b6a9fc 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -97,3 +97,4 @@ C1261072659-POCLOUD C1261072654-POCLOUD C1254854453-LARC_CLOUD C1254855648-LARC_CLOUD +C1254854962-LARC_CLOUD From 4cfe63c65e9f275110a39eb47937d1620134e378 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 22:45:51 +0000 Subject: [PATCH 046/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index e1b6a9fc..520ebc3d 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -98,3 +98,4 @@ C1261072654-POCLOUD C1254854453-LARC_CLOUD C1254855648-LARC_CLOUD C1254854962-LARC_CLOUD +C1247485682-LARC_CLOUD From f1cfe540492b7d411b61f423171f7566d636eec4 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 23:00:53 +0000 Subject: [PATCH 047/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 520ebc3d..a1fd0a58 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -99,3 +99,4 @@ C1254854453-LARC_CLOUD C1254855648-LARC_CLOUD C1254854962-LARC_CLOUD C1247485682-LARC_CLOUD +C1247485690-LARC_CLOUD From 0a38fd1ee201f5fd0926ba32d7281a194548a265 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 19 Jan 2024 23:30:59 +0000 Subject: [PATCH 048/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index a1fd0a58..20db20f8 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -100,3 +100,4 @@ C1254855648-LARC_CLOUD C1254854962-LARC_CLOUD C1247485682-LARC_CLOUD C1247485690-LARC_CLOUD +C1247485685-LARC_CLOUD From a86899b6600ee59fe9d9f33f82efc54a35e2c370 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 21:31:15 +0000 Subject: [PATCH 049/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 20db20f8..c4161881 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -101,3 +101,4 @@ C1254854962-LARC_CLOUD C1247485682-LARC_CLOUD C1247485690-LARC_CLOUD C1247485685-LARC_CLOUD +C1242274079-POCLOUD From 83006d4ff5d74148059b4481cb165e2be8c1a440 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 21:45:34 +0000 Subject: [PATCH 050/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index c4161881..48a91b4e 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -102,3 +102,4 @@ C1247485682-LARC_CLOUD C1247485690-LARC_CLOUD C1247485685-LARC_CLOUD C1242274079-POCLOUD +C1240739526-POCLOUD From 8074ecc86e398b5fab2832f287c03f26465f7386 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 22:00:43 +0000 Subject: [PATCH 051/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 48a91b4e..710aa042 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -103,3 +103,4 @@ C1247485690-LARC_CLOUD C1247485685-LARC_CLOUD C1242274079-POCLOUD C1240739526-POCLOUD +C1261072651-POCLOUD From f644022695e7a2bcaf31de88603883ea09346363 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 22:15:30 +0000 Subject: [PATCH 052/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 710aa042..1ae6f1a4 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -104,3 +104,4 @@ C1247485685-LARC_CLOUD C1242274079-POCLOUD C1240739526-POCLOUD C1261072651-POCLOUD +C1261072650-POCLOUD From 8418f31159eaf3ec3432987537f07caf4414bf15 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 22:30:58 +0000 Subject: [PATCH 053/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 1ae6f1a4..481f9535 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -105,3 +105,4 @@ C1242274079-POCLOUD C1240739526-POCLOUD C1261072651-POCLOUD C1261072650-POCLOUD +C1242274070-POCLOUD From b4a42d1cd455c66eeedc1c93b17a00717593e9cd Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 22:45:27 +0000 Subject: [PATCH 054/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 481f9535..23b5cd3c 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -106,3 +106,4 @@ C1240739526-POCLOUD C1261072651-POCLOUD C1261072650-POCLOUD C1242274070-POCLOUD +C1240739691-POCLOUD From 6d02bde825ec92369310b9ab1e06f58b49de59ff Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 23:01:25 +0000 Subject: [PATCH 055/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 23b5cd3c..05ff68da 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -107,3 +107,4 @@ C1261072651-POCLOUD C1261072650-POCLOUD C1242274070-POCLOUD C1240739691-POCLOUD +C1257081729-POCLOUD From 3bbff2ff6c423034ebd93b120784f35e9bca7fae Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 23:15:24 +0000 Subject: [PATCH 056/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 05ff68da..7fa652a0 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -108,3 +108,4 @@ C1261072650-POCLOUD C1242274070-POCLOUD C1240739691-POCLOUD C1257081729-POCLOUD +C1261072661-POCLOUD From b3663c0205afd07e0faa63dd483db1be6f74ec85 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 23:30:18 +0000 Subject: [PATCH 057/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 7fa652a0..cc67fa75 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -109,3 +109,4 @@ C1242274070-POCLOUD C1240739691-POCLOUD C1257081729-POCLOUD C1261072661-POCLOUD +C1261072652-POCLOUD From 7549e5bb3b5e9c88f3b277ae19557968ac72f3db Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Tue, 6 Feb 2024 23:45:32 +0000 Subject: [PATCH 058/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index cc67fa75..85dbb7da 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -110,3 +110,4 @@ C1240739691-POCLOUD C1257081729-POCLOUD C1261072661-POCLOUD C1261072652-POCLOUD +C1261072662-POCLOUD From 932271366d3acc674bf7a109e88fadd1a0e7af7c Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 00:00:31 +0000 Subject: [PATCH 059/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 85dbb7da..a0bf2f95 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -111,3 +111,4 @@ C1257081729-POCLOUD C1261072661-POCLOUD C1261072652-POCLOUD C1261072662-POCLOUD +C1261072660-POCLOUD From ba7294c690e20cf4e8275d7f862b195c500b201b Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 15:45:47 +0000 Subject: [PATCH 060/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index a0bf2f95..f41a31c0 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -112,3 +112,4 @@ C1261072661-POCLOUD C1261072652-POCLOUD C1261072662-POCLOUD C1261072660-POCLOUD +C1261645986-LARC_CLOUD From bc6b37628a6e03ba91e9505c640523fdc51335cd Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 20:30:59 +0000 Subject: [PATCH 061/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index ae6456c5..5ab3844a 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -86,3 +86,4 @@ C2799465538-POCLOUD C2799465544-POCLOUD C2799465542-POCLOUD C2799465428-POCLOUD +C2799438350-POCLOUD From 47399a9f8c7bc195e6e7aadc6e57baa0de94b82c Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 21:00:55 +0000 Subject: [PATCH 062/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 5ab3844a..5749c471 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -87,3 +87,4 @@ C2799465544-POCLOUD C2799465542-POCLOUD C2799465428-POCLOUD C2799438350-POCLOUD +C2799438351-POCLOUD From 7c1404fbd16f76919e7c857781083035c2f36ce1 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 22:15:26 +0000 Subject: [PATCH 063/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 5749c471..1e2dc8a8 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -88,3 +88,4 @@ C2799465542-POCLOUD C2799465428-POCLOUD C2799438350-POCLOUD C2799438351-POCLOUD +C2799438353-POCLOUD From 2ab503fce02c6f69b27e9c1e4687c544c0e2cd8b Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 7 Feb 2024 22:30:34 +0000 Subject: [PATCH 064/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 1e2dc8a8..1b324498 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -89,3 +89,4 @@ C2799465428-POCLOUD C2799438350-POCLOUD C2799438351-POCLOUD C2799438353-POCLOUD +C2296989388-POCLOUD From e685f5567c22ac5faef7b5726b1e28d213ff4a31 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Thu, 8 Feb 2024 19:30:45 +0000 Subject: [PATCH 065/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index f41a31c0..7440f007 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -113,3 +113,4 @@ C1261072652-POCLOUD C1261072662-POCLOUD C1261072660-POCLOUD C1261645986-LARC_CLOUD +C1258237266-POCLOUD From a1283a5012f962c155441fc096dcbdb5257f8307 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Thu, 8 Feb 2024 19:45:55 +0000 Subject: [PATCH 066/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 7440f007..8aaccdc8 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -114,3 +114,4 @@ C1261072662-POCLOUD C1261072660-POCLOUD C1261645986-LARC_CLOUD C1258237266-POCLOUD +C1259966654-POCLOUD From 5d9ed3955f9234010ed998f6913e9699ec42327a Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Thu, 8 Feb 2024 20:00:38 +0000 Subject: [PATCH 067/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 8aaccdc8..7d058efd 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -115,3 +115,4 @@ C1261072660-POCLOUD C1261645986-LARC_CLOUD C1258237266-POCLOUD C1259966654-POCLOUD +C1258237267-POCLOUD From 31d134684b23563c007a9ee0f2dc2fa278b968a1 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 01:46:11 +0000 Subject: [PATCH 068/124] Update uat_associations.txt with new collections --- cmr/uat_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/uat_associations.txt b/cmr/uat_associations.txt index 7d058efd..4f408724 100644 --- a/cmr/uat_associations.txt +++ b/cmr/uat_associations.txt @@ -116,3 +116,4 @@ C1261645986-LARC_CLOUD C1258237266-POCLOUD C1259966654-POCLOUD C1258237267-POCLOUD +C1240739686-POCLOUD From 854cc417dc147aea54a08aeca97b8d6fb2af83c3 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 01:46:11 +0000 Subject: [PATCH 069/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 1b324498..611cf278 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -90,3 +90,4 @@ C2799438350-POCLOUD C2799438351-POCLOUD C2799438353-POCLOUD C2296989388-POCLOUD +C2205553958-POCLOUD From 1239557421a2abcb1c53a78d0b35c1e0f9efed33 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 02:00:38 +0000 Subject: [PATCH 070/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 611cf278..4944b545 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -91,3 +91,4 @@ C2799438351-POCLOUD C2799438353-POCLOUD C2296989388-POCLOUD C2205553958-POCLOUD +C2706513160-POCLOUD From a749e96fd2cfb56648eed3b0866d356f69ffe6e4 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 04:00:59 +0000 Subject: [PATCH 071/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 4944b545..f9106a37 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -92,3 +92,4 @@ C2799438353-POCLOUD C2296989388-POCLOUD C2205553958-POCLOUD C2706513160-POCLOUD +C2147480877-POCLOUD From 0103b4d5f9874e9c774606f40d459024590753db Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 04:15:50 +0000 Subject: [PATCH 072/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index f9106a37..d796befe 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -93,3 +93,4 @@ C2296989388-POCLOUD C2205553958-POCLOUD C2706513160-POCLOUD C2147480877-POCLOUD +C2147478146-POCLOUD From 23b44803f4829c1eb7e9d39b311a0373092daab3 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Fri, 9 Feb 2024 04:30:55 +0000 Subject: [PATCH 073/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index d796befe..1f22df75 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -94,3 +94,4 @@ C2205553958-POCLOUD C2706513160-POCLOUD C2147480877-POCLOUD C2147478146-POCLOUD +C2730520815-POCLOUD From 5885e5ecc7d472f2f88a5db46623eb764d8807f6 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 14 Feb 2024 00:45:38 +0000 Subject: [PATCH 074/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 1f22df75..911bd465 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -95,3 +95,4 @@ C2706513160-POCLOUD C2147480877-POCLOUD C2147478146-POCLOUD C2730520815-POCLOUD +C2799465509-POCLOUD From 448dbc6c8047a344b2ba13ee038418b40e207a51 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 14 Feb 2024 01:00:54 +0000 Subject: [PATCH 075/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 911bd465..1c33dc7b 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -96,3 +96,4 @@ C2147480877-POCLOUD C2147478146-POCLOUD C2730520815-POCLOUD C2799465509-POCLOUD +C2799465518-POCLOUD From 1bc6eb6e5ae4746df3f63189eb605c4969f2ce8f Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 14 Feb 2024 01:30:31 +0000 Subject: [PATCH 076/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 1c33dc7b..5ddc401f 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -97,3 +97,4 @@ C2147478146-POCLOUD C2730520815-POCLOUD C2799465509-POCLOUD C2799465518-POCLOUD +C2799465522-POCLOUD From 95892f21a1bd7bee3f279ae0dadc6a637333a5f1 Mon Sep 17 00:00:00 2001 From: jonathansmolenski Date: Wed, 14 Feb 2024 02:47:56 +0000 Subject: [PATCH 077/124] Update ops_associations.txt with new collections --- cmr/ops_associations.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt index 5ddc401f..3ff0104d 100644 --- a/cmr/ops_associations.txt +++ b/cmr/ops_associations.txt @@ -98,3 +98,4 @@ C2730520815-POCLOUD C2799465509-POCLOUD C2799465518-POCLOUD C2799465522-POCLOUD +C2068529568-POCLOUD From 6fdeeb21746b063252fb5a9286ae99790137afad Mon Sep 17 00:00:00 2001 From: ank1m <154441323+ank1m@users.noreply.github.com> Date: Wed, 14 Feb 2024 13:14:10 -0500 Subject: [PATCH 078/124] Issue #96: ensure the created dimension is sorted (#101) * implement sorting of the output queue according to the order of the input queue to satisfy issue #96 * Update CHANGELOG.md with issue-96 fix --- CHANGELOG.md | 2 ++ podaac/merger/harmony/download_worker.py | 10 +++++----- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 05076576..b87313e2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added ### Changed + - [issues/96](https://github.com/podaac/concise/issues/96): + - impelemented sorting after [multi_core_download](https://github.com/podaac/concise/blob/23b44803f4829c1eb7e9d39b311a0373092daab3/podaac/merger/harmony/download_worker.py#L15) to preserve the input file order in the ### Deprecated ### Removed ### Fixed diff --git a/podaac/merger/harmony/download_worker.py b/podaac/merger/harmony/download_worker.py index 465b46ed..f4f3e2c9 100644 --- a/podaac/merger/harmony/download_worker.py +++ b/podaac/merger/harmony/download_worker.py @@ -44,8 +44,8 @@ def multi_core_download(urls, destination_dir, access_token, cfg, process_count= url_queue = manager.Queue(len(urls)) path_list = manager.list() - for url in urls: - url_queue.put(url) + for iurl, url in enumerate(urls): + url_queue.put((iurl, url)) # Spawn worker processes processes = [] @@ -64,7 +64,7 @@ def multi_core_download(urls, destination_dir, access_token, cfg, process_count= path_list = deepcopy(path_list) # ensure GC can cleanup multiprocessing - return [Path(path) for path in path_list] + return [Path(path) for ipath, path in sorted(path_list)] def _download_worker(url_queue, path_list, destination_dir, access_token, cfg): @@ -91,7 +91,7 @@ def _download_worker(url_queue, path_list, destination_dir, access_token, cfg): while not url_queue.empty(): try: - url = url_queue.get_nowait() + iurl, url = url_queue.get_nowait() except queue.Empty: break @@ -105,4 +105,4 @@ def _download_worker(url_queue, path_list, destination_dir, access_token, cfg): else: logger.warning('Origin filename could not be assertained - %s', url) - path_list.append(str(path)) + path_list.append((iurl, str(path))) From 643e0881f6c6271aebd96441a1cd1fb7cea03815 Mon Sep 17 00:00:00 2001 From: concise bot Date: Wed, 14 Feb 2024 18:16:41 +0000 Subject: [PATCH 079/124] /version 0.8.0a4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 94297702..8b801000 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.8.0a3" +version = "0.8.0a4" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 4353bf4b81fc0997ccf928b4d93253d2ca5ffa95 Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 1 Mar 2024 18:13:59 +0000 Subject: [PATCH 080/124] /version 0.9.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0e752aed..13542e94 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.9.0a0" +version = "0.9.0a1" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From d77e96b9606e5b26d43e2e30124968f952c52aa2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 May 2024 09:06:52 -0700 Subject: [PATCH 081/124] Bump idna from 3.4 to 3.7 (#108) Bumps [idna](https://github.com/kjd/idna) from 3.4 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](https://github.com/kjd/idna/compare/v3.4...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 9eeb2f8c..dc4254cc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "alabaster" @@ -568,13 +568,13 @@ urllib3 = ">=1.26.9,<1.27.0" [[package]] name = "idna" -version = "3.4" +version = "3.7" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.5" files = [ - {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"}, - {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"}, + {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, + {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, ] [[package]] @@ -1293,6 +1293,7 @@ files = [ {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"}, {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"}, {file = "PyYAML-6.0.1-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:40df9b996c2b73138957fe23a16a4f0ba614f4c0efce1e9406a184b6d07fa3a9"}, + {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef"}, {file = "PyYAML-6.0.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:6c22bec3fbe2524cde73d7ada88f6566758a8f7227bfbf93a408a9d86bcc12a0"}, {file = "PyYAML-6.0.1-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4"}, {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"}, From 8def2fe6676bace798fb1f2d470cf67f2f92080d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 May 2024 09:07:09 -0700 Subject: [PATCH 082/124] Bump tqdm from 4.66.1 to 4.66.3 (#109) Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.66.1 to 4.66.3. - [Release notes](https://github.com/tqdm/tqdm/releases) - [Commits](https://github.com/tqdm/tqdm/compare/v4.66.1...v4.66.3) --- updated-dependencies: - dependency-name: tqdm dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index dc4254cc..41b3ac14 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1858,13 +1858,13 @@ files = [ [[package]] name = "tqdm" -version = "4.66.1" +version = "4.66.3" description = "Fast, Extensible Progress Meter" optional = false python-versions = ">=3.7" files = [ - {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"}, - {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"}, + {file = "tqdm-4.66.3-py3-none-any.whl", hash = "sha256:4f41d54107ff9a223dca80b53efe4fb654c67efaba7f47bada3ee9d50e05bd53"}, + {file = "tqdm-4.66.3.tar.gz", hash = "sha256:23097a41eba115ba99ecae40d06444c15d1c0c698d527a01c6c8bd1c5d0647e5"}, ] [package.dependencies] From 51cfba4a047e8152bb3048b7962f288abadcc93e Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 6 May 2024 16:10:12 +0000 Subject: [PATCH 083/124] /version 0.9.0a2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 13542e94..9db6c476 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.9.0a1" +version = "0.9.0a2" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 19d9cdc860e6390c7d51f82acba88d755f0f6dd9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 May 2024 11:42:28 -0700 Subject: [PATCH 084/124] Bump jinja2 from 3.1.3 to 3.1.4 (#110) Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.3...3.1.4) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 41b3ac14..964b002b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -637,13 +637,13 @@ requirements-deprecated-finder = ["pip-api", "pipreqs"] [[package]] name = "jinja2" -version = "3.1.3" +version = "3.1.4" description = "A very fast and expressive template engine." optional = false python-versions = ">=3.7" files = [ - {file = "Jinja2-3.1.3-py3-none-any.whl", hash = "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa"}, - {file = "Jinja2-3.1.3.tar.gz", hash = "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90"}, + {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"}, + {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"}, ] [package.dependencies] From 826e4a8ad43d3ea8d6c90afce75e6a4a58721f04 Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 13 May 2024 18:45:28 +0000 Subject: [PATCH 085/124] /version 0.9.0a3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9db6c476..32c63184 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.9.0a2" +version = "0.9.0a3" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 2b2ae35362b7c3125f06a254a09ab39f13c02469 Mon Sep 17 00:00:00 2001 From: James Wood Date: Wed, 15 May 2024 14:22:18 -0700 Subject: [PATCH 086/124] Feature/cleanup tests (#112) * update dependency versions * Removed CMR testing * update actions versions --------- Co-authored-by: James Wood --- .github/workflows/add-collection-test.yml | 156 -- .github/workflows/build-pipeline.yml | 6 +- .pylintrc | 4 +- CHANGELOG.md | 5 +- add_collection_test.py | 307 ---- cmr/ops_associations.txt | 101 -- cmr/uat_associations.txt | 119 -- poetry.lock | 1960 ++++++++++++--------- pyproject.toml | 20 +- remove_association.py | 101 -- 10 files changed, 1112 insertions(+), 1667 deletions(-) delete mode 100644 .github/workflows/add-collection-test.yml delete mode 100644 add_collection_test.py delete mode 100644 cmr/ops_associations.txt delete mode 100644 cmr/uat_associations.txt delete mode 100644 remove_association.py diff --git a/.github/workflows/add-collection-test.yml b/.github/workflows/add-collection-test.yml deleted file mode 100644 index 9cd69436..00000000 --- a/.github/workflows/add-collection-test.yml +++ /dev/null @@ -1,156 +0,0 @@ -# This is a test pipeline, that verifies and updates the associations in cmr -name: Add Collection Test -# Controls when the workflow will run -on: - # Allows you to run this workflow manually from the Actions tab - workflow_dispatch: - -jobs: - # First job in the workflow installs and verifies the software - build: - name: Test Execution - # The type of runner that the job will run on - runs-on: ubuntu-latest - steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Create Output Directory - run: mkdir test_output - - name: Set environment variables - run: | - echo "UAT_OUTPUT_FILE=test_output/output/uat_output_json.txt" >> $GITHUB_ENV - echo "OPS_OUTPUT_FILE=test_output/output/ops_output_json.txt" >> $GITHUB_ENV - echo "OUTPUT_DIR=test_output/output" >> $GITHUB_ENV - echo "UAT_SUCCESS_FILE=uat_success.txt" >> $GITHUB_ENV - echo "OPS_SUCCESS_FILE=ops_success.txt" >> $GITHUB_ENV - echo "UAT_FAILURE_FILE=uat_fail.txt" >> $GITHUB_ENV - echo "OPS_FAILURE_FILE=ops_fail.txt" >> $GITHUB_ENV - echo "SLACK_REPORT_CONTENT=" >> $GITHUB_ENV - - name: Set environment variables for notebook - run: | - echo "OPS_USERNAME=${{ secrets.EDL_USER }}" >> $GITHUB_ENV - echo "OPS_PASSWORD=${{ secrets.EDL_PASS }}" >> $GITHUB_ENV - echo "UAT_USERNAME=${{ secrets.EDL_USER }}" >> $GITHUB_ENV - echo "UAT_PASSWORD=${{ secrets.EDL_PASS }}" >> $GITHUB_ENV - - name: Create prerequisites - run: | - mkdir ${{ env.OUTPUT_DIR }} - realpath ${{ env.OUTPUT_DIR }} - - name: Install dependencies - run: | - pip3 install --upgrade pip - pip3 install black - pip3 install netCDF4 - pip3 install git+https://github.com/nasa/harmony-py.git - pip3 install git+https://github.com/podaac/cmr-umm-updater.git - pip3 install git+https://github.com/podaac/cmr-association-diff.git - pip3 install python-dateutil --upgrade - - name: Run CMR Association diff scripts - run: | - cmr_association_diff -e uat -t service -a "cmr/uat_associations.txt" -p POCLOUD -n 'PODAAC Concise' -o ${{ env.UAT_OUTPUT_FILE }} --token ${{ secrets.LAUNCHPAD_TOKEN_UAT }} - cmr_association_diff -e ops -t service -a "cmr/ops_associations.txt" -p POCLOUD -n 'PODAAC Concise' -o ${{ env.OPS_OUTPUT_FILE }} --token ${{ secrets.LAUNCHPAD_TOKEN_OPS }} - - name: Run Add Collection Test - run: | - python3 add_collection_test.py -e uat -i ${{ env.UAT_OUTPUT_FILE }} -o ${{ env.OUTPUT_DIR }} - python3 add_collection_test.py -e ops -i ${{ env.OPS_OUTPUT_FILE }} -o ${{ env.OUTPUT_DIR }} - - name: Check UAT files - id: check_UAT_output_files - run: | - echo "::set-output name=SUCCESS_EXISTS::$(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.UAT_SUCCESS_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "::set-output name=FAIL_EXISTS::$(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.UAT_FAILURE_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "::set-output name=SUCCESS_CONTENT::$(cat ${{ env.OUTPUT_DIR }}/${{ env.UAT_SUCCESS_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo "::set-output name=FAIL_CONTENT::$(cat ${{ env.OUTPUT_DIR }}/${{ env.UAT_FAILURE_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo - echo - echo "Success File: $(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.UAT_SUCCESS_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "Failed File: $(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.UAT_FAILURE_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "Success Content: $(cat ${{ env.OUTPUT_DIR }}/${{ env.UAT_SUCCESS_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo - echo "Failed Content: $(cat ${{ env.OUTPUT_DIR }}/${{ env.UAT_FAILURE_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - - name: Check OPS files - id: check_OPS_output_files - run: | - echo "::set-output name=SUCCESS_EXISTS::$(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.OPS_SUCCESS_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "::set-output name=FAIL_EXISTS::$(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.OPS_FAILURE_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "::set-output name=SUCCESS_CONTENT::$(cat ${{ env.OUTPUT_DIR }}/${{ env.OPS_SUCCESS_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo "::set-output name=FAIL_CONTENT::$(cat ${{ env.OUTPUT_DIR }}/${{ env.OPS_FAILURE_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo - echo - echo "Success File: $(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.OPS_SUCCESS_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "Failed File: $(if [ -f ${{ env.OUTPUT_DIR }}/${{ env.OPS_FAILURE_FILE }} ]; then echo "true"; else echo "false"; fi)" - echo "Success Content: $(cat ${{ env.OUTPUT_DIR }}/${{ env.OPS_SUCCESS_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - echo - echo "Failed Content: $(cat ${{ env.OUTPUT_DIR }}/${{ env.OPS_FAILURE_FILE }} | sed 's/$/,/' | tr '\n' ' ')" - - name: Slack Report update - Add info for UAT check - SUCCESS - if: | - steps.check_UAT_output_files.outputs.SUCCESS_EXISTS == 'true' - run: | - echo "SLACK_REPORT_CONTENT=${{ env.SLACK_REPORT_CONTENT }}\ncollection-test UAT result: SUCCESS\nSuccessfully ran Concise Notebook on the following collections:\n${{ steps.check_UAT_output_files.outputs.SUCCESS_CONTENT }}\n" >> $GITHUB_ENV - - name: Slack Report update - Add info for UAT check - FAILURE - if: | - steps.check_UAT_output_files.outputs.FAIL_EXISTS == 'true' - run: | - echo "SLACK_REPORT_CONTENT=${{ env.SLACK_REPORT_CONTENT }}\ncollection-test UAT result: FAILURE\nFailed to run Concise Notebook on the following collections:\n${{ steps.check_UAT_output_files.outputs.FAIL_CONTENT }}\n" >> $GITHUB_ENV - - name: Slack Report update - Add info for OPS check - SUCCESS - if: | - steps.check_OPS_output_files.outputs.SUCCESS_EXISTS == 'true' - run: | - echo "SLACK_REPORT_CONTENT=${{ env.SLACK_REPORT_CONTENT }}\ncollection-test OPS result: SUCCESS\nSuccessfully ran Concise Notebook on the following collections:\n${{ steps.check_OPS_output_files.outputs.SUCCESS_CONTENT }}\n" >> $GITHUB_ENV - - name: Slack Report update - Add info for OPS check - FAILURE - if: | - steps.check_OPS_output_files.outputs.FAIL_EXISTS == 'true' - run: | - echo "SLACK_REPORT_CONTENT=${{ env.SLACK_REPORT_CONTENT }}\ncollection-test OPS result: FAILURE\nFailed to run Concise Notebook on the following collections:\n${{ steps.check_OPS_output_files.outputs.FAIL_CONTENT }}\n" >> $GITHUB_ENV - - name: Slack Report update - Add action link on Failure - if: | - steps.check_UAT_output_files.outputs.FAIL_EXISTS == 'true' || - steps.check_OPS_output_files.outputs.FAIL_EXISTS == 'true' - run: | - echo "SLACK_REPORT_CONTENT=${{ env.SLACK_REPORT_CONTENT }}\nExecution link:\ngithub.com/${{ github.repository }}/actions/runs/${{ github.run_id }}" >> $GITHUB_ENV - echo ${{ env.SLACK_REPORT_CONTENT }} - - name: Send Report to Slack - uses: slackapi/slack-github-action@v1.21.0 - if: | - env.SLACK_REPORT_CONTENT != '' - with: - payload: | - { - "status": "${{ env.SLACK_REPORT_CONTENT }}" - } - env: - SLACK_WEBHOOK_URL: ${{ secrets.SLACK_BOT_WEBHOOK }} - - name: Remove UAT collections on FAIL - if: | - steps.check_UAT_output_files.outputs.FAIL_EXISTS == 'true' - run: | - python3 "remove_association.py" -p POCLOUD -n 'PODAAC Concise' -e uat -i '${{ env.OUTPUT_DIR }}/${{ env.UAT_FAILURE_FILE }}' --token ${{ secrets.LAUNCHPAD_TOKEN_UAT }} - - name: Remove OPS collections on FAIL - if: | - steps.check_OPS_output_files.outputs.FAIL_EXISTS == 'true' - run: | - python3 "remove_association.py" -p POCLOUD -n 'PODAAC Concise' -e ops -i '${{ env.OUTPUT_DIR }}/${{ env.OPS_FAILURE_FILE }}' --token ${{ secrets.LAUNCHPAD_TOKEN_OPS }} - - name: Update UAT collections on SUCCESS - if: | - steps.check_UAT_output_files.outputs.SUCCESS_EXISTS == 'true' - # Add a new line to the EOF if there isn't any, so the merging will start in a new line not after the last character - run: | - vi -escwq ./cmr/uat_associations.txt - cat ${{ env.OUTPUT_DIR }}/${{ env.UAT_SUCCESS_FILE }} >> ./cmr/uat_associations.txt - git config user.name "${GITHUB_ACTOR}" - git config user.email "${GITHUB_ACTOR}@users.noreply.github.com" - git commit -am "Update uat_associations.txt with new collections" - git push - - name: Update OPS collections on SUCCESS - if: | - steps.check_OPS_output_files.outputs.SUCCESS_EXISTS == 'true' - # Add a new line to the EOF if there isn't any, so the merging will start in a new line not after the last character - run: | - vi -escwq ./cmr/ops_associations.txt - cat ${{ env.OUTPUT_DIR }}/${{ env.OPS_SUCCESS_FILE }} >> ./cmr/ops_associations.txt - git config user.name "${GITHUB_ACTOR}" - git config user.email "${GITHUB_ACTOR}@users.noreply.github.com" - git commit -am "Update ops_associations.txt with new collections" - git push diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index bfe739fb..6c83eb3d 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -23,8 +23,8 @@ jobs: runs-on: ubuntu-latest steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ env.PYTHON_VERSION }} - name: Install Poetry @@ -190,7 +190,7 @@ jobs: - name: Build Python Artifact run: | poetry build - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: python-artifact path: dist/* diff --git a/.pylintrc b/.pylintrc index 203538f6..cd720bde 100644 --- a/.pylintrc +++ b/.pylintrc @@ -307,8 +307,8 @@ min-public-methods=2 [EXCEPTIONS] # Exceptions that will emit a warning when caught. -overgeneral-exceptions=BaseException, - Exception +overgeneral-exceptions=builtins.BaseException, + builtins.Exception [FORMAT] diff --git a/CHANGELOG.md b/CHANGELOG.md index 11fe38a9..3c8e867c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,9 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added -### Changed +### Changed + - Updated python libraries ### Deprecated ### Removed + - Removed CMR testing. Now done in [concise-autotest](https://github.com/podaac/concise-autotest) repo + - Moved add_collection_test.py test to verify_collection.py (in concise-autotest repo) ### Fixed diff --git a/add_collection_test.py b/add_collection_test.py deleted file mode 100644 index a3bc1db4..00000000 --- a/add_collection_test.py +++ /dev/null @@ -1,307 +0,0 @@ -import os -from os import path -from urllib.parse import urlparse -import itertools -import unittest -import numpy as np -import netCDF4 as nc -import requests -import json -from harmony import BBox, Client, Collection, Request, Environment -import argparse -from utils import FileHandler -from utils.enums import Venue - - -def parse_args(): - """ - Parses the program arguments - Returns - ------- - args - """ - - parser = argparse.ArgumentParser( - description='Update CMR with latest profile', - formatter_class=argparse.ArgumentDefaultsHelpFormatter - ) - - parser.add_argument('-e', '--env', - help='CMR environment used to pull results from.', - required=True, - choices=["uat", "ops", "ngap_uat", "ngap_ops"], - metavar='uat or ops') - - parser.add_argument('-n', '--notebook', - help='Notebook to run', - required=False, - metavar='') - - parser.add_argument('-i', '--input_file', - help='File of json collections', - required=True, - metavar='') - - parser.add_argument('-o', '--output_path', - help='output path for success and fails', - required=False, - metavar='') - - args = parser.parse_args() - return args - - -def get_username_and_password(venue): - if venue.lower() == "uat": - return os.environ.get("UAT_USERNAME"), os.environ.get("UAT_PASSWORD") - elif venue.lower() == "ops": - return os.environ.get('OPS_USERNAME'), os.environ.get('OPS_PASSWORD') - else: - raise ValueError("Invalid venue") - - -def get_x_y_variables(variables): - x_var_candidates = ["lon", "longitude", "beam_clon", "sp_lon", "cellon"] - y_var_candidates = ["lat", "latitude", "beam_clat", "sp_lat", "cellat"] - - x_var, y_var = None, None - for var in variables: - if x_var is None and var in x_var_candidates: - x_var = var - if y_var is None and var in y_var_candidates: - y_var = var - if x_var and y_var: - break - - return x_var, y_var - - -def verify_dims(merged_group, origin_group, both_merged): - for dim in origin_group.dimensions: - if both_merged: - unittest.TestCase().assertEqual(merged_group.dimensions[dim].size, origin_group.dimensions[dim].size) - else: - unittest.TestCase().assertGreaterEqual(merged_group.dimensions[dim].size, origin_group.dimensions[dim].size) - - -def verify_attrs(merged_obj, origin_obj, both_merged): - ignore_attributes = [ - 'request-bounding-box', 'request-bounding-box-description', 'PODAAC-dataset-shortname', - 'PODAAC-persistent-ID', 'time_coverage_end', 'time_coverage_start' - ] - - merged_attrs = merged_obj.ncattrs() - origin_attrs = origin_obj.ncattrs() - - for attr in origin_attrs: - if attr in ignore_attributes: - # Skip attributes which are present in the Java implementation, - # but not (currently) present in the Python implementation - continue - - if not both_merged and attr not in merged_attrs: - # Skip attributes which are not present in both merged and origin. - # This is normal operation as some attributes may be omited b/c - # they're inconsistent between granules - continue - - merged_attr = merged_obj.getncattr(attr) - if both_merged and isinstance(merged_attr, int): - # Skip integer values - the Java implementation seems to omit - # these values due to its internal handling of all values as - # Strings - continue - - origin_attr = origin_obj.getncattr(attr) - if isinstance(origin_attr, np.ndarray): - unittest.TestCase().assertTrue(np.array_equal(merged_attr, origin_attr)) - else: - if attr != "history_json": - unittest.TestCase().assertEqual(merged_attr, origin_attr) - - -def verify_variables(merged_group, origin_group, subset_index, both_merged): - for var in origin_group.variables: - merged_var = merged_group.variables[var] - origin_var = origin_group.variables[var] - - verify_attrs(merged_var, origin_var, both_merged) - - if both_merged: - # both groups require subset indexes - merged_data = merged_var[subset_index[0]] - origin_data = origin_var[subset_index[1]] - else: - # merged group requires a subset index - merged_data = np.resize(merged_var[subset_index], origin_var.shape) - origin_data = origin_var - - equal_nan = True - if merged_data.dtype.kind == 'S': - equal_nan = False - - # verify variable data - if isinstance(origin_data, str): - unittest.TestCase().assertEqual(merged_data, origin_data) - else: - unittest.TestCase().assertTrue(np.array_equal(merged_data, origin_data, equal_nan=equal_nan)) - - -def verify_groups(merged_group, origin_group, subset_index, file=None, both_merged=False): - if file: - print("verifying groups ....." + file) - - verify_dims(merged_group, origin_group, both_merged) - verify_attrs(merged_group, origin_group, both_merged) - verify_variables(merged_group, origin_group, subset_index, both_merged) - - for child_group in origin_group.groups: - merged_subgroup = merged_group[child_group] - origin_subgroup = origin_group[child_group] - verify_groups(merged_subgroup, origin_subgroup, subset_index, both_merged=both_merged) - - -# GET TOKEN FROM CMR -def get_token(cmr_root, username, password): - token_api = "https://{}/api/users/tokens".format(cmr_root) - response = requests.get(token_api, auth=(username, password)) - content = response.json() - if len(content) > 0: - return content[0].get('access_token') - else: - create_token_api = "https://{}/api/users/token".format(cmr_root) - response = requests.post(create_token_api, auth=(username, password)) - content = response.json() - return content.get('access_token') - - -def download_file(url, local_path, headers): - response = requests.get(url, stream=True, headers=headers) - if response.status_code == 200: - with open(local_path, 'wb') as file: - for chunk in response.iter_content(chunk_size=8192): - file.write(chunk) - print("Original File downloaded successfully. " + local_path) - else: - print(f"Failed to download the file. Status code: {response.status_code}") - - -def test(collection_id, venue): - - max_results = 2 - - username, password = get_username_and_password(venue) - environment = Environment.UAT if venue.lower() == "uat" else Environment.PROD - harmony_client = Client(auth=(username, password), env=environment) - - collection = Collection(id=collection_id) - - request = Request( - collection=collection, - concatenate=True, - max_results=max_results, - skip_preview=True, - format="application/x-netcdf4", - ) - - request.is_valid() - - print(harmony_client.request_as_curl(request)) - - job1_id = harmony_client.submit(request) - - print(f'\n{job1_id}') - - print(harmony_client.status(job1_id)) - - print('\nWaiting for the job to finish') - - results = harmony_client.result_json(job1_id) - - print('\nDownloading results:') - - futures = harmony_client.download_all(job1_id) - file_names = [f.result() for f in futures] - print('\nDone downloading.') - - filename = file_names[0] - - # Handle time dimension and variables dropping - merge_dataset = nc.Dataset(filename, 'r') - - cmr_base_url = "https://cmr.earthdata.nasa.gov/search/granules.umm_json?readable_granule_name=" - edl_root = 'urs.earthdata.nasa.gov' - - if venue.lower() == 'uat': - cmr_base_url = "https://cmr.uat.earthdata.nasa.gov/search/granules.umm_json?readable_granule_name=" - edl_root = 'uat.urs.earthdata.nasa.gov' - - token = get_token(edl_root, username, password) - headers = { - "Authorization": f"Bearer {token}" - } - - original_files = merge_dataset.variables['subset_files'] - history_json = json.loads(merge_dataset.history_json) - assert len(original_files) == max_results - - for url in history_json[0].get("derived_from"): - local_file_name = os.path.basename(url) - download_file(url, local_file_name, headers) - - for i, file in enumerate(original_files): - origin_dataset = nc.Dataset(file) - verify_groups(merge_dataset, origin_dataset, i, file=file) - - -def run(): - """ - Run from command line. - - Returns - ------- - """ - - _args = parse_args() - environment = _args.env - notebook = _args.notebook - inputFile = _args.input_file - output_location = _args.output_path if _args.output_path else '.' - - success = [] - fails = [] - - if path.exists(inputFile): - venue = Venue.from_str(environment) - collections = FileHandler.get_file_content_list_per_line(inputFile) - print(collections) - # limit number of collections tested to 1 - for collection in itertools.islice(collections, 1): - if "POCLOUD" not in collection and venue == "uat": - continue - - try: - print(collection) - test(collection, venue.name) - success.append(collection) - except Exception as ex: - print(ex) - fails.append(collection) - - # Create output files - if output_location: - success_outfile = path.realpath(f'{output_location}/{_args.env}_success.txt') - fail_outfile = path.realpath(f'{output_location}/{_args.env}_fail.txt') - - if success: - with open(success_outfile, 'w') as the_file: - the_file.writelines(x + '\n' for x in success) - - if fails: - with open(fail_outfile, 'w') as the_file: - the_file.writelines(x + '\n' for x in fails) - - -if __name__ == '__main__': - print("Start running test .......") - run() diff --git a/cmr/ops_associations.txt b/cmr/ops_associations.txt deleted file mode 100644 index 3ff0104d..00000000 --- a/cmr/ops_associations.txt +++ /dev/null @@ -1,101 +0,0 @@ -C1940473819-POCLOUD -C1940475563-POCLOUD -C2205618215-POCLOUD -C2205618339-POCLOUD -C2205121384-POCLOUD -C2205121394-POCLOUD -C2152044763-POCLOUD -C2158344213-POCLOUD -C2254232941-POCLOUD -C2147947806-POCLOUD -C2247621105-POCLOUD -C2158348170-POCLOUD -C2205121315-POCLOUD -C2152046451-POCLOUD -C2158348264-POCLOUD -C2158350299-POCLOUD -C2152045877-POCLOUD -C1996881636-POCLOUD -C2251465126-POCLOUD -C2075141524-POCLOUD -C1940471193-POCLOUD -C2251464384-POCLOUD -C1940472420-POCLOUD -C1940470304-POCLOUD -C2205121449-POCLOUD -C2596983413-POCLOUD -C2596986276-POCLOUD -C2036882072-POCLOUD -C2075141638-POCLOUD 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b/pyproject.toml index 32c63184..031553b4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,21 +15,21 @@ packages = [ ] [tool.poetry.dependencies] -python = "^3.9" +python = "^3.10" netCDF4 = "^1.5.6" numpy = "^1.20.3" -harmony-service-lib = "^1.0.20" -importlib-metadata = "^6.0.0" +harmony-service-lib = "^1.0.26" +importlib-metadata = "^7.1.0" [tool.poetry.group.dev.dependencies] -setuptools = "^66.0.0" -pytest = "~7" -flake8 = "~6" -pytest-cov = "~4" -pylint = "~2" -Sphinx = "^4.0" +setuptools = "^69.5.1" +pytest = "^8.2.0" +flake8 = "^7.0.0" +pytest-cov = "^5.0.0" +pylint = "^3.2.0" +Sphinx = "^7.3.7" requests = "^2.25.1" -sphinx-rtd-theme = "^1.0" +sphinx-rtd-theme = "^2.0.0" papermill = "^2.3.4" [tool.poetry.scripts] diff --git a/remove_association.py b/remove_association.py deleted file mode 100644 index 8166f225..00000000 --- a/remove_association.py +++ /dev/null @@ -1,101 +0,0 @@ -import argparse -import cmr - -from podaac.umms_updater.util import create_assoc -from podaac.umms_updater.util import svc_update - -def parse_args(): - """ - Parses the program arguments - Returns - ------- - args - """ - - parser = argparse.ArgumentParser( - description='Remove collection association from CMR', - formatter_class=argparse.ArgumentDefaultsHelpFormatter - ) - - parser.add_argument('-e', '--env', - help='CMR environment used to pull results from.', - required=False, - choices=["uat", "ops", "sit"], - metavar='uat or ops') - - parser.add_argument('-i', '--input_file', - help='File of json collections to remove', - required=False, - metavar='') - - parser.add_argument('-t', '--token', - help='Launchpad token string', - default=None, - required=True, - metavar='Launchpad token') - - parser.add_argument('-p', '--provider', - help='A provider ID identifies a provider and is' - 'composed of a combination of upper case' - ' letters, digits, and underscores.' - 'The maximum length is 10 characters.' - 'Concept ID is provided if UMM-S record already' - 'exists and needs to be updated.', - required=False, - default='POCLOUD', - metavar='POCLOUD') - - parser.add_argument('-n', '--umm_name', - help='Name of the umm tool or service', - required=True, - metavar='') - - - args = parser.parse_args() - return args - -def run(): - """ - Run from command line. - - Returns - ------- - """ - - _args = parse_args() - - collection_json = _args.input_file - environment = _args.env - service_name = _args.umm_name - - header = { - 'Content-type': "application/json", - 'Authorization': str(_args.token), - } - url_prefix = svc_update.cmr_environment_url(_args.env) - - mode = cmr.queries.CMR_OPS - if environment == 'uat': - mode = cmr.queries.CMR_UAT - - service_query = cmr.queries.ServiceQuery(mode=mode).provider(_args.provider).name(service_name).get() - service_concept_id = service_query[0].get('concept_id') - - with open(collection_json) as afile: - assoc_concept_ids = afile.readlines() - exception_happen = False - failed_remove = [] - for i, assoc_concept_id in enumerate(assoc_concept_ids): - collection_concept_id = assoc_concept_id.strip('\n') - print(f"Removing {collection_concept_id} from CMR association") - resp = create_assoc.remove_association(url_prefix, service_concept_id, collection_concept_id, header) - print(f'Response: {resp}') - if resp.status_code != 200: - exception_happen = True - failed_remove.append(assoc_concept_ids) - if exception_happen: - print(failed_remove) - raise Exception("Failure to remove a collection from CMR") - -if __name__ == '__main__': - run() From 619b1b6858bb23bf501f0cdac391764a6c9be125 Mon Sep 17 00:00:00 2001 From: concise bot Date: Wed, 15 May 2024 21:25:03 +0000 Subject: [PATCH 087/124] /version 0.9.0a4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 031553b4..11aa1c07 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.9.0a3" +version = "0.9.0a4" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 9e4a089a6cf5bc4cc74f0d6dbbc06c597bf3dacd Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Fri, 24 May 2024 10:17:24 -0400 Subject: [PATCH 088/124] add type annotations and args to docstrings (#115) * add type annotations and args to docstrings * update CHANGELOG.md --- CHANGELOG.md | 1 + podaac/merger/merge.py | 30 ++++++++++++------- podaac/merger/merge_worker.py | 48 ++++++++++++++++++++---------- podaac/merger/path_utils.py | 9 +++--- podaac/merger/preprocess_worker.py | 39 +++++++++++++++--------- 5 files changed, 84 insertions(+), 43 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c8e867c..1840fe9d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added ### Changed - Updated python libraries + - [issue #114](https://github.com/podaac/concise/issues/114): add type annotations ### Deprecated ### Removed - Removed CMR testing. Now done in [concise-autotest](https://github.com/podaac/concise-autotest) repo diff --git a/podaac/merger/merge.py b/podaac/merger/merge.py index c2cd9edc..44a20503 100644 --- a/podaac/merger/merge.py +++ b/podaac/merger/merge.py @@ -1,5 +1,5 @@ """Main module containing merge implementation""" - +from pathlib import Path from time import perf_counter from logging import getLogger from os import cpu_count @@ -11,9 +11,9 @@ from podaac.merger.preprocess_worker import run_preprocess -def is_file_empty(parent_group): +def is_file_empty(parent_group: nc.Dataset | nc.Group) -> bool: """ - Function to test if a all variable size in a dataset is 0 + Function to test if any variable size in a dataset is zero """ for var in parent_group.variables.values(): @@ -24,17 +24,23 @@ def is_file_empty(parent_group): return True -def merge_netcdf_files(original_input_files, output_file, granule_urls, logger=getLogger(__name__), perf_stats=None, process_count=None): # pylint: disable=too-many-locals +def merge_netcdf_files(original_input_files: list[Path], # pylint: disable=too-many-locals + output_file: str, + granule_urls, + logger=getLogger(__name__), + perf_stats: dict = None, + process_count: int = None): """ Main entrypoint to merge implementation. Merges n >= 2 granules together as a single - granule. Named in reference to original Java implementation. + granule. Named in reference to the original Java implementation. Parameters ---------- - input_files: list - list of string paths to NetCDF4 files to merge + original_input_files: list + list of Paths to NetCDF4 files to merge output_file: str output path for merged product + granule_urls logger: logger logger object perf_stats: dict @@ -113,7 +119,7 @@ def merge_netcdf_files(original_input_files, output_file, granule_urls, logger=g logger.info('Done!') -def clean_metadata(metadata): +def clean_metadata(metadata: dict) -> None: """ Prepares metadata dictionary for insertion by removing inconsistent entries and performing escaping of attribute names @@ -141,9 +147,13 @@ def clean_metadata(metadata): del metadata[key] -def init_dataset(merged_dataset, groups, var_info, max_dims, input_files): +def init_dataset(merged_dataset: nc.Dataset, + groups: list[str], + var_info: dict, + max_dims: dict, + input_files: list[Path]) -> None: """ - Initialize the dataset utilizing data gathered from preprocessing + Initialize the dataset using data gathered from preprocessing Parameters ---------- diff --git a/podaac/merger/merge_worker.py b/podaac/merger/merge_worker.py index 7a16faf5..d43ee66a 100644 --- a/podaac/merger/merge_worker.py +++ b/podaac/merger/merge_worker.py @@ -1,19 +1,20 @@ """Preprocessing methods and the utilities to automagically run them in single-thread/multiprocess modes""" - +import logging import math -import multiprocessing -from multiprocessing.shared_memory import SharedMemory import queue import time import os import shutil +import multiprocessing +from multiprocessing.shared_memory import SharedMemory +from pathlib import Path import netCDF4 as nc import numpy as np from podaac.merger.path_utils import resolve_dim, resolve_group -def shared_memory_size(): +def shared_memory_size() -> int: """ try to get the shared memory space size by reading the /dev/shm on linux machines """ @@ -26,9 +27,8 @@ def shared_memory_size(): return int(default_memory_size) -def max_var_memory(file_list, var_info, max_dims): - """ - function to get the maximum shared memory that will be used for variables +def max_var_memory(file_list: list[Path], var_info: dict, max_dims) -> int: + """Function to get the maximum shared memory that will be used for variables Parameters ---------- @@ -36,6 +36,7 @@ def max_var_memory(file_list, var_info, max_dims): List of file paths to be processed var_info : dict Dictionary of variable paths and associated VariableInfo + max_dims """ max_var_mem = 0 @@ -57,7 +58,12 @@ def max_var_memory(file_list, var_info, max_dims): return max_var_mem -def run_merge(merged_dataset, file_list, var_info, max_dims, process_count, logger): +def run_merge(merged_dataset: nc.Dataset, + file_list: list[Path], + var_info: dict, + max_dims: dict, + process_count: int, + logger: logging.Logger): """ Automagically run merging in an optimized mode determined by the environment @@ -73,6 +79,7 @@ def run_merge(merged_dataset, file_list, var_info, max_dims, process_count, logg Dictionary of dimension paths and maximum dimensions found during preprocessing process_count : int Number of worker processes to run (expected >= 1) + logger """ if process_count == 1: @@ -91,7 +98,11 @@ def run_merge(merged_dataset, file_list, var_info, max_dims, process_count, logg _run_single_core(merged_dataset, file_list, var_info, max_dims, logger) -def _run_single_core(merged_dataset, file_list, var_info, max_dims, logger): +def _run_single_core(merged_dataset: nc.Dataset, + file_list: list[Path], + var_info: dict, + max_dims: dict, + logger: logging.Logger): """ Run the variable merge in the current thread/single-core mode @@ -105,6 +116,7 @@ def _run_single_core(merged_dataset, file_list, var_info, max_dims, logger): Dictionary of variable paths and associated VariableInfo max_dims : dict Dictionary of dimension paths and maximum dimensions found during preprocessing + logger """ logger.info("Running single core ......") @@ -129,7 +141,12 @@ def _run_single_core(merged_dataset, file_list, var_info, max_dims, logger): merged_var[i] = resized -def _run_multi_core(merged_dataset, file_list, var_info, max_dims, process_count, logger): # pylint: disable=too-many-locals +def _run_multi_core(merged_dataset: nc.Dataset, # pylint: disable=too-many-locals + file_list: list[Path], + var_info: dict, + max_dims: dict, + process_count: int, + logger: logging.Logger): """ Run the variable merge in multi-core mode. This method creates (process_count - 1) read processes which read data from an origin granule, resize it, then queue it @@ -150,6 +167,7 @@ def _run_multi_core(merged_dataset, file_list, var_info, max_dims, process_count Dictionary of dimension paths and maximum dimensions found during preprocessing process_count : int Number of worker processes to run (expected >= 2) + logger """ logger.info("Running multicore ......") @@ -266,7 +284,7 @@ def _run_worker(in_queue, out_queue, max_dims, var_info, memory_limit, lock): shared_mem.close() -def _check_exit(processes): +def _check_exit(processes: list): """ Ensure that all processes have exited without error by checking their exitcode if they're no longer running. Processes that have exited properly are removed @@ -286,7 +304,7 @@ def _check_exit(processes): raise RuntimeError(f'Merging failed - exit code: {process.exitcode}') -def resize_var(var, var_info, max_dims): +def resize_var(var: nc.Variable, var_info, max_dims: dict) -> np.ndarray: """ Resizes a variable's data to the maximum dimensions found in preprocessing. This method will never downscale a variable and only performs bottom and @@ -296,8 +314,8 @@ def resize_var(var, var_info, max_dims): ---------- var : nc.Variable variable to be resized - group_path : str - group path to this variable + var_info + contains a group path to this variable max_dims : dict dictionary of maximum dimensions found during preprocessing @@ -310,7 +328,7 @@ def resize_var(var, var_info, max_dims): if var.ndim == 0: return var[:] - # generate ordered array of new widths + # generate an ordered array of new widths dims = [resolve_dim(max_dims, var_info.group_path, dim.name) - dim.size for dim in var.get_dims()] widths = [[0, dim] for dim in dims] diff --git a/podaac/merger/path_utils.py b/podaac/merger/path_utils.py index 9cf7ebbe..8a93c9fe 100644 --- a/podaac/merger/path_utils.py +++ b/podaac/merger/path_utils.py @@ -2,9 +2,10 @@ Utilities used throughout the merging implementation to simplify group path resolution and generation """ +import netCDF4 as nc -def get_group_path(group, resource): +def get_group_path(group: nc.Group, resource: str) -> str: """ Generates a Unix-like path from a group and resource to be accessed @@ -27,7 +28,7 @@ def get_group_path(group, resource): return group.path + '/' + resource -def resolve_group(dataset, path): +def resolve_group(dataset: nc.Dataset, path: str): """ Resolves a group path into two components: the group and the resource's name @@ -50,10 +51,10 @@ def resolve_group(dataset, path): if len(components[0]) > 0: group = dataset[components[0]] - return (group, components[1]) + return group, components[1] -def resolve_dim(dims, group_path, dim_name): +def resolve_dim(dims: dict, group_path: str, dim_name: str): """ Attempt to resolve dim name starting from top-most group going down to the root group diff --git a/podaac/merger/preprocess_worker.py b/podaac/merger/preprocess_worker.py index 9edefabe..4bedba33 100644 --- a/podaac/merger/preprocess_worker.py +++ b/podaac/merger/preprocess_worker.py @@ -1,10 +1,10 @@ """Preprocessing methods and the utilities to automagically run them in single-thread/multiprocess modes""" - +from pathlib import Path import json import queue from copy import deepcopy from datetime import datetime, timezone -from multiprocessing import Manager, Process +from multiprocessing import Manager, Process, Queue import importlib_metadata import netCDF4 as nc @@ -14,7 +14,7 @@ from podaac.merger.variable_info import VariableInfo -def run_preprocess(file_list, process_count, granule_urls): +def run_preprocess(file_list: list[Path], process_count: int, granule_urls: str) -> dict: """ Automagically run preprocessing in an optimized mode determined by the environment @@ -24,6 +24,7 @@ def run_preprocess(file_list, process_count, granule_urls): List of file paths to be processed process_count : int Number of worker processes to run (expected >= 1) + granule_urls """ if process_count == 1: @@ -50,7 +51,7 @@ def merge_max_dims(merged_max_dims, subset_max_dims): merged_max_dims[dim_name] = subset_dim_size -def merge_metadata(merged_metadata, subset_metadata): +def merge_metadata(merged_metadata: dict, subset_metadata: dict) -> None: """ Perform aggregation of metadata. Intended for use in multithreaded mode only @@ -75,7 +76,7 @@ def merge_metadata(merged_metadata, subset_metadata): merged_attrs[attr_name] = False # mark as inconsistent -def construct_history(input_files, granule_urls): +def construct_history(input_files: list[Path], granule_urls: str) -> dict: """ Construct history JSON entry for this concatenation operation https://wiki.earthdata.nasa.gov/display/TRT/In-File+Provenance+Metadata+-+TRT-42 @@ -84,6 +85,7 @@ def construct_history(input_files, granule_urls): ---------- input_files : list List of input files + granule_urls : str Returns ------- @@ -123,7 +125,7 @@ def retrieve_history(dataset): return json.loads(history_json) -def _run_single_core(file_list, granule_urls): +def _run_single_core(file_list: list[Path], granule_urls: str) -> dict: """ Run the granule preprocessing in the current thread/single-core mode @@ -131,6 +133,7 @@ def _run_single_core(file_list, granule_urls): ---------- file_list : list List of file paths to be processed + granule_urls Returns ------- @@ -167,7 +170,9 @@ def _run_single_core(file_list, granule_urls): } -def _run_multi_core(file_list, process_count, granule_urls): +def _run_multi_core(file_list: list[Path], + process_count: int, + granule_urls: str) -> dict: """ Run the granule preprocessing in multi-core mode. This method spins up the number of processes defined by process_count which process granules @@ -181,6 +186,7 @@ def _run_multi_core(file_list, process_count, granule_urls): List of file paths to be processed process_count : int Number of worker processes to run (expected >= 2) + granule_urls Returns ------- @@ -262,11 +268,11 @@ def _run_multi_core(file_list, process_count, granule_urls): } -def _run_worker(in_queue, results): +def _run_worker(in_queue: Queue, results: list[dict]) -> None: """ A method to be executed in a separate process which runs preprocessing on granules from the input queue and stores the results internally. When the queue is empty - (processing is complete), the local results are transfered to the external results + (processing is complete), the local results are transferred to the external results array to be merged by the main process. If the process never processed any granules which is possible if the input queue is underfilled, the process just exits without appending to the array @@ -311,7 +317,12 @@ def _run_worker(in_queue, results): }) -def process_groups(parent_group, group_list, max_dims, group_metadata, var_metadata, var_info): +def process_groups(parent_group: nc.Dataset | nc.Group, + group_list: list, + max_dims: dict, + group_metadata: dict, + var_metadata: dict, + var_info: dict): """ Perform preprocessing of a group and recursively process each child group @@ -345,7 +356,7 @@ def process_groups(parent_group, group_list, max_dims, group_metadata, var_metad process_groups(child_group, group_list, max_dims, group_metadata, var_metadata, var_info) -def get_max_dims(group, max_dims): +def get_max_dims(group: nc.Dataset | nc.Group, max_dims: dict) -> None: """ Aggregates dimensions from each group and creates a dictionary of the largest dimension sizes for each group @@ -365,7 +376,7 @@ def get_max_dims(group, max_dims): max_dims[dim_path] = dim.size -def get_metadata(group, metadata): +def get_metadata(group: nc.Dataset | nc.Group | nc.Variable, metadata: dict) -> None: """ Aggregates metadata from various NetCDF4 objects into a dictionary @@ -386,7 +397,7 @@ def get_metadata(group, metadata): metadata[attr_name] = False # mark as inconsistent -def attr_eq(attr_1, attr_2): +def attr_eq(attr_1, attr_2) -> bool: """ Helper function to check if one attribute value is equal to another (no, a simple == was not working) @@ -408,7 +419,7 @@ def attr_eq(attr_1, attr_2): return True -def get_variable_data(group, var_info, var_metadata): +def get_variable_data(group: nc.Dataset | nc.Group, var_info: dict, var_metadata: dict) -> None: """ Aggregate variable metadata and attributes. Primarily utilized in process_groups From e9a7860c8e8b675695efba0a8465555baee0c503 Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 24 May 2024 14:20:00 +0000 Subject: [PATCH 089/124] /version 0.9.0a5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 11aa1c07..9dd260b5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.9.0a4" +version = "0.9.0a5" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 3cea513b958690ed2873f03daaa0d201f60717e1 Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 10 Jun 2024 20:35:01 +0000 Subject: [PATCH 090/124] /version 0.10.0a1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c4038ba5..44632527 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a0" +version = "0.10.0a1" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 0e2b72e67887ec138c129f1c5ccabb828908a140 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 27 Jun 2024 09:01:59 -0700 Subject: [PATCH 091/124] Bump urllib3 from 1.26.18 to 1.26.19 (#119) Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.18 to 1.26.19. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/1.26.19/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.18...1.26.19) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- poetry.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 5f53affe..4dff6f48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "aiohttp" @@ -1350,8 +1350,8 @@ astroid = ">=3.2.2,<=3.3.0-dev0" colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""} dill = [ {version = ">=0.2", markers = "python_version < \"3.11\""}, - {version = ">=0.3.6", markers = "python_version >= \"3.11\""}, {version = ">=0.3.7", markers = "python_version >= \"3.12\""}, + {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""}, ] isort = ">=4.2.5,<5.13.0 || >5.13.0,<6" mccabe = ">=0.6,<0.8" @@ -2119,13 +2119,13 @@ files = [ [[package]] name = "urllib3" -version = "1.26.18" +version = "1.26.19" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ - {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"}, - {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"}, + {file = "urllib3-1.26.19-py2.py3-none-any.whl", hash = "sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3"}, + {file = "urllib3-1.26.19.tar.gz", hash = "sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429"}, ] [package.extras] From 55b3132326e59147a6570b70cef4394fa1b17f1f Mon Sep 17 00:00:00 2001 From: concise bot Date: Thu, 27 Jun 2024 16:04:54 +0000 Subject: [PATCH 092/124] /version 0.10.0a2 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 44632527..dfb7edfc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a1" +version = "0.10.0a2" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 3e93b87741d276d8583aaa0ef035e853e8d3302f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Aug 2024 09:11:35 -0700 Subject: [PATCH 093/124] Bump aiohttp from 3.9.5 to 3.10.2 (#127) Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.9.5 to 3.10.2. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](https://github.com/aio-libs/aiohttp/compare/v3.9.5...v3.10.2) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... 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+python-versions = ">=3.7" +files = [ + {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"}, + {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"}, +] + [[package]] name = "attrs" version = "23.2.0" From 728b57ce830d2292825177d66b8505e09a6ed7ac Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 12 Aug 2024 16:14:24 +0000 Subject: [PATCH 094/124] /version 0.10.0a3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index dfb7edfc..81147f56 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a2" +version = "0.10.0a3" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 58aba18647eb7f7ee1c67259d400cdfe9dcd0693 Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Thu, 15 Aug 2024 12:40:00 -0700 Subject: [PATCH 095/124] Fix Merging of variables (#128) * update code pylint and flake8 * remove print * add harmony deployment * update harmony deployment url * update changelog * update changelog --- .github/workflows/build-pipeline.yml | 13 ++++++ CHANGELOG.md | 5 ++- deployment/harmony_deploy.py | 67 ++++++++++++++++++++++++++++ podaac/merger/preprocess_worker.py | 12 ++--- 4 files changed, 88 insertions(+), 9 deletions(-) create mode 100644 deployment/harmony_deploy.py diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index c28f1a0e..62e6b393 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -243,6 +243,19 @@ jobs: pull: true tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} + + - name: Deploy Harmony + env: + ENV: ${{ env.venue }} + CMR_USER: ${{ secrets.CMR_USER }} + CMR_PASS: ${{ secrets.CMR_PASS }} + if: | + github.ref == 'refs/heads/main' || + startsWith(github.ref, 'refs/heads/release') + working-directory: deployment + run: + poetry run python harmony_deploy.py --tag ${{ env.software_version }} + # As of 2023/01/23 these steps below for scanning the Docker image with Snyk are failing. I've tried both the official Snyk # action https://github.com/snyk/actions/tree/master/docker and this method below of manually calling the CLI. # The error when using the official Snyk action is diff --git a/CHANGELOG.md b/CHANGELOG.md index b676846a..69746444 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,11 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] ### Added -### Changed + - Update Github Actions + - Added harmony deployment into github actions. ### Changed ### Deprecated ### Removed ### Fixed + - Variable Merging + - Fixed way we merge variables when granules in a collection have varying variables. ## [0.9.0] diff --git a/deployment/harmony_deploy.py b/deployment/harmony_deploy.py new file mode 100644 index 00000000..38035bef --- /dev/null +++ b/deployment/harmony_deploy.py @@ -0,0 +1,67 @@ +import os +import requests +import json +import logging +import argparse +from requests.auth import HTTPBasicAuth + +# Environment variables +ENV = os.getenv('ENV') +CMR_USER = os.getenv('CMR_USER') +CMR_PASS = os.getenv('CMR_PASS') + +def bearer_token() -> str: + tokens = [] + headers = {'Accept': 'application/json'} + url = f"https://{'uat.' if ENV == 'uat' else ''}urs.earthdata.nasa.gov/api/users" + + # First just try to get a token that already exists + try: + resp = requests.get(url + "/tokens", headers=headers, auth=HTTPBasicAuth(CMR_USER, CMR_PASS)) + response_content = json.loads(resp.content) + + for x in response_content: + tokens.append(x['access_token']) + + except Exception: # noqa E722 + logging.warning("Error getting the token - check user name and password", exc_info=True) + + # No tokens exist, try to create one + if not tokens: + try: + resp = requests.post(url + "/token", headers=headers, auth=HTTPBasicAuth(CMR_USER, CMR_PASS)) + response_content = json.loads(resp.content) + tokens.append(response_content['access_token']) + except Exception: # noqa E722 + logging.warning("Error getting the token - check user name and password", exc_info=True) + + # If still no token, then we can't do anything + if not tokens: + raise RuntimeError("Unable to get bearer token from EDL") + + return next(iter(tokens)) + +if __name__ == "__main__": + + parser = argparse.ArgumentParser(description="Update the service image tag.") + parser.add_argument("--tag", help="The new tag version to update.", required=True) + args = parser.parse_args() + + url = f"https://harmony.{'uat.' if ENV == 'uat' else ''}earthdata.nasa.gov/service-image-tag/podaac-concise" + token = bearer_token() + + headers = { + "Authorization": f"Bearer {token}", + "Content-type": "application/json" + } + data = { + "tag": args.tag + } + + response = requests.put(url, headers=headers, json=data) + + print(response.status_code) + try: + print(response.json()) + except json.JSONDecodeError: + print("Response content is not in JSON format") diff --git a/podaac/merger/preprocess_worker.py b/podaac/merger/preprocess_worker.py index 4bedba33..7dd98022 100644 --- a/podaac/merger/preprocess_worker.py +++ b/podaac/merger/preprocess_worker.py @@ -236,14 +236,10 @@ def _run_multi_core(file_list: list[Path], if var_info is None: var_info = result['var_info'] elif var_info != result['var_info']: - if set(var_info.keys()).difference(result['var_info']): - # If not all variables match, only compare variables that intersect - intersecting_vars = set(var_info).intersection(result['var_info']) - if list( - map(var_info.get, intersecting_vars) - ) != list(map(result['var_info'].get, intersecting_vars)): - raise RuntimeError('Variable schemas are inconsistent between granules') - var_info.update(result['var_info']) + intersecting_vars = set(var_info).intersection(result['var_info']) + if any(var_info[var] != result['var_info'][var] for var in intersecting_vars): + raise RuntimeError('Variable schemas are inconsistent between granules') + var_info.update(result['var_info']) # The following data requires accumulation methods merge_max_dims(max_dims, result['max_dims']) From ea3a3dd6d9bfd5d4089fc17781aba83eb86304bf Mon Sep 17 00:00:00 2001 From: concise bot Date: Thu, 15 Aug 2024 19:42:46 +0000 Subject: [PATCH 096/124] /version 0.10.0a4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 81147f56..44c1a916 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a3" +version = "0.10.0a4" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From e075f160aa4a3cb18d2abef5656621ecd7be1d7c Mon Sep 17 00:00:00 2001 From: James Wood Date: Fri, 16 Aug 2024 09:30:21 -0700 Subject: [PATCH 097/124] release 0.10.0 --- CHANGELOG.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 69746444..92d1693d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] +### Added +### Changed +### Deprecated +### Removed +### Fixed + + +## [0.10.0] + ### Added - Update Github Actions - Added harmony deployment into github actions. From 6f9dfb8baf4c114a2b8b3a2c5e7deee0ca3a3973 Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 16 Aug 2024 16:32:57 +0000 Subject: [PATCH 098/124] /version 0.10.0rc1 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 44c1a916..c9c53ce0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a4" +version = "0.10.0rc1" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 2dd2c50b19ba9c53cbc1990f02a071af2c59ea2a Mon Sep 17 00:00:00 2001 From: James Wood Date: Fri, 16 Aug 2024 10:11:17 -0700 Subject: [PATCH 099/124] update versions --- poetry.lock | 1215 +++++++++++++++++++++++++----------------------- pyproject.toml | 4 +- 2 files changed, 634 insertions(+), 585 deletions(-) diff --git a/poetry.lock b/poetry.lock index d2ac522d..b07f963e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,104 +2,103 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22:28:26 +0000 Subject: [PATCH 103/124] /version 0.10.0rc3 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 00285e43..e89a058b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc2" +version = "0.10.0rc3" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 73ca7987ce1ad394620216252315e610893c677a Mon Sep 17 00:00:00 2001 From: James Wood Date: Thu, 7 Nov 2024 14:29:46 -0800 Subject: [PATCH 104/124] deploy From 6a2f17064407e6548502cea879a3a63ce84506d1 Mon Sep 17 00:00:00 2001 From: concise bot Date: Thu, 7 Nov 2024 22:32:19 +0000 Subject: [PATCH 105/124] /version 0.10.0rc4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e89a058b..e10240cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc3" +version = "0.10.0rc4" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 0c52464e43fe8a87f5be322d71b8951d7cc668cc Mon Sep 17 00:00:00 2001 From: Daniel Kaufman <114174502+danielfromearth@users.noreply.github.com> Date: Thu, 14 Nov 2024 17:49:53 -0500 Subject: [PATCH 106/124] Feature/issue 117 improve name of output file (#121) * update poetry.lock * typo * modify filename to include first url's name and last datetime * remove surplus lines * update CHANGELOG.md * fix failing test to match new output name * debug commit * unquote symbols in time string * fix failing test * debug * debug * remove debug lines * change from isoformat extended to basic, and remove url parsing in test * match timestamp format in test * fix invalid nested string quotes --- CHANGELOG.md | 1 + podaac/merger/harmony/service.py | 9 +- poetry.lock | 244 +++++++++++++++---------------- tests/test_harmony.py | 10 +- 4 files changed, 135 insertions(+), 129 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 69746444..a592b317 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Update Github Actions - Added harmony deployment into github actions. ### Changed + - [issue #117](https://github.com/podaac/concise/issues/117): Add part of URL to output file name ### Deprecated ### Removed ### Fixed diff --git a/podaac/merger/harmony/service.py b/podaac/merger/harmony/service.py index d8013196..e2d5be51 100644 --- a/podaac/merger/harmony/service.py +++ b/podaac/merger/harmony/service.py @@ -32,7 +32,7 @@ def invoke(self): Primary entrypoint into the service wrapper. Overrides BaseHarmonyAdapter.invoke """ if not self.catalog: - # Message-only support is being depreciated in Harmony so we should expect to + # Message-only support is being depreciated in Harmony, so we should expect to # only see requests with catalogs when invoked with a newer Harmony instance # https://github.com/nasa/harmony-service-lib-py/blob/21bcfbda17caf626fb14d2ac4f8673be9726b549/harmony/adapter.py#L71 raise RuntimeError('Invoking CONCISE without a STAC catalog is not supported') @@ -42,7 +42,7 @@ def invoke(self): def process_catalog(self, catalog: Catalog): """ Recursively process a catalog and all its children. Adapted from - BaseHarmonyAdapter._process_catalog_recursive to specfifically + BaseHarmonyAdapter._process_catalog_recursive to specifically support our particular use case for many-to-one Parameters @@ -85,7 +85,10 @@ def process_catalog(self, catalog: Catalog): # -- Perform merging -- collection = self._get_item_source(items[0]).collection - filename = f'{collection}_merged.nc4' + first_granule_url = [] + get_granule_url(items[0], first_granule_url) + first_url_name = Path(first_granule_url[0]).stem + filename = f'{first_url_name}_{datetimes[1].strftime("%Y%m%dT%H%M%SZ")}_{collection}_merged.nc4' with TemporaryDirectory() as temp_dir: self.logger.info('Starting granule downloads') diff --git a/poetry.lock b/poetry.lock index d2ac522d..72c30584 100644 --- a/poetry.lock +++ b/poetry.lock @@ -204,17 +204,17 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"] [[package]] name = "boto3" -version = "1.34.123" +version = "1.34.139" description = "The AWS SDK for Python" 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"sha256:953d4e6ad24357bceffbc9707bc74349aca9d245f68eb65419cf0c249a1949a2"}, + {file = "tenacity-8.5.0-py3-none-any.whl", hash = "sha256:b594c2a5945830c267ce6b79a166228323ed52718f30302c1359836112346687"}, + {file = "tenacity-8.5.0.tar.gz", hash = "sha256:8bc6c0c8a09b31e6cad13c47afbed1a567518250a9a171418582ed8d9c20ca78"}, ] [package.extras] diff --git a/tests/test_harmony.py b/tests/test_harmony.py index 9df29b89..08b81845 100644 --- a/tests/test_harmony.py +++ b/tests/test_harmony.py @@ -1,3 +1,4 @@ +from datetime import datetime import json from shutil import rmtree import sys @@ -75,14 +76,17 @@ def test_service_invoke(self): self.assertEqual(item['bbox'], [-4, -3, 4, 3]) self.assertEqual(properties['start_datetime'], '2020-01-01T00:00:00+00:00') self.assertEqual(properties['end_datetime'], '2020-01-05T23:59:59+00:00') - # -- Asset Verification -- data = item['assets']['data'] collection_name = in_message['sources'][0]['collection'] # Sanity checks on metadata - self.assertTrue(data['href'].endswith(f'/{collection_name}_merged.nc4')) - self.assertEqual(data['title'], f'{collection_name}_merged.nc4') + self.assertTrue(data['href'].endswith( + f"{datetime.fromisoformat(properties['end_datetime']).strftime('%Y%m%dT%H%M%SZ')}_{collection_name}_merged.nc4" + )) + self.assertTrue(data['title'].endswith( + f"{datetime.fromisoformat(properties['end_datetime']).strftime('%Y%m%dT%H%M%SZ')}_{collection_name}_merged.nc4" + )) self.assertEqual(data['type'], 'application/x-netcdf4') self.assertEqual(data['roles'], ['data']) From f6678500b01678e03275f59ec88675aebfd48201 Mon Sep 17 00:00:00 2001 From: concise bot Date: Thu, 14 Nov 2024 22:52:43 +0000 Subject: [PATCH 107/124] /version 0.10.0a5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 44c1a916..6c1a9e62 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a4" +version = "0.10.0a5" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From b6eb801841e319b12e1ed4ce31243e7f37133b8f Mon Sep 17 00:00:00 2001 From: James Wood Date: Mon, 2 Dec 2024 14:59:07 -0800 Subject: [PATCH 108/124] updated harmony lib version --- podaac/merger/harmony/cli.py | 8 ++++---- podaac/merger/harmony/download_worker.py | 4 ++-- podaac/merger/harmony/service.py | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/podaac/merger/harmony/cli.py b/podaac/merger/harmony/cli.py index 3f0399bf..c8d88c1f 100644 --- a/podaac/merger/harmony/cli.py +++ b/podaac/merger/harmony/cli.py @@ -1,7 +1,7 @@ """A Harmony CLI wrapper around Concise""" from argparse import ArgumentParser -import harmony +import harmony_service_lib from podaac.merger.harmony.service import ConciseService @@ -9,11 +9,11 @@ def main(config=None): """Main Harmony CLI entrypoint""" parser = ArgumentParser() - harmony.setup_cli(parser) + harmony_service_lib.setup_cli(parser) args = parser.parse_args() - if harmony.is_harmony_cli(args): - harmony.run_cli(parser, args, ConciseService, cfg=config) + if harmony_service_lib.is_harmony_cli(args): + harmony_service_lib.run_cli(parser, args, ConciseService, cfg=config) else: parser.error("Only --harmony CLIs are supported") diff --git a/podaac/merger/harmony/download_worker.py b/podaac/merger/harmony/download_worker.py index f4f3e2c9..51c8d03c 100644 --- a/podaac/merger/harmony/download_worker.py +++ b/podaac/merger/harmony/download_worker.py @@ -8,8 +8,8 @@ import re from urllib.parse import urlparse -from harmony.logging import build_logger -from harmony.util import download +from harmony_service_lib.logging import build_logger +from harmony_service_lib.util import download def multi_core_download(urls, destination_dir, access_token, cfg, process_count=None): diff --git a/podaac/merger/harmony/service.py b/podaac/merger/harmony/service.py index e2d5be51..e1ff275f 100644 --- a/podaac/merger/harmony/service.py +++ b/podaac/merger/harmony/service.py @@ -7,8 +7,8 @@ from urllib.parse import urlsplit from uuid import uuid4 -from harmony.adapter import BaseHarmonyAdapter -from harmony.util import bbox_to_geometry, stage +from harmony_service_lib import BaseHarmonyAdapter +from harmony_service_lib.util import bbox_to_geometry, stage from pystac import Catalog, Item from pystac.item import Asset From ed68654879d3132fa9a7e6d3c4a2d955cf9bd855 Mon Sep 17 00:00:00 2001 From: concise bot Date: Mon, 2 Dec 2024 23:01:41 +0000 Subject: [PATCH 109/124] /version 0.10.0rc5 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c3a089bf..0a0a82df 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc4" +version = "0.10.0rc5" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From dcbfbb6c0fa075f118ae1e6d6a16ce5ae745ad3f Mon Sep 17 00:00:00 2001 From: Simon Liu <69875423+sliu008@users.noreply.github.com> Date: Fri, 6 Dec 2024 12:46:16 -0800 Subject: [PATCH 110/124] Feature/update error logging (#138) * update python libraries * fix pylint * poetry update * update changelog * poetry update * add tests for concise exception class * more test coverage * update license --- .pylintrc | 3 +- CHANGELOG.md | 3 + LICENSE | 2 +- podaac/merger/harmony/cli.py | 2 +- podaac/merger/harmony/download_worker.py | 4 +- podaac/merger/harmony/service.py | 149 +- poetry.lock | 2599 ++++++++++++---------- pyproject.toml | 14 +- tests/test_concise_exception.py | 97 + 9 files changed, 1629 insertions(+), 1244 deletions(-) create mode 100644 tests/test_concise_exception.py diff --git a/.pylintrc b/.pylintrc index cd720bde..45714749 100644 --- a/.pylintrc +++ b/.pylintrc @@ -416,7 +416,8 @@ disable=raw-checker-failed, useless-suppression, deprecated-pragma, use-symbolic-message-instead, - too-many-arguments + too-many-arguments, + too-many-positional-arguments # Enable the message, report, category or checker with the given id(s). You can # either give multiple identifier separated by comma (,) or put this option diff --git a/CHANGELOG.md b/CHANGELOG.md index a592b317..c0646db9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added harmony deployment into github actions. ### Changed - [issue #117](https://github.com/podaac/concise/issues/117): Add part of URL to output file name + - Update python libraries + - Update harmony service lib that changed project structure + - Add Concise exception to propogate up to harmony api calls ### Deprecated ### Removed ### Fixed diff --git a/LICENSE b/LICENSE index f49a4e16..adb76827 100644 --- a/LICENSE +++ b/LICENSE @@ -186,7 +186,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright 2024 California Institute of Technology Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/podaac/merger/harmony/cli.py b/podaac/merger/harmony/cli.py index 3f0399bf..ece999ad 100644 --- a/podaac/merger/harmony/cli.py +++ b/podaac/merger/harmony/cli.py @@ -1,7 +1,7 @@ """A Harmony CLI wrapper around Concise""" from argparse import ArgumentParser -import harmony +import harmony_service_lib as harmony from podaac.merger.harmony.service import ConciseService diff --git a/podaac/merger/harmony/download_worker.py b/podaac/merger/harmony/download_worker.py index f4f3e2c9..51c8d03c 100644 --- a/podaac/merger/harmony/download_worker.py +++ b/podaac/merger/harmony/download_worker.py @@ -8,8 +8,8 @@ import re from urllib.parse import urlparse -from harmony.logging import build_logger -from harmony.util import download +from harmony_service_lib.logging import build_logger +from harmony_service_lib.util import download def multi_core_download(urls, destination_dir, access_token, cfg, process_count=None): diff --git a/podaac/merger/harmony/service.py b/podaac/merger/harmony/service.py index e2d5be51..a38deae0 100644 --- a/podaac/merger/harmony/service.py +++ b/podaac/merger/harmony/service.py @@ -6,9 +6,12 @@ from shutil import copyfile from urllib.parse import urlsplit from uuid import uuid4 +import traceback +import sys -from harmony.adapter import BaseHarmonyAdapter -from harmony.util import bbox_to_geometry, stage +from harmony_service_lib.adapter import BaseHarmonyAdapter +from harmony_service_lib.util import bbox_to_geometry, stage +from harmony_service_lib.exceptions import HarmonyException from pystac import Catalog, Item from pystac.item import Asset @@ -20,6 +23,37 @@ NETCDF4_MIME = 'application/x-netcdf4' # pylint: disable=invalid-name +class ConciseException(HarmonyException): + """Concise Exception class for custom error messages to see in harmony api calls.""" + def __init__(self, original_exception): + # Ensure we can extract traceback information + if original_exception.__traceback__ is None: + # Capture the current traceback if not already present + try: + raise original_exception + except type(original_exception): + original_exception.__traceback__ = sys.exc_info()[2] + + # Extract the last traceback entry (most recent call) for the error location + tb = traceback.extract_tb(original_exception.__traceback__)[-1] + + # Get the error details: file, line, function, and message + filename = tb.filename + lineno = tb.lineno + funcname = tb.name + error_msg = str(original_exception) + + # Format the error message to be more readable + readable_message = (f"Error in file '{filename}', line {lineno}, in function '{funcname}': " + f"{error_msg}") + + # Call the parent class constructor with the formatted message and category + super().__init__(readable_message, 'podaac/concise') + + # Store the original exception for potential further investigation + self.original_exception = original_exception + + class ConciseService(BaseHarmonyAdapter): """ A harmony-service-lib wrapper around the Concise module. This wrapper does @@ -55,63 +89,68 @@ def process_catalog(self, catalog: Catalog): pystac.Catalog A new catalog containing the results from the merge """ - result = catalog.clone() - result.id = str(uuid4()) - result.clear_children() - # Get all the items from the catalog, including from child or linked catalogs - items = list(self.get_all_catalog_items(catalog)) + try: + result = catalog.clone() + result.id = str(uuid4()) + result.clear_children() + + # Get all the items from the catalog, including from child or linked catalogs + items = list(self.get_all_catalog_items(catalog)) + + # Quick return if catalog contains no items + if len(items) == 0: + return result + + # -- Process metadata -- + bbox = [] + granule_urls = [] + datetimes = [ + datetime.max.replace(tzinfo=timezone.utc), # start + datetime.min.replace(tzinfo=timezone.utc) # end + ] + + for item in items: + get_bbox(item, bbox) + get_granule_url(item, granule_urls) + get_datetime(item, datetimes) + + # Items did not have a bbox; valid under spec + if len(bbox) == 0: + bbox = None + + # -- Perform merging -- + collection = self._get_item_source(items[0]).collection + first_granule_url = [] + get_granule_url(items[0], first_granule_url) + first_url_name = Path(first_granule_url[0]).stem + filename = f'{first_url_name}_{datetimes[1].strftime("%Y%m%dT%H%M%SZ")}_{collection}_merged.nc4' + + with TemporaryDirectory() as temp_dir: + self.logger.info('Starting granule downloads') + input_files = multi_core_download(granule_urls, temp_dir, self.message.accessToken, self.config) + self.logger.info('Finished granule downloads') + + output_path = Path(temp_dir).joinpath(filename).resolve() + merge_netcdf_files(input_files, output_path, granule_urls, logger=self.logger) + staged_url = self._stage(str(output_path), filename, NETCDF4_MIME) + + # -- Output to STAC catalog -- + result.clear_items() + properties = { + "start_datetime": datetimes[0].isoformat(), + "end_datetime": datetimes[1].isoformat() + } + + item = Item(str(uuid4()), bbox_to_geometry(bbox), bbox, None, properties) + asset = Asset(staged_url, title=filename, media_type=NETCDF4_MIME, roles=['data']) + item.add_asset('data', asset) + result.add_item(item) - # Quick return if catalog contains no items - if len(items) == 0: return result - # -- Process metadata -- - bbox = [] - granule_urls = [] - datetimes = [ - datetime.max.replace(tzinfo=timezone.utc), # start - datetime.min.replace(tzinfo=timezone.utc) # end - ] - - for item in items: - get_bbox(item, bbox) - get_granule_url(item, granule_urls) - get_datetime(item, datetimes) - - # Items did not have a bbox; valid under spec - if len(bbox) == 0: - bbox = None - - # -- Perform merging -- - collection = self._get_item_source(items[0]).collection - first_granule_url = [] - get_granule_url(items[0], first_granule_url) - first_url_name = Path(first_granule_url[0]).stem - filename = f'{first_url_name}_{datetimes[1].strftime("%Y%m%dT%H%M%SZ")}_{collection}_merged.nc4' - - with TemporaryDirectory() as temp_dir: - self.logger.info('Starting granule downloads') - input_files = multi_core_download(granule_urls, temp_dir, self.message.accessToken, self.config) - self.logger.info('Finished granule downloads') - - output_path = Path(temp_dir).joinpath(filename).resolve() - merge_netcdf_files(input_files, output_path, granule_urls, logger=self.logger) - staged_url = self._stage(str(output_path), filename, NETCDF4_MIME) - - # -- Output to STAC catalog -- - result.clear_items() - properties = { - "start_datetime": datetimes[0].isoformat(), - "end_datetime": datetimes[1].isoformat() - } - - item = Item(str(uuid4()), bbox_to_geometry(bbox), bbox, None, properties) - asset = Asset(staged_url, title=filename, media_type=NETCDF4_MIME, roles=['data']) - item.add_asset('data', asset) - result.add_item(item) - - return result + except Exception as ex: + raise ConciseException(ex) from ex def _stage(self, local_filename, remote_filename, mime): """ diff --git a/poetry.lock b/poetry.lock index 72c30584..d3cd69e1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,109 +1,109 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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"6ca15121fb8a03d8a41d00a1c173ccdd0ed25733d0193c97165932d35928a329" diff --git a/pyproject.toml b/pyproject.toml index 6c1a9e62..ab9994ca 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -17,19 +17,19 @@ packages = [ [tool.poetry.dependencies] python = "^3.10" netCDF4 = "^1.5.6" -numpy = "^1.20.3" -harmony-service-lib = "^1.0.27" -importlib-metadata = "^7.1.0" +numpy = "^2.1.3" +harmony-service-lib = "^2.3.0" +importlib-metadata = "^8.5.0" [tool.poetry.group.dev.dependencies] -setuptools = "^70.0.0" +setuptools = "^75.6.0" pytest = "^8.2.0" flake8 = "^7.0.0" -pytest-cov = "^5.0.0" +pytest-cov = "^6.0.0" pylint = "^3.2.0" -Sphinx = "^7.3.7" +Sphinx = "^8.1.3" requests = "^2.25.1" -sphinx-rtd-theme = "^2.0.0" +sphinx-rtd-theme = "^3.0.2" papermill = "^2.3.4" [tool.poetry.scripts] diff --git a/tests/test_concise_exception.py b/tests/test_concise_exception.py new file mode 100644 index 00000000..f879b818 --- /dev/null +++ b/tests/test_concise_exception.py @@ -0,0 +1,97 @@ +import pytest +import traceback +import sys +from podaac.merger.harmony.service import ConciseException + + +def test_exception_message_formatting(): + """ + Test that the ConciseException correctly formats the error message + with file, line, function, and original error details. + """ + try: + # Simulate an error by intentionally causing a division by zero + 1 / 0 + except ZeroDivisionError as original_error: + concise_exception = ConciseException(original_error) + + # Detailed assertions with informative error messages + error_str = str(concise_exception) + error_msg = concise_exception.message + + assert "Error in file" in error_msg, f"Expected file context, got: {error_msg}" + assert "line" in error_msg, f"Expected line number, got: {error_msg}" + assert "in function" in error_msg, f"Expected function context, got: {error_msg}" + assert "division by zero" in error_msg, f"Expected original error message, got: {error_msg}" + assert concise_exception.category == 'podaac/concise' + +def test_exception_traceback_details(): + """ + Verify that the exception captures the correct traceback information. + """ + def inner_function(): + # Another function to add depth to the traceback + 1 / 0 + + try: + inner_function() + except ZeroDivisionError as original_error: + concise_exception = ConciseException(original_error) + + # Extract expected details + tb = traceback.extract_tb(original_error.__traceback__)[-1] + expected_filename = tb.filename + expected_lineno = tb.lineno + expected_funcname = tb.name + + error_msg = concise_exception.message + assert expected_filename in error_msg, f"Filename not found, got: {error_msg}" + assert str(expected_lineno) in error_msg, f"Line number not found, got: {error_msg}" + assert expected_funcname in error_msg, f"Function name not found, got: {error_msg}" + +def test_original_error_type_preservation(): + """ + Ensure that the original error type is preserved in the traceback. + """ + try: + raise ValueError("Test error message") + except ValueError as original_error: + concise_exception = ConciseException(original_error) + + error_msg = concise_exception.message + assert "Test error message" in error_msg, f"Original error message not found, got: {error_msg}" + assert isinstance(concise_exception.original_exception, ValueError) + +def test_module_identifier(): + """ + Verify that the module identifier is set correctly. + """ + try: + raise RuntimeError("Sample error") + except RuntimeError as original_error: + concise_exception = ConciseException(original_error) + + assert concise_exception.category == 'podaac/concise' + +def test_exception_with_no_traceback(): + """ + Test handling of an exception without an existing traceback. + """ + # Create an exception without a traceback + try: + raise ValueError("Test exception without traceback") + except ValueError as original_error: + # Deliberately remove the traceback + original_error.__traceback__ = None + + # Create ConciseException + concise_exception = ConciseException(original_error) + + # Verify that a traceback was generated + assert concise_exception.original_exception is not None + + # Check that the message is still formatted + error_msg = concise_exception.message + assert "Error in file" in error_msg + assert "in function" in error_msg + assert "Test exception without traceback" in error_msg From 9ecc008dace259669cbf3abb87486625a2dd6cbe Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 6 Dec 2024 20:49:04 +0000 Subject: [PATCH 111/124] /version 0.10.0a6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index ab9994ca..0f00940b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0a5" +version = "0.10.0a6" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 602dd681c0583f8f5c5f1184203686b1d938c368 Mon Sep 17 00:00:00 2001 From: James Wood Date: Fri, 6 Dec 2024 14:14:33 -0800 Subject: [PATCH 112/124] renamed back to harmony --- podaac/merger/harmony/cli.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/podaac/merger/harmony/cli.py b/podaac/merger/harmony/cli.py index 6ae54635..ece999ad 100644 --- a/podaac/merger/harmony/cli.py +++ b/podaac/merger/harmony/cli.py @@ -9,11 +9,11 @@ def main(config=None): """Main Harmony CLI entrypoint""" parser = ArgumentParser() - harmony_service_lib.setup_cli(parser) + harmony.setup_cli(parser) args = parser.parse_args() - if harmony_service_lib.is_harmony_cli(args): - harmony_service_lib.run_cli(parser, args, ConciseService, cfg=config) + if harmony.is_harmony_cli(args): + harmony.run_cli(parser, args, ConciseService, cfg=config) else: parser.error("Only --harmony CLIs are supported") From e0704aa93308676b7645827edbaf8dab9321bfde Mon Sep 17 00:00:00 2001 From: concise bot Date: Fri, 6 Dec 2024 22:17:06 +0000 Subject: [PATCH 113/124] /version 0.10.0rc6 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 65e8ae8e..e4c2b0c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc5" +version = "0.10.0rc6" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 4c35e34c21a1b94679020157d15495b9b0453ba0 Mon Sep 17 00:00:00 2001 From: James Wood <8115931+jamesfwood@users.noreply.github.com> Date: Wed, 18 Dec 2024 11:28:12 -0800 Subject: [PATCH 114/124] Update harmony_deploy.py Needs to fail if can't update service version --- deployment/harmony_deploy.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/deployment/harmony_deploy.py b/deployment/harmony_deploy.py index 38035bef..df0c913f 100644 --- a/deployment/harmony_deploy.py +++ b/deployment/harmony_deploy.py @@ -59,9 +59,6 @@ def bearer_token() -> str: } response = requests.put(url, headers=headers, json=data) + response.raise_for_status() - print(response.status_code) - try: - print(response.json()) - except json.JSONDecodeError: - print("Response content is not in JSON format") + print(f"Response JSON: {response.json()}") From e6ac8ae8ee9378885d368f7cb687f4779f60abb5 Mon Sep 17 00:00:00 2001 From: concise bot Date: Wed, 18 Dec 2024 19:31:10 +0000 Subject: [PATCH 115/124] /version 0.10.0rc7 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index e4c2b0c9..93702713 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc6" +version = "0.10.0rc7" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 97dc05f562b07268a3e6b705bdecba73bb36e02e Mon Sep 17 00:00:00 2001 From: James Wood Date: Wed, 18 Dec 2024 11:43:00 -0800 Subject: [PATCH 116/124] update dep versions --- poetry.lock | 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insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c3ad40b1..5a9de34f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "podaac-concise" -version = "0.10.0rc9" +version = "0.10.0rc10" description = "Harmony service that merges granules" authors = ["podaac-tva "] license = "Apache-2.0" From 26cc26c13d8ddb754d16df7bc83791dae7d31421 Mon Sep 17 00:00:00 2001 From: James Wood Date: Thu, 2 Jan 2025 13:11:59 -0800 Subject: [PATCH 122/124] update --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3b65ee11..acb92c03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,7 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [issue #117](https://github.com/podaac/concise/issues/117): Add part of URL to output file name - Update python libraries - Update harmony service lib that changed project structure - - Add Concise exception to propogate up to harmony api calls + - Add Concise exception to propogate up to harmony api calls. ### Deprecated ### Removed ### Fixed From 963d4ed22673767bedca43025bd0142f209dcfaa Mon Sep 17 00:00:00 2001 From: James Wood Date: Thu, 2 Jan 2025 13:16:57 -0800 Subject: [PATCH 123/124] Update to latest action --- .github/workflows/build-pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build-pipeline.yml b/.github/workflows/build-pipeline.yml index 641952c5..3bed15f8 100644 --- a/.github/workflows/build-pipeline.yml +++ b/.github/workflows/build-pipeline.yml @@ -85,7 +85,7 @@ jobs: run: | poetry run pytest --junitxml=build/reports/pytest.xml --cov=podaac/ --cov-report=xml:build/reports/coverage.xml -m "not aws and not integration" tests/ - name: SonarCloud Scan - uses: sonarsource/sonarcloud-github-action@master + uses: sonarsource/sonarqube-scan-action@v4 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }} 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