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/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/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/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'), 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), 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/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' 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, - 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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" + } } ], - "organ": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/5.3.7/organ_ontology", - "ontology": "UBERON:0002048", - "ontology_label": "Lung", - "text": "Lung" - }, - "preservation_storage": { - "describedBy": "https://schema.humancellatlas.org/module/biomaterial/6.1.1/preservation_storage", - "storage_method": "frozen at -80C" + "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)" }, "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" } ], - "is_living": "unknown", - "organism_age": "2", - "organism_age_unit": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/5.3.5/time_unit_ontology", - "ontology": "UO:0000034", - "ontology_label": "week", - "text": "week" - }, - "provenance": { - "describedBy": "https://schema.humancellatlas.org/system/1.1.0/provenance", - "document_id": "ee1f02ff-cfee-4f99-ab44-6ac896965815", - "submission_date": "2022-11-15T21:08:17.062047Z", - "submitter_id": "Shuyang.Zhao.cchmc@lungmap.net", - "update_date": "2024-05-20T19:59:14.828160Z", - "updater_id": "josh.fortriede.cchmc@lungmap.net" - }, - "schema_type": "biomaterial", - "sex": "male" - }, - "collection_protocol/3e396673-63c9-4fdb-b869-012fdd638137": { - "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol", - "method": { - "describedBy": "https://schema.humancellatlas.org/module/ontology/5.3.5/process_type_ontology", - "text": "" - }, - "protocol_core": { - "describedBy": "https://schema.humancellatlas.org/core/protocol/5.2.5/protocol_core", - 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"email": "jeffrey.whitsett@cchmc.org", - "institution": "Cincinnati Children's Hospital Medical Center", - "laboratory": "Division of Neonatology, Perinatal and Pulmonary Biology", - "name": "Jeffrey A. 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" }, - "publications": [ - { - "authors": [], - "describedBy": "https://schema.humancellatlas.org/module/project/7.0.0/publication", - "doi": "10.1164/rccm.202210-2015OC", - "official_hca_publication": false, - "pmid": 37463497, - "title": "Single Cell Multiomics Identifies Cells and Genetic Networks Underlying Alveolar Capillary Dysplasia", - "url": "https://www.atsjournals.org/doi/10.1164/rccm.202210-2015OC" - } - ], - "schema_type": "project", - "schema_version": "15.0.0", - "supplementary_links": [] + "schema_type": "biomaterial" } }, "links": { diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json index ba63ed7de7..9df2b6dc80 100644 --- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json +++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json @@ -1,44 +1,5 @@ { "manifest": { - "supplementary_file/22561f93-d5e0-57eb-a54e-2d9d565cc234": { - "name": "22561f93-d5e0-57eb-a54e-2d9d565cc234_file_name.fmt", - 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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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"protocol_id": "library_protocol_1", - "protocol_name": "10x 3' v2 library preparation", - "protocol_description": "A total of 7,000-8,000 viable cells per sample were loaded for single cell capturing and cDNA library generation using the 10X Chromium 3\u2019 library construction kit v2 following the manufacturer\u2019s instructions (including 3 washes to minimize ambient RNA)." - }, - "cell_barcode": { - "barcode_read": "Read 1", - "barcode_offset": 0, - "barcode_length": 16 - }, - "input_nucleic_acid_molecule": { - "text": "polyA RNA", - "ontology": "OBI:0000869", - "ontology_label": "polyA RNA" - }, - "nucleic_acid_source": "single cell", - "library_construction_method": { - "text": "10x 3' V2 sequencing", - "ontology": "EFO:0009899", - "ontology_label": "10x 3' v2" + "protocol_id": "analysis_protocol_1", + "protocol_name": "Raw gene expression analysis", + "protocol_description": "Paired-end reads were processed and mapped to the GRCh38-3.0.0 human genome using Cell Ranger v3.0. 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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"ontology_label": "breast" - }, - "diseases": [ - { - "text": "normal", - "ontology": "PATO:0000461", - "ontology_label": "normal" - } - ], + "estimated_cell_count": 7500, "provenance": { - "document_id": "10dfef3f-6932-41bf-8ad2-b76c70e8cbb3", - "submission_date": "2022-07-26T00:16:46.135Z", - "update_date": "2022-08-23T17:15:17.722Z", - "schema_major_version": 10, - "schema_minor_version": 5 + "document_id": "194914ee-3e84-4df3-befd-963b9e7dd873", + "submission_date": "2022-07-26T00:16:46.389Z", + "update_date": "2022-08-23T17:15:17.950Z", + "schema_major_version": 13, + "schema_minor_version": 3 } }, - "specimen_from_organism/12574b13-e36d-43e8-95b4-083e8d23ac7b": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.5.0/specimen_from_organism", + "cell_suspension/287cbe05-3074-4f1b-9e2e-02c0a54cce73": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SAMN20423002", - 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}, - "diseases": [ - { - "text": "normal", - "ontology": "PATO:0000461", - "ontology_label": "normal" - } - ], - "provenance": { - "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": 5 - } - }, - "cell_suspension/194914ee-3e84-4df3-befd-963b9e7dd873": { - "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", - "schema_type": "biomaterial", - "biomaterial_core": { - "biomaterial_id": "SRX11559748", - "biomaterial_name": "GSM5474112", - "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", - "ncbi_taxon_id": [ - 9606 - ], - "biosamples_accession": "SAMN20422994" - }, - "genus_species": [ - { - "text": "Homo sapiens", - "ontology": "NCBITaxon:9606", + "ontology": "NCBITaxon:9606", "ontology_label": "Homo sapiens" } ], "estimated_cell_count": 7500, "provenance": { - "document_id": "194914ee-3e84-4df3-befd-963b9e7dd873", - "submission_date": "2022-07-26T00:16:46.389Z", - "update_date": "2022-08-23T17:15:17.950Z", + "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 } }, - "cell_suspension/287cbe05-3074-4f1b-9e2e-02c0a54cce73": { + "cell_suspension/ce845e4e-69ff-4c83-b96b-8b1169140551": { "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension", "schema_type": "biomaterial", "biomaterial_core": { - "biomaterial_id": "SRX11559746", - "biomaterial_name": "GSM5474110", + "biomaterial_id": "SRX11559755", + "biomaterial_name": "GSM5474119", "biomaterial_description": "cell suspension from mammary tissue for scRNAseq", "ncbi_taxon_id": [ 9606 ], - "biosamples_accession": "SAMN20422996" + "biosamples_accession": "SAMN20423003" }, "genus_species": [ { @@ -731,24 +426,24 @@ ], "estimated_cell_count": 7500, "provenance": { - "document_id": "287cbe05-3074-4f1b-9e2e-02c0a54cce73", - "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", + 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"PATO:0000461", + "ontology_label": "normal" } ], - "data_use_restriction": "NRES", "provenance": { - "document_id": "9b876d31-0739-4e96-9846-f76e6a427279", - "submission_date": "2022-05-31T17:34:57.200Z", - "update_date": "2024-10-18T09:51:03.155Z", - "schema_major_version": 19, - "schema_minor_version": 0 + "document_id": "a0ed2c89-ddd9-4f38-a801-dcaf1f8809cb", + "submission_date": "2022-07-26T00:16:46.216Z", + "update_date": "2022-08-23T17:15:17.779Z", + "schema_major_version": 10, + "schema_minor_version": 5 } }, - "enrichment_protocol/34455725-aa8e-4bf6-b6b6-763d3aa695e4": { - "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol", - "schema_type": "protocol", - "protocol_core": { - "protocol_id": "enrichment_protocol_1", - "protocol_name": "cell size selection", - "protocol_description": "For scRNA-seq, cells were treated for 5 minutes with TrypLE (Gibco 12605010), filtered through a 40 \u03bcm strainer, resuspended in PBS containing 0.04% BSA, counted manually under the microscope, and loaded onto the 10X Chromium platform immediately." + "specimen_from_organism/a252e8e8-c833-49c6-8daa-930bef8bd105": { + "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.5.0/specimen_from_organism", + "schema_type": "biomaterial", + "biomaterial_core": { + "biomaterial_id": "SAMN20422999", + "biomaterial_name": "mammary tissue specimen", + "biomaterial_description": "mammary tissue,Mammary tissue,Reductive,RAD51C,31,Premenopausal,4,1,Black,No,No", + "ncbi_taxon_id": [ + 9606 + ], + "biosamples_accession": "SAMN20422999", + "insdc_sample_accession": "SRS9598104" }, - "method": { - "text": "cell size selection", - "ontology": "EFO:0009337", - "ontology_label": "cell size selection" + "genus_species": [ + { + "text": "Homo sapiens", + "ontology_label": "Homo sapiens" + } + ], + "organ": { + "text": "breast", + "ontology": "UBERON:0000310", + "ontology_label": "breast" }, - "maximum_size": 40, + "diseases": [ + { + "text": "normal", + "ontology": "PATO:0000461", + "ontology_label": "normal" + } + ], "provenance": { - "document_id": "34455725-aa8e-4bf6-b6b6-763d3aa695e4", - "submission_date": "2022-07-26T00:16:46.540Z", - "update_date": "2022-07-27T20:39:39.177Z", - "schema_major_version": 3, - "schema_minor_version": 1 + "document_id": "a252e8e8-c833-49c6-8daa-930bef8bd105", + "submission_date": "2022-07-26T00:16:46.123Z", + "update_date": "2022-08-23T17:15:17.714Z", + "schema_major_version": 10, + "schema_minor_version": 5 } }, - "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." + "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 } } }, diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py index 69f586e2fc..94f81f1b9f 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 ( @@ -180,8 +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 @@ -189,23 +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): """ @@ -296,7 +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]: @@ -433,6 +442,7 @@ 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', ] @@ -442,10 +452,28 @@ 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) + 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, *, @@ -456,10 +484,10 @@ 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) + self.assertEqual(test_bundle.stitched, emulated_bundle.stitched) class TestTDRSourceList(AzulUnitTestCase):