Schemas
module-attribute
¶
GENOME_STATUS_SCHEMA = load(f)
Schema for the genome status JSON file.
Schema Content: genome_status_schema.json
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/NPLinker/nplinker/main/src/nplinker/schemas/genome_status_schema.json",
"title": "Status of genomes",
"description": "A list of genome status objects, each of which contains information about a single genome",
"type": "object",
"required": [
"genome_status",
"version"
],
"properties": {
"genome_status": {
"type": "array",
"title": "Genome status",
"description": "A list of genome status objects",
"items": {
"type": "object",
"required": [
"original_id",
"resolved_refseq_id",
"resolve_attempted",
"bgc_path"
],
"properties": {
"original_id": {
"type": "string",
"title": "Original ID",
"description": "The original ID of the genome",
"minLength": 1
},
"resolved_refseq_id": {
"type": "string",
"title": "Resolved RefSeq ID",
"description": "The RefSeq ID that was resolved for this genome"
},
"resolve_attempted": {
"type": "boolean",
"title": "Resolve Attempted",
"description": "Whether or not an attempt was made to resolve this genome"
},
"bgc_path": {
"type": "string",
"title": "BGC Path",
"description": "The path to the downloaded BGC file for this genome"
}
}
},
"minItems": 1,
"uniqueItems": true
},
"version": {
"type": "string",
"enum": [
"1.0"
]
}
},
"additionalProperties": false
}
module-attribute
¶
GENOME_BGC_MAPPINGS_SCHEMA = load(f)
Schema for genome BGC mappings JSON file.
Schema Content: genome_bgc_mappings_schema.json
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/NPLinker/nplinker/main/src/nplinker/schemas/genome_bgc_mappings_schema.json",
"title": "Mappings from genome ID to BGC IDs",
"description": "A list of mappings from genome ID to BGC (biosynthetic gene cluster) IDs",
"type": "object",
"required": [
"mappings",
"version"
],
"properties": {
"mappings": {
"type": "array",
"title": "Mappings from genome ID to BGC IDs",
"description": "A list of mappings from genome ID to BGC IDs",
"items": {
"type": "object",
"required": [
"genome_ID",
"BGC_ID"
],
"properties": {
"genome_ID": {
"type": "string",
"title": "Genome ID",
"description": "The genome ID used in BGC database such as antiSMASH",
"minLength": 1
},
"BGC_ID": {
"type": "array",
"title": "BGC ID",
"description": "A list of BGC IDs",
"items": {
"type": "string",
"minLength": 1
},
"minItems": 1,
"uniqueItems": true
}
}
},
"minItems": 1,
"uniqueItems": true
},
"version": {
"type": "string",
"enum": [
"1.0"
]
}
},
"additionalProperties": false
}
module-attribute
¶
STRAIN_MAPPINGS_SCHEMA = load(f)
Schema for strain mappings JSON file.
Schema Content: strain_mappings_schema.json
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/NPLinker/nplinker/main/src/nplinker/schemas/strain_mappings_schema.json",
"title": "Strain mappings",
"description": "A list of mappings from strain ID to strain aliases",
"type": "object",
"required": [
"strain_mappings",
"version"
],
"properties": {
"strain_mappings": {
"type": "array",
"title": "Strain mappings",
"description": "A list of strain mappings",
"items": {
"type": "object",
"required": [
"strain_id",
"strain_alias"
],
"properties": {
"strain_id": {
"type": "string",
"title": "Strain ID",
"description": "Strain ID, which could be any strain name or accession number",
"minLength": 1
},
"strain_alias": {
"type": "array",
"title": "Strain aliases",
"description": "A list of strain aliases, which could be any names that refer to the same strain",
"items": {
"type": "string",
"minLength": 1
},
"minItems": 1,
"uniqueItems": true
}
}
},
"minItems": 1,
"uniqueItems": true
},
"version": {
"type": "string",
"enum": [
"1.0"
]
}
},
"additionalProperties": false
}
module-attribute
¶
USER_STRAINS_SCHEMA = load(f)
Schema for user strains JSON file.
Schema Content: user_strains.json
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/NPLinker/nplinker/main/src/nplinker/schemas/user_strains.json",
"title": "User specified strains",
"description": "A list of strain IDs specified by user",
"type": "object",
"required": [
"strain_ids"
],
"properties": {
"strain_ids": {
"type": "array",
"title": "Strain IDs",
"description": "A list of strain IDs specified by user. The strain IDs must be the same as the ones in the strain mappings file.",
"items": {
"type": "string",
"minLength": 1
},
"minItems": 1,
"uniqueItems": true
},
"version": {
"type": "string",
"enum": [
"1.0"
]
}
},
"additionalProperties": false
}
module-attribute
¶
PODP_ADAPTED_SCHEMA = load(f)
Schema for PODP JSON file.
The PODP JSON file is the project JSON file downloaded from PODP platform. For example, for PODP project MSV000079284, its JSON file is https://pairedomicsdata.bioinformatics.nl/api/projects/4b29ddc3-26d0-40d7-80c5-44fb6631dbf9.4.
Schema Content: podp_adapted_schema.json
{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "https://raw.githubusercontent.com/NPLinker/nplinker/main/src/nplinker/schemas/podp_adapted_schema.json",
"title": "Adapted Paired Omics Data Platform Schema for NPLinker",
"description": "This schema is adapted from PODP schema (https://pairedomicsdata.bioinformatics.nl/schema.json) for NPLinker. It's used to validate the input data for NPLinker. Thus, only required fields for NPLinker are kept in this schema, and some fields are modified to fit NPLinker's requirements.",
"type": "object",
"required": [
"version",
"metabolomics",
"genomes",
"genome_metabolome_links"
],
"properties": {
"version": {
"type": "string",
"readOnly": true,
"default": "3",
"enum": [
"3"
]
},
"metabolomics": {
"type": "object",
"title": "2. Metabolomics Information",
"description": "Please provide basic information on the publicly available metabolomics project from which paired data is available. Currently, we allow for links to mass spectrometry data deposited in GNPS-MaSSIVE or MetaboLights.",
"properties": {
"project": {
"type": "object",
"required": [
"molecular_network"
],
"title": "GNPS-MassIVE",
"properties": {
"GNPSMassIVE_ID": {
"type": "string",
"title": "GNPS-MassIVE identifier",
"description": "Please provide the GNPS-MassIVE identifier of your metabolomics data set, e.g., MSV000078839.",
"pattern": "^MSV[0-9]{9}$"
},
"MaSSIVE_URL": {
"type": "string",
"title": "Link to MassIVE upload",
"description": "Please provide the link to the MassIVE upload, e.g., <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=a507232a787243a5afd69a6c6fa1e508&view=advanced_view\">https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=a507232a787243a5afd69a6c6fa1e508&view=advanced_view</a>. Warning, there cannot be spaces in the URI.",
"format": "uri"
},
"molecular_network": {
"type": "string",
"pattern": "^[0-9a-z]{32}$",
"title": "Molecular Network Task ID",
"description": "If you have run a Molecular Network on GNPS, please provide the task ID of the Molecular Network job. It can be found in the URL of the Molecular Networking job, e.g., in <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c36f90ba29fe44c18e96db802de0c6b9\">https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c36f90ba29fe44c18e96db802de0c6b9</a> the task ID is c36f90ba29fe44c18e96db802de0c6b9."
}
}
}
},
"required": [
"project"
],
"additionalProperties": true
},
"genomes": {
"type": "array",
"title": "3. (Meta)genomics Information",
"description": "Please add all genomes and/or metagenomes for which paired data is available as separate entries.",
"items": {
"type": "object",
"required": [
"genome_ID",
"genome_label"
],
"properties": {
"genome_ID": {
"type": "object",
"title": "Genome accession",
"description": "At least one of the three identifiers is required.",
"anyOf": [
{
"required": [
"GenBank_accession"
]
},
{
"required": [
"RefSeq_accession"
]
},
{
"required": [
"JGI_Genome_ID"
]
}
],
"properties": {
"GenBank_accession": {
"type": "string",
"title": "GenBank accession number",
"description": "If the publicly available genome got a GenBank accession number assigned, e.g., <a href=\"https://www.ncbi.nlm.nih.gov/nuccore/AL645882\" target=\"_blank\" rel=\"noopener noreferrer\">AL645882</a>, please provide it here. The genome sequence must be submitted to GenBank/ENA/DDBJ (and an accession number must be received) before this form can be filled out. In case of a whole genome sequence, please use master records. At least one identifier must be entered.",
"minLength": 1
},
"RefSeq_accession": {
"type": "string",
"title": "RefSeq accession number",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/NC_003888.3\">NC_003888.3</a>",
"minLength": 1
},
"JGI_Genome_ID": {
"type": "string",
"title": "JGI IMG genome ID",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641228474\">641228474</a>",
"minLength": 1
}
}
},
"genome_label": {
"type": "string",
"title": "Genome label",
"description": "Please assign a unique Genome Label for this genome or metagenome to help you recall it during the linking step. For example 'Streptomyces sp. CNB091'",
"minLength": 1
}
}
},
"minItems": 1
},
"genome_metabolome_links": {
"type": "array",
"title": "6. Genome - Proteome - Metabolome Links",
"description": "Create a linked pair by selecting the Genome Label and optional Proteome label as provided earlier. Subsequently links to the metabolomics data file belonging to that genome/proteome with appropriate experimental methods.",
"items": {
"type": "object",
"required": [
"genome_label",
"metabolomics_file"
],
"properties": {
"genome_label": {
"type": "string",
"title": "Genome/Metagenome",
"description": "Please select the Genome Label to be linked to a metabolomics data file."
},
"metabolomics_file": {
"type": "string",
"title": "Location of metabolomics data file",
"description": "Please provide a direct link to the metabolomics data file location, e.g. <a href=\"ftp://massive.ucsd.edu/MSV000078839/spectrum/R5/CNB091_R5_M.mzXML\" target=\"_blank\" rel=\"noopener noreferrer\">ftp://massive.ucsd.edu/MSV000078839/spectrum/R5/CNB091_R5_M.mzXML</a> found in the FTP download of a MassIVE dataset or <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ebi.ac.uk/metabolights/MTBLS307/files/Urine_44_fullscan1_pos.mzXML\">https://www.ebi.ac.uk/metabolights/MTBLS307/files/Urine_44_fullscan1_pos.mzXML</a> found in the Files section of a MetaboLights study. Warning, there cannot be spaces in the URI.",
"format": "uri"
}
},
"additionalProperties": true
},
"minItems": 1
}
},
"additionalProperties": true
}
validate_podp_json(json_data: dict) -> None
Validate JSON data against the PODP JSON schema.
All validation error messages are collected and raised as a single ValueError.
Parameters:
-
json_data(dict) –The JSON data to validate.
Raises:
-
ValueError–If the JSON data does not match the schema.
Examples:
Download PODP JSON file for project MSV000079284 from
https://pairedomicsdata.bioinformatics.nl/api/projects/4b29ddc3-26d0-40d7-80c5-44fb6631dbf9.4
and save it as podp_project.json.
Validate it:
>>> with open(podp_project.json, "r") as f:
... json_data = json.load(f)
>>> validate_podp_json(json_data)