Converts HCA pre-ingest JSON to ENA XML and packages it as a zip.
Tests take an example output, generates ENA XML files and validates each against ENA schemas. The XML files are then packaged into a zip file.
handler.py ./examples/metadata_spleen_v5_20180313_userFriendlyHeaders.json
Will create a directory in /tmp containing the XML and a corresponding ZIP of the directory.
serverless invoke local --function convert --path ./examples/metadata_spleen_v5_20180313_userFriendlyHeaders.json
The code is also deployed as a AWS Lambda with a HTTP endpoint.
curl -X POST \
https://n8b51jauvh.execute-api.us-east-1.amazonaws.com/dev/convert \
-H 'Accept: application/zip' \
-H 'Cache-Control: no-cache' \
-H 'Content-Type: application/json' \
-d '[ {
"schema_type" : "project",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/project/5.0.1/project",
"schema_version" : "5.0.1",
"schema_type" : "project",
"project_core" : {
"project_shortname" : "Tissue_stability",
"project_title" : "Testing ischaemic sensitivity of human tissue using single cell RNA seq",
"project_description" : "Assessment of ischaemic sensitivity of three human tissues using 10x 3'\'' single cell RNA sequencing - this submission is ONLY for the first spleen sample; further samples to be collected. Ultimately we aim to collect data from three tissues expected to have different sensitivity to ischaemia: spleen (expected least sensitive), oesophagus (in the middle) and liver (expected most sensitive). Samples will be collected '\''fresh'\'' (ie as soon as possible) and at 12h, 24h and 72h post onset of ischaemia in the donor. Single cell RNA sequencing data will be generated at each time point using the 10x genomics single cell 3'\'' method.",
"describedBy" : "https://schema.humancellatlas.org/core/project/5.0.0/project_core",
"schema_version" : "5.0.0"
},
"supplementary_files" : [ "Experimental_report.docx", "Human_spleen_dissociation_protocol.pdf", "Clinical_metadata.xlsx", "284C_IMAGE_spleen_annotated.jpeg", "10x_protocol.pdf" ]
} ]
}, {
"schema_type" : "biomaterial",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/donor_organism",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "284C-A1",
"biomaterial_name" : "284C-spleen",
"biomaterial_description" : "Spleen",
"ncbi_taxon_id" : [ 9606 ],
"supplementary_files" : [ "Clinical_metadata.xlsx" ],
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"death" : {
"cause_of_death" : "Hypoxic brain damage",
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/death"
},
"medical_history" : {
"alcohol_history" : "3-6 units/day",
"smoking_history" : "Smoker, 20/day for 25 years, stopped 2000",
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/medical_history"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"organism_age" : "55-60",
"organism_age_unit" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/time_unit_ontology",
"text" : "year"
},
"development_stage" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/development_stage_ontology",
"text" : "adult"
},
"disease" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/disease_ontology",
"text" : "normal"
} ],
"height" : "1.75-1.8",
"height_unit" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/length_unit_ontology",
"text" : "meter"
},
"is_living" : false,
"biological_sex" : "male",
"weight" : "80-85",
"weight_unit" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/mass_unit_ontology",
"text" : "kg"
}
} ],
"links" : [ {
"source_type" : "biomaterial",
"source_id" : "284C-A1",
"destination_type" : "process",
"destination_ids" : [ "" ]
} ]
}, {
"schema_type" : "biomaterial",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/specimen_from_organism",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL5",
"biomaterial_name" : "284C_spleen_fresh",
"biomaterial_description" : "fresh spleen",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "284C-A1",
"supplementary_files" : [ "284C_IMAGE_spleen_annotated.jpeg" ],
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"organ" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_ontology",
"text" : "spleen"
},
"organ_part" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_part_ontology",
"text" : "spleen"
},
"state_of_specimen" : {
"gross_image" : [ "284C_IMAGE_spleen_annotated.jpg" ],
"ischemic_time" : 7200,
"postmortem_interval" : 19800,
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/state_of_specimen"
}
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/specimen_from_organism",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL6",
"biomaterial_name" : "284C_spleen_12h",
"biomaterial_description" : "spleen at 12h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "284C-A1",
"supplementary_files" : [ "284C_IMAGE_spleen_annotated.jpeg" ],
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"organ" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_ontology",
"text" : "spleen"
},
"organ_part" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_part_ontology",
"text" : "spleen"
},
"state_of_specimen" : {
"gross_image" : [ "284C_IMAGE_spleen_annotated.jpg" ],
"ischemic_time" : 43200,
"postmortem_interval" : 54300,
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/state_of_specimen"
}
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/specimen_from_organism",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL7",
"biomaterial_name" : "284C_spleen_24h",
"biomaterial_description" : "spleen at 24h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "284C-A1",
"supplementary_files" : [ "284C_IMAGE_spleen_annotated.jpeg" ],
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"organ" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_ontology",
"text" : "spleen"
},
"organ_part" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_part_ontology",
"text" : "spleen"
},
"state_of_specimen" : {
"gross_image" : [ "284C_IMAGE_spleen_annotated.jpg" ],
"ischemic_time" : 86400,
"postmortem_interval" : 97200,
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/state_of_specimen"
}
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/specimen_from_organism",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL8",
"biomaterial_name" : "284C_spleen_72h",
"biomaterial_description" : "spleen at 72h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "284C-A1",
"supplementary_files" : [ "284C_IMAGE_spleen_annotated.jpeg" ],
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"organ" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_ontology",
"text" : "spleen"
},
"organ_part" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/organ_part_ontology",
"text" : "spleen"
},
"state_of_specimen" : {
"gross_image" : [ "284C_IMAGE_spleen_annotated.jpg" ],
"ischemic_time" : 259200,
"postmortem_interval" : 269100,
"describedBy" : "https://schema.humancellatlas.org/module/biomaterial/5.0.0/state_of_specimen"
}
} ],
"links" : [ {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL5",
"destination_type" : "organ",
"destination_ids" : [ "UBERON:0002106" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL5",
"destination_type" : "process",
"destination_ids" : [ "enrichment_process_1" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL6",
"destination_type" : "organ",
"destination_ids" : [ "UBERON:0002106" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL6",
"destination_type" : "process",
"destination_ids" : [ "enrichment_process_1" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL7",
"destination_type" : "organ",
"destination_ids" : [ "UBERON:0002106" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL7",
"destination_type" : "process",
"destination_ids" : [ "enrichment_process_1" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL8",
"destination_type" : "organ",
"destination_ids" : [ "UBERON:0002106" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL8",
"destination_type" : "process",
"destination_ids" : [ "enrichment_process_1" ]
} ]
}, {
"schema_type" : "biomaterial",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/cell_suspension",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL5_cells",
"biomaterial_name" : "cells from fresh spleen",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "A1-Spl-0-TL5",
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"total_estimated_cells" : 39300000
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/cell_suspension",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL6_cells",
"biomaterial_name" : "cells from spleen at 12h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "A1-Spl-0-TL6",
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"total_estimated_cells" : 25200000
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/cell_suspension",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL7_cells",
"biomaterial_name" : "cells from spleen at 24h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "A1-Spl-0-TL7",
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"total_estimated_cells" : 65240000
}, {
"describedBy" : "https://schema.humancellatlas.org/type/biomaterial/5.0.0/cell_suspension",
"schema_version" : "5.0.0",
"schema_type" : "biomaterial",
"biomaterial_core" : {
"biomaterial_id" : "A1-Spl-0-TL8_cells",
"biomaterial_name" : "cells from spleen at 72h ischaemic time",
"ncbi_taxon_id" : [ 9606 ],
"has_input_biomaterial" : "A1-Spl-0-TL8",
"describedBy" : "https://schema.humancellatlas.org/core/biomaterial/5.0.0/biomaterial_core",
"schema_version" : "5.0.0"
},
"genus_species" : [ {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/species_ontology",
"text" : "Homo sapiens"
} ],
"total_estimated_cells" : 39250000
} ],
"links" : [ {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL5_cells",
"destination_type" : "process",
"destination_ids" : [ "" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL6_cells",
"destination_type" : "process",
"destination_ids" : [ "" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL7_cells",
"destination_type" : "process",
"destination_ids" : [ "" ]
}, {
"source_type" : "biomaterial",
"source_id" : "A1-Spl-0-TL8_cells",
"destination_type" : "process",
"destination_ids" : [ "" ]
} ]
}, {
"schema_type" : "process",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.0.0/dissociation_process",
"schema_version" : "5.0.0",
"schema_type" : "process",
"process_core" : {
"process_id" : "dissociation_process_1",
"process_name" : "Dissociation of spleen tissue sample into cell suspension",
"describedBy" : "https://schema.humancellatlas.org/core/process/5.0.0/process_core",
"schema_version" : "5.0.0"
},
"dissociation_method" : "mechanical",
"nucleic_acid_source" : "single cell"
} ],
"links" : [ {
"source_type" : "process",
"source_id" : "dissociation_process_1",
"destination_type" : "protocol",
"destination_ids" : [ "Human_spleen_dissociation_protocol" ]
} ]
}, {
"schema_type" : "process",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.0.0/enrichment_process",
"schema_version" : "5.0.0",
"schema_type" : "process",
"process_core" : {
"process_id" : "enrichment_process_1",
"process_name" : "Enrichment for live cells",
"describedBy" : "https://schema.humancellatlas.org/core/process/5.0.0/process_core",
"schema_version" : "5.0.0"
},
"enrichment_method" : "MACS",
"markers" : "LiveCells"
} ],
"links" : [ {
"source_type" : "process",
"source_id" : "enrichment_process_1",
"destination_type" : "protocol",
"destination_ids" : [ "Human_spleen_dissociation_protocol" ]
} ]
}, {
"schema_type" : "process",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/process/sequencing/5.0.0/library_preparation_process",
"schema_version" : "5.0.0",
"schema_type" : "process",
"process_core" : {
"process_id" : "library_preparation_process_1",
"describedBy" : "https://schema.humancellatlas.org/core/process/5.0.0/process_core",
"schema_version" : "5.0.0"
},
"input_nucleic_acid_molecule" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/biological_macromolecule_ontology",
"text" : "polyA RNA"
},
"library_construction_approach" : "10x_v2",
"end_bias" : "3 prime tag",
"strand" : "second"
} ],
"links" : [ {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "cell",
"destination_ids" : [ "Read 1" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "cell",
"destination_ids" : [ "0" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "cell",
"destination_ids" : [ "16" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "umi",
"destination_ids" : [ "Read 1" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "umi",
"destination_ids" : [ "16" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "umi",
"destination_ids" : [ "10" ]
}, {
"source_type" : "process",
"source_id" : "library_preparation_process_1",
"destination_type" : "protocol",
"destination_ids" : [ "10x_sequencing_protocol" ]
} ]
}, {
"schema_type" : "process",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/process/sequencing/5.0.0/sequencing_process",
"schema_version" : "5.0.0",
"schema_type" : "process",
"process_core" : {
"process_id" : "sequencing_process_1",
"process_name" : "10x_v2 sequencing",
"describedBy" : "https://schema.humancellatlas.org/core/process/5.0.0/process_core",
"schema_version" : "5.0.0"
},
"instrument_manufacturer_model" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/instrument_ontology",
"text" : "Illumina HiSeq 4000"
},
"paired_ends" : true
} ],
"links" : [ {
"source_type" : "process",
"source_id" : "sequencing_process_1",
"destination_type" : "protocol",
"destination_ids" : [ "10x_sequencing_protocol" ]
} ]
}, {
"schema_type" : "protocol",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/protocol/5.0.0/protocol",
"schema_version" : "5.0.0",
"schema_type" : "protocol",
"protocol_core" : {
"protocol_id" : "Human_spleen_dissociation_protocol",
"protocol_name" : "Spleen dissociation protocol",
"document" : "Human_spleen_dissociation_protocol.pdf",
"describedBy" : "https://schema.humancellatlas.org/core/protocol/5.0.0/protocol_core",
"schema_version" : "5.0.0"
},
"protocol_type" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/protocol_type_ontology",
"text" : "EFO:0003809"
}
}, {
"describedBy" : "https://schema.humancellatlas.org/type/protocol/5.0.0/protocol",
"schema_version" : "5.0.0",
"schema_type" : "protocol",
"protocol_core" : {
"protocol_id" : "10x_sequencing_protocol",
"protocol_name" : "10X Genomics protocol - including loading single cells and library prep",
"protocol_description" : "ChromiumTM Single Cell 3'\'' Library & Gel Bead Kit v2",
"document" : "10x_protocol.pdf",
"describedBy" : "https://schema.humancellatlas.org/core/protocol/5.0.0/protocol_core",
"schema_version" : "5.0.0"
},
"protocol_type" : {
"describedBy" : "https://schema.humancellatlas.org/module/ontology/5.0.0/protocol_type_ontology",
"text" : "EFO:0007832"
}
} ]
}, {
"schema_type" : "file",
"content" : [ {
"describedBy" : "https://schema.humancellatlas.org/type/file/5.0.0/sequence_file",
"schema_version" : "5.0.0",
"schema_type" : "file",
"file_core" : {
"file_name" : "HCATisStabAug177078016_S1_L001_I1_001.fastq.gz",
"file_format" : "fastq.gz",
"describedBy" : "https://schema.humancellatlas.org/core/file/5.0.0/file_core",
"schema_version" : "5.0.0"
},
"read_index" : "index1",
"lane_index" : 1
}, {
"describedBy" : "https://schema.humancellatlas.org/type/file/5.0.0/sequence_file",
"schema_version" : "5.0.0",
"schema_type" : "file",
"file_core" : {
"file_name" : "HCATisStabAug177078016_S1_L001_R1_001.fastq.gz",
"file_format" : "fastq.gz",
"describedBy" : "https://schema.humancellatlas.org/core/file/5.0.0/file_core",
"schema_version" : "5.0.0"
},
"read_index" : "read1",
"lane_index" : 1
}, {
"describedBy" : "https://schema.humancellatlas.org/type/file/5.0.0/sequence_file",
"schema_version" : "5.0.0",
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