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hubmapconsortium / search-api

HuBMAP search service and associated pieces to create an index
https://search.api.hubmapconsortium.org
MIT License
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Investigate Elasticsearch `circuit_breaking_exception` "Data too large" #819

Closed yuanzhou closed 2 months ago

yuanzhou commented 2 months ago

Full reindex on DEV to test out the round 5 efficiency updates from Karl's changes, but encounter hundreds of such errors:

[2024-06-22 07:00:07] ERROR in es_writer:95: Failed to write doc of uuid: d7c64854d6eb06792fccc500ab4d9009 to index: hm_613_dev_consortium_portal
[2024-06-22 07:00:07] ERROR in es_writer:96: Error Message: {"error":{"root_cause":[{"type":"circuit_breaking_exception","reason":"[parent] Data too large, data for [indices:data/write/bulk[s]] would be [8185875406/7.6gb], which is larger than the limit of [8160437862/7.5gb], real usage: [8185583904/7.6gb], new bytes reserved: [291502/284.6kb], usages [request=0/0b, fielddata=1612197/1.5mb, in_flight_requests=600866/586.7kb, accounting=375790156/358.3mb]","bytes_wanted":8185875406,"bytes_limit":8160437862,"durability":"PERMANENT"}],"type":"circuit_breaking_exception","reason":"[parent] Data too large, data for [indices:data/write/bulk[s]] would be [8185875406/7.6gb], which is larger than the limit of [8160437862/7.5gb], real usage: [8185583904/7.6gb], new bytes reserved: [291502/284.6kb], usages [request=0/0b, fielddata=1612197/1.5mb, in_flight_requests=600866/586.7kb, accounting=375790156/358.3mb]","bytes_wanted":8185875406,"bytes_limit":8160437862,"durability":"PERMANENT"},"status":429}

Did another full reindex over the weekend and still same issue.

yuanzhou commented 2 months ago

Request body is only 142K:

{"ancestor_counts": {"entity_type": {"Donor": 1, "Sample": 1}}, "ancestor_ids": ["411319bc691ba1e91dadac6262193507", "142d18f0a749d3d02d8b1addbca15589"], "ancestors": [{"created_by_user_displayname": "Daniel Cotter", "created_by_user_email": "Daniel.cotter@stanford.edu", "created_timestamp": 1649696763380, "data_access_level": "public", "description": "Small intestine from donor B011 / W192", "entity_type": "Sample", "group_name": "Stanford TMC", "group_uuid": "def5fd76-ed43-11e8-b56a-0e8017bdda58", "hubmap_id": "HBM342.SZCR.585", "lab_tissue_sample_id": "B011-A-XXX", "last_modified_timestamp": 1649697562748, "mapped_data_access_level": "Public", "mapped_last_modified_timestamp": "2022-04-11 17:19:22", "mapped_organ": "Small Intestine", "mapped_sample_category": "Organ", "organ": "SI", "protocol_url": "dx.doi.org/10.17504/protocols.io.biqpkdvn", "sample_category": "organ", "submission_id": "STAN0014-SI", "uuid": "411319bc691ba1e91dadac6262193507"}, {"created_by_user_displayname": "Daniel Cotter", "created_by_user_email": "Daniel.cotter@stanford.edu", "created_timestamp": 1649351465116, "data_access_level": "public", "description": "W192 is WUSTL ID", "entity_type": "Donor", "group_name": "Stanford TMC", "group_uuid": "def5fd76-ed43-11e8-b56a-0e8017bdda58", "hubmap_id": "HBM275.QBCZ.562", "lab_donor_id": "B011", "label": "B011", "last_modified_timestamp": 1649351465116, "mapped_data_access_level": "Public", "mapped_last_modified_timestamp": "2022-04-07 17:11:05", "mapped_metadata": {"abo_blood_group_system": ["Blood Type A"], "age_unit": ["year"], "age_value": [54.0], "body_mass_index_unit": ["kg/m2"], "body_mass_index_value": [20.5], "cause_of_death": ["Anoxia"], "height_unit": ["cm"], "height_value": [147.3], "mechanism_of_injury": ["Cardiovascular"], "medical_history": ["Hypertension", "Type 2 Diabetes Mellitus"], "race": ["Black or African American"], "sex": ["Female"], "weight_unit": ["kg"], "weight_value": [44.5]}, "metadata": {"organ_donor_data": [{"code": "424144002", "concept_id": "C0001779", "data_type": "Numeric", "data_value": "54", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "424144002", "grouping_concept": "C0001779", "grouping_concept_preferred_term": "Age", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "EQ", "preferred_term": "Age", "sab": "SNOMEDCT_US", "start_datetime": "", "units": "year"}, {"code": "112144000", "concept_id": "C0427620", "data_type": "Nominal", "data_value": "ABO Blood Group", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "63915006", "grouping_concept": "C0000778", "grouping_concept_preferred_term": "ABO blood group system", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Blood Type A", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "60621009", "concept_id": "C1305855", "data_type": "Numeric", "data_value": "20.5", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "60621009", "grouping_concept": "C1305855", "grouping_concept_preferred_term": "Body Mass Index", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "EQ", "preferred_term": "Body Mass Index", "sab": "SNOMEDCT_US", "start_datetime": "", "units": "kg/m2"}, {"code": "29658002", "concept_id": "C0003130", "data_type": "Nominal", "data_value": "Anoxia", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "184305005", "grouping_concept": "C0007465", "grouping_concept_preferred_term": "Cause of Death", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Anoxia", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "50373000", "concept_id": "C0005890", "data_type": "Numeric", "data_value": "147.3", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "50373000", "grouping_concept": "C0005890", "grouping_concept_preferred_term": "Height", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "EQ", "preferred_term": "Height", "sab": "SNOMEDCT_US", "start_datetime": "", "units": "cm"}, {"code": "405617006", "concept_id": "C1320716", "data_type": "Nominal", "data_value": "Cardiovascular", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "246078001", "grouping_concept": "C0449413", "grouping_concept_preferred_term": "Mechanism of Injury", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Cardiovascular", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "38341003", "concept_id": "C0020538", "data_type": "Nominal", "data_value": "Hypertension", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "392521001", "grouping_concept": "C0262926", "grouping_concept_preferred_term": "Medical History", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Hypertension", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "44054006", "concept_id": "C0011860", "data_type": "Nominal", "data_value": "Type 2 Diabetes Mellitus", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "392521001", "grouping_concept": "C0262926", "grouping_concept_preferred_term": "Medical History", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Type 2 Diabetes Mellitus", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "413464008", "concept_id": "C0027567", "data_type": "Nominal", "data_value": "Race", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "415229000", "grouping_concept": "C0034510", "grouping_concept_preferred_term": "Race", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Black or African American", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "1086007", "concept_id": "C0086287", "data_type": "Nominal", "data_value": "Sex", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "57312000", "grouping_concept": "C1522384", "grouping_concept_preferred_term": "Sex", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "", "preferred_term": "Female", "sab": "SNOMEDCT_US", "start_datetime": "", "units": ""}, {"code": "27113001", "concept_id": "C0005910", "data_type": "Numeric", "data_value": "44.5", "end_datetime": "", "graph_version": "UMLS2022AA", "grouping_code": "27113001", "grouping_concept": "C0005910", "grouping_concept_preferred_term": "Weight", "grouping_sab": "SNOMEDCT_US", "numeric_operator": "EQ", "preferred_term": "Weight", "sab": "SNOMEDCT_US", "start_datetime": "", "units": "kg"}]}, "protocol_url": "dx.doi.org/10.17504/protocols.io.bin8kdhw", "submission_id": "STAN0014", "uuid": "142d18f0a749d3d02d8b1addbca15589"}], "created_by_user_displayname": "Daniel Cotter", "created_by_user_email": "Daniel.cotter@stanford.edu", "created_timestamp": 1649781177879, "data_access_level": "public", "descendant_counts": {"dataset_type": {"ATACseq": 1, "ATACseq [SnapATAC]": 2, "CODEX": 1, "CODEX [Cytokit + SPRM]": 5, "RNAseq": 1, "RNAseq [Salmon]": 1}, "entity_type": {"Dataset": 11, "Sample": 1}}, "descendant_ids": ["c1a9f7ac0babf65af4a280846c91b7f7", "4f20058fbdca73ddbf8a0fe4e7553fca", "a24771788dc2d572e267badeb701161d", "f16a9a988bd572da2c3d7658fc236b46", "f4e830056221a0a296eb8a879739e952", "4152e68d6b2b157c33f1d2858c959066", "4839e7564bc7676e781b8f3f9bfbf35b", "a5f09e7c23d5018c24208e6b14251ba5", "cfeb38aafe8830ba7fa0bd44cdfd1fdc", "08da48ab256abd9baec281ebe6c65abd", "573a6dbec068677a6dd9660cf92c95a5", "89e4944336dd47d32a50fe8aac049db1"], "descendants": [{"created_by_user_displayname": "Daniel Cotter", "created_by_user_email": "Daniel.cotter@stanford.edu", "created_timestamp": 1649887585901, "data_access_level": "public", "description": "Sample of duodenum of small intestine from donor B011 / W192", "entity_type": "Sample", "group_name": "Stanford TMC", "group_uuid": "def5fd76-ed43-11e8-b56a-0e8017bdda58", "hubmap_id": "HBM937.MZGP.398", "lab_tissue_sample_id": "B011-A-501", "last_modified_timestamp": 1654708954632, "protocol_url": "https://dx.doi.org/10.17504/protocols.io.bqm5mu86", "rui_location": "{\"@context\": \"https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld\", \"@id\": \"http://purl.org/ccf/1.5/d1085194-4902-4252-95fd-faf03afd9288\", \"@type\": \"SpatialEntity\", \"ccf_annotations\": [\"http://purl.obolibrary.org/obo/UBERON_0002115\", \"http://purl.obolibrary.org/obo/UBERON_0002114\", \"http://purl.obolibrary.org/obo/FMA_14926\", \"http://purl.obolibrary.org/obo/FMA_14928\"], \"creation_date\": \"2022-06-08\", \"creator\": \"Yiing Lin\", \"creator_first_name\": \"Yiing\", \"creator_last_name\": \"Lin\", \"dimension_units\": \"millimeter\", \"placement\": {\"@context\": \"https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld\", \"@id\": \"http://purl.org/ccf/1.5/d1085194-4902-4252-95fd-faf03afd9288_placement\", \"@type\": \"SpatialPlacement\", \"placement_date\": \"2022-06-08\", \"rotation_order\": \"XYZ\", \"rotation_units\": \"degree\", \"scaling_units\": \"ratio\", \"target\": \"http://purl.org/ccf/latest/ccf.owl#VHFSmallIntestine\", \"translation_units\": \"millimeter\", \"x_rotation\": 0, \"x_scaling\": 1, \"x_translation\": 33.438, \"y_rotation\": 0, \"y_scaling\": 1, \"y_translation\": 196.307, \"z_rotation\": -37, \"z_scaling\": 1, \"z_translation\": 15.419}, \"x_dimension\": 3, \"y_dimension\": 30, \"z_dimension\": 15}", "sample_category": "block", "submission_id": "STAN0014-SI-1-1", "uuid": "c1a9f7ac0babf65af4a280846c91b7f7"}, {"contacts": [{"affiliation": "Stanford University", "first_name": "Annika", "is_contact": "TRUE", "last_name": "Weimer", "middle_name_or_initial": "", "name": "Annika Weimer", "orcid_id": "0000-0001-9944-8769", "version": "1"}, {"affiliation": "Stanford University", "first_name": "Bei", "is_contact": "TRUE", "last_name": "Wei", "middle_name_or_initial": "", "name": "Bei Wei", "orcid_id": "0000-0003-1516-8802", "version": "1"}], "contains_human_genetic_sequences": true, "contributors": [{"affiliation": "Stanford University", "first_name": "Annika", "is_contact": "TRUE", "last_name": "Weimer", "middle_name_or_initial": "", "name": "Annika Weimer", "orcid_id": "0000-0001-9944-8769", "version": "1"}, {"affiliation": "Stanford University", "first_name": "Bei", "is_contact": "TRUE", "last_name": "Wei", "middle_name_or_initial": "", "name": "Bei Wei", "orcid_id": "0000-0003-1516-8802", "version": "1"}], "created_by_user_displayname": "HuBMAP Process", "created_by_user_email": "hubmap@hubmapconsortium.org", "created_timestamp": 1665591464742, "creation_action": "Create Dataset Activity", "data_access_level": "protected", "data_types": ["snRNAseq-10xGenomics-v3"], "dataset_type": "RNAseq", "dbgap_sra_experiment_url": "https://www.ncbi.nlm.nih.gov/sra/SRX20680554", "dbgap_study_url": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002272", "description": "Colon & heart multiome snRNAseq data : B011/B011-A-501", "doi_url": "https://doi.org/10.35079/HBM439.LWSZ.467", "entity_type": "Dataset", "files": [], "group_name": "Stanford TMC", "group_uuid": "def5fd76-ed43-11e8-b56a-0e8017bdda58", "hubmap_id": "HBM439.LWSZ.467", "last_modified_timestamp": 1666795105041, "metadata": {"dag_provenance_list": [{"hash": "7a5be2c", "origin": "https://github.com/hubmapconsortium/ingest-pipeline.git"}], "extra_metadata": {"collectiontype": "generic_metadatatsv"}, "files": [], "metadata": {"acquisition_instrument_model": "NovaSeq", "acquisition_instrument_vendor": "Illumina", "analyte_class": "RNA", "assay_category": "sequence", "assay_type": "snRNAseq-10xGenomics-v3", "cell_barcode_offset": "0", "cell_barcode_read": "R1", "cell_barcode_size": "16", "contributors_path": "extras/contributors.tsv", "execution_datetime": "2021-03-18 09:30", "is_targeted": "FALSE", "is_technical_replicate": "FALSE", "library_adapter_sequence": "AGATCGGAAGAGCACACGT", "library_average_fragment_size": 475, "library_construction_protocols_io_doi": "10.17504/protocols.io.bffvjjn6", "library_final_yield_unit": "ng", "library_final_yield_value": 440, "library_id": "B011-A-501", "library_layout": "paired-end", "library_pcr_cycles": 7, "library_pcr_cycles_for_sample_index": 13, "operator": "Bei Wei, Kristina Paul", "operator_email": "wbei@stanford.edu", "pi": "Mike Snyder", "pi_email": "mpsnyder@stanford.edu", "protocols_io_doi": "10.17504/protocols.io.bvbmn2k6", "rnaseq_assay_input": 666, "rnaseq_assay_method": "10x Chromium multiome Reagent Kits", "sc_isolation_cell_number": 880000, "sc_isolation_enrichment": "none", "sc_isolation_entity": "nucleus", "sc_isolation_protocols_io_doi": "10.17504/protocols.io.6t8herw", "sc_isolation_quality_metric": "OK", "sc_isolation_tissue_dissociation": "dounce", "sequencing_phix_percent": 1, "sequencing_read_format": "28/10/10/90", "sequencing_read_percent_q30": 95.0, "sequencing_reagent_kit": "NovaSeq"}}, "provider_info": "Colon & heart multiome snRNAseq data : B011/B011-A-501", "published_timestamp": 1666795105041, "registered_doi": "10.35079/HBM439.LWSZ.467", "status": "Published", "title": "RNAseq data from the small intestine of a 54-year-old black or african american female", "uuid": "4f20058fbdca73ddbf8a0fe4e7553fca"}, {"contains_human_genetic_sequences": false, "created_by_user_displayname": "HuBMAP Process", "created_by_user_email": "hubmap@hubmapconsortium.org", "created_timestamp": 1665804514573, "creation_action": "Central Process", "data_access_level": "public", "data_types": ["salmon_sn_rnaseq_10x"], "dataset_info": "salmon_rnaseq_10x_sn__4f20058fbdca73ddbf8a0fe4e7553fca__salmon-rnaseq", "dataset_type": "RNAseq [Salmon]", "entity_type": "Dataset", "files": [{"description": "Disperson plot of gene expression", "edam_term": "EDAM_1.24.format_3508", "is_qa_qc": false, "rel_path": "dispersion_plot.pdf", "size": 754512, "type": "pdf"}, {"description": "Genome build information in JSON format", "edam_term": "EDAM_1.24.format_3464", "is_qa_qc": false, "rel_path": "genome_build.json", "size": 106, "type": "json"}, {"description": "Normalized gene expression with additional metadata, in HDF5 format, readable with the 'anndata' Python package", "edam_term": "EDAM_1.24.format_3590", "is_data_product": true, "is_qa_qc": false, "rel_path": "secondary_analysis.h5ad", "size": 91618659, "type": "h5ad"}, {"description": "Quality control report in JSON format", "edam_term": "EDAM_1.24.format_3464", "is_qa_qc": true, "rel_path": "qc_results.json", "size": 451, "type": "json"}, {"description": "scVelo RNA velocity grid plot", "edam_term": "EDAM_1.24.format_3508", "is_qa_qc": false, "rel_path": "scvelo_embedding_grid.pdf", "size": 186676, "type": "pdf"}, {"description": "RNA velocity results, in HDF5 format, readable with the 'anndata' Python package", "edam_term": "EDAM_1.24.format_3590", "is_data_product": true, "is_qa_qc": false, "rel_path": "scvelo_annotated.h5ad", "size": 33826008, "type": "h5ad"}, {"description": "UMAP plot of cells, colored by Leiden cluster ID", "edam_term": "EDAM_1.24.format_3508", "is_qa_qc": false, "rel_path": "umap_by_leiden_cluster.pdf", "size": 14683, "type": "pdf"}, {"description": "Raw gene expression, in HDF5 format, readable with the 'anndata' Python package, intronic counts as AnnData layer", "edam_term": "EDAM_1.24.format_3590", "is_data_product": true, "is_qa_qc": false, "rel_path": "expr.h5ad", "size": 38107932, "type": "h5ad"}, {"description": "UMAP plot of cells, colored by embedding density", "edam_term": "EDAM_1.24.format_3508", "is_qa_qc": false, "rel_path": "umap_embedding_density.pdf", "size": 59868, "type": "pdf"}, {"description": "Quality control results from Scanpy, per-cell and per-gene, in HDF5 format", "edam_term": "EDAM_1.24.format_3590", "is_qa_qc": true, "rel_path": "qc_results.hdf5", "size": 3047572, "type": "hdf5"}, {"description": "Raw gene expression, in HDF5 format, readable with the 'anndata' Python package, intronic counts as AnnData layer", "edam_term": "EDAM_1.24.format_3590", "is_qa_qc": false, "rel_path": "raw_expr.h5ad", "size": 23302224, "type": "h5ad"}, {"description": "FastQC report of input FASTQ file", "edam_term": "EDAM_1.24.format_2331", "is_qa_qc": true, "rel_path": "fastqc_output/Bei_CO2-8_B011-A-501-GCACTGAGAA-TTCACGCATA_S16_L003_R2_001_fastqc.html", "size": 621099, "type": "unknown"}, {"description": "FastQC report of input FASTQ file", "edam_term": "EDAM_1.24.format_2331", "is_qa_qc": true, "rel_path": "fastqc_output/Bei_CO2-8_B011-A-501-GCACTGAGAA-TTCACGCATA_S16_L001_I1_001_fastqc.html", "size": 504613, "type": "unknown"}, {"description": "FastQC report of input FASTQ file", "edam_term": "EDAM_1.24.format_2331", "is_qa_qc": true, "rel_path": "fastqc_output/Bei_CO2-8_B011-A-501-GCACTGAGAA-TTCACGCATA_S16_L001_R1_001_fastqc.html", "size": 520246, "type": "unknown"}, {"description": "FastQC report of input FASTQ file", "edam_term": "EDAM_1.24.format_2331", "is_qa_qc": true, "rel_path": 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