From e59b94b48a835692b089478337a4b443c7a21e3c Mon Sep 17 00:00:00 2001 From: Abraham Chavez Date: Fri, 16 Oct 2026 12:19:51 -0700 Subject: [PATCH 1/9] [r] Index GTEX snapshots held back from anvil15 (#8392) --- deployments/anvilprod/environment.py | 6 ++++++ deployments/hammerbox/environment.py | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/deployments/anvilprod/environment.py b/deployments/anvilprod/environment.py index 851d70a7f4..96467af871 100644 --- a/deployments/anvilprod/environment.py +++ b/deployments/anvilprod/environment.py @@ -1408,6 +1408,12 @@ def union(previous_catalog: dict[DatasetName, SourceItem | None], source('ee5a23e4', 'DepMap_HMB_20240827_ANV6_202607080056', no_ma_mirror), source('ce3811eb', 'ENCORE_293T_20260708_ANV6_202607081759'), source('42923ab3', 'ENCORE_RS293_20260708_ANV6_202607081737'), + source('c112acbb', 'GTEx_V7_hg19_20260821_ANV6_202608241432', no_ma_mirror), + source('c81bf322', 'GTEx_V8_hg38_20240116_ANV6_202608211533', no_ma_mirror), + source('532caa61', 'GTEx_V9_hg38_20260821_ANV6_202608251459', no_ma_mirror), + source('cb6c0630', 'GTEx_public_data_20260821_ANV6_202608211401'), + source('5aa27a7c', 'GTEx_v10_hg38_20260821_ANV6_202608241349', no_ma_mirror), + source('63c68539', 'GTEx_v11_hg38_20260126_ANV6_202608211606', no_ma_mirror), source('6ae39c14', 'GUARDD_US_GRU_R2_20260709_ANV6_202607091806', no_ma_mirror), source('2de712ea', 'GUARDD_US_HMB_R2_20260709_ANV6_202607091814', no_ma_mirror), source('6e7af669', 'HPRC_20260121_ANV6_202607080129'), diff --git a/deployments/hammerbox/environment.py b/deployments/hammerbox/environment.py index 6a7f20d228..7e4e779ef5 100644 --- a/deployments/hammerbox/environment.py +++ b/deployments/hammerbox/environment.py @@ -1410,6 +1410,12 @@ def union(previous_catalog: dict[DatasetName, SourceItem | None], source('ee5a23e4', 'DepMap_HMB_20240827_ANV6_202607080056', no_ma_mirror), source('ce3811eb', 'ENCORE_293T_20260708_ANV6_202607081759'), source('42923ab3', 'ENCORE_RS293_20260708_ANV6_202607081737'), + source('c112acbb', 'GTEx_V7_hg19_20260821_ANV6_202608241432', no_ma_mirror), + source('c81bf322', 'GTEx_V8_hg38_20240116_ANV6_202608211533', no_ma_mirror), + source('532caa61', 'GTEx_V9_hg38_20260821_ANV6_202608251459', no_ma_mirror), + source('cb6c0630', 'GTEx_public_data_20260821_ANV6_202608211401'), + source('5aa27a7c', 'GTEx_v10_hg38_20260821_ANV6_202608241349', no_ma_mirror), + source('63c68539', 'GTEx_v11_hg38_20260126_ANV6_202608211606', no_ma_mirror), source('6ae39c14', 'GUARDD_US_GRU_R2_20260709_ANV6_202607091806', no_ma_mirror), source('2de712ea', 'GUARDD_US_HMB_R2_20260709_ANV6_202607091814', no_ma_mirror), source('6e7af669', 'HPRC_20260121_ANV6_202607080129'), From 5e6a3f1ca588310404f0382f3010fe85cca741e9 Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Tue, 20 Oct 2026 12:26:43 -0700 Subject: [PATCH 2/9] [u] Four inaccessible LungMAP snapshots in dev (#8421, #8412) --- UPGRADING.rst | 11 +++++++++++ deployments/dev/environment.py | 4 +++- deployments/sandbox/environment.py | 4 +++- 3 files changed, 17 insertions(+), 2 deletions(-) diff --git a/UPGRADING.rst b/UPGRADING.rst index 8ec2507748..23e82d83a1 100644 --- a/UPGRADING.rst +++ b/UPGRADING.rst @@ -23,6 +23,17 @@ Note that as of September 2026, the issue number(s) must be occur in parentheses and at the end of section titles, instead of the beginning. +Four inaccessible LungMAP snapshots in dev (#8421) +================================================== + +Everyone +~~~~~~~~ + +Drop the ``lungmap`` atlas from personal deployments colocated with ``dev``. Use +the ``sandbox`` deployment's ``environment.py`` as a model. Remove the ``lm2`` +and ``lm2-it`` catalogs from your personal deployments. + + Claude Code monitors run without the environment the hook provides (#8323) ========================================================================== diff --git a/deployments/dev/environment.py b/deployments/dev/environment.py index 24e8cba208..29f87676cb 100644 --- a/deployments/dev/environment.py +++ b/deployments/dev/environment.py @@ -308,7 +308,9 @@ def env() -> Mapping[str, str | None]: sources=condense(sources)) for atlas, catalog, sources, mirror_limit, it_mirror_limit, in [ ('hca', 'dcp3', dcp3_min_sources, int(1.5 * 1024 ** 3), int(1.5 * 1024 ** 3)), - ('lungmap', 'lm2', lm2_sources, -1, -1) + # FIXME: Decommission LungMAP + # https://github.com/DataBiosphere/azul/issues/8412 + # ('lungmap', 'lm2', lm2_sources, -1, -1) ] for suffix, is_it in [ ('', False), diff --git a/deployments/sandbox/environment.py b/deployments/sandbox/environment.py index 953e23d8c8..86d7ff6089 100644 --- a/deployments/sandbox/environment.py +++ b/deployments/sandbox/environment.py @@ -321,7 +321,9 @@ def env() -> Mapping[str, str | None]: sources=condense(sources)) for atlas, catalog, sources, mirror_limit, it_mirror_limit, in [ ('hca', 'dcp3', dcp3_min_sources, int(1.5 * 1024 ** 3), int(1.5 * 1024 ** 3)), - ('lungmap', 'lm2', lm2_sources, -1, -1) + # FIXME: Decommission LungMAP + # https://github.com/DataBiosphere/azul/issues/8412 + # ('lungmap', 'lm2', lm2_sources, -1, -1) ] for suffix, is_it in [ ('', False), From 43bf9f784f86c92120847e4cc6c4892251d4f461 Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 00:12:53 -0700 Subject: [PATCH 3/9] Remove manifest entry UUIDs from a canned bundle's stitched set The `stitched` attribute of a canned HCA bundle is a set of the UUIDs of the entities that were stitched into that bundle. The canned TDR HCA bundle 4426adc5 also listed, for each stitched file, the UUID of that file's manifest entry. The plugin only ever adds an entity's own UUID, so the canner cannot have produced those six surplus entries. They were inert, because `Bundle.not_stitched` matches the set against each entity's `document_id`, which a manifest entry UUID never equals. The surplus went unnoticed because `_test_fetch_bundle` compared every other attribute of a canned bundle against that of the emulated one, but not `stitched`. It now does. The canned DSS bundles carry the same surplus, tracked in #8423. Co-Authored-By: Claude Opus 5 (1M context) --- .../data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 6 ------ test/indexer/test_tdr.py | 1 + 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json index f1e47f9431..18fe139baf 100644 --- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json +++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json @@ -829,21 +829,15 @@ "33e31f6f-fe78-45bd-ae57-10d2d14253cf", "5b503dcb-dca6-4e4f-988b-f7100c030dc5", "5d82b884-7db4-47fa-9ccd-03054065c509", - "6578c322-7060-4c82-8469-9e54100e6b44", "6f5ddf2c-382d-4c0a-a506-3a5286067c83", "7a015307-6db9-541f-aaae-db9fdb41000f", "8f8b9587-237f-4995-9461-c96eac53d615", "a06cb5d5-2675-4d64-aeb8-79e0103715f3", - "bf92ef4a-c422-44fb-bfc1-c2f86528b86b", "c0d18b81-0b54-4a11-864b-cd3f43b7e7bf", - "c8e93df7-2623-5e86-890a-aca3e925795e", - "cd8e02d1-d0f9-4094-9a31-329931df60dc", "dd7f3d64-4b79-48f0-9d8c-4324594fe820", "e738a267-87fc-4070-abc7-b3be6442c6d0", - "ebf2947d-76d2-405b-a559-68c6ebb1b2d5", "eca2ab79-ad61-411f-815a-4f6d936d992b", "ee7404a4-c183-4a75-8bd1-34b5fc140e81", - "f4132e3a-c468-4ca3-ad7b-b97b61054151", "fcba26aa-658c-4120-ab31-cc5a5a00f759" ] } \ No newline at end of file diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index 69f586e2fc..476f70858b 100644 --- a/test/indexer/test_tdr.py +++ b/test/indexer/test_tdr.py @@ -460,6 +460,7 @@ def _test_fetch_bundle(self, self.assertEqual(test_bundle.manifest, emulated_bundle.manifest) self.assertEqual(test_bundle.metadata, emulated_bundle.metadata) self.assertEqual(test_bundle.links, emulated_bundle.links) + self.assertEqual(test_bundle.stitched, emulated_bundle.stitched) class TestTDRSourceList(AzulUnitTestCase): From bd3ca5160ad2fc75500f3f4c7b66ac6d96e3aa8e Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 09:35:09 -0700 Subject: [PATCH 4/9] Remove a comment claiming an order that no assertion checks The comment stated that the manifest and the metadata of a bundle are both sorted by entity UUID. The assertions below it compare dictionaries, which are equal regardless of the order of their entries, so nothing verified that claim. The claim was inaccurate, too. The entries are grouped by entity type and only sorted by UUID within such a group. The order of the groups is that of a set's iteration. Co-Authored-By: Claude Opus 5 (1M context) --- test/indexer/test_tdr.py | 1 - 1 file changed, 1 deletion(-) diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index 476f70858b..ed497a5581 100644 --- a/test/indexer/test_tdr.py +++ b/test/indexer/test_tdr.py @@ -456,7 +456,6 @@ def _test_fetch_bundle(self, self.assertEqual(test_bundle.fqid, emulated_bundle.fqid) assert isinstance(emulated_bundle, TDRHCABundle) - # Manifest and metadata should both be sorted by entity UUID self.assertEqual(test_bundle.manifest, emulated_bundle.manifest) self.assertEqual(test_bundle.metadata, emulated_bundle.metadata) self.assertEqual(test_bundle.links, emulated_bundle.links) From ab3bf993a04712ea8daf1a6234e117a8098c77e6 Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 09:40:41 -0700 Subject: [PATCH 5/9] Sort the manifest and metadata entries when canning a bundle A plugin groups those entries by entity type, in the iteration order of a set, which varies with Python's hash seed. Canning one bundle twice could therefore yield two files that differ only in the order of their entries. The canner now sorts both by entity reference. The entries of the canned TDR HCA bundles are reordered accordingly. They are otherwise unchanged, and so are the other attributes of those bundles. Only the canned file is normalized. The order of the entries of a bundle in memory still varies between processes. Co-Authored-By: Claude Opus 5 (1M context) --- scripts/can_bundle.py | 10 + ...4-dbba-33e6-9e40-6a9b3fe8585f.tdr.hca.json | 1280 +++--- ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json | 1192 ++--- ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 738 +-- ...3-429a-4260-9b1b-9c1e9844c80b.tdr.hca.json | 4064 ++++++++--------- 5 files changed, 3647 insertions(+), 3637 deletions(-) diff --git a/scripts/can_bundle.py b/scripts/can_bundle.py index db29e6025e..396137124c 100644 --- a/scripts/can_bundle.py +++ b/scripts/can_bundle.py @@ -39,6 +39,7 @@ AnyJSON, AnyMutableJSON, json_dict, + json_mapping, ) from azul.logging import ( configure_script_logging, @@ -150,6 +151,15 @@ def save_bundle(bundle: Bundle, output_dir: str) -> None: bundle_json = bundle.to_json() # We can bundles without the FQID so that we can mock it during tests bundle_json.pop('fqid') + # Plugins group these entries by entity type, in the iteration order of + # a set, which varies based on Python's hash seed. + for key in ('manifest', 'metadata'): + try: + entries = json_mapping(bundle_json[key]) + except KeyError: + pass + else: + bundle_json[key] = dict(sorted(entries.items())) with write_file_atomically(path) as f: json.dump(bundle_json, f, indent=4) log.info('Successfully wrote %s', path) diff --git a/test/indexer/data/1928ae54-dbba-33e6-9e40-6a9b3fe8585f.tdr.hca.json b/test/indexer/data/1928ae54-dbba-33e6-9e40-6a9b3fe8585f.tdr.hca.json index 9787792dea..737c881435 100644 --- a/test/indexer/data/1928ae54-dbba-33e6-9e40-6a9b3fe8585f.tdr.hca.json +++ b/test/indexer/data/1928ae54-dbba-33e6-9e40-6a9b3fe8585f.tdr.hca.json @@ -1,44 +1,5 @@ { "manifest": { - "sequence_file/002ebcd6-722d-434d-b21b-13a06e659a67": { - "uuid": "002ebcd6-722d-434d-b21b-13a06e659a67", - "name": "ACD3_snRNA_S33_L001_R2_001.fastq.gz", - "version": "2025-01-07T21:14:38.055401Z", - "drs_uri": "drs://dg.4503:696f302b-ecd9-4bcc-a750-56c22b496f02", - "size": 4845312460, - "sha256": "d9440b3d1d7dbaa98b93fa6e8686f0334fcc271e4621a77b75cdab3dde46b110", - "crc32c": "808a4ad6", - "sha1": null, - "s3_etag": null, - "content-type": ".gz", - "indexed": false - }, - "sequence_file/563ab2c6-6a71-474b-859b-206cb49ad5e3": { - "uuid": "563ab2c6-6a71-474b-859b-206cb49ad5e3", - "name": "ACD1_snATAC.demultiplexed.R1.fastq.gz", - "version": "2025-01-07T21:14:38.102511Z", - "drs_uri": "drs://dg.4503:d184f3fb-4544-4ba8-850f-3ce366e28901", - "size": 15144424495, - "sha256": "90e585e99ac28ef24cb5feae76e981abbf61b983048252adf5b3ee338d48f028", - "crc32c": "e32d7982", - "sha1": null, - "s3_etag": null, - "content-type": ".gz", - "indexed": false - }, - "sequence_file/9c41c821-ebb1-49c7-9fbf-f76000fd2a39": { - "uuid": "9c41c821-ebb1-49c7-9fbf-f76000fd2a39", - "name": "ACD4_Multiome_RNA_S4_L001_R1_001.fastq.gz", - "version": "2025-01-07T21:14:38.463212Z", - "drs_uri": "drs://dg.4503:3872df96-cfbb-48fd-b5d6-19307dc302d1", - "size": 4698100692, - "sha256": "337ee1ec1dc7ffcc0c1f03c6f3c2f83768474cdf38b05286efe2c0661749e90c", - "crc32c": "d6e430a7", - "sha1": null, - "s3_etag": null, - "content-type": ".gz", - "indexed": false - }, "analysis_file/005f71ed-fcba-4026-bc97-a8c9707f26ee": { "uuid": "005f71ed-fcba-4026-bc97-a8c9707f26ee", "name": "ACD2_snATAC_barcodes.tsv.gz", @@ -77,78 +38,48 @@ "s3_etag": null, "content-type": "application/x-gzip", "indexed": false - } - }, - "metadata": { + }, "sequence_file/002ebcd6-722d-434d-b21b-13a06e659a67": { - "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file", - "file_core": { - "checksum": "cf9bfa79726cea64ce6dd108d1ea9ada", - "describedBy": "https://schema.humancellatlas.org/core/file/6.2.0/file_core", - "file_name": "ACD3_snRNA_S33_L001_R2_001.fastq.gz", - "file_source": "LungMAP", - "format": "fastq.gz" - }, - "lane_index": 1, - "library_prep_id": "ACD3_snRNA_S33", - "provenance": { - "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "002ebcd6-722d-434d-b21b-13a06e659a67", - "submission_date": "2022-11-14T15:49:13.374432Z", - "submitter_id": "Shuyang.Zhao.cchmc@lungmap.net", - "update_date": "2025-01-07T21:14:38.055401Z", - "updater_id": "josh.fortriede.cchmc@lungmap.net" - }, - "read_index": "read2", - "schema_type": "file", - "schema_version": "9.3.0" + "uuid": "002ebcd6-722d-434d-b21b-13a06e659a67", + "name": "ACD3_snRNA_S33_L001_R2_001.fastq.gz", + "version": "2025-01-07T21:14:38.055401Z", + "drs_uri": "drs://dg.4503:696f302b-ecd9-4bcc-a750-56c22b496f02", + "size": 4845312460, + "sha256": "d9440b3d1d7dbaa98b93fa6e8686f0334fcc271e4621a77b75cdab3dde46b110", + "crc32c": "808a4ad6", + "sha1": null, + "s3_etag": null, + "content-type": ".gz", + "indexed": false }, "sequence_file/563ab2c6-6a71-474b-859b-206cb49ad5e3": { - "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file", - "file_core": { - "checksum": "368eb50aa056bcc37aaca065f3021494", - "describedBy": "https://schema.humancellatlas.org/core/file/6.2.0/file_core", - "file_name": "ACD1_snATAC.demultiplexed.R1.fastq.gz", - "file_source": "LungMAP", - "format": "fastq.gz" - }, - "lane_index": 1, - "library_prep_id": "ACD1_snATAC", - "provenance": { - "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "563ab2c6-6a71-474b-859b-206cb49ad5e3", - "submission_date": "2022-11-14T15:43:50.799759Z", - "submitter_id": "Shuyang.Zhao.cchmc@lungmap.net", - "update_date": "2025-01-07T21:14:38.102511Z", - "updater_id": "josh.fortriede.cchmc@lungmap.net" - }, - "read_index": "read1", - "schema_type": "file", - "schema_version": "9.3.0" + "uuid": "563ab2c6-6a71-474b-859b-206cb49ad5e3", + "name": "ACD1_snATAC.demultiplexed.R1.fastq.gz", + "version": "2025-01-07T21:14:38.102511Z", + "drs_uri": "drs://dg.4503:d184f3fb-4544-4ba8-850f-3ce366e28901", + "size": 15144424495, + "sha256": "90e585e99ac28ef24cb5feae76e981abbf61b983048252adf5b3ee338d48f028", + "crc32c": "e32d7982", + "sha1": null, + "s3_etag": null, + "content-type": ".gz", + "indexed": false }, "sequence_file/9c41c821-ebb1-49c7-9fbf-f76000fd2a39": { - "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file", - "file_core": { - "checksum": "374070d742f5e8f61860aa91e8d43695", - "describedBy": "https://schema.humancellatlas.org/core/file/6.2.0/file_core", - "file_name": "ACD4_Multiome_RNA_S4_L001_R1_001.fastq.gz", - "file_source": "LungMAP", - "format": "fastq.gz" - }, - "lane_index": 1, - "library_prep_id": "ACD4_Multiome_S4_RNA", - "provenance": { - "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "9c41c821-ebb1-49c7-9fbf-f76000fd2a39", - "submission_date": "2022-11-14T15:46:24.851947Z", - "submitter_id": "Shuyang.Zhao.cchmc@lungmap.net", - "update_date": "2025-01-07T21:14:38.463212Z", - "updater_id": "josh.fortriede.cchmc@lungmap.net" - }, - "read_index": "read1", - "schema_type": "file", - "schema_version": "9.3.0" 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The cellular and transcriptional mechanisms by which FOXF1 deficiency disrupts human lung formation are unknown. To identify cell types, gene networks, and cell-cell interactions underlying the pathogenesis of ACDMPV. We used single-nucleus RNA and assay for transposase-accessible chromatin sequencing, immunofluorescence confocal microscopy, and RNA in situ hybridization to identify cell types and molecular networks influenced by FOXF1 in ACDMPV lungs. Pathogenic single-nucleotide variants and copy-number variant deletions involving the FOXF1 gene locus in all subjects with ACDMPV (n = 6) were accompanied by marked changes in lung structure, including deficient alveolar development and a paucity of pulmonary microvasculature. Single-nucleus RNA and assay for transposase-accessible chromatin sequencing identified alterations in cell number and gene expression in endothelial cells (ECs), pericytes, fibroblasts, and epithelial cells in ACDMPV lungs. Distinct cell-autonomous roles for FOXF1 in capillary ECs and pericytes were identified. Pathogenic variants involving the FOXF1 gene locus disrupt gene expression in EC progenitors, inhibiting the differentiation or survival of capillary 2 ECs and cell-cell interactions necessary for both pulmonary vasculogenesis and alveolar type 1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA (vascular endothelial growth factor A) signaling and marked expansion of systemic bronchial ECs expressing COL15A1 (collagen type XV \u03b1 1 chain). Distinct FOXF1 gene regulatory networks were identified in subsets of pulmonary endothelial and fibroblast progenitors, providing both cellular and molecular targets for the development of therapies for ACDMPV and other diffuse lung diseases of infancy.", + "project_short_name": "Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV)", + "project_title": "Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV)" }, "provenance": { "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "1aa2900c-7572-4bda-b518-2d458d789ff5", - "submission_date": "2022-12-15T12:33:03.922626Z", - "submitter_id": "josh.fortriede.cchmc@lungmap.net", - "update_date": "2022-12-15T12:34:55.602005Z", + "document_id": "fdadee7e-2097-45d5-bf81-cc280bd8348e", + "schema_major_version": 1, + "schema_minor_version": 1, + "schema_version": "1.1.0", + "submission_date": "2022-11-10T16:57:48.457844Z", + "submitter_id": "Shuyang.Zhao@cchmc.org", + "update_date": "2024-06-25T15:12:06.304736Z", "updater_id": "josh.fortriede.cchmc@lungmap.net" }, - 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"schema_type": "biomaterial", - "sex": "male" + "schema_type": "biomaterial" }, - "donor_organism/ee1f02ff-cfee-4f99-ab44-6ac896965815": { + "specimen_from_organism/aedbc237-e962-4584-b99e-75a7b9656974": { "biomaterial_core": { - "biomaterial_description": "ACD1", - "biomaterial_id": "ee1f02ff-cfee-4f99-ab44-6ac896965815", - "biomaterial_name": "ACD1", + "biomaterial_id": "aedbc237-e962-4584-b99e-75a7b9656974", + "biomaterial_name": "ACD1 lung", "describedBy": "https://schema.humancellatlas.org/core/biomaterial/8.2.0/biomaterial_core", - "ncbi_taxon_id": [] - }, - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism", - "development_stage": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/5.3.6/development_stage_ontology", - "ontology": "HsapDv:0000082", - "ontology_label": "newborn human stage", - "text": "newborn human stage" + "ncbi_taxon_id": [ + 9606 + ] }, + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism", "diseases": [ { "describedBy": "https://schema.humancellatlas.org/module/ontology/5.3.8/disease_ontology", @@ -1108,158 +1241,25 @@ "text": "Homo sapiens" } ], - 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Whitsett", - "project_role": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/1.0.0/contributor_role_ontology", - "text": "principal investigator" - } - }, - { - "corresponding_contributor": true, - "describedBy": "https://schema.humancellatlas.org/module/project/8.0.1/contact", - "email": "minzhe.guo@cchmc.org", - "institution": "Cincinnati Children's Hospital Medical Center", - "laboratory": "Division of Neonatology, Perinatal and Pulmonary Biology", - "name": "Minzhe Guo", - "project_role": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/1.0.0/contributor_role_ontology", - "ontology": "EFO:0009742", - "ontology_label": "computational scientist", - "text": "computational scientist" - } - }, - { - "corresponding_contributor": false, - "describedBy": "https://schema.humancellatlas.org/module/project/8.0.1/contact", - "email": "Kathryn.Wikenheiser-Brokamp@cchmc.org", - "institution": "Cincinnati Children's Hospital Medical Center", - "laboratory": "Division of Pathology & Laboratory Medicine", - "name": "Kathryn A Wikenheiser-Brokamp", - "project_role": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/1.0.0/contributor_role_ontology", - "ontology": "EFO:0009738", - "ontology_label": "pathologist", - "text": "pathologist" - } - }, - { - "corresponding_contributor": false, - "describedBy": "https://schema.humancellatlas.org/module/project/8.0.1/contact", - "email": "Yan.Xu@cchmc.org", - "institution": "Cincinnati Children's Hospital Medical Center", - "laboratory": "Neonatology & Pulmonary Biology Perinatal Institute", - "name": "Yan Xu", - "project_role": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/1.0.0/contributor_role_ontology", - "ontology": "EFO:0001739", - "ontology_label": "investigator", - "text": "investigator" - } - }, - { - "corresponding_contributor": false, - "describedBy": "https://schema.humancellatlas.org/module/project/8.0.1/contact", - "email": "kevin.burns@cchmc.org", - "institution": "DMCC", - "name": "Kevin Burns", - "project_role": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/1.0.0/contributor_role_ontology", - "ontology": "EFO:0009737", - "ontology_label": "data curator", - "text": "data curator" - } - } - ], - "describedBy": "https://schema.humancellatlas.org/type/project/15.0.0/project", - "funders": [], - "geo_series_accessions": [], - "insdc_project_accessions": [], - "insdc_study_accessions": [], - "project_core": { - "describedBy": "https://schema.humancellatlas.org/core/project/7.0.5/project_core", - "project_description": "ACDMPV is a lethal developmental disorder of lung morphogenesis caused by insufficiency of FOXF1 (forkhead box F1) transcription factor function. The cellular and transcriptional mechanisms by which FOXF1 deficiency disrupts human lung formation are unknown. To identify cell types, gene networks, and cell-cell interactions underlying the pathogenesis of ACDMPV. We used single-nucleus RNA and assay for transposase-accessible chromatin sequencing, immunofluorescence confocal microscopy, and RNA in situ hybridization to identify cell types and molecular networks influenced by FOXF1 in ACDMPV lungs. Pathogenic single-nucleotide variants and copy-number variant deletions involving the FOXF1 gene locus in all subjects with ACDMPV (n = 6) were accompanied by marked changes in lung structure, including deficient alveolar development and a paucity of pulmonary microvasculature. Single-nucleus RNA and assay for transposase-accessible chromatin sequencing identified alterations in cell number and gene expression in endothelial cells (ECs), pericytes, fibroblasts, and epithelial cells in ACDMPV lungs. Distinct cell-autonomous roles for FOXF1 in capillary ECs and pericytes were identified. Pathogenic variants involving the FOXF1 gene locus disrupt gene expression in EC progenitors, inhibiting the differentiation or survival of capillary 2 ECs and cell-cell interactions necessary for both pulmonary vasculogenesis and alveolar type 1 cell differentiation. Loss of the pulmonary microvasculature was associated with increased VEGFA (vascular endothelial growth factor A) signaling and marked expansion of systemic bronchial ECs expressing COL15A1 (collagen type XV \u03b1 1 chain). Distinct FOXF1 gene regulatory networks were identified in subsets of pulmonary endothelial and fibroblast progenitors, providing both cellular and molecular targets for the development of therapies for ACDMPV and other diffuse lung diseases of infancy.", - "project_short_name": "Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV)", - "project_title": "Alveolar capillary dysplasia with misalignment of the pulmonary veins (ACDMPV)" + "preservation_storage": { + "describedBy": "https://schema.humancellatlas.org/module/biomaterial/6.1.1/preservation_storage", + "storage_method": "frozen at -80C" }, "provenance": { "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "fdadee7e-2097-45d5-bf81-cc280bd8348e", - "schema_major_version": 1, - "schema_minor_version": 1, - "schema_version": "1.1.0", - "submission_date": "2022-11-10T16:57:48.457844Z", - "submitter_id": "Shuyang.Zhao@cchmc.org", - "update_date": "2024-06-25T15:12:06.304736Z", + "document_id": "aedbc237-e962-4584-b99e-75a7b9656974", + "submission_date": "2022-12-15T12:32:55.338580Z", + "submitter_id": "josh.fortriede.cchmc@lungmap.net", + "update_date": "2022-12-15T12:34:55.591879Z", "updater_id": "josh.fortriede.cchmc@lungmap.net" }, - 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We have identified PU.1, IRF8 and BATF3 transcription factors (TFs) to reprogram human fibroblasts into DC type 1 (DC1). Induced DCs acquire a step-wise DC1 transcriptional signature at the single cell level as assessed with droplet based scRNA-seq. Hence, we provide evidence that antigen presentation can be dynamically programmed by a small combination of TFs in human cells. Moreover, it represents a platform for generating autologous DC1, the most attractive DC subset for cancer immunotherapy." }, - "file_description": "Make/amplify cDNA for each cell", + "contributors": [ + { + "name": "Filipe,,Pereira", + "email": "filipe.pereira@med.lu.se", + "phone": "+46 72 243 00 14", + "institution": "Lund University", + "laboratory": "Department of Laboratory Medicine", + "address": "S\u00f6lvegatan 17, BMC A12,\u00a0Lund", + "country": "Sweden", + "corresponding_contributor": true, + "project_role": { + "text": "Principal investigator", + "ontology": "EFO:0009736", + "ontology_label": "principal investigator" + }, + "orcid_id": "0000-0002-9724-1382" + }, + { + "name": "F\u00e1bio,,Rosa", + "email": "fabio.rosa.1993@gmail.com", + "phone": "+351 914 765 335", + "institution": "Lund University", + "laboratory": "Department of Laboratory Medicine", + "address": "S\u00f6lvegatan 17, BMC A12,\u00a0Lund", + "country": "Sweden", + "corresponding_contributor": false, + "project_role": { + "text": "Experimental scientist", + "ontology": "EFO:0009741", + "ontology_label": "experimental scientist" + }, + "orcid_id": "0000-0002-7714-5852" + }, + { + "name": "Cristiana,,Pires", + "email": "cristiana.pires@med.lu.se", + "phone": "+351 916 838 690", + "institution": "Lund University", + "laboratory": "Department of Laboratory Medicine", + "address": "S\u00f6lvegatan 17, BMC A12,\u00a0Lund", + "country": "Sweden", + "corresponding_contributor": false, + "project_role": { + "text": "Experimental scientist", + "ontology": "EFO:0009741", + "ontology_label": "experimental scientist" + }, + "orcid_id": "0000-0003-3100-0903" + }, + { + "name": "Ilia,,Kurochkin", + "email": "ilia.kurochkin@skolkovotech.ru", + "phone": "+79 151 16 49 52", + "institution": "Skolkovo Institute of Science and Technology", + "laboratory": "Center for Neurobiology and Brain Restoration", + "address": "Moscow, 121205, Russia", + "country": "Russia", + "corresponding_contributor": false, + "project_role": { + "text": "Computational scientist", + "ontology": "EFO:0009742", + "ontology_label": "computational scientist" + }, + "orcid_id": "0000-0003-2985-6323" + }, + { + "name": "Enrique,,Sapena Ventura", + "email": "enrique@ebi.ac.uk", + "institution": "European Bioinformatics Institute", + "laboratory": "Human Cell Atlas Data coordination Platform", + "country": "UK", + "corresponding_contributor": false, + "project_role": { + "text": "HCA Data Wrangler", + "ontology": "EFO:0009737", + "ontology_label": "data curator" + } + } + ], + "funders": [ + { + "grant_title": "4-year career package: Wallenberg Centre for Molecular Medicine and Faculty of Medicine at Lund University", + "grant_id": "Not provided", + "organization": "Wallenberg Foundation" + }, + { + "grant_title": "Generating Dendritic Cells by Direct Reprogramming", + "grant_id": "20180864", + "organization": "Crafoord Foundation\u00a0(Lund)" + }, + { + "grant_title": "Generating Dendritic Cells by Direct Reprogramming", + "grant_id": "CAN 2017/745", + "organization": "Cancerfonden\u00a0(Lund)" + }, + { + "grant_title": "ReproDC: Generating Antigen Presenting Cells by Direct Reprogramming", + "grant_id": "CENTRO-01-0145-FEDER-030013", + "organization": "FCT\u00a0Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia (Lisbon)" + }, + { + "grant_title": "Generating Dendritic Cells by Direct Cell Reprogramming", + "grant_id": "2018-02442", + "organization": "Swedish research council\u00a0(Lund)" + } + ], "provenance": { - 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Filtering eliminated genes detected in <20 cells, and discarded cells with (1) UMI counts < 1,000, (2) gene counts < 500 or > 8,000, and (3) mitochondrial gene ratio > 10%, resulting in the detection of 20,437 genes in 52,681 cells (see Table S5) across a total of 16 samples, with a median of approximately 3,000 cells from each sample. A median of 1,756 genes and 6,116 transcripts were captured per cell." }, - "library_construction_kit": { - "manufacturer": "10X Genomics" + "type": { + "text": "data transformation", + "ontology": "OBI:0200000", + "ontology_label": "data transformation" }, - "end_bias": "3 prime tag", - "primer": "poly-dT", - "strand": "first", - "umi_barcode": { - "barcode_read": "Read 1", - "barcode_offset": 16, - "barcode_length": 10 + "computational_method": "Cell Ranger v3.0", + "matrix": { + "derivation_process": [ + "quantification" + ] }, "provenance": { - "document_id": "090eef67-013e-4c09-a507-d595ef50ac02", - "submission_date": "2022-07-26T00:16:46.551Z", - "update_date": "2022-07-27T20:39:39.178Z", - "schema_major_version": 6, - "schema_minor_version": 3 + "document_id": "3809d420-b97a-4194-9ec9-d2a6c1c00519", + "submission_date": "2022-07-26T00:16:46.575Z", + "update_date": "2022-07-27T20:39:39.180Z", + "schema_major_version": 9, + "schema_minor_version": 2 } }, - "specimen_from_organism/10dfef3f-6932-41bf-8ad2-b76c70e8cbb3": { - 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"submission_date": "2022-07-26T00:16:46.363Z", - "update_date": "2022-08-23T17:15:17.919Z", + "document_id": "ce845e4e-69ff-4c83-b96b-8b1169140551", + "submission_date": "2022-07-26T00:16:46.475Z", + "update_date": "2022-08-23T17:15:18.062Z", "schema_major_version": 13, "schema_minor_version": 3 } }, - "cell_suspension/3fe887bd-7ddd-4139-9c2b-3f38d5e0a158": { + "cell_suspension/d431a352-e6a1-4b28-8374-cfa08a4a549b": { "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559754", - "biomaterial_name": "GSM5474118", + "biomaterial_id": "SRX11559747", + "biomaterial_name": "GSM5474111", "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20423004" + "biosamples_accession": "SAMN20422995" }, "genus_species": [ { @@ -759,24 +454,24 @@ ], "estimated_cell_count": 7500, "provenance": { - "document_id": "3fe887bd-7ddd-4139-9c2b-3f38d5e0a158", - "submission_date": "2022-07-26T00:16:46.463Z", - "update_date": "2022-08-23T17:15:18.047Z", + "document_id": "d431a352-e6a1-4b28-8374-cfa08a4a549b", + "submission_date": "2022-07-26T00:16:46.376Z", + "update_date": "2022-08-23T17:15:17.935Z", "schema_major_version": 13, "schema_minor_version": 3 } }, - "cell_suspension/57fdd10e-e5a6-4998-92e7-6fb0c905468b": { + "cell_suspension/ee8e1d61-d43b-4acc-8f77-d1ea968938f9": { "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559752", - "biomaterial_name": "GSM5474116", + "biomaterial_id": "SRX11559753", + "biomaterial_name": "GSM5474117", "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422990" + "biosamples_accession": "SAMN20423005" }, "genus_species": [ { @@ -787,24 +482,24 @@ ], "estimated_cell_count": 7500, "provenance": { - "document_id": "57fdd10e-e5a6-4998-92e7-6fb0c905468b", - "submission_date": "2022-07-26T00:16:46.437Z", - "update_date": "2022-08-23T17:15:18.017Z", + "document_id": "ee8e1d61-d43b-4acc-8f77-d1ea968938f9", + "submission_date": "2022-07-26T00:16:46.450Z", + "update_date": "2022-08-23T17:15:18.031Z", "schema_major_version": 13, "schema_minor_version": 3 } }, - "cell_suspension/694af37a-0253-4cef-bf82-65f27d8b4eda": { + "cell_suspension/fe3e7365-6847-416e-9dde-c9ae36f73513": { "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559751", - "biomaterial_name": "GSM5474115", + "biomaterial_id": "SRX11559742", + "biomaterial_name": "GSM5474106", "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422991" + "biosamples_accession": "SAMN20423000" }, "genus_species": [ { @@ -815,80 +510,75 @@ ], "estimated_cell_count": 7500, "provenance": { - "document_id": "694af37a-0253-4cef-bf82-65f27d8b4eda", - "submission_date": "2022-07-26T00:16:46.426Z", - "update_date": "2022-08-23T17:15:18.003Z", + "document_id": "fe3e7365-6847-416e-9dde-c9ae36f73513", + "submission_date": "2022-07-26T00:16:46.315Z", + "update_date": "2022-08-23T17:15:17.852Z", "schema_major_version": 13, "schema_minor_version": 3 } }, - "cell_suspension/86095244-35e6-4d38-9849-35a6403f2d21": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", - "schema_type": "biomaterial", - "biomaterial_core": { - "biomaterial_id": "SRX11559756", - "biomaterial_name": "GSM5474104", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", - "ncbi_taxon_id": [ - 9606 - ], - "biosamples_accession": "SAMN20423002" + "collection_protocol/f5bf4e91-b9a2-484a-9ec9-7f165e13dcd5": { + "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol", + "schema_type": "protocol", + "protocol_core": { + "protocol_id": "collection_protocol_1", + "protocol_name": "surgical resection", + "protocol_description": "Specimens were obtained from Brigham & Women\u2019s Hospital or Faulkner Hospital on the day of surgery, processed to single cells and analyzed by scRNA-seq on the same day" + }, + "method": { + "text": "surgical resection", + "ontology": "EFO:0009744", + "ontology_label": "surgical resection" }, - "genus_species": [ - { - "text": "Homo sapiens", - "ontology": "NCBITaxon:9606", - "ontology_label": "Homo sapiens" - } - ], - "estimated_cell_count": 7500, "provenance": { - "document_id": "86095244-35e6-4d38-9849-35a6403f2d21", - "submission_date": "2022-07-26T00:16:46.487Z", - "update_date": "2022-08-23T17:15:18.093Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "f5bf4e91-b9a2-484a-9ec9-7f165e13dcd5", + "submission_date": "2022-07-26T00:16:46.515Z", + "update_date": "2022-07-27T20:39:39.171Z", + "schema_major_version": 9, + "schema_minor_version": 2 } }, - "cell_suspension/a81fb1dc-f3c2-4ed7-a75b-83634f07c351": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", - "schema_type": "biomaterial", - "biomaterial_core": { - "biomaterial_id": "SRX11559744", - "biomaterial_name": "GSM5474108", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", - "ncbi_taxon_id": [ - 9606 - ], - "biosamples_accession": "SAMN20422998" + "dissociation_protocol/71df9d7e-c283-4379-9292-f497c56bb615": { + "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol", + "schema_type": "protocol", + "protocol_core": { + "protocol_id": "dissociation_protocol_1", + "protocol_name": "mechanical dissociation", + "protocol_description": "Cells were then pelleted by centrifugation, further dissociated by sequentially pipetting with 10, 5, and 1-ml pipette tips, and recentrifuged. The resulting cell pellet was used directly to establish organoid culture as previously described (Rosenbluth et al., 2020) or further dissociated into single cells for scRNA-seq or CyTOF analysis." + }, + "method": { + "text": "mechinical dissociation", + "ontology": "EFO:0009129", + "ontology_label": "mechinical dissociation" }, - "genus_species": [ - { - "text": "Homo sapiens", - "ontology": "NCBITaxon:9606", - "ontology_label": "Homo sapiens" - } - ], - "estimated_cell_count": 7500, "provenance": { - "document_id": "a81fb1dc-f3c2-4ed7-a75b-83634f07c351", - "submission_date": "2022-07-26T00:16:46.338Z", - "update_date": "2022-08-23T17:15:17.885Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "71df9d7e-c283-4379-9292-f497c56bb615", + "submission_date": "2022-07-26T00:16:46.527Z", + "update_date": "2022-07-27T20:39:39.175Z", + "schema_major_version": 6, + "schema_minor_version": 2 } }, - "cell_suspension/ae418af2-0db6-402d-a8cf-e303be76aa9b": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/185c2967-3195-49a2-8ad4-c44aa91b433e": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559743", - "biomaterial_name": "GSM5474107", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_11", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor with history of breast cancer", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422999" + "genotype": "BRCA2 (c.8487+3A>G)" + }, + "human_specific": { + "ethnicity": [ + { + "text": "White", + "ontology": "HANCESTRO:0005", + "ontology_label": "European" + } + ] }, "genus_species": [ { @@ -897,26 +587,57 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "33.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], + "medical_history": { + "treatment": "Chemotherapy and anti-HER2 therapy, neoadjuvant" + }, "provenance": { - "document_id": "ae418af2-0db6-402d-a8cf-e303be76aa9b", - "submission_date": "2022-07-26T00:16:46.326Z", - "update_date": "2022-08-23T17:15:17.870Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "185c2967-3195-49a2-8ad4-c44aa91b433e", + "submission_date": "2022-07-26T00:16:46.040Z", + "update_date": "2022-08-23T17:15:17.669Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/aec73517-4e8b-4120-b083-5f87a151c490": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/5863a7ac-cfdb-4c3e-a7a6-5eee912237df": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559749", - "biomaterial_name": "GSM5474113", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_06", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422993" + "genotype": "BRCA1 (del exons 21-24)" + }, + "human_specific": { + "ethnicity": [ + { + "text": "White", + "ontology": "HANCESTRO:0005", + "ontology_label": "European" + } + ] }, "genus_species": [ { @@ -925,26 +646,54 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "35.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], "provenance": { - "document_id": "aec73517-4e8b-4120-b083-5f87a151c490", - "submission_date": "2022-07-26T00:16:46.401Z", - "update_date": "2022-08-23T17:15:17.963Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "5863a7ac-cfdb-4c3e-a7a6-5eee912237df", + "submission_date": "2022-07-26T00:16:45.976Z", + "update_date": "2022-08-23T17:15:17.640Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/b1ea2c38-e8b4-4155-879a-f1b977de52b9": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/58722446-c05b-43cd-8b70-a38df65e5790": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559757", - "biomaterial_name": "GSM5474105", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_07", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor with history of breast cancer", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20423001" + "genotype": "BRCA1 (c.5266dupC (p.GLn1756Profs*74))" + }, + "human_specific": { + "ethnicity": [ + { + "text": "Jewish", + "ontology": "HANCESTRO:0324", + "ontology_label": "Ashkenazi Jew" + } + ] }, "genus_species": [ { @@ -953,26 +702,57 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "52.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], + "medical_history": { + "treatment": "Chemotherapy, for contralateral breast cancer > 1 year ago" + }, "provenance": { - "document_id": "b1ea2c38-e8b4-4155-879a-f1b977de52b9", - "submission_date": "2022-07-26T00:16:46.501Z", - "update_date": "2022-08-23T17:15:18.113Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "58722446-c05b-43cd-8b70-a38df65e5790", + "submission_date": "2022-07-26T00:16:45.988Z", + "update_date": "2022-08-23T17:15:17.646Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/b6fe2669-4e44-4e93-9ac3-400a368aa024": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/60d8f5ae-1b05-4819-b3c9-cbd5120003cb": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559745", - "biomaterial_name": "GSM5474109", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_14", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422997" + "genotype": "BRCA2 (c.8575delC (p.Gln2859Lysfs*4))" + }, + "human_specific": { + "ethnicity": [ + { + "text": "White", + "ontology": "HANCESTRO:0005", + "ontology_label": "European" + } + ] }, "genus_species": [ { @@ -981,26 +761,57 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "57.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], + "medical_history": { + "treatment": "Chemotherapy + Avastin for prior ovarian cancer > 1 year ago" + }, "provenance": { - "document_id": "b6fe2669-4e44-4e93-9ac3-400a368aa024", - "submission_date": "2022-07-26T00:16:46.350Z", - "update_date": "2022-08-23T17:15:17.901Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "60d8f5ae-1b05-4819-b3c9-cbd5120003cb", + "submission_date": "2022-07-26T00:16:46.076Z", + "update_date": "2022-08-23T17:15:17.685Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/b95f0aae-4c86-449d-b3e1-ba918a837ea8": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/673222e2-9081-4058-a49c-8d2599a11d93": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559750", - "biomaterial_name": "GSM5474114", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_01", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422992" + "genotype": "WT" + }, + "human_specific": { + "ethnicity": [ + { + "text": "Black", + "ontology": "HANCESTRO:0568", + "ontology_label": "African American" + } + ] }, "genus_species": [ { @@ -1009,26 +820,54 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "36.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], "provenance": { - "document_id": "b95f0aae-4c86-449d-b3e1-ba918a837ea8", - "submission_date": "2022-07-26T00:16:46.414Z", - "update_date": "2022-08-23T17:15:17.988Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "673222e2-9081-4058-a49c-8d2599a11d93", + "submission_date": "2022-07-26T00:16:45.913Z", + "update_date": "2022-08-23T17:15:17.601Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/ce845e4e-69ff-4c83-b96b-8b1169140551": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/6fe2f7fa-22ce-468f-b279-9eb56855fda9": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559755", - "biomaterial_name": "GSM5474119", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_12", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor with history of breast cancer", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20423003" + "genotype": "BRCA2 (c.5796_5797delTA (p.His1932fs))" + }, + "human_specific": { + "ethnicity": [ + { + "text": "White", + "ontology": "HANCESTRO:0005", + "ontology_label": "European" + } + ] }, "genus_species": [ { @@ -1037,26 +876,57 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "39.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + "ontology_label": "human adult stage" + }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], + "medical_history": { + "treatment": "Chemotherapy, neoadjuvant" + }, "provenance": { - "document_id": "ce845e4e-69ff-4c83-b96b-8b1169140551", - "submission_date": "2022-07-26T00:16:46.475Z", - "update_date": "2022-08-23T17:15:18.062Z", - "schema_major_version": 13, - "schema_minor_version": 3 + "document_id": "6fe2f7fa-22ce-468f-b279-9eb56855fda9", + "submission_date": "2022-07-26T00:16:46.052Z", + "update_date": "2022-08-23T17:15:17.675Z", + "schema_major_version": 15, + "schema_minor_version": 6 } }, - "cell_suspension/d431a352-e6a1-4b28-8374-cfa08a4a549b": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", + "donor_organism/79e2e6d6-6288-4dbf-a6bb-e2ac8affbf55": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.6.0/donor_organism", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559747", - "biomaterial_name": "GSM5474111", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", + "biomaterial_id": "Individual_09", + "biomaterial_name": "mammary tissue donor", + "biomaterial_description": "mammary tissue donor with history of breast cancer", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422995" + "genotype": "BRCA1 (IVS10-2A>T)" + }, + "human_specific": { + "ethnicity": [ + { + "text": "White", + "ontology": "HANCESTRO:0005", + "ontology_label": "European" + } + ] }, "genus_species": [ { @@ -1065,26 +935,45 @@ "ontology_label": "Homo sapiens" } ], - "estimated_cell_count": 7500, + "sex": "female", + "is_living": "yes", + "organism_age": "55.0", + "organism_age_unit": { + "text": "year", + "ontology": "UO:0000036", + "ontology_label": "year" + }, + "development_stage": { + "text": "human adult stage", + "ontology": "HsapDv:0000087", + 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and 1-ml pipette tips, and recentrifuged. The resulting cell pellet was used directly to establish organoid culture as previously described (Rosenbluth et al., 2020) or further dissociated into single cells for scRNA-seq or CyTOF analysis." + "specimen_from_organism/ceb55be8-123a-47f5-864e-30b9081a86db": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.5.0/specimen_from_organism", + "schema_type": "biomaterial", + "biomaterial_core": { + "biomaterial_id": "SAMN20422994", + "biomaterial_name": "mammary tissue specimen", + "biomaterial_description": "mammary tissue,Mammary tissue,Prophylactic,BRCA1 (IVS10-2A>T),55,Surgical menopause,4,2,White,Yes,No", + "ncbi_taxon_id": [ + 9606 + ], + "biosamples_accession": "SAMN20422994", + "insdc_sample_accession": "SRS9598109" }, - "method": { - "text": "mechinical dissociation", - "ontology": "EFO:0009129", - "ontology_label": "mechinical dissociation" + "genus_species": [ + { + "text": "Homo sapiens", + "ontology_label": "Homo sapiens" + } + ], + "organ": { + "text": "breast", + "ontology": "UBERON:0000310", + "ontology_label": "breast" }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], "provenance": { - "document_id": "71df9d7e-c283-4379-9292-f497c56bb615", - "submission_date": "2022-07-26T00:16:46.527Z", - "update_date": "2022-07-27T20:39:39.175Z", - "schema_major_version": 6, - "schema_minor_version": 2 + "document_id": "ceb55be8-123a-47f5-864e-30b9081a86db", + "submission_date": "2022-07-26T00:16:46.189Z", + "update_date": "2022-08-23T17:15:17.760Z", + "schema_major_version": 10, + "schema_minor_version": 5 } }, - "sequencing_protocol/71ab4e5a-9475-49e6-b061-09f8854ebd09": { - "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol", - "schema_type": "protocol", - "protocol_core": { - "protocol_id": "sequencing_protocol_1", - "protocol_name": "Illumina HiSeq X Ten sequencing", - "protocol_description": "Libraries were sequenced by Illumina HiSeq X Ten. Paired-end reads were processed and mapped to the GRCh38-3.0.0 human genome using Cell Ranger v3.0." + "specimen_from_organism/d8c6c2fa-51a4-4164-a7e5-ebcf565373dc": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.5.0/specimen_from_organism", + "schema_type": "biomaterial", + "biomaterial_core": { + "biomaterial_id": "SAMN20423005", + "biomaterial_name": "mammary tissue specimen", + "biomaterial_description": "mammary tissue,Mammary tissue,Prophylactic,BRCA2 (c.8575delC (p.Gln2859Lysfs*4)),57,Surgical menopause,2,2,White,No,No", + "ncbi_taxon_id": [ + 9606 + ], + "biosamples_accession": "SAMN20423005", + "insdc_sample_accession": "SRS9598114" }, - "instrument_manufacturer_model": { - "text": "Illumina HiSeq X Ten", - "ontology": "EFO:0008567", - "ontology_label": "Illumina HiSeq X" + "genus_species": [ + { + "text": "Homo sapiens", + "ontology_label": "Homo sapiens" + } + ], + "organ": { + "text": "breast", + "ontology": "UBERON:0000310", + "ontology_label": "breast" }, - "paired_end": false, - "method": { - "text": "tag based single cell RNA sequencing", - "ontology": "EFO:0008440", - "ontology_label": "tag based single cell RNA sequencing" + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], + "provenance": { + "document_id": "d8c6c2fa-51a4-4164-a7e5-ebcf565373dc", + "submission_date": "2022-07-26T00:16:46.253Z", + "update_date": "2022-08-23T17:15:17.805Z", + "schema_major_version": 10, + "schema_minor_version": 5 + } + }, + "specimen_from_organism/f371f5fd-bb50-433d-8c96-ac9ee2e9cad5": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.5.0/specimen_from_organism", + "schema_type": "biomaterial", + "biomaterial_core": { + "biomaterial_id": "SAMN20423000", + "biomaterial_name": "mammary tissue specimen", + "biomaterial_description": "mammary tissue,Mammary tissue,Reductive,WT,41,Premenopausal,1,1,White,No,No", + "ncbi_taxon_id": [ + 9606 + ], + "biosamples_accession": "SAMN20423000", + "insdc_sample_accession": "SRS9598103" }, - "10x": { - "fastq_method": "Cellranger mkfastq", - "fastq_method_version": "Cell Ranger v3.0" + "genus_species": [ + { + "text": "Homo sapiens", + "ontology_label": "Homo sapiens" + } + ], + "organ": { + "text": "breast", + "ontology": "UBERON:0000310", + "ontology_label": "breast" }, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], "provenance": { - "document_id": "71ab4e5a-9475-49e6-b061-09f8854ebd09", - "submission_date": "2022-07-26T00:16:46.563Z", - "update_date": "2022-07-27T20:39:39.179Z", + "document_id": "f371f5fd-bb50-433d-8c96-ac9ee2e9cad5", + "submission_date": "2022-07-26T00:16:46.111Z", + "update_date": "2022-08-23T17:15:17.705Z", "schema_major_version": 10, - "schema_minor_version": 1 + "schema_minor_version": 5 } } }, From 29a33fe575534bdbf93ec1cf6861bb107e7c8c3c Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 08:55:07 -0700 Subject: [PATCH 6/9] Add a second upstream bundle to the canned stitching fixture (#8393) The canned bundles of `test_subgraph_stitching` formed a chain, so the plugin retrieved them one at a time, in the order the chain dictated. The order of the merged links only varies when one batch holds more than one bundle, a shape that fixture could not produce. The root bundle now consumes a second file, produced by a new bundle whose own input is a cell suspension rather than a file. That bundle is therefore self-contained, and the traversal retrieves it together with the first upstream bundle, in one batch. A batch is a set, whose iteration order varies between processes, so this test now fails in roughly half of all runs, until the commit that merges the links in a deterministic order. The new bundle, its process and the file it produces are synthetic. All other entities they reference already exist in the canned tables. Co-Authored-By: Claude Opus 5 (1M context) --- ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 73 +++++++++++++++ ...39f-4e7d-9161-b720953432ce.tables.tdr.json | 92 +++++++++++++++++++ test/indexer/test_tdr.py | 3 +- 3 files changed, 167 insertions(+), 1 deletion(-) diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json index 8b59671ae2..6cad3d9ae0 100644 --- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json +++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json @@ -26,6 +26,19 @@ "content-type": "application/octet-stream", "indexed": false }, + "sequence_file/448f32ab-6505-44a1-ba27-1e2ee012146f": { + "uuid": "caaef0b3-685d-4071-abd7-7a7592ccf1b1", + "name": "22167_8#272_1.fastq.gz", + "version": "2020-08-10T21:24:26.174274Z", + "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_cd4fd46d-79d9-461b-9f38-347930019613", + "size": 761919, + "sha256": "6a8d9a6b14043d69828b15e3711311bd4ed283e62ef7fc18205c8043eac9dc33", + "crc32c": "9f4a1c07", + "sha1": "a2dc257d81b97c05232c1b41adb85cc1cf0e54cf", + "s3_etag": "b1c2d3e4f5a6978877665544332211ff", + "content-type": "application/gzip", + "indexed": false + }, "sequence_file/8f8b9587-237f-4995-9461-c96eac53d615": { "uuid": "f4132e3a-c468-4ca3-ad7b-b97b61054151", "name": "22167_7#271_2.fastq.gz", @@ -365,6 +378,18 @@ "update_date": "2019-05-14T11:06:42.648Z" } }, + "process/0d58cccc-8479-49a9-8598-71d2b28371b7": { + "process_core": { + "process_id": "proc_22167_8#272" + }, + "schema_type": "process", + "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process", + "provenance": { + "document_id": "0d58cccc-8479-49a9-8598-71d2b28371b7", + "submission_date": "2020-08-10T21:20:11.987Z", + "update_date": "2020-08-10T21:24:26.174Z" + } + }, "process/33e31f6f-fe78-45bd-ae57-10d2d14253cf": { "process_core": { "process_id": "process_id_4334" @@ -523,6 +548,21 @@ "schema_minor_version": 1 } }, + "sequence_file/448f32ab-6505-44a1-ba27-1e2ee012146f": { + "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file", + "schema_type": "file", + "file_core": { + "file_name": "22167_8#272_1.fastq.gz", + "format": "fastq.gz" + }, + "read_index": "read1", + "lane_index": 8, + "provenance": { + "document_id": "448f32ab-6505-44a1-ba27-1e2ee012146f", + "submission_date": "2020-08-10T21:20:11.987Z", + "update_date": "2020-08-10T21:24:26.174Z" + } + }, "sequence_file/8f8b9587-237f-4995-9461-c96eac53d615": { "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file", "schema_type": "file", @@ -659,6 +699,10 @@ { "input_id": "8f8b9587-237f-4995-9461-c96eac53d615", "input_type": "sequence_file" + }, + { + "input_id": "448f32ab-6505-44a1-ba27-1e2ee012146f", + "input_type": "sequence_file" } ], "link_type": "process_link", @@ -677,6 +721,33 @@ } ] }, + { + "link_type": "process_link", + "process_type": "process", + "process_id": "0d58cccc-8479-49a9-8598-71d2b28371b7", + "inputs": [ + { + "input_type": "cell_suspension", + "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6" + } + ], + "outputs": [ + { + "output_type": "sequence_file", + "output_id": "448f32ab-6505-44a1-ba27-1e2ee012146f" + } + ], + "protocols": [ + { + "protocol_type": "library_preparation_protocol", + "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5" + }, + { + "protocol_type": "sequencing_protocol", + "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b" + } + ] + }, { "inputs": [ { @@ -824,9 +895,11 @@ }, "stitched": [ "01a1d04b-05d0-4904-b627-68b0dc02bc17", + "0d58cccc-8479-49a9-8598-71d2b28371b7", "201ae4d0-c7c6-4777-947f-18f5268884b6", "3211ef8f-a60c-4892-ae55-91d6752dcd75", "33e31f6f-fe78-45bd-ae57-10d2d14253cf", + "448f32ab-6505-44a1-ba27-1e2ee012146f", "5b503dcb-dca6-4e4f-988b-f7100c030dc5", "5d82b884-7db4-47fa-9ccd-03054065c509", "6f5ddf2c-382d-4c0a-a506-3a5286067c83", diff --git a/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json b/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json index a9c4c42dde..386fc74dbd 100644 --- a/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json +++ b/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json @@ -1112,6 +1112,39 @@ "content_type": "application/gzip", "size": 718443 } + }, + { + "sequence_file_id": "448f32ab-6505-44a1-ba27-1e2ee012146f", + "version": "2020-08-10T21:24:26.174274Z", + "content": { + "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file", + "schema_type": "file", + "file_core": { + "file_name": "22167_8#272_1.fastq.gz", + "format": "fastq.gz" + }, + "read_index": "read1", + "lane_index": 8, + "provenance": { + "document_id": "448f32ab-6505-44a1-ba27-1e2ee012146f", + "submission_date": "2020-08-10T21:20:11.987Z", + "update_date": "2020-08-10T21:24:26.174Z" + } + }, + "file_id": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_cd4fd46d-79d9-461b-9f38-347930019613", + "descriptor": { + "describedBy": "https://schema.humancellatlas.org/system/2.1.0/file_descriptor", + "schema_type": "file_descriptor", + "crc32c": "9f4a1c07", + "sha1": "a2dc257d81b97c05232c1b41adb85cc1cf0e54cf", + "sha256": "6a8d9a6b14043d69828b15e3711311bd4ed283e62ef7fc18205c8043eac9dc33", + "s3_etag": "b1c2d3e4f5a6978877665544332211ff", + "file_name": "22167_8#272_1.fastq.gz", + "file_version": "2020-08-10T21:24:26.174274Z", + "file_id": "caaef0b3-685d-4071-abd7-7a7592ccf1b1", + "content_type": "application/gzip", + "size": 761919 + } } ] }, @@ -1641,6 +1674,22 @@ "update_date": "2019-05-14T12:26:53.666Z" } } + }, + { + "process_id": "0d58cccc-8479-49a9-8598-71d2b28371b7", + "version": "2020-08-10T21:24:26.174274Z", + "content": { + "process_core": { + "process_id": "proc_22167_8#272" + }, + "schema_type": "process", + "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process", + "provenance": { + "document_id": "0d58cccc-8479-49a9-8598-71d2b28371b7", + "submission_date": "2020-08-10T21:20:11.987Z", + "update_date": "2020-08-10T21:24:26.174Z" + } + } } ] }, @@ -1659,6 +1708,10 @@ { "input_id": "8f8b9587-237f-4995-9461-c96eac53d615", "input_type": "sequence_file" + }, + { + "input_id": "448f32ab-6505-44a1-ba27-1e2ee012146f", + "input_type": "sequence_file" } ], "link_type": "process_link", @@ -2046,6 +2099,45 @@ ] }, "project_id": "116965f3-f094-4769-9d28-ae675c1b569c" + }, + { + "links_id": "a5e0fc4d-b1e2-4827-9853-48918e488f9c", + "version": "2020-08-10T21:24:26.174274Z", + "content": { + "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links", + "schema_type": "links", + "schema_version": "2.1.1", + "links": [ + { + "link_type": "process_link", + "process_type": "process", + "process_id": "0d58cccc-8479-49a9-8598-71d2b28371b7", + "inputs": [ + { + "input_type": "cell_suspension", + "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6" + } + ], + "outputs": [ + { + "output_type": "sequence_file", + "output_id": "448f32ab-6505-44a1-ba27-1e2ee012146f" + } + ], + "protocols": [ + { + "protocol_type": "library_preparation_protocol", + "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5" + }, + { + "protocol_type": "sequencing_protocol", + "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b" + } + ] + } + ] + }, + "project_id": "116965f3-f094-4769-9d28-ae675c1b569c" } ] }, diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index ed497a5581..16fb068a4f 100644 --- a/test/indexer/test_tdr.py +++ b/test/indexer/test_tdr.py @@ -433,6 +433,7 @@ def test_fetch_bundle(self): def test_subgraph_stitching(self): downstream_uuid = '4426adc5-b3c5-5aab-ab86-51d8ce44dfbe' upstream_uuids = [ + 'a5e0fc4d-b1e2-4827-9853-48918e488f9c', 'b0c2c714-45ee-4759-a32b-8ccbbcf911d4', 'bd4939c1-a078-43bd-8477-99ae59ceb555', ] @@ -442,7 +443,7 @@ def test_subgraph_stitching(self): assert len(bundle.stitched) > 0 with self.assertLogs(plugin_log, level=logging.DEBUG) as cm: self._test_fetch_bundle(bundle, load_tables=True) - record = one(r for r in cm.records if 'Stitched 2 bundle(s): ' in r.message) + record = one(r for r in cm.records if 'Stitched 3 bundle(s): ' in r.message) for upstream_uuid in upstream_uuids: self.assertIn("uuid='" + upstream_uuid, record.message) From f5c76a6659451c0ce7f957a8e6633e70c7c49d52 Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 13:51:46 -0700 Subject: [PATCH 7/9] Assert that merged links don't depend on the stitching order (#8393) The stitched bundles of one batch are the elements of a set, so the order in which the plugin emits them, and with it the order of the merged links, varies between processes. The preceding commit made the fixture produce such a batch, but a single run of the test still covers only whichever order that process happens to produce. The new test merges the links of the stitched bundles in every permutation and expects the result of the canned bundle each time. It fails until the next commit, which merges them in a deterministic order. Co-Authored-By: Claude Opus 5 (1M context) --- test/indexer/test_tdr.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index 16fb068a4f..67337629cb 100644 --- a/test/indexer/test_tdr.py +++ b/test/indexer/test_tdr.py @@ -4,6 +4,9 @@ from io import ( BytesIO, ) +from itertools import ( + permutations, +) import json import logging from operator import ( @@ -447,6 +450,24 @@ def test_subgraph_stitching(self): for upstream_uuid in upstream_uuids: self.assertIn("uuid='" + upstream_uuid, record.message) + def test_merge_links(self): + """ + Ensure that _merge_links is deterministic and insensitive to the order + in which _stitch_bundles emits the stitched bundles + """ + downstream_uuid = '4426adc5-b3c5-5aab-ab86-51d8ce44dfbe' + fqid = self.bundle_fqid(uuid=downstream_uuid, + version='2020-08-10T21:24:26.174274Z') + expected_bundle = self._load_canned_bundle(fqid) + self._make_mock_tables(fqid.source) + entities, root_entities, links_jsons = self.plugin._stitch_bundles(expected_bundle) + root, *stitched = links_jsons + self.assertEqual(downstream_uuid, root['links_id']) + for permutation in permutations(stitched): + with self.subTest(stitched=[row['links_id'] for row in permutation]): + actual_links = self.plugin._merge_links([root, *permutation]) + self.assertEqual(expected_bundle.links, actual_links) + def _test_fetch_bundle(self, test_bundle: TDRHCABundle, *, From dc00356141d1393339497523ea980dd18aafde93 Mon Sep 17 00:00:00 2001 From: Abraham Chavez Date: Mon, 19 Oct 2026 15:28:33 -0700 Subject: [PATCH 8/9] [r] Merge links of stitched HCA bundles in a deterministic order (#8393) The TDR HCA plugin merged the links in the order in which it retrieved the stitched bundles. That is the iteration order of a set and differs between indexer invocations, so every partition of a stitched bundle could produce a links replica with a different content hash. In prod, one bundle has 101 replicas that differ only in the order of their links. The links of the root bundle now come first, followed by those of the other bundles in the order of their UUID. Co-Authored-By: Claude Opus 5.5 --- src/azul/plugins/repository/tdr_hca/__init__.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py index f089ea74ec..128c63bd8a 100644 --- a/src/azul/plugins/repository/tdr_hca/__init__.py +++ b/src/azul/plugins/repository/tdr_hca/__init__.py @@ -467,11 +467,18 @@ def _find_upstream_bundles(self, def _merge_links(self, links_jsons: MutableJSONs) -> MutableJSON: """ Merge the links.json documents from multiple stitched bundles into a - single document. + single document, ensuring that the result does not depend on the order + of the stitched bundles. + + :param links_jsons: The links entities of the root bundle, followed by + those of the bundles stitched to it. """ root, *stitched = links_jsons if stitched: - source_contents = [row['content'] for row in links_jsons] + # The stitched bundles are in the iteration order of a set, which + # varies between processes. + stitched.sort(key=itemgetter('links_id')) + source_contents = [row['content'] for row in [root, *stitched]] # FIXME: Explicitly verify compatible schema versions for stitched subgraphs # https://github.com/DataBiosphere/azul/issues/3215 schema_type = 'links' From dfe1faf3cb52550f01522176edea2778511eb189 Mon Sep 17 00:00:00 2001 From: Hannes Schmidt Date: Wed, 21 Oct 2026 14:06:55 -0700 Subject: [PATCH 9/9] Start a BigQuery emulator for every test, not every test class A test used to drop the tables it had created, so that the next test of the class could create them again in the same emulator. Dropping them grew more expensive the longer that emulator had been in use, from 4.7s in the first test of a class to 11.6s in the fifth, and dominated the run time of both affected test classes. A test now gets an emulator of its own and discards it afterwards. Launching one costs 0.3s and makes dropping the tables unnecessary. Running test_tdr and test_anvil together takes 59s instead of 142s, for the same 29 tests. Replacing the nineteen table deletions with a single deletion of the dataset was tried first. That deletion degrades just like the ones it replaces, so it saved only 12%. Co-Authored-By: Claude Opus 5 (1M context) --- test/indexer/test_tdr.py | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index 67337629cb..94f81f1b9f 100644 --- a/test/indexer/test_tdr.py +++ b/test/indexer/test_tdr.py @@ -183,8 +183,6 @@ def _patch_tdr_client(cls): source = cls.source.ref.spec credentials_provider = MockCredentialsProvider(project_id=source.subdomain) tdr = MockTDRClient(credentials_provider=credentials_provider) - assert cls.netloc is not None - MockTDRClient.netloc = cls.netloc cls.addClassPatch(mock.patch.object(TDRPlugin, '_tdr', return_value=tdr)) @cached_property @@ -192,23 +190,32 @@ def plugin(self) -> TDR_PLUGIN: plugin_cls = self._plugin_cls() return plugin_cls(catalog=self.catalog) - netloc: tuple[str, int] | None = None - @classmethod def setUpClass(cls): super().setUpClass() - image = resolve_docker_image_for_launch('bigquery_emulator') - cls.netloc = cls._create_container(image=image, - container_port=9050, - command=[ - '--log-level=debug', - '--port=9050', - '--project=' + cls.source.ref.spec.subdomain, - '--dataset=' + cls.source.ref.spec.name - ]) cls._patch_tdr_client() cls._patch_timestamp_conversion() + def setUp(self): + super().setUp() + # Intuitively we would want to share a container between test methods + # and only drop the tables in between, but for some unknown reason + # dropping tables is slower than restarting the whole container. + source = self.source.ref.spec + image = resolve_docker_image_for_launch('bigquery_emulator') + MockTDRClient.netloc = self._create_container(image=image, + container_port=9050, + command=[ + '--log-level=debug', + '--port=9050', + '--project=' + source.subdomain, + '--dataset=' + source.name + ]) + + def tearDown(self): + self._kill_containers() + super().tearDown() + @classmethod def _patch_timestamp_conversion(cls): """ @@ -299,7 +306,6 @@ def dump_row(row: JSON) -> JSON: # noinspection PyTypeChecker table = bigquery.Table(table_name, schema) bq.create_table(table=table) - self.addCleanup(bq.delete_table, table) bq.insert_rows(table=table, selected_fields=schema, rows=map(dump_row, rows)) def _bq_schema_from_row(self, row: BigQueryRow) -> list[bigquery.SchemaField]: