Backport production fixes (#5791, #5824, #3631)

deployments/prod/environment.py

@@ -967,7 +967,7 @@ def mkdict(previous_catalog: dict[str, str],
     mksrc('datarepo-5f867d37', 'hca_prod_dbd836cfbfc241f0983441cc6c0b235a__20220212_dcp2_20231102_dcp33', 9)
 ]))
 
-dcp34_sources = mkdict(dcp33_sources, 428, mkdelta([
+dcp34_sources = mkdict(dcp33_sources, 427, mkdelta([
     mksrc('datarepo-a2f2ced7', 'hca_prod_08fb10df32e5456c9882e33fcd49077a__20231212_dcp2_20231213_dcp34', 44),
     mksrc('datarepo-cd738b8d', 'hca_prod_10a845f7036146fa92a32a36483136b1__20231212_dcp2_20231213_dcp34', 102),
     mksrc('datarepo-6fec2801', 'hca_prod_1538d572bcb7426b8d2c84f3a7f87bb0__20220630_dcp2_20231213_dcp34', 12),
@@ -979,14 +979,12 @@ def mkdict(previous_catalog: dict[str, str],
     mksrc('datarepo-078dbc55', 'hca_prod_34c9a62ca6104e31b3438fb7be676f8c__20221101_dcp2_20231213_dcp34', 179),
     mksrc('datarepo-a0115d6e', 'hca_prod_3cfcdff5dee14a7ba591c09c6e850b11__20220112_dcp2_20231213_dcp34', 9),
     mksrc('datarepo-66dbe882', 'hca_prod_415eb773cadb43d1ab897d160d5cfc7d__20231212_dcp2_20231213_dcp34', 2),
-    mksrc('datarepo-52544dd5', 'hca_prod_41fb1734a121461695c73b732c9433c7__20220113_dcp2_20231213_dcp34', 13),
     mksrc('datarepo-37f63790', 'hca_prod_58028aa80ed249cab60f15e2ed5989d5__20220117_dcp2_20231213_dcp34', 5),
     mksrc('datarepo-9f64fc88', 'hca_prod_581de139461f4875b40856453a9082c7__20231212_dcp2_20231213_dcp34', 704),
     mksrc('datarepo-78a292c4', 'hca_prod_5b910a437fb54ea7b9d643dbd1bf2776__20220729_dcp2_20231213_dcp34', 13),
     mksrc('datarepo-84d96baf', 'hca_prod_65cbfea55c544255a1d014549a86a5c1__20230616_dcp2_20231213_dcp34', 33),
     mksrc('datarepo-96cc1349', 'hca_prod_6735ff731a04422eb500730202e46f8a__20231212_dcp2_20231213_dcp34', 19),
     mksrc('datarepo-e8198e31', 'hca_prod_6874b7eb344547ec877375141430e169__20231213_dcp2_20231213_dcp34', 82),
-    mksrc('datarepo-b289fd01', 'hca_prod_77780d5603c0481faade2038490cef9f__20220330_dcp2_20231213_dcp34', 95),
     mksrc('datarepo-43f096b1', 'hca_prod_77dedd59137648879bcadc42b56d5b7a__20230201_dcp2_20231213_dcp34', 51),
     mksrc('datarepo-594e57c3', 'hca_prod_78b2406dbff246fc8b6120690e602227__20220117_dcp2_20231213_dcp34', 218),
     mksrc('datarepo-13c1e76b', 'hca_prod_8185730f411340d39cc3929271784c2b__20220117_dcp2_20231213_dcp34', 12),
@@ -996,23 +994,17 @@ def mkdict(previous_catalog: dict[str, str],
     mksrc('datarepo-40731b27', 'hca_prod_894ae6ac5b4841a8a72f315a9b60a62e__20231212_dcp2_20231213_dcp34', 34),
     mksrc('datarepo-e7931a4c', 'hca_prod_925f9a4ccac0444aad2c612656ab3a85__20231212_dcp2_20231213_dcp34', 192),
     mksrc('datarepo-96344c2b', 'hca_prod_957261f72bd64358a6ed24ee080d5cfc__20220330_dcp2_20231213_dcp34', 605),
-    mksrc('datarepo-2b1ee49d', 'hca_prod_9a23ac2d93dd4bac9bb8040e6426db9d__20220906_dcp2_20231213_dcp34', 14),
-    mksrc('datarepo-877e7541', 'hca_prod_a2a2f324cf24409ea859deaee871269c__20220330_dcp2_20231213_dcp34', 18),
     mksrc('datarepo-7f53a7f2', 'hca_prod_abe1a013af7a45ed8c26f3793c24a1f4__20220118_dcp2_20231213_dcp34', 46),
-    mksrc('datarepo-ab3f90ec', 'hca_prod_aecfd908674c4d4eb36e0c1ceab02245__20231101_dcp2_20231213_dcp34', 76),
-    mksrc('datarepo-bc200810', 'hca_prod_aff9c3cd6b844fc2abf2b9c0b3038277__20220330_dcp2_20231213_dcp34', 18),
     mksrc('datarepo-1e2e46c4', 'hca_prod_bfaedc29fe844e72a46175dc8aabbd1b__20230929_dcp2_20231213_dcp34', 5),
     mksrc('datarepo-2901e79b', 'hca_prod_c05184453b3b49c6b8fcc41daa4eacba__20220213_dcp2_20231213_dcp34', 7),
     mksrc('datarepo-5b1e55df', 'hca_prod_c16a754f5da346ed8c1e6426af2ef625__20220519_dcp2_20231213_dcp34', 112),
     mksrc('datarepo-94d17e05', 'hca_prod_c1a9a93dd9de4e659619a9cec1052eaa__20220118_dcp2_20231213_dcp34', 47),
-    mksrc('datarepo-29c0cb3e', 'hca_prod_c302fe54d22d451fa130e24df3d6afca__20220606_dcp2_20231213_dcp34', 9),
     mksrc('datarepo-d12842d9', 'hca_prod_c4077b3c5c984d26a614246d12c2e5d7__20220118_dcp2_20231213_dcp34', 366),
     mksrc('datarepo-abaa9315', 'hca_prod_c844538b88544a95bd01aacbaf86d97f__20230427_dcp2_20231213_dcp34', 14),
     mksrc('datarepo-02709814', 'hca_prod_cbd3d2769f244af98381b11f6cdbdc4b__20231212_dcp2_20231213_dcp34', 57),
     mksrc('datarepo-7da203ad', 'hca_prod_cfece4d2f18d44ada46a42bbcb5cb3b7__20230929_dcp2_20231213_dcp34', 2),
     mksrc('datarepo-45fc3b21', 'hca_prod_da77bd0643ae4012a774e4d62797df51__20231212_dcp2_20231213_dcp34', 20),
     mksrc('datarepo-0bc51bfc', 'hca_prod_daf9d9827ce643f6ab51272577290606__20220119_dcp2_20231213_dcp34', 43),
-    mksrc('datarepo-e88e52d4', 'hca_prod_e255b1c611434fa683a8528f15b41038__20220330_dcp2_20231213_dcp34', 107),
     mksrc('datarepo-8ecfd261', 'hca_prod_e49e556ada5a442ab45c8691b457623e__20231212_dcp2_20231213_dcp34', 201),
     mksrc('datarepo-99284b34', 'hca_prod_e526d91dcf3a44cb80c5fd7676b55a1d__20220119_dcp2_20231213_dcp34', 606),
     mksrc('datarepo-88582dc4', 'hca_prod_ede2e0b46652464fabbc0b2d964a25a0__20220118_dcp2_20231213_dcp34', 13),

src/azul/plugins/repository/tdr_hca/__init__.py

@@ -289,8 +289,9 @@ def _parse_drs_uri(self,
                 else:
                     # FIXME: Support non-null DRS URIs in file descriptors
                     #        https://github.com/DataBiosphere/azul/issues/3631
-                    require(external_drs_uri is None,
-                            'Non-null `drs_uri` in file descriptor', external_drs_uri)
+                    if external_drs_uri is not None:
+                        log.warning('Non-null `drs_uri` in file descriptor (%s)', external_drs_uri)
+                        external_drs_uri = None
                     return external_drs_uri
             else:
                 return file_id