From 1e1a4051d9ae2626d36797132e5700149d7db4ac Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Wed, 31 Jan 2024 15:10:07 +0100 Subject: [PATCH 1/9] Update submission schema --- CHANGELOG.md | 1 + preClinVar/resources/submission_schema.json | 1442 +++++++++-------- .../submission_schema_before_221121.json | 1024 ------------ 3 files changed, 751 insertions(+), 1716 deletions(-) delete mode 100644 preClinVar/resources/submission_schema_before_221121.json diff --git a/CHANGELOG.md b/CHANGELOG.md index ff5cee7..e2d83d1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,7 @@ ## [unreleased] ### Changed - Updated version of external images in GitHub actions +- Updated API submission schema to the latest ### Fixed - Bump certifi from 2022.12.7 to 2023.7.22 - Description of the response returned by dry run endpoint in README file diff --git a/preClinVar/resources/submission_schema.json b/preClinVar/resources/submission_schema.json index 98babcd..6a2f149 100644 --- a/preClinVar/resources/submission_schema.json +++ b/preClinVar/resources/submission_schema.json @@ -1,17 +1,64 @@ { "$schema": "http://json-schema.org/draft-07/schema#", "type": "object", - "anyOf": [ - {"required": ["clinvarSubmission"]}, - {"required": ["clinvarDeletion"]} - ], "properties": { + "assertionCriteria": { + "type": "object", + "description": "\"Assertion criteria\" refers to documentation of the criteria that your organization uses to classify variants. It can be provided as a database identifier, like a PubMed ID, or a file that is submitted to ClinVar, but not both. Only one document may be provided for assertion criteria. These fields are equivalent to the \"Assertion method citation\" column in the spreadsheet. Note that only one single assertion criteria (a citation or an electronic document) may be provided for a submission. This assertion criteria will be applied to all interpretations in the submission. For assertion criteria submitted as a database identifier, an assertion criteria name will be calculated based on the citation details. For assertion criteria submitted as a file, you may provide an assertion criteria name during file upload on your Organization page in Submission Portal.", + "properties": { + "db": { + "type": "string", + "enum": [ + "PubMed", + "DOI", + "pmc" + ] + }, + "id": { + "type": "string", + "description": "The document identifier. Formats are: \nPubMed: the PubMed ID, digits only, e.g. 10862036\npmc: the PubMedCentral ID, digits only, e.g. 2746682\nDOI: the full DOI including prefix, forward slash, and suffix, e.g. 10.1038/gim.2015.30", + "errors": { + "pattern": "The identifier value is considered an invalid citation. Please provide only one identifier as the citation for your assertion criteria." + }, + "pattern": "^[^;]+$" + }, + "url": { + "type": "string", + "description": " The URL for a file that you have already submitted to ClinVar as assertion criteria. If you need to find this URL or if you need to submit new assertion criteria, please go to the \"View/add assertion criteria files\" tab on your Organization page in Submission Portal.", + "errors": { + "pattern": "The URL for assertion criteria must be the URL provided by ClinVar. If you need to find this URL or if you need to submit new assertion criteria, Please go to the \"View/add assertion criteria files\" tab on your Organization page in Submission Portal." + }, + "pattern": "^https://[qd]?submit.ncbi.nlm.nih.gov/(api/2.0/files|ft/byid)/.*" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "url" + ] + }, + { + "required": [ + "db", + "id" + ] + } + ] + }, + "behalfOrgID": { + "type": "integer", + "description": "Optional. When submitting on behalf of another organization, this specifies the other organization's ID", + "minimum": 1 + }, "clinvarDeletion": { "type": "object", "items": { "type": "object", "title": "ClinVar Deletions", - "required": ["accessionSet"], + "required": [ + "accessionSet" + ], "properties": { "accessionSet": { "type": "array", @@ -20,12 +67,14 @@ "items": { "type": "object", "title": "Clinvar accession and reason for deleting", - "required": ["accession"], + "required": [ + "accession" + ], "properties": { "accession": { "type": "string", - "pattern": "^SCV[0123456789]{9}$", - "description": "The SCV accession for your submitted record to delete (not the RCV or the VCV)." + "description": "The SCV accession for your submitted record to delete (not the RCV or the VCV), e.g. SCV000123456.", + "pattern": "^SCV[0123456789]{9}$" }, "reason": { "type": "string", @@ -42,66 +91,28 @@ "title": "ClinVar Submission Set", "minItems": 1, "maxItems": 10000, - "items": - { - "type": "object", - "title": "ClinVar Submission", - "description": "Submissions to ClinVar are considered 'variant-level' (not case-level or patient-specific), because they are focused on the variant or set of variants that was interpreted. One of variantSet, haplotypeSet, haplotypeSingleVariantSet, phaseUnknownSet, distinctChromosomesSet, diplotypeSet, compoundHeterozygoteSet is required to define the variant or set of variants that was interpreted.", - "required": [ - "recordStatus", - "clinicalSignificance", - "observedIn", - "conditionSet" - ], - "oneOf": [ - { - "required": [ - "variantSet" - ] - }, - { - "required": [ - "haplotypeSet" - ] - }, - { - "required": [ - "haplotypeSingleVariantSet" - ] - }, - { - "required": [ - "phaseUnknownSet" - ] - }, - { - "required": [ - "distinctChromosomesSet" - ] - }, - { - "required": [ - "diplotypeSet" - ] - }, - { - "required": [ - "compoundHeterozygoteSet" - ] - } - ], - "properties": { - "clinicalSignificance": { - "type": "object", - "description": "Clinical significance", - "required": [ - "clinicalSignificanceDescription" - ], - "properties": { - "citation": { + "items": { + "type": "object", + "title": "ClinVar Submission", + "description": "Submissions to ClinVar are considered 'variant-level' (not case-level or patient-specific), because they are focused on the variant or set of variants that was interpreted. One of variantSet, haplotypeSet, haplotypeSingleVariantSet, phaseUnknownSet, distinctChromosomesSet, diplotypeSet, compoundHeterozygoteSet is required to define the variant or set of variants that was interpreted.", + "required": [ + "recordStatus", + "clinicalSignificance", + "observedIn", + "conditionSet" + ], + "properties": { + "clinicalSignificance": { + "type": "object", + "description": "Clinical significance", + "required": [ + "clinicalSignificanceDescription" + ], + "properties": { + "citation": { "type": "array", - "items": - { + "minItems": 1, + "items": { "type": "object", "description": "Citations that were used by the submitter to evaluate the clinical significance of the variant. More than one citation may be provided. Each citation can be provided as a database identifier, like a PubMed ID, or a URL, but not both.", "properties": { @@ -115,7 +126,8 @@ ] }, "id": { - "type": "string" + "type": "string", + "description": "The document identifier. Formats are: \nPubMed: the PubMed ID, digits only, e.g. 10862036\npmc: the PubMedCentral ID, digits only, e.g. 2746682\nDOI: the full DOI including prefix, forward slash, and suffix, e.g. 10.1038/gim.2015.30\nBookShelf: the Bookshelf ID including the prefix, e.g. NBK1384" }, "url": { "type": "string" @@ -129,316 +141,379 @@ "id" ] }, - { + { "required": [ "url" ] - } ] - }}, - "clinicalSignificanceDescription": { + } + }, + "clinicalSignificanceDescription": { + "type": "string", + "description": "The interpretation, or clinical significance, of the variant for the submitted condition, equivalent to Clinical significance in the submission spreadsheet.", + "enum": [ + "Pathogenic", + "Likely pathogenic", + "Uncertain significance", + "Likely benign", + "Benign", + "Pathogenic, low penetrance", + "Uncertain risk allele", + "Likely pathogenic, low penetrance", + "Established risk allele", + "Likely risk allele", + "affects", + "association", + "drug response", + "confers sensitivity", + "protective", + "other", + "not provided" + ] + }, + "comment": { + "type": "string", + "description": "Optional, but highly encouraged. Free text describing the rationale for the clinical significance." + }, + "customAssertionScore": { + "type": "number", + "description": "The final score, or point value, calculated when the assertion method uses a point-based scoring system, e.g. ACMG/ClinGen CNV Guidelines, 2019 (PMID: 31690835). The assertion method must also be provided. " + }, + "dateLastEvaluated": { + "type": "string", + "description": "The date that the clinical significance was last evaluated by the submitter (not the date the phenotype of the patient was evaluated), equivalent to Date last evaluated in the submission spreadsheet. Use the format yyyy-mm-dd. If only month/year is known, use the first day of the month. If only year is known, use Jan. 1.", + "pattern": "^[1-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]$" + }, + "explanationOfDrugResponse": { + "type": "string", + "description": "Required for a record with clinical significance of 'drug response'. Please provide a value describing the drug response, e.g. 'likely responsive'. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + }, + "explanationOfOtherClinicalSignificance": { + "type": "string", + "description": "Required if 'other' is selected for clinical significance. Please provide the new value for clinical significance, e.g. pseudodeficiency allele. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + }, + "modeOfInheritance": { + "type": "string", + "description": "The mode of inheritance specific to the variant-disease pair, not generally for the disease.", + "enum": [ + "Autosomal dominant inheritance", + "Autosomal recessive inheritance", + "Mitochondrial inheritance", + "Genetic anticipation", + "Sporadic", + "Sex-limited autosomal dominant", + "X-linked recessive inheritance", + "X-linked dominant inheritance", + "Y-linked inheritance", + "Other", + "X-linked inheritance", + "Codominant", + "Semidominant inheritance", + "Autosomal unknown", + "Autosomal dominant inheritance with maternal imprinting", + "Autosomal dominant inheritance with paternal imprinting", + "Multifactorial inheritance", + "Unknown mechanism", + "Oligogenic inheritance" + ] + } + }, + "additionalProperties": false + }, + "clinvarAccession": { + "type": "string", + "description": "Required for updated records and for novel records if accession numbers were reserved. Provide the SCV number for your submitted record (not the RCV number), e.g. SCV000123456." + }, + "compoundHeterozygoteSet": { + "$ref": "#/definitions/compoundHeterozygoteSetType" + }, + "conditionSet": { + "type": "object", + "description": "The condition for which the variant is interpreted. Detailed information about reporting condition is available at https://www.ncbi.nlm.nih.gov/clinvar/docs/faq_submitters/#pheno If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records. i.e. this variant causes condition A in some individuals and causes disease B in other individuals. Provide only one name or identifier for a condition; do not provide multiple names or identifiers for the same condition.", + "properties": { + "condition": { + "description": "The condition must be provided as either a database identifier or a name, but not both. A database identifier is preferred by ClinVar; a name should be provided only if there is no database identifier available.", + "$ref": "#/definitions/conditionType" + }, + "drugResponse": { + "description": "The drug Response evaluated specified by database ID or drug name, but not both", + "$ref": "#/definitions/drugResponseType" + }, + "multipleConditionExplanation": { + "type": "string", + "description": "Variants in ClinVar are typically classified for a single condition (disease or drug response). If more than one condition is provided in the conditionSet, this field is required and explains why multiple conditions are valid. Options are \"Novel disease\" when a new disease is unnamed and only described by a set of clinical features (HPO ids); \"Uncertain\" when a variant is classified for several related diseases and it may be uncertain whether the variant causes one or several of them; and \"Co-occurring\" when a variant causes more than one disease in the same individual (this is expected to be rare).", + "enum": [ + "Novel disease", + "Uncertain", + "Co-occurring" + ] + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "condition" + ] + }, + { + "allOf": [ + { + "required": [ + "drugResponse" + ] + }, + { + "not": { + "required": [ + "multipleConditionExplanation" + ] + } + } + ] + } + ] + }, + "diplotypeSet": { + "$ref": "#/definitions/diplotypeSetType" + }, + "distinctChromosomesSet": { + "$ref": "#/definitions/distinctChromosomesSetType" + }, + "haplotypeSet": { + "$ref": "#/definitions/haplotypeSetType" + }, + "haplotypeSingleVariantSet": { + "$ref": "#/definitions/haplotypeSingleVariantSetType" + }, + "localID": { + "type": "string", + "description": "Optional, but highly recommended. The stable unique identifier your organization uses to identifiy this variant. This identifier will be public so should not include protected health information." + }, + "localKey": { + "type": "string", + "description": "Your unique local identifier for the variant-condition pair, equivalent to the Linking ID in the submission spreadsheet." + }, + "observedIn": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "required": [ + "alleleOrigin", + "affectedStatus", + "collectionMethod" + ], + "properties": { + "affectedStatus": { "type": "string", - "description": "The interpretation, or clinical significance, of the variant for the submitted condition, equivalent to Clinical significance in the submission spreadsheet.", + "description": "Indicates whether or not the individual(s) in each observation were affected by the condition for the interpretation", "enum": [ - "Pathogenic", - "Likely pathogenic", - "Uncertain significance", - "Likely benign", - "Benign", - "Pathogenic, low penetrance", - "Uncertain risk allele", - "Likely pathogenic, low penetrance", - "Established risk allele", - "Likely risk allele", - "affects", - "association", - "drug response", - "confers sensitivity", - "protective", - "other", - "not provided" + "yes", + "no", + "unknown", + "not provided", + "not applicable" ] }, - "comment": { + "alleleOrigin": { "type": "string", - "description": "Optional, but highly encouraged. Free text describing the rationale for the clinical significance." + "description": "The genetic origin of the variant for individuals in each aggregate observation. For de novo variants, please indicate 'de novo', not the origin of the chromosome.", + "enum": [ + "germline", + "somatic", + "de novo", + "unknown", + "inherited", + "maternal", + "paternal", + "biparental", + "not applicable" + ] + }, + "clinicalFeatures": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "description": "Clinical features that were observed by the submitter in an individual with the variant. More than one feature may be provided. Each clinical feature may be described by a database identifier or by a name, but not both. These fields are equivalent to the \"Clinical features\" column in the spreadsheet.", + "required": [ + "clinicalFeaturesAffectedStatus" + ], + "properties": { + "clinicalFeaturesAffectedStatus": { + "type": "string", + "description": "To indicate whether each clinical feature was present, absent, or not tested in the individual(s) observed. ", + "enum": [ + "present", + "absent", + "not tested" + ] + }, + "db": { + "type": "string", + "enum": [ + "HP" + ] + }, + "id": { + "type": "string", + "description": "The HPO identifier including the prefix, e.g. HP:0000815" + }, + "name": { + "type": "string" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "name" + ] + } + ] + } }, - "dateLastEvaluated": { + "clinicalFeaturesComment": { "type": "string", - "pattern": "^[1-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]$", - "description": "The date that the clinical significance was last evaluated by the submitter (not the date the phenotype of the patient was evaluated), equivalent to Date last evaluated in the submission spreadsheet. Use the format yyyy-mm-dd. If only month/year is known, use the first day of the month. If only year is known, use Jan. 1." + "description": "To provide a free text explanation of clinical features provided in the previous column, e.g. to describe the progression of disease or diagnosis. Please use this comment to expand on the information in 'clinicalFeatures'" }, - "modeOfInheritance": { + "collectionMethod": { "type": "string", - "description": "The mode of inheritance specific to the variant-disease pair, not generally for the disease.", + "description": "The method used to collect the data for each observation, e.g. clinical testing or research. See https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#collection", "enum": [ - "Autosomal dominant inheritance", - "Autosomal recessive inheritance", - "Mitochondrial inheritance", - "Somatic mutation", - "Genetic anticipation", - "Sporadic", - "Sex-limited autosomal dominant", - "X-linked recessive inheritance", - "X-linked dominant inheritance", - "Y-linked inheritance", - "Other", - "X-linked inheritance", - "Codominant", - "Semidominant inheritance", - "Autosomal unknown", - "Autosomal dominant inheritance with maternal imprinting", - "Autosomal dominant inheritance with paternal imprinting", - "Multifactorial inheritance", - "Unknown mechanism", - "Oligogenic inheritance" + "curation", + "literature only", + "reference population", + "provider interpretation", + "phenotyping only", + "case-control", + "clinical testing", + "in vitro", + "in vivo", + "research", + "not provided" ] }, - "customAssertionScore": { - "type": "number", - "description": "The final score, or point value, calculated when the assertion method uses a point-based scoring system, e.g. ACMG/ClinGen CNV Guidelines, 2019 (PMID: 31690835). The assertion method must also be provided. " - }, - "explanationOfDrugResponse": { - "type": "string", - "description": "Required for a record with clinical significance of 'drug response'. Please provide a value describing the drug response, e.g. 'likely responsive'. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + "numberOfIndividuals": { + "type": "integer", + "description": "The total number of individuals with the variant observed by the submitter.", + "minimum": 0 }, - "explanationOfOtherClinicalSignificance": { + "structVarMethodType": { "type": "string", - "description": "Required if 'other' is selected for clinical significance. Please provide the new value for clinical significance, e.g. pseudodeficiency allele. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + "description": "The method and type of analysis used to identify a structural variant, i.e. any variant >50 nt, equivalent to \"Structural variant method/analysis type\" in the submission spreadsheet. Allowed values are enumerated in the schema. Although optional in the JSON, this field is required for variants that are >50 nt (and in scope for dbVar).", + "enum": [ + "SNP array", + "Oligo array", + "Read depth", + "Paired-end mapping", + "One end anchored assembly", + "Sequence alignment", + "Optical mapping", + "Curated,PCR" + ] } }, "additionalProperties": false - }, - "clinvarAccession": { - "type": "string", - "description": "Required for updated records and for novel records if accession numbers were reserved. Provide the SCV number for your submitted record (not the RCV number). For novel records without reserved accessions: the SCV accession number will be returned to you after your submission file is processed. You should provide that accession number back to ClinVar when you update your SCV record. " - }, + } + }, + "phaseUnknownSet": { + "$ref": "#/definitions/phaseUnknownSetType" + }, + "recordStatus": { + "type": "string", + "description": "If you include SCV accessions for 'clinvarAccession', you must indicate whether each record is novel (and accessions were reserved prior to submission) or is an update to an existing SCV record.", + "enum": [ + "novel", + "update" + ] + }, + "variantSet": { + "$ref": "#/definitions/variantSetType" + } + }, + "additionalProperties": false, + "else": { + "properties": { "conditionSet": { - "type": "object", - "description": "The condition for which the variant is interpreted. Detailed information about reporting condition is available at https://www.ncbi.nlm.nih.gov/clinvar/docs/faq_submitters/#pheno If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records. i.e. this variant causes condition A in some individuals and causes disease B in other individuals. Provide only one name or identifier for a condition; do not provide multiple names or identifiers for the same condition.", - "oneOf": [ - { - "required": ["condition"] - }, - { - "required": ["drugResponse"] - } + "required": [ + "condition" ], + "errors": { + "required": "conditionSet.drugResponse is allowed only when clinicalSignificanceDescription is \"drug response\"" + } + } + } + }, + "if": { + "properties": { + "clinicalSignificance": { "properties": { - "condition": { - "description": "The condition must be provided as either a database identifier or a name, but not both. A database identifier is preferred by ClinVar; a name should be provided only if there is no database identifier available.", - "$ref": "#/definitions/conditionType" - }, - "drugResponse": { - "description": "The drug Response evaluated specified by database ID or drug name, but not both", - "$ref": "#/definitions/drugResponseType" - } - }, - "additionalProperties": false - }, - "localID": { - "type": "string", - "description": "Optional, but highly recommended. The stable unique identifier your organization uses to identifiy this variant. This identifier will be public so should not include protected health information." - }, - "localKey": { - "type": "string", - "description": "Your unique local identifier for the variant-condition pair, equivalent to the Linking ID in the submission spreadsheet." - }, - "observedIn": { - "type": "array", - "minItems": 1, - "items": - { - "type": "object", - "required": [ - "alleleOrigin", - "affectedStatus", - "collectionMethod" - - ], - "properties": { - "affectedStatus": { - "type": "string", - "description": "Indicates whether or not the individual(s) in each observation were affected by the condition for the interpretation", - "enum": [ - "yes", - "no", - "unknown", - "not provided", - "not applicable" - ] - }, - "alleleOrigin": { - "type": "string", - "description": "The genetic origin of the variant for individuals in each aggregate observation. For de novo variants, please indicate 'de novo', not the origin of the chromosome.", - "enum": [ - "germline", - "somatic", - "de novo", - "unknown", - "inherited", - "maternal", - "paternal", - "biparental", - "not applicable" - ] - }, - "clinicalFeatures": { - "type": "array", - "items": - { - "type": "object", - "description": "Clinical features that were observed by the submitter in an individual with the variant. More than one feature may be provided. Each clinical feature may be described by a database identifier or by a name, but not both. These fields are equivalent to the \"Clinical features\" column in the spreadsheet.", - "properties": { - "db": { - "type": "string", - "enum": [ - "HP" - ] - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - }, - "clinicalFeaturesAffectedStatus": { - "type": "string", - "description": "To indicate whether each clinical feature was present, absent, or not tested in the individual(s) observed. ", - "enum": [ - "present", - "absent", - "not tested" - ] - } - }, - "required": [ - "clinicalFeaturesAffectedStatus" - ], - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "name" - ] - } - ] - } - - }, - "clinicalFeaturesComment": { - "type": "string", - "description": "To provide a free text explanation of clinical features provided in the previous column, e.g. to describe the progression of disease or diagnosis. Please use this comment to expand on the information in 'clinicalFeatures'" - }, - "collectionMethod": { - "type": "string", - "description": "The method used to collect the data for each observation, e.g. clinical testing or research. See https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#collection", - "enum": [ - "curation", - "literature only", - "reference population", - "provider interpretation", - "phenotyping only", - "case-control", - "clinical testing", - "in vitro", - "in vivo", - "research", - "not provided" - ] - }, - "numberOfIndividuals": { - "type": "integer", - "minimum": 0, - "description": "The total number of individuals with the variant observed by the submitter." - }, - "structVarMethodType": { - "type": "string", - "description": "The method and type of analysis used to identify a structural variant, i.e. any variant >50 nt, equivalent to \"Structural variant method/analysis type\" in the submission spreadsheet. Allowed values are enumerated in the schema. Although optional in the JSON, this field is required for variants that are >50 nt (and in scope for dbVar).", - "enum": [ - "SNP array", - "Oligo array", - "Read depth", - "Paired-end mapping", - "One end anchored assembly", - "Sequence alignment", - "Optical mapping", - "Curated,PCR" - ] - } - }, - "additionalProperties": false + "clinicalSignificanceDescription": { + "const": "drug response" } - }, - "recordStatus": { - "type": "string", - "description": "If you include SCV accessions for 'clinvarAccession', you must indicate whether each record is novel (and accessions were reserved prior to submission) or is an update to an existing SCV record.", - "enum": [ - "novel", - "update" - ] - }, - "variantSet": { - "$ref": "#/definitions/variantSetType" - }, - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - }, - "phaseUnknownSet": { - "$ref": "#/definitions/phaseUnknownSetType" - }, - "distinctChromosomesSet": { - "$ref": "#/definitions/distinctChromosomesSetType" - }, - "diplotypeSet": { - "$ref": "#/definitions/diplotypeSetType" - }, - "compoundHeterozygoteSet": { - "$ref": "#/definitions/compoundHeterozygoteSetType" + } } + } + }, + "oneOf": [ + { + "required": [ + "variantSet" + ] }, - "additionalProperties": false, - "if": { - "properties": { - "clinicalSignificance": { - "properties" : { - "clinicalSignificanceDescription": { "const": "drug response" } - } - } - } + { + "required": [ + "haplotypeSet" + ] }, - "then": { - "properties": { - "conditionSet": { - "required": ["drugResponse"], - "errors": {"required": "when clinicalSignificanceDescription is \"drug response\", conditionSet.drugResponse is a required property"} - } - } + { + "required": [ + "haplotypeSingleVariantSet" + ] }, - "else" : { - "properties": { - "conditionSet": { - "required": ["condition"], - "errors": {"required": "conditionSet.drugResponse is allowed only when clinicalSignificanceDescription is \"drug response\""} - } - } + { + "required": [ + "phaseUnknownSet" + ] + }, + { + "required": [ + "distinctChromosomesSet" + ] + }, + { + "required": [ + "diplotypeSet" + ] + }, + { + "required": [ + "compoundHeterozygoteSet" + ] + } + ], + "then": { + "properties": { + "conditionSet": { + "required": [ + "drugResponse" + ], + "errors": { + "required": "when clinicalSignificanceDescription is \"drug response\", conditionSet.drugResponse is a required property" + } + } } } - - }, - "submissionName": { - "type": "string", - "description": "Optional. The name for this submission. If not provided, it will be the submission id." + } }, "clinvarSubmissionReleaseStatus": { "type": "string", @@ -448,56 +523,329 @@ "hold until published" ] }, - "assertionCriteria": { + "submissionName": { + "type": "string", + "description": "Optional. The name for this submission. If not provided, it will be the submission id." + } + }, + "additionalProperties": false, + "anyOf": [ + { + "required": [ + "clinvarSubmission" + ] + }, + { + "required": [ + "clinvarDeletion" + ] + } + ], + "definitions": { + "compoundHeterozygoteSetType": { "type": "object", - "description": "\"Assertion criteria\" refers to documentation of the criteria that your organization uses to classify variants. It can be provided as a database identifier, like a PubMed ID, or a file that is submitted to ClinVar, but not both. Only one document may be provided for assertion criteria. These fields are equivalent to the \"Assertion method citation\" column in the spreadsheet. Note that only one single assertion criteria (a citation or an electronic document) may be provided for a submission. This assertion criteria will be applied to all interpretations in the submission. For assertion criteria submitted as a database identifier, an assertion criteria name will be calculated based on the citation details. For assertion criteria submitted as a file, you may provide an assertion criteria name during file upload on your Organization page in Submission Portal.", + "description": "Complex variants on different chromosomes, affecting multiple polypeptide chains.", + "required": [ + "hgvs", + "variantSets" + ], "properties": { - "db": { + "hgvs": { "type": "string", - "enum": [ - "PubMed", - "DOI", - "pmc" - ] + "description": "A single, valid HGVS expression" }, - "id": { + "variantSets": { + "type": "array", + "description": "Sets of variants grouped by chromosome", + "minItems": 2, + "maxItems": 2, + "items": { + "type": "object", + "properties": { + "variantSet": { + "$ref": "#/definitions/variantSetType" + } + }, + "additionalProperties": false + }, + "errors": { + "minItems": "Only allow exactly two sets of variants.", + "maxItems": "Only allow exactly two sets of variants." + } + } + }, + "additionalProperties": false + }, + "conditionType": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "properties": { + "db": { + "type": "string", + "enum": [ + "OMIM", + "MedGen", + "Orphanet", + "MeSH", + "HP", + "MONDO" + ] + }, + "id": { + "type": "string", + "description": "The database identifier for the condition. Formats are:\nOMIM: the six digit OMIM number for the disease (not the gene), e.g. 300957; or the Phenotypic Series number including the PS prefix, e.g. PS200600\nMedGen: the MedGen UID, e.g. 751520.\nOrphanet: the Orphanet ID including the prefix, e.g. ORPHA71290\nMeSH: the MeSH ID, e.g. D009634\nHP: the HPO ID including the prefix, e.g. HP:0000815\nMondo: the Mondo ID including the prefix, e.g. MONDO:0100038\n" + }, + "name": { + "type": "string" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "name" + ] + } + ] + }, + "errors": { + "minItems": "Empty condition not allowed" + } + }, + "diplotypeSetType": { + "type": "object", + "description": "A genotype consisting of two haplotypes.", + "required": [ + "hgvs", + "haplotypeSets" + ], + "properties": { + "haplotypeSets": { + "type": "array", + "description": "A container for a combination of exactly two sets, which may be any combination of haplotypeSet and/or haplotypeSingleVariantSet", + "minItems": 2, + "maxItems": 2, + "items": { + "type": "object", + "properties": { + "haplotypeSet": { + "$ref": "#/definitions/haplotypeSetType" + }, + "haplotypeSingleVariantSet": { + "$ref": "#/definitions/haplotypeSingleVariantSetType" + } + }, + "additionalProperties": false + }, + "errors": { + "minItems": "Only allow exactly two sets of variants.", + "maxItems": "Only allow exactly two sets of variants." + } + }, + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the diplotype." + }, + "starAlleleName": { + "type": "string", + "description": "The star allele name for the diplotype" + } + }, + "additionalProperties": false + }, + "distinctChromosomesSetType": { + "type": "object", + "description": "Linked variant data from more than one chromosome", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "Set level HGVS" + }, + "variants": { + "type": "array", + "description": "The linked variants from more than one chromosome", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "At least two variants are required." + } + } + }, + "additionalProperties": false + }, + "drugResponseType": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "properties": { + "condition": { + "description": "The conditions for which the drug is used specified by database ID or name, but not both.", + "$ref": "#/definitions/conditionType" + }, + "db": { + "type": "string", + "enum": [ + "OMIM", + "MedGen", + "Orphanet", + "MeSH", + "HP", + "MONDO" + ] + }, + "drugName": { + "type": "string", + "description": "Name of the drug for which the response is evaluated." + }, + "id": { + "type": "string", + "description": "The MedGen UID for the drug response, e.g. 148193" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "drugName" + ] + } + ] + }, + "errors": { + "minItems": "Empty drugResponse not allowed" + } + }, + "haplotypeSetType": { + "type": "object", + "description": "A set of two or more variants on the same chromosome, typically in the same gene, that were classified together.", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the haplotype." + }, + "starAlleleName": { "type": "string", - "pattern": "^[^;]+$", + "description": "The star allele name for the haplotype." + }, + "variants": { + "type": "array", + "description": "List of variants that make up the haplotype", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, "errors": { - "pattern": "The identifier value is considered an invalid citation. Please provide only one identifier as the citation for your assertion criteria." + "minItems": "At least two variants are required." } + } + }, + "additionalProperties": false + }, + "haplotypeSingleVariantSetType": { + "type": "object", + "description": "A haplotype that is defined by a single variant; likely only expected for pharmacogenomic genes where a single variant may represent the haplotype across an entire gene.", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the haplotype." }, - "url": { + "starAlleleName": { "type": "string", - "description": " The URL for a file that you have already submitted to ClinVar as assertion criteria. If you need to find this URL or if you need to submit new assertion criteria, please go to the \"View/add assertion criteria files\" tab on your Organization page in Submission Portal.", - "pattern": "^https://[qd]?submit.ncbi.nlm.nih.gov/(api/2.0/files|ft/byid)/.*", + "description": "Star allele name for haplotype." + }, + "variants": { + "type": "array", + "description": "The variant that makes up the haplotype", + "minItems": 1, + "maxItems": 1, + "items": { + "$ref": "#/definitions/variantType" + }, "errors": { - "pattern": "The URL for assertion criteria must be the URL provided by ClinVar. If you need to find this URL or if you need to submit new assertion criteria, Please go to the \"View/add assertion criteria files\" tab on your Organization page in Submission Portal." + "minItems": "Only allow exact one variant", + "maxItems": "Only allow exact one variant" } } }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "url" - ] + "additionalProperties": false + }, + "phaseUnknownSetType": { + "type": "object", + "description": "A set of two or more variants that were classified together, but the phasing has not been established", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression." }, - { - "required": [ - "db", - "id" - ] + "variants": { + "type": "array", + "description": "The linked variants with unknown phase", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "At least two variants are required." + } + } + }, + "additionalProperties": false + }, + "variantSetType": { + "type": "object", + "description": "A single variant that was classified; this is the most common type of set for variants in ClinVar. The interpreted variant must be described either by HGVS or by chromosome coordinates, but not both.", + "required": [ + "variant" + ], + "properties": { + "variant": { + "type": "array", + "minItems": 1, + "maxItems": 1, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "Only allow exact one variant", + "maxItems": "Only allow exact one variant" + } } - ] + }, + "additionalProperties": false }, - "behalfOrgID": { - "type": "integer", - "minimum": 1, - "description": "Optional. When submitting on behalf of another organization, this specifies the other organization's ID" - } - }, - "definitions": { "variantType": { "type": "object", "description": "type of variant", @@ -507,7 +855,8 @@ "description": "The location of the variant in chromosome coordinates. Use only 1-based coordinates, not 0-based. For large variants (> 50 nt.), if the exact coordinates (to basepair resolution) of the variant call are known, provide only the start and stop coordinates. Otherwise, use outer_start (lower value) and inner_start (upper value) to define the interval in which the call begins. Likewise, use inner_stop (lower value) and outer_stop (upper value) to define the interval in which the call ends. If only the minimal region is known, use inner_start and inner_stop. If only the maximum region is known, use outer_start and outer_stop. You must provide either one set of coordinates (start and stop, outers only, or inners only) or two sets of coordinates (inners and outers).", "properties": { "accession": { - "type": "string" + "type": "string", + "description": "The accession and version number for the chromosome, e.g. NC_000007.14." }, "alternateAllele": { "type": "string", @@ -558,23 +907,23 @@ }, "innerStart": { "type": "integer", - "minimum": 0, - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)" + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 }, "innerStop": { "type": "integer", - "minimum": 0, - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)" + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 }, "outerStart": { "type": "integer", - "minimum": 0, - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)" + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 }, "outerStop": { "type": "integer", - "minimum": 0, - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)" + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 }, "referenceAllele": { "type": "string", @@ -582,18 +931,18 @@ }, "start": { "type": "integer", - "minimum": 0, - "description": "The start location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate." + "description": "The start location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", + "minimum": 0 }, "stop": { "type": "integer", - "minimum": 0, - "description": "The stop location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate." + "description": "The stop location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", + "minimum": 0 }, "variantLength": { "type": "integer", - "minimum": 0, - "description": "Required for structural variants if outer start/stop is provided but inner start/stop is not provided" + "description": "Required for structural variants if outer start/stop is provided but inner start/stop is not provided", + "minimum": 0 } }, "additionalProperties": false, @@ -617,14 +966,15 @@ }, "gene": { "type": "array", + "minItems": 1, "items": { "type": "object", "description": "Gene symbol should be provided only to indicate the gene-disease relationship supporting the variant interpretation. Gene symbol is not expected for CNVs or cytogenetic variants, except to make a statement that a specific gene within the variant has a relationship to the interpreted condition. Gene symbol can be provided as either the HGNC official symbol or as the NCBI Gene ID, but not both.", "properties": { "id": { "type": "integer", - "minimum": 0, - "description": "NCBI Gene ID" + "description": "NCBI Gene ID", + "minimum": 0 }, "symbol": { "type": "string", @@ -652,8 +1002,8 @@ }, "referenceCopyNumber": { "type": "integer", - "minimum": 0, - "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The reference copy number is an integer and is typically \"2\", as most genes and variants are on autosomes." + "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The reference copy number is an integer and is typically \"2\", as most genes and variants are on autosomes.", + "minimum": 0 }, "variantType": { "type": "string", @@ -684,298 +1034,6 @@ ] } ] - }, - "variantSetType": { - "type": "object", - "description": "A single variant that was classified; this is the most common type of set for variants in ClinVar. The interpreted variant must be described either by HGVS or by chromosome coordinates, but not both.", - "required": [ - "variant" - ], - "properties": { - "variant": { - "type": "array", - "items": { - "$ref": "#/definitions/variantType" - }, - "minItems": 1, - "maxItems": 1, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "haplotypeSetType": { - "type": "object", - "description": "A set of two or more variants on the same chromosome, typically in the same gene, that were classified together.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the haplotype." - }, - "variants": { - "type": "array", - "description": "List of variants that make up the haplotype", - "items": { - "$ref": "#/definitions/variantType" - }, - "minItems": 2, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "haplotypeSingleVariantSetType": { - "type": "object", - "description": "A haplotype that is defined by a single variant; likely only expected for pharmacogenomic genes where a single variant may represent the haplotype across an entire gene.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "Star allele name for haplotype." - }, - "variants": { - "type": "array", - "description": "The variant that makes up the haplotype", - "items": { - "$ref": "#/definitions/variantType" - }, - "minItems": 1, - "maxItems": 1, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "phaseUnknownSetType": { - "type": "object", - "description": "A set of two or more variants that were classified together, but the phasing has not been established", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression." - }, - "variants": { - "type": "array", - "description": "The linked variants with unknown phase", - "items": { - "$ref": "#/definitions/variantType" - }, - "minItems": 2, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "distinctChromosomesSetType": { - "type": "object", - "description": "Linked variant data from more than one chromosome", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "Set level HGVS" - }, - "variants": { - "type": "array", - "description": "The linked variants from more than one chromosome", - "items": { - "$ref": "#/definitions/variantType" - }, - "minItems": 2, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "diplotypeSetType": { - "type": "object", - "description": "A genotype consisting of two haplotypes.", - "required": [ - "hgvs", - "haplotypeSets" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the diplotype." - }, - "haplotypeSets": { - "type": "array", - "description": "A container for a combination of exactly two sets, which may be any combination of haplotypeSet and/or haplotypeSingleVariantSet", - "items": { - "type": "object", - "properties": { - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - } - }, - "additionalProperties": false - }, - "minItems": 2, - "maxItems": 2, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the diplotype" - } - }, - "additionalProperties": false - }, - "compoundHeterozygoteSetType": { - "type": "object", - "description": "Complex variants on different chromosomes, affecting multiple polypeptide chains.", - "required": [ - "hgvs", - "variantSets" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression" - }, - "variantSets": { - "type": "array", - "description": "Sets of variants grouped by chromosome", - "items": { - "type": "object", - "properties": { - "variantSet": { - "$ref": "#/definitions/variantSetType" - } - }, - "additionalProperties": false - }, - "minItems": 2, - "maxItems": 2, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - } - }, - "additionalProperties": false - }, - "conditionType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "id": {"type": "string"}, - "name": {"type": "string"} - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": ["name"] - } - ] - }, - "errors": {"minItems": "Empty condition not allowed"} - }, - "drugResponseType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "id": { - "description": "The identifier for the drug response", - "type": "string" - }, - "drugName": { - "description": "Name of the drug for which the response is evaluated.", - "type": "string" - }, - "condition": { - "description": "The conditions for which the drug is used specified by database ID or name, but not both.", - "$ref": "#/definitions/conditionType" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": ["drugName"] - } - ] - }, - "errors": {"minItems": "Empty drugResponse not allowed"} } - }, - "additionalProperties": false + } } diff --git a/preClinVar/resources/submission_schema_before_221121.json b/preClinVar/resources/submission_schema_before_221121.json deleted file mode 100644 index 180f2c2..0000000 --- a/preClinVar/resources/submission_schema_before_221121.json +++ /dev/null @@ -1,1024 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "behalfOrgID": { - "type": "integer", - "description": "Optional. When submitting on behalf of another organization, this specifies the other organization's ID", - "minimum": 1 - }, - "clinvarDeletion": { - "type": "object", - "items": { - "type": "object", - "title": "ClinVar Deletions", - "required": [ - "accessionSet" - ], - "properties": { - "accessionSet": { - "type": "array", - "minItems": 1, - "maxItems": 10000, - "items": { - "type": "object", - "title": "Clinvar accession and reason for deleting", - "required": [ - "accession" - ], - "properties": { - "accession": { - "type": "string", - "description": "The SCV accession for your submitted record to delete (not the RCV or the VCV).", - "pattern": "^SCV[0123456789]{9}$" - }, - "reason": { - "type": "string", - "description": "A public comment explaining why this record is being deleted." - } - } - } - } - } - } - }, - "clinvarSubmission": { - "type": "array", - "title": "ClinVar Submission Set", - "minItems": 1, - "maxItems": 10000, - "items": { - "type": "object", - "title": "ClinVar Submission", - "description": "Submissions to ClinVar are considered 'variant-level' (not case-level or patient-specific), because they are focused on the variant or set of variants that was interpreted. One of variantSet, haplotypeSet, haplotypeSingleVariantSet, phaseUnknownSet, distinctChromosomesSet, diplotypeSet, compoundHeterozygoteSet is required to define the variant or set of variants that was interpreted.", - "required": [ - "recordStatus", - "releaseStatus", - "clinicalSignificance", - "observedIn", - "conditionSet" - ], - "properties": { - "assertionCriteria": { - "type": "object", - "required": [ - "method", - "citation" - ], - "properties": { - "citation": { - "type": "object", - "description": "\"Assertion criteria\" refers to documentation of the criteria that your organization uses to classify variants. It can be provided as a database identifier, like a PubMed ID, or a file that is submitted to ClinVar, but not both. Only one document may be provided for assertion criteria. These fields are equivalent to the \"Assertion method citation\" column in the spreadsheet.", - "properties": { - "db": { - "type": "string", - "enum": [ - "PubMed", - "BookShelf", - "DOI", - "pmc" - ] - }, - "id": { - "type": "string" - }, - "url": { - "type": "string", - "description": "The URL for a file that you have already submitted to ClinVar as assertion criteria.", - "errors": { - "pattern": "The URL for assertion criteria must be the URL provided by ClinVar. Contact clinvar@ncbi.nlm.nih.gov if you need to find this URL or if you need to submit new assertion criteria." - }, - "pattern": "^https://[qd]?submit.ncbi.nlm.nih.gov/ft/byid/.*" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "url" - ] - }, - { - "required": [ - "db", - "id" - ] - } - ] - }, - "method": { - "type": "string", - "description": "A name for your assertion criteria is required. We'll use the file name if a file is cited so the submitter does not need to provide a separate name. The submitter must provide a name if a database identifier is cited. This field is equivalent to the \"Assertion method\" column in the spreadsheet." - } - }, - "additionalProperties": false - }, - "clinicalSignificance": { - "type": "object", - "description": "Clinical significance", - "required": [ - "clinicalSignificanceDescription" - ], - "properties": { - "citation": { - "type": "array", - "items": { - "type": "object", - "description": "Citations that were used by the submitter to evaluate the clinical significance of the variant. More than one citation may be provided. Each citation can be provided as a database identifier, like a PubMed ID, or a URL, but not both.", - "properties": { - "db": { - "type": "string", - "enum": [ - "PubMed", - "BookShelf", - "DOI", - "pmc" - ] - }, - "id": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "db", - "id" - ] - }, - { - "required": [ - "url" - ] - } - ] - } - }, - "clinicalSignificanceDescription": { - "type": "string", - "description": "The interpretation, or clinical significance, of the variant for the submitted condition, equivalent to Clinical significance in the submission spreadsheet.", - "enum": [ - "Pathogenic", - "Likely pathogenic", - "Uncertain significance", - "Likely benign", - "Benign", - "Pathogenic, low penetrance", - "Uncertain risk allele", - "Likely pathogenic, low penetrance", - "Established risk allele", - "Likely risk allele", - "affects", - "association", - "drug response", - "confers sensitivity", - "protective", - "other", - "not provided" - ] - }, - "comment": { - "type": "string", - "description": "Optional, but highly encouraged. Free text describing the rationale for the clinical significance." - }, - "customAssertionScore": { - "type": "number", - "description": "The final score, or point value, calculated when the assertion method uses a point-based scoring system, e.g. ACMG/ClinGen CNV Guidelines, 2019 (PMID: 31690835). The assertion method must also be provided. " - }, - "dateLastEvaluated": { - "type": "string", - "description": "The date that the clinical significance was last evaluated by the submitter (not the date the phenotype of the patient was evaluated), equivalent to Date last evaluated in the submission spreadsheet. Use the format yyyy-mm-dd. If only month/year is known, use the first day of the month. If only year is known, use Jan. 1.", - "pattern": "^[1-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]$" - }, - "explanationOfDrugResponse": { - "type": "string", - "description": "Required for a record with clinical significance of 'drug response'. Please provide a value describing the drug response, e.g. 'likely responsive'. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." - }, - "explanationOfOtherClinicalSignificance": { - "type": "string", - "description": "Required if 'other' is selected for clinical significance. Please provide the new value for clinical significance, e.g. pseudodeficiency allele. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." - }, - "modeOfInheritance": { - "type": "string", - "description": "The mode of inheritance specific to the variant-disease pair, not generally for the disease.", - "enum": [ - "Autosomal dominant inheritance", - "Autosomal recessive inheritance", - "Mitochondrial inheritance", - "Somatic mutation", - "Genetic anticipation", - "Sporadic", - "Sex-limited autosomal dominant", - "X-linked recessive inheritance", - "X-linked dominant inheritance", - "Y-linked inheritance", - "Other", - "X-linked inheritance", - "Codominant", - "Semidominant inheritance", - "Autosomal unknown", - "Autosomal dominant inheritance with maternal imprinting", - "Autosomal dominant inheritance with paternal imprinting", - "Multifactorial inheritance", - "Unknown mechanism", - "Oligogenic inheritance" - ] - } - }, - "additionalProperties": false - }, - "clinvarAccession": { - "type": "string", - "description": "Required for updated records and for novel records if accession numbers were reserved. Provide the SCV number for your submitted record (not the RCV number). For novel records without reserved accessions: the SCV accession number will be returned to you after your submission file is processed. You should provide that accession number back to ClinVar when you update your SCV record. " - }, - "compoundHeterozygoteSet": { - "$ref": "#/definitions/compoundHeterozygoteSetType" - }, - "conditionSet": { - "type": "object", - "description": "The condition for which the variant is interpreted. Detailed information about reporting condition is available at https://www.ncbi.nlm.nih.gov/clinvar/docs/faq_submitters/#pheno If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records. i.e. this variant causes condition A in some individuals and causes disease B in other individuals. Provide only one name or identifier for a condition; do not provide multiple names or identifiers for the same condition.", - "properties": { - "condition": { - "description": "The condition must be provided as either a database identifier or a name, but not both. A database identifier is preferred by ClinVar; a name should be provided only if there is no database identifier available.", - "$ref": "#/definitions/conditionType" - }, - "drugResponse": { - "description": "The drug Response evaluated specified by database ID or drug name, but not both", - "$ref": "#/definitions/drugResponseType" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "condition" - ] - }, - { - "required": [ - "drugResponse" - ] - } - ] - }, - "diplotypeSet": { - "$ref": "#/definitions/diplotypeSetType" - }, - "distinctChromosomesSet": { - "$ref": "#/definitions/distinctChromosomesSetType" - }, - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - }, - "localID": { - "type": "string", - "description": "Optional, but highly recommended. The stable unique identifier your organization uses to identifiy this variant. This identifier will be public so should not include protected health information." - }, - "localKey": { - "type": "string", - "description": "Your unique local identifier for the variant-condition pair, equivalent to the Linking ID in the submission spreadsheet." - }, - "observedIn": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "required": [ - "alleleOrigin", - "affectedStatus", - "collectionMethod" - ], - "properties": { - "affectedStatus": { - "type": "string", - "description": "Indicates whether or not the individual(s) in each observation were affected by the condition for the interpretation", - "enum": [ - "yes", - "no", - "unknown", - "not provided", - "not applicable" - ] - }, - "alleleOrigin": { - "type": "string", - "description": "The genetic origin of the variant for individuals in each aggregate observation. For de novo variants, please indicate 'de novo', not the origin of the chromosome.", - "enum": [ - "germline", - "somatic", - "de novo", - "unknown", - "inherited", - "maternal", - "paternal", - "biparental", - "not applicable" - ] - }, - "clinicalFeatures": { - "type": "array", - "items": { - "type": "object", - "description": "Clinical features that were observed by the submitter in an individual with the variant. More than one feature may be provided. Each clinical feature may be described by a database identifier or by a name, but not both. These fields are equivalent to the \"Clinical features\" column in the spreadsheet.", - "required": [ - "clinicalFeaturesAffectedStatus" - ], - "properties": { - "clinicalFeaturesAffectedStatus": { - "type": "string", - "description": "To indicate whether each clinical feature was present, absent, or not tested in the individual(s) observed. ", - "enum": [ - "present", - "absent", - "not tested" - ] - }, - "db": { - "type": "string", - "enum": [ - "HP" - ] - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "name" - ] - } - ] - } - }, - "clinicalFeaturesComment": { - "type": "string", - "description": "To provide a free text explanation of clinical features provided in the previous column, e.g. to describe the progression of disease or diagnosis. Please use this comment to expand on the information in 'clinicalFeatures'" - }, - "collectionMethod": { - "type": "string", - "description": "The method used to collect the data for each observation, e.g. clinical testing or research. See https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#collection", - "enum": [ - "curation", - "literature only", - "reference population", - "provider interpretation", - "phenotyping only", - "case-control", - "clinical testing", - "in vitro", - "in vivo", - "research", - "not provided" - ] - }, - "numberOfIndividuals": { - "type": "integer", - "description": "The total number of individuals with the variant observed by the submitter.", - "minimum": 0 - }, - "structVarMethodType": { - "type": "string", - "description": "The method and type of analysis used to identify a structural variant, i.e. any variant >50 nt, equivalent to \"Structural variant method/analysis type\" in the submission spreadsheet. Allowed values are enumerated in the schema. Although optional in the JSON, this field is required for variants that are >50 nt (and in scope for dbVar).", - "enum": [ - "SNP array", - "Oligo array", - "Read depth", - "Paired-end mapping", - "One end anchored assembly", - "Sequence alignment", - "Optical mapping", - "Curated,PCR" - ] - } - }, - "additionalProperties": false - } - }, - "phaseUnknownSet": { - "$ref": "#/definitions/phaseUnknownSetType" - }, - "recordStatus": { - "type": "string", - "description": "If you include SCV accessions for 'clinvarAccession', you must indicate whether each record is novel (and accessions were reserved prior to submission) or is an update to an existing SCV record.", - "enum": [ - "novel", - "update" - ] - }, - "releaseStatus": { - "type": "string", - "description": "\"hold until published\" allows a temporary hold on data being presented publicly. If no value is provided, the default is public.", - "enum": [ - "public", - "hold until published" - ] - }, - "variantSet": { - "$ref": "#/definitions/variantSetType" - } - }, - "additionalProperties": false, - "else": { - "properties": { - "conditionSet": { - "required": [ - "condition" - ], - "errors": { - "required": "conditionSet.drugResponse is allowed only when clinicalSignificanceDescription is \"drug response\"" - } - } - } - }, - "if": { - "properties": { - "clinicalSignificance": { - "properties": { - "clinicalSignificanceDescription": { - "const": "drug response" - } - } - } - } - }, - "oneOf": [ - { - "required": [ - "variantSet" - ] - }, - { - "required": [ - "haplotypeSet" - ] - }, - { - "required": [ - "haplotypeSingleVariantSet" - ] - }, - { - "required": [ - "phaseUnknownSet" - ] - }, - { - "required": [ - "distinctChromosomesSet" - ] - }, - { - "required": [ - "diplotypeSet" - ] - }, - { - "required": [ - "compoundHeterozygoteSet" - ] - } - ], - "then": { - "properties": { - "conditionSet": { - "required": [ - "drugResponse" - ], - "errors": { - "required": "when clinicalSignificanceDescription is \"drug response\", conditionSet.drugResponse is a required property" - } - } - } - } - } - }, - "submissionName": { - "type": "string", - "description": "Optional. The name for this submission. If not provided, it will be the submission id." - } - }, - "additionalProperties": false, - "anyOf": [ - { - "required": [ - "clinvarSubmission" - ] - }, - { - "required": [ - "clinvarDeletion" - ] - } - ], - "definitions": { - "compoundHeterozygoteSetType": { - "type": "object", - "description": "Complex variants on different chromosomes, affecting multiple polypeptide chains.", - "required": [ - "hgvs", - "variantSets" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression" - }, - "variantSets": { - "type": "array", - "description": "Sets of variants grouped by chromosome", - "minItems": 2, - "maxItems": 2, - "items": { - "type": "object", - "properties": { - "variantSet": { - "$ref": "#/definitions/variantSetType" - } - }, - "additionalProperties": false - }, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - } - }, - "additionalProperties": false - }, - "conditionType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "name" - ] - } - ] - }, - "errors": { - "minItems": "Empty condition not allowed" - } - }, - "diplotypeSetType": { - "type": "object", - "description": "A genotype consisting of two haplotypes.", - "required": [ - "hgvs", - "haplotypeSets" - ], - "properties": { - "haplotypeSets": { - "type": "array", - "description": "A container for a combination of exactly two sets, which may be any combination of haplotypeSet and/or haplotypeSingleVariantSet", - "minItems": 2, - "maxItems": 2, - "items": { - "type": "object", - "properties": { - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - } - }, - "additionalProperties": false - }, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - }, - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the diplotype." - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the diplotype" - } - }, - "additionalProperties": false - }, - "distinctChromosomesSetType": { - "type": "object", - "description": "Linked variant data from more than one chromosome", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "Set level HGVS" - }, - "variants": { - "type": "array", - "description": "The linked variants from more than one chromosome", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "drugResponseType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "condition": { - "description": "The conditions for which the drug is used specified by database ID or name, but not both.", - "$ref": "#/definitions/conditionType" - }, - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "drugName": { - "type": "string", - "description": "Name of the drug for which the response is evaluated." - }, - "id": { - "type": "string", - "description": "The identifier for the drug response" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "drugName" - ] - } - ] - }, - "errors": { - "minItems": "Empty drugResponse not allowed" - } - }, - "haplotypeSetType": { - "type": "object", - "description": "A set of two or more variants on the same chromosome, typically in the same gene, that were classified together.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the haplotype." - }, - "variants": { - "type": "array", - "description": "List of variants that make up the haplotype", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "haplotypeSingleVariantSetType": { - "type": "object", - "description": "A haplotype that is defined by a single variant; likely only expected for pharmacogenomic genes where a single variant may represent the haplotype across an entire gene.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "Star allele name for haplotype." - }, - "variants": { - "type": "array", - "description": "The variant that makes up the haplotype", - "minItems": 1, - "maxItems": 1, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "phaseUnknownSetType": { - "type": "object", - "description": "A set of two or more variants that were classified together, but the phasing has not been established", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression." - }, - "variants": { - "type": "array", - "description": "The linked variants with unknown phase", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "variantSetType": { - "type": "object", - "description": "A single variant that was classified; this is the most common type of set for variants in ClinVar. The interpreted variant must be described either by HGVS or by chromosome coordinates, but not both.", - "required": [ - "variant" - ], - "properties": { - "variant": { - "type": "array", - "minItems": 1, - "maxItems": 1, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "variantType": { - "type": "object", - "description": "type of variant", - "properties": { - "chromosomeCoordinates": { - "type": "object", - "description": "The location of the variant in chromosome coordinates. Use only 1-based coordinates, not 0-based. For large variants (> 50 nt.), if the exact coordinates (to basepair resolution) of the variant call are known, provide only the start and stop coordinates. Otherwise, use outer_start (lower value) and inner_start (upper value) to define the interval in which the call begins. Likewise, use inner_stop (lower value) and outer_stop (upper value) to define the interval in which the call ends. If only the minimal region is known, use inner_start and inner_stop. If only the maximum region is known, use outer_start and outer_stop. You must provide either one set of coordinates (start and stop, outers only, or inners only) or two sets of coordinates (inners and outers).", - "properties": { - "accession": { - "type": "string" - }, - "alternateAllele": { - "type": "string", - "description": "The alternate allele for the submitted variant. This is used only for small variants (up to 50 nt.)" - }, - "assembly": { - "type": "string", - "description": "The genome assembly that was used to call the variant.", - "enum": [ - "GRCh38", - "hg38", - "GRCh37", - "hg19", - "NCBI36", - "hg18" - ] - }, - "chromosome": { - "type": "string", - "description": "The chromosome for the location of the variant. Values are 1-22, X, Y, and MT. If the location is pseudoautosomal, submit on X and ClinVar will calculate the Y location.", - "enum": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "X", - "Y", - "MT" - ] - }, - "innerStart": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "innerStop": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "outerStart": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "outerStop": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "referenceAllele": { - "type": "string", - "description": "The reference allele for the submitted variant. This is used only for small variants (up to 50 nt.)" - }, - "start": { - "type": "integer", - "description": "The start location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", - "minimum": 0 - }, - "stop": { - "type": "integer", - "description": "The stop location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", - "minimum": 0 - }, - "variantLength": { - "type": "integer", - "description": "Required for structural variants if outer start/stop is provided but inner start/stop is not provided", - "minimum": 0 - } - }, - "additionalProperties": false, - "anyOf": [ - { - "required": [ - "assembly", - "chromosome" - ] - }, - { - "required": [ - "accession" - ] - } - ] - }, - "copyNumber": { - "type": "string", - "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The observed copy number is a string, to allow for cases where the copy number is ambiguous and a range is provided, e.g. 3,4." - }, - "gene": { - "type": "array", - "items": { - "type": "object", - "description": "Gene symbol should be provided only to indicate the gene-disease relationship supporting the variant interpretation. Gene symbol is not expected for CNVs or cytogenetic variants, except to make a statement that a specific gene within the variant has a relationship to the interpreted condition. Gene symbol can be provided as either the HGNC official symbol or as the NCBI Gene ID, but not both.", - "properties": { - "id": { - "type": "integer", - "description": "NCBI Gene ID", - "minimum": 0 - }, - "symbol": { - "type": "string", - "description": "HGNC official gene symbol." - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id" - ] - }, - { - "required": [ - "symbol" - ] - } - ] - } - }, - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the variant on a nucleotide sequence." - }, - "referenceCopyNumber": { - "type": "integer", - "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The reference copy number is an integer and is typically \"2\", as most genes and variants are on autosomes.", - "minimum": 0 - }, - "variantType": { - "type": "string", - "description": "The type of variant; provided for larger variants instead of reference and alternate alleles. Required for any variant for which the reference and alternate alleles are not specified. In practice, this will occur for structural variants and for deletions or duplications described only by genomic coordinates.", - "enum": [ - "Insertion", - "Deletion", - "Duplication", - "Tandem duplication", - "copy number loss", - "copy number gain", - "Inversion", - "Translocation", - "Complex" - ] - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "chromosomeCoordinates" - ] - }, - { - "required": [ - "hgvs" - ] - } - ] - } - } -} From 4ada01243484a50f4fa5cc4c3a80385ae2237c72 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Wed, 31 Jan 2024 15:15:07 +0100 Subject: [PATCH 2/9] Revert file --- .../submission_schema_bedore_221121.json | 1024 +++++++++++++++++ 1 file changed, 1024 insertions(+) create mode 100644 preClinVar/resources/submission_schema_bedore_221121.json diff --git a/preClinVar/resources/submission_schema_bedore_221121.json b/preClinVar/resources/submission_schema_bedore_221121.json new file mode 100644 index 0000000..62a7d4b --- /dev/null +++ b/preClinVar/resources/submission_schema_bedore_221121.json @@ -0,0 +1,1024 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "behalfOrgID": { + "type": "integer", + "description": "Optional. When submitting on behalf of another organization, this specifies the other organization's ID", + "minimum": 1 + }, + "clinvarDeletion": { + "type": "object", + "items": { + "type": "object", + "title": "ClinVar Deletions", + "required": [ + "accessionSet" + ], + "properties": { + "accessionSet": { + "type": "array", + "minItems": 1, + "maxItems": 10000, + "items": { + "type": "object", + "title": "Clinvar accession and reason for deleting", + "required": [ + "accession" + ], + "properties": { + "accession": { + "type": "string", + "description": "The SCV accession for your submitted record to delete (not the RCV or the VCV).", + "pattern": "^SCV[0123456789]{9}$" + }, + "reason": { + "type": "string", + "description": "A public comment explaining why this record is being deleted." + } + } + } + } + } + } + }, + "clinvarSubmission": { + "type": "array", + "title": "ClinVar Submission Set", + "minItems": 1, + "maxItems": 10000, + "items": { + "type": "object", + "title": "ClinVar Submission", + "description": "Submissions to ClinVar are considered 'variant-level' (not case-level or patient-specific), because they are focused on the variant or set of variants that was interpreted. One of variantSet, haplotypeSet, haplotypeSingleVariantSet, phaseUnknownSet, distinctChromosomesSet, diplotypeSet, compoundHeterozygoteSet is required to define the variant or set of variants that was interpreted.", + "required": [ + "recordStatus", + "releaseStatus", + "clinicalSignificance", + "observedIn", + "conditionSet" + ], + "properties": { + "assertionCriteria": { + "type": "object", + "required": [ + "method", + "citation" + ], + "properties": { + "citation": { + "type": "object", + "description": "\"Assertion criteria\" refers to documentation of the criteria that your organization uses to classify variants. It can be provided as a database identifier, like a PubMed ID, or a file that is submitted to ClinVar, but not both. Only one document may be provided for assertion criteria. These fields are equivalent to the \"Assertion method citation\" column in the spreadsheet.", + "properties": { + "db": { + "type": "string", + "enum": [ + "PubMed", + "BookShelf", + "DOI", + "pmc" + ] + }, + "id": { + "type": "string" + }, + "url": { + "type": "string", + "description": "The URL for a file that you have already submitted to ClinVar as assertion criteria.", + "errors": { + "pattern": "The URL for assertion criteria must be the URL provided by ClinVar. Contact clinvar@ncbi.nlm.nih.gov if you need to find this URL or if you need to submit new assertion criteria." + }, + "pattern": "^https://[qd]?submit.ncbi.nlm.nih.gov/ft/byid/.*" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "url" + ] + }, + { + "required": [ + "db", + "id" + ] + } + ] + }, + "method": { + "type": "string", + "description": "A name for your assertion criteria is required. We'll use the file name if a file is cited so the submitter does not need to provide a separate name. The submitter must provide a name if a database identifier is cited. This field is equivalent to the \"Assertion method\" column in the spreadsheet." + } + }, + "additionalProperties": false + }, + "clinicalSignificance": { + "type": "object", + "description": "Clinical significance", + "required": [ + "clinicalSignificanceDescription" + ], + "properties": { + "citation": { + "type": "array", + "items": { + "type": "object", + "description": "Citations that were used by the submitter to evaluate the clinical significance of the variant. More than one citation may be provided. Each citation can be provided as a database identifier, like a PubMed ID, or a URL, but not both.", + "properties": { + "db": { + "type": "string", + "enum": [ + "PubMed", + "BookShelf", + "DOI", + "pmc" + ] + }, + "id": { + "type": "string" + }, + "url": { + "type": "string" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "db", + "id" + ] + }, + { + "required": [ + "url" + ] + } + ] + } + }, + "clinicalSignificanceDescription": { + "type": "string", + "description": "The interpretation, or clinical significance, of the variant for the submitted condition, equivalent to Clinical significance in the submission spreadsheet.", + "enum": [ + "Pathogenic", + "Likely pathogenic", + "Uncertain significance", + "Likely benign", + "Benign", + "Pathogenic, low penetrance", + "Uncertain risk allele", + "Likely pathogenic, low penetrance", + "Established risk allele", + "Likely risk allele", + "affects", + "association", + "drug response", + "confers sensitivity", + "protective", + "other", + "not provided" + ] + }, + "comment": { + "type": "string", + "description": "Optional, but highly encouraged. Free text describing the rationale for the clinical significance." + }, + "customAssertionScore": { + "type": "number", + "description": "The final score, or point value, calculated when the assertion method uses a point-based scoring system, e.g. ACMG/ClinGen CNV Guidelines, 2019 (PMID: 31690835). The assertion method must also be provided. " + }, + "dateLastEvaluated": { + "type": "string", + "description": "The date that the clinical significance was last evaluated by the submitter (not the date the phenotype of the patient was evaluated), equivalent to Date last evaluated in the submission spreadsheet. Use the format yyyy-mm-dd. If only month/year is known, use the first day of the month. If only year is known, use Jan. 1.", + "pattern": "^[1-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]$" + }, + "explanationOfDrugResponse": { + "type": "string", + "description": "Required for a record with clinical significance of 'drug response'. Please provide a value describing the drug response, e.g. 'likely responsive'. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + }, + "explanationOfOtherClinicalSignificance": { + "type": "string", + "description": "Required if 'other' is selected for clinical significance. Please provide the new value for clinical significance, e.g. pseudodeficiency allele. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." + }, + "modeOfInheritance": { + "type": "string", + "description": "The mode of inheritance specific to the variant-disease pair, not generally for the disease.", + "enum": [ + "Autosomal dominant inheritance", + "Autosomal recessive inheritance", + "Mitochondrial inheritance", + "Somatic mutation", + "Genetic anticipation", + "Sporadic", + "Sex-limited autosomal dominant", + "X-linked recessive inheritance", + "X-linked dominant inheritance", + "Y-linked inheritance", + "Other", + "X-linked inheritance", + "Codominant", + "Semidominant inheritance", + "Autosomal unknown", + "Autosomal dominant inheritance with maternal imprinting", + "Autosomal dominant inheritance with paternal imprinting", + "Multifactorial inheritance", + "Unknown mechanism", + "Oligogenic inheritance" + ] + } + }, + "additionalProperties": false + }, + "clinvarAccession": { + "type": "string", + "description": "Required for updated records and for novel records if accession numbers were reserved. Provide the SCV number for your submitted record (not the RCV number). For novel records without reserved accessions: the SCV accession number will be returned to you after your submission file is processed. You should provide that accession number back to ClinVar when you update your SCV record. " + }, + "compoundHeterozygoteSet": { + "$ref": "#/definitions/compoundHeterozygoteSetType" + }, + "conditionSet": { + "type": "object", + "description": "The condition for which the variant is interpreted. Detailed information about reporting condition is available at https://www.ncbi.nlm.nih.gov/clinvar/docs/faq_submitters/#pheno If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records. i.e. this variant causes condition A in some individuals and causes disease B in other individuals. Provide only one name or identifier for a condition; do not provide multiple names or identifiers for the same condition.", + "properties": { + "condition": { + "description": "The condition must be provided as either a database identifier or a name, but not both. A database identifier is preferred by ClinVar; a name should be provided only if there is no database identifier available.", + "$ref": "#/definitions/conditionType" + }, + "drugResponse": { + "description": "The drug Response evaluated specified by database ID or drug name, but not both", + "$ref": "#/definitions/drugResponseType" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "condition" + ] + }, + { + "required": [ + "drugResponse" + ] + } + ] + }, + "diplotypeSet": { + "$ref": "#/definitions/diplotypeSetType" + }, + "distinctChromosomesSet": { + "$ref": "#/definitions/distinctChromosomesSetType" + }, + "haplotypeSet": { + "$ref": "#/definitions/haplotypeSetType" + }, + "haplotypeSingleVariantSet": { + "$ref": "#/definitions/haplotypeSingleVariantSetType" + }, + "localID": { + "type": "string", + "description": "Optional, but highly recommended. The stable unique identifier your organization uses to identifiy this variant. This identifier will be public so should not include protected health information." + }, + "localKey": { + "type": "string", + "description": "Your unique local identifier for the variant-condition pair, equivalent to the Linking ID in the submission spreadsheet." + }, + "observedIn": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "required": [ + "alleleOrigin", + "affectedStatus", + "collectionMethod" + ], + "properties": { + "affectedStatus": { + "type": "string", + "description": "Indicates whether or not the individual(s) in each observation were affected by the condition for the interpretation", + "enum": [ + "yes", + "no", + "unknown", + "not provided", + "not applicable" + ] + }, + "alleleOrigin": { + "type": "string", + "description": "The genetic origin of the variant for individuals in each aggregate observation. For de novo variants, please indicate 'de novo', not the origin of the chromosome.", + "enum": [ + "germline", + "somatic", + "de novo", + "unknown", + "inherited", + "maternal", + "paternal", + "biparental", + "not applicable" + ] + }, + "clinicalFeatures": { + "type": "array", + "items": { + "type": "object", + "description": "Clinical features that were observed by the submitter in an individual with the variant. More than one feature may be provided. Each clinical feature may be described by a database identifier or by a name, but not both. These fields are equivalent to the \"Clinical features\" column in the spreadsheet.", + "required": [ + "clinicalFeaturesAffectedStatus" + ], + "properties": { + "clinicalFeaturesAffectedStatus": { + "type": "string", + "description": "To indicate whether each clinical feature was present, absent, or not tested in the individual(s) observed. ", + "enum": [ + "present", + "absent", + "not tested" + ] + }, + "db": { + "type": "string", + "enum": [ + "HP" + ] + }, + "id": { + "type": "string" + }, + "name": { + "type": "string" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "name" + ] + } + ] + } + }, + "clinicalFeaturesComment": { + "type": "string", + "description": "To provide a free text explanation of clinical features provided in the previous column, e.g. to describe the progression of disease or diagnosis. Please use this comment to expand on the information in 'clinicalFeatures'" + }, + "collectionMethod": { + "type": "string", + "description": "The method used to collect the data for each observation, e.g. clinical testing or research. See https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#collection", + "enum": [ + "curation", + "literature only", + "reference population", + "provider interpretation", + "phenotyping only", + "case-control", + "clinical testing", + "in vitro", + "in vivo", + "research", + "not provided" + ] + }, + "numberOfIndividuals": { + "type": "integer", + "description": "The total number of individuals with the variant observed by the submitter.", + "minimum": 0 + }, + "structVarMethodType": { + "type": "string", + "description": "The method and type of analysis used to identify a structural variant, i.e. any variant >50 nt, equivalent to \"Structural variant method/analysis type\" in the submission spreadsheet. Allowed values are enumerated in the schema. Although optional in the JSON, this field is required for variants that are >50 nt (and in scope for dbVar).", + "enum": [ + "SNP array", + "Oligo array", + "Read depth", + "Paired-end mapping", + "One end anchored assembly", + "Sequence alignment", + "Optical mapping", + "Curated,PCR" + ] + } + }, + "additionalProperties": false + } + }, + "phaseUnknownSet": { + "$ref": "#/definitions/phaseUnknownSetType" + }, + "recordStatus": { + "type": "string", + "description": "If you include SCV accessions for 'clinvarAccession', you must indicate whether each record is novel (and accessions were reserved prior to submission) or is an update to an existing SCV record.", + "enum": [ + "novel", + "update" + ] + }, + "releaseStatus": { + "type": "string", + "description": "\"hold until published\" allows a temporary hold on data being presented publicly. If no value is provided, the default is public.", + "enum": [ + "public", + "hold until published" + ] + }, + "variantSet": { + "$ref": "#/definitions/variantSetType" + } + }, + "additionalProperties": false, + "else": { + "properties": { + "conditionSet": { + "required": [ + "condition" + ], + "errors": { + "required": "conditionSet.drugResponse is allowed only when clinicalSignificanceDescription is \"drug response\"" + } + } + } + }, + "if": { + "properties": { + "clinicalSignificance": { + "properties": { + "clinicalSignificanceDescription": { + "const": "drug response" + } + } + } + } + }, + "oneOf": [ + { + "required": [ + "variantSet" + ] + }, + { + "required": [ + "haplotypeSet" + ] + }, + { + "required": [ + "haplotypeSingleVariantSet" + ] + }, + { + "required": [ + "phaseUnknownSet" + ] + }, + { + "required": [ + "distinctChromosomesSet" + ] + }, + { + "required": [ + "diplotypeSet" + ] + }, + { + "required": [ + "compoundHeterozygoteSet" + ] + } + ], + "then": { + "properties": { + "conditionSet": { + "required": [ + "drugResponse" + ], + "errors": { + "required": "when clinicalSignificanceDescription is \"drug response\", conditionSet.drugResponse is a required property" + } + } + } + } + } + }, + "submissionName": { + "type": "string", + "description": "Optional. The name for this submission. If not provided, it will be the submission id." + } + }, + "additionalProperties": false, + "anyOf": [ + { + "required": [ + "clinvarSubmission" + ] + }, + { + "required": [ + "clinvarDeletion" + ] + } + ], + "definitions": { + "compoundHeterozygoteSetType": { + "type": "object", + "description": "Complex variants on different chromosomes, affecting multiple polypeptide chains.", + "required": [ + "hgvs", + "variantSets" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression" + }, + "variantSets": { + "type": "array", + "description": "Sets of variants grouped by chromosome", + "minItems": 2, + "maxItems": 2, + "items": { + "type": "object", + "properties": { + "variantSet": { + "$ref": "#/definitions/variantSetType" + } + }, + "additionalProperties": false + }, + "errors": { + "minItems": "Only allow exactly two sets of variants.", + "maxItems": "Only allow exactly two sets of variants." + } + } + }, + "additionalProperties": false + }, + "conditionType": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "properties": { + "db": { + "type": "string", + "enum": [ + "OMIM", + "MedGen", + "Orphanet", + "MeSH", + "HP", + "MONDO" + ] + }, + "id": { + "type": "string" + }, + "name": { + "type": "string" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "name" + ] + } + ] + }, + "errors": { + "minItems": "Empty condition not allowed" + } + }, + "diplotypeSetType": { + "type": "object", + "description": "A genotype consisting of two haplotypes.", + "required": [ + "hgvs", + "haplotypeSets" + ], + "properties": { + "haplotypeSets": { + "type": "array", + "description": "A container for a combination of exactly two sets, which may be any combination of haplotypeSet and/or haplotypeSingleVariantSet", + "minItems": 2, + "maxItems": 2, + "items": { + "type": "object", + "properties": { + "haplotypeSet": { + "$ref": "#/definitions/haplotypeSetType" + }, + "haplotypeSingleVariantSet": { + "$ref": "#/definitions/haplotypeSingleVariantSetType" + } + }, + "additionalProperties": false + }, + "errors": { + "minItems": "Only allow exactly two sets of variants.", + "maxItems": "Only allow exactly two sets of variants." + } + }, + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the diplotype." + }, + "starAlleleName": { + "type": "string", + "description": "The star allele name for the diplotype" + } + }, + "additionalProperties": false + }, + "distinctChromosomesSetType": { + "type": "object", + "description": "Linked variant data from more than one chromosome", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "Set level HGVS" + }, + "variants": { + "type": "array", + "description": "The linked variants from more than one chromosome", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "At least two variants are required." + } + } + }, + "additionalProperties": false + }, + "drugResponseType": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "properties": { + "condition": { + "description": "The conditions for which the drug is used specified by database ID or name, but not both.", + "$ref": "#/definitions/conditionType" + }, + "db": { + "type": "string", + "enum": [ + "OMIM", + "MedGen", + "Orphanet", + "MeSH", + "HP", + "MONDO" + ] + }, + "drugName": { + "type": "string", + "description": "Name of the drug for which the response is evaluated." + }, + "id": { + "type": "string", + "description": "The identifier for the drug response" + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id", + "db" + ] + }, + { + "required": [ + "drugName" + ] + } + ] + }, + "errors": { + "minItems": "Empty drugResponse not allowed" + } + }, + "haplotypeSetType": { + "type": "object", + "description": "A set of two or more variants on the same chromosome, typically in the same gene, that were classified together.", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the haplotype." + }, + "starAlleleName": { + "type": "string", + "description": "The star allele name for the haplotype." + }, + "variants": { + "type": "array", + "description": "List of variants that make up the haplotype", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "At least two variants are required." + } + } + }, + "additionalProperties": false + }, + "haplotypeSingleVariantSetType": { + "type": "object", + "description": "A haplotype that is defined by a single variant; likely only expected for pharmacogenomic genes where a single variant may represent the haplotype across an entire gene.", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the haplotype." + }, + "starAlleleName": { + "type": "string", + "description": "Star allele name for haplotype." + }, + "variants": { + "type": "array", + "description": "The variant that makes up the haplotype", + "minItems": 1, + "maxItems": 1, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "Only allow exact one variant", + "maxItems": "Only allow exact one variant" + } + } + }, + "additionalProperties": false + }, + "phaseUnknownSetType": { + "type": "object", + "description": "A set of two or more variants that were classified together, but the phasing has not been established", + "required": [ + "hgvs", + "variants" + ], + "properties": { + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression." + }, + "variants": { + "type": "array", + "description": "The linked variants with unknown phase", + "minItems": 2, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "At least two variants are required." + } + } + }, + "additionalProperties": false + }, + "variantSetType": { + "type": "object", + "description": "A single variant that was classified; this is the most common type of set for variants in ClinVar. The interpreted variant must be described either by HGVS or by chromosome coordinates, but not both.", + "required": [ + "variant" + ], + "properties": { + "variant": { + "type": "array", + "minItems": 1, + "maxItems": 1, + "items": { + "$ref": "#/definitions/variantType" + }, + "errors": { + "minItems": "Only allow exact one variant", + "maxItems": "Only allow exact one variant" + } + } + }, + "additionalProperties": false + }, + "variantType": { + "type": "object", + "description": "type of variant", + "properties": { + "chromosomeCoordinates": { + "type": "object", + "description": "The location of the variant in chromosome coordinates. Use only 1-based coordinates, not 0-based. For large variants (> 50 nt.), if the exact coordinates (to basepair resolution) of the variant call are known, provide only the start and stop coordinates. Otherwise, use outer_start (lower value) and inner_start (upper value) to define the interval in which the call begins. Likewise, use inner_stop (lower value) and outer_stop (upper value) to define the interval in which the call ends. If only the minimal region is known, use inner_start and inner_stop. If only the maximum region is known, use outer_start and outer_stop. You must provide either one set of coordinates (start and stop, outers only, or inners only) or two sets of coordinates (inners and outers).", + "properties": { + "accession": { + "type": "string" + }, + "alternateAllele": { + "type": "string", + "description": "The alternate allele for the submitted variant. This is used only for small variants (up to 50 nt.)" + }, + "assembly": { + "type": "string", + "description": "The genome assembly that was used to call the variant.", + "enum": [ + "GRCh38", + "hg38", + "GRCh37", + "hg19", + "NCBI36", + "hg18" + ] + }, + "chromosome": { + "type": "string", + "description": "The chromosome for the location of the variant. Values are 1-22, X, Y, and MT. If the location is pseudoautosomal, submit on X and ClinVar will calculate the Y location.", + "enum": [ + "1", + "2", + "3", + "4", + "5", + "6", + "7", + "8", + "9", + "10", + "11", + "12", + "13", + "14", + "15", + "16", + "17", + "18", + "19", + "20", + "21", + "22", + "X", + "Y", + "MT" + ] + }, + "innerStart": { + "type": "integer", + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 + }, + "innerStop": { + "type": "integer", + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 + }, + "outerStart": { + "type": "integer", + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 + }, + "outerStop": { + "type": "integer", + "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", + "minimum": 0 + }, + "referenceAllele": { + "type": "string", + "description": "The reference allele for the submitted variant. This is used only for small variants (up to 50 nt.)" + }, + "start": { + "type": "integer", + "description": "The start location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", + "minimum": 0 + }, + "stop": { + "type": "integer", + "description": "The stop location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", + "minimum": 0 + }, + "variantLength": { + "type": "integer", + "description": "Required for structural variants if outer start/stop is provided but inner start/stop is not provided", + "minimum": 0 + } + }, + "additionalProperties": false, + "anyOf": [ + { + "required": [ + "assembly", + "chromosome" + ] + }, + { + "required": [ + "accession" + ] + } + ] + }, + "copyNumber": { + "type": "string", + "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The observed copy number is a string, to allow for cases where the copy number is ambiguous and a range is provided, e.g. 3,4." + }, + "gene": { + "type": "array", + "items": { + "type": "object", + "description": "Gene symbol should be provided only to indicate the gene-disease relationship supporting the variant interpretation. Gene symbol is not expected for CNVs or cytogenetic variants, except to make a statement that a specific gene within the variant has a relationship to the interpreted condition. Gene symbol can be provided as either the HGNC official symbol or as the NCBI Gene ID, but not both.", + "properties": { + "id": { + "type": "integer", + "description": "NCBI Gene ID", + "minimum": 0 + }, + "symbol": { + "type": "string", + "description": "HGNC official gene symbol." + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "id" + ] + }, + { + "required": [ + "symbol" + ] + } + ] + } + }, + "hgvs": { + "type": "string", + "description": "A single, valid HGVS expression to describe the variant on a nucleotide sequence." + }, + "referenceCopyNumber": { + "type": "integer", + "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The reference copy number is an integer and is typically \"2\", as most genes and variants are on autosomes.", + "minimum": 0 + }, + "variantType": { + "type": "string", + "description": "The type of variant; provided for larger variants instead of reference and alternate alleles. Required for any variant for which the reference and alternate alleles are not specified. In practice, this will occur for structural variants and for deletions or duplications described only by genomic coordinates.", + "enum": [ + "Insertion", + "Deletion", + "Duplication", + "Tandem duplication", + "copy number loss", + "copy number gain", + "Inversion", + "Translocation", + "Complex" + ] + } + }, + "additionalProperties": false, + "oneOf": [ + { + "required": [ + "chromosomeCoordinates" + ] + }, + { + "required": [ + "hgvs" + ] + } + ] + } + } +} \ No newline at end of file From 2922d871be0aa9a41f1dd9cbfc464dddb869769c Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 07:47:39 +0100 Subject: [PATCH 3/9] Replace deprecated pkg_resources with importlib_resources --- CHANGELOG.md | 3 +- poetry.lock | 818 +++++++++++++++++++------------ preClinVar/demo/__init__.py | 35 +- preClinVar/resources/__init__.py | 8 +- pyproject.toml | 1 + 5 files changed, 515 insertions(+), 350 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ff5cee7..b30ab63 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,8 @@ - Updated version of external images in GitHub actions ### Fixed - Bump certifi from 2022.12.7 to 2023.7.22 -- Description of the response returned by dry run endpoint in README file +- Description of the response returned by dry run endpoint in README file +- Migrate from deprecated `pkg_resources` lib to `importlib_resources` ## [2.3.1] ### Fixed diff --git a/poetry.lock b/poetry.lock index bb95856..59f88df 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,83 +1,65 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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(>=10.0)"] [[package]] name = "zipp" -version = "3.8.0" +version = "3.17.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"}, - {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"}, + {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, + {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, ] [package.extras] -docs = ["jaraco.packaging (>=9)", "rst.linker (>=1.9)", "sphinx"] -testing = ["func-timeout", "jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] +docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] +testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "0e8d3a4b70c90117a9fad7a0299fa155837dcf633f5653e3d3a2e1ee585d47ea" +content-hash = "b6e3362a8e2254decbc6c7c56c340ed32a69901b57dc24ad1b2fdc220afca855" diff --git a/preClinVar/demo/__init__.py b/preClinVar/demo/__init__.py index 9de6ee7..867fcee 100644 --- a/preClinVar/demo/__init__.py +++ b/preClinVar/demo/__init__.py @@ -1,4 +1,6 @@ -import pkg_resources +from importlib_resources import files + +BASE_PATH = "preClinVar.demo" ###### .csv files ###### casedata_old_csv = "CaseData_before_221121.csv" @@ -11,27 +13,14 @@ casedata_sv_csv = "CaseData_sv.csv" ###### Path to .csv files ###### -casedata_old_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_old_csv]) -) -variants_old_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_old_csv]) -) -casedata_snv_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_snv_csv]) -) -casedata_sv_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", casedata_sv_csv]) -) -variants_hgvs_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_hgvs_csv]) -) -variants_sv_breakpoints_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_sv_breakpoints_csv]) -) -variants_sv_range_coords_csv_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["demo", variants_sv_range_coords_csv]) -) +casedata_old_csv_path = str(files(BASE_PATH).joinpath(casedata_old_csv)) +variants_old_csv_path = str(files(BASE_PATH).joinpath(variants_old_csv)) +casedata_snv_csv_path = str(files(BASE_PATH).joinpath(casedata_snv_csv)) +casedata_sv_csv_path = str(files(BASE_PATH).joinpath(casedata_sv_csv)) +variants_hgvs_csv_path = str(files(BASE_PATH).joinpath(variants_hgvs_csv)) +variants_sv_breakpoints_csv_path = str(files(BASE_PATH).joinpath(variants_sv_breakpoints_csv)) +variants_sv_range_coords_csv_path = str(files(BASE_PATH).joinpath(variants_sv_range_coords_csv)) + ###### Example of a json file submission ###### subm_json = "submission.json" -subm_json_path = pkg_resources.resource_filename("preClinVar", "/".join(["demo", subm_json])) +subm_json_path = str(files(BASE_PATH).joinpath(subm_json)) diff --git a/preClinVar/resources/__init__.py b/preClinVar/resources/__init__.py index 7270749..0ec0e52 100644 --- a/preClinVar/resources/__init__.py +++ b/preClinVar/resources/__init__.py @@ -1,10 +1,10 @@ -import pkg_resources +from importlib_resources import files + +BASE_PATH = "preClinVar.resources" ###### submission schema json file ###### subm_schema = "submission_schema.json" ###### Path to submission schema file ###### -subm_schema_path = pkg_resources.resource_filename( - "preClinVar", "/".join(["resources", subm_schema]) -) +subm_schema_path = str(files(BASE_PATH).joinpath(subm_schema)) diff --git a/pyproject.toml b/pyproject.toml index 05d107f..5af4709 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ black = "^22.6.0" python-multipart = "^0.0.5" jsonschema = "^4.6.1" responses = "^0.21.0" +importlib-resources = "^6.1.1" [tool.poetry.dev-dependencies] pytest = "^7.1.2" From fe8925b91eb294455da1ffb5a17f17039d1f37a2 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 08:02:27 +0100 Subject: [PATCH 4/9] Downgrade anyio lib --- poetry.lock | 18 ++++++++---------- pyproject.toml | 1 + 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/poetry.lock b/poetry.lock index 59f88df..cc71c29 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,25 +2,23 @@ [[package]] name = "anyio" -version = "4.2.0" +version = "3.6.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.8" +python-versions = ">=3.6.2" files = [ - {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, - {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, + {file = "anyio-3.6.1-py3-none-any.whl", hash = "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be"}, + {file = "anyio-3.6.1.tar.gz", hash = "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b"}, ] [package.dependencies] -exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" -typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] -trio = ["trio (>=0.23)"] +doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] +trio = ["trio (>=0.16)"] [[package]] name = "attrs" @@ -908,4 +906,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "b6e3362a8e2254decbc6c7c56c340ed32a69901b57dc24ad1b2fdc220afca855" +content-hash = "065789b44cf7f2f552812973579825e0bca7015946549f471a419aa4549c3eac" diff --git a/pyproject.toml b/pyproject.toml index 5af4709..fca06d9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,6 +16,7 @@ python-multipart = "^0.0.5" jsonschema = "^4.6.1" responses = "^0.21.0" importlib-resources = "^6.1.1" +anyio = "3.6.1" [tool.poetry.dev-dependencies] pytest = "^7.1.2" From af991560a817774d4bd046ce2d86834087bdba2d Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 08:29:11 +0100 Subject: [PATCH 5/9] Try fixing lock file --- poetry.lock | 18 ++++++++++-------- pyproject.toml | 1 - 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/poetry.lock b/poetry.lock index cc71c29..59f88df 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,23 +2,25 @@ [[package]] name = "anyio" -version = "3.6.1" +version = "4.2.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false -python-versions = ">=3.6.2" +python-versions = ">=3.8" files = [ - {file = "anyio-3.6.1-py3-none-any.whl", hash = "sha256:cb29b9c70620506a9a8f87a309591713446953302d7d995344d0d7c6c0c9a7be"}, - {file = "anyio-3.6.1.tar.gz", hash = "sha256:413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b"}, + {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"}, + {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"}, ] [package.dependencies] +exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] -test = ["contextlib2", "coverage[toml] (>=4.5)", "hypothesis (>=4.0)", "mock (>=4)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (<0.15)", "uvloop (>=0.15)"] -trio = ["trio (>=0.16)"] +doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints (>=1.2.0)", "sphinx-rtd-theme"] +test = ["anyio[trio]", "coverage[toml] (>=7)", "exceptiongroup (>=1.2.0)", "hypothesis (>=4.0)", "psutil (>=5.9)", "pytest (>=7.0)", "pytest-mock (>=3.6.1)", "trustme", "uvloop (>=0.17)"] +trio = ["trio (>=0.23)"] [[package]] name = "attrs" @@ -906,4 +908,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "065789b44cf7f2f552812973579825e0bca7015946549f471a419aa4549c3eac" +content-hash = "b6e3362a8e2254decbc6c7c56c340ed32a69901b57dc24ad1b2fdc220afca855" diff --git a/pyproject.toml b/pyproject.toml index fca06d9..5af4709 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,6 @@ python-multipart = "^0.0.5" jsonschema = "^4.6.1" responses = "^0.21.0" importlib-resources = "^6.1.1" -anyio = "3.6.1" [tool.poetry.dev-dependencies] pytest = "^7.1.2" From 09209438b5647ea1be811f14c2ae0bbeafa6e891 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 08:46:30 +0100 Subject: [PATCH 6/9] Revert liibs --- poetry.lock | 818 +++++++++++++++++++------------------------------ pyproject.toml | 1 - 2 files changed, 322 insertions(+), 497 deletions(-) diff --git a/poetry.lock b/poetry.lock index 59f88df..bb95856 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,65 +1,83 @@ -# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. 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"jaraco.itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.0.1)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" python-versions = "^3.8" -content-hash = "b6e3362a8e2254decbc6c7c56c340ed32a69901b57dc24ad1b2fdc220afca855" +content-hash = "0e8d3a4b70c90117a9fad7a0299fa155837dcf633f5653e3d3a2e1ee585d47ea" diff --git a/pyproject.toml b/pyproject.toml index 5af4709..05d107f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,6 @@ black = "^22.6.0" python-multipart = "^0.0.5" jsonschema = "^4.6.1" responses = "^0.21.0" -importlib-resources = "^6.1.1" [tool.poetry.dev-dependencies] pytest = "^7.1.2" From c11f57320a4a6dfc062039ce86aef43e5e23aa1a Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 08:56:05 +0100 Subject: [PATCH 7/9] Removed old submission schema --- .../submission_schema_bedore_221121.json | 1024 ----------------- 1 file changed, 1024 deletions(-) delete mode 100644 preClinVar/resources/submission_schema_bedore_221121.json diff --git a/preClinVar/resources/submission_schema_bedore_221121.json b/preClinVar/resources/submission_schema_bedore_221121.json deleted file mode 100644 index 62a7d4b..0000000 --- a/preClinVar/resources/submission_schema_bedore_221121.json +++ /dev/null @@ -1,1024 +0,0 @@ -{ - "$schema": "http://json-schema.org/draft-07/schema#", - "type": "object", - "properties": { - "behalfOrgID": { - "type": "integer", - "description": "Optional. When submitting on behalf of another organization, this specifies the other organization's ID", - "minimum": 1 - }, - "clinvarDeletion": { - "type": "object", - "items": { - "type": "object", - "title": "ClinVar Deletions", - "required": [ - "accessionSet" - ], - "properties": { - "accessionSet": { - "type": "array", - "minItems": 1, - "maxItems": 10000, - "items": { - "type": "object", - "title": "Clinvar accession and reason for deleting", - "required": [ - "accession" - ], - "properties": { - "accession": { - "type": "string", - "description": "The SCV accession for your submitted record to delete (not the RCV or the VCV).", - "pattern": "^SCV[0123456789]{9}$" - }, - "reason": { - "type": "string", - "description": "A public comment explaining why this record is being deleted." - } - } - } - } - } - } - }, - "clinvarSubmission": { - "type": "array", - "title": "ClinVar Submission Set", - "minItems": 1, - "maxItems": 10000, - "items": { - "type": "object", - "title": "ClinVar Submission", - "description": "Submissions to ClinVar are considered 'variant-level' (not case-level or patient-specific), because they are focused on the variant or set of variants that was interpreted. One of variantSet, haplotypeSet, haplotypeSingleVariantSet, phaseUnknownSet, distinctChromosomesSet, diplotypeSet, compoundHeterozygoteSet is required to define the variant or set of variants that was interpreted.", - "required": [ - "recordStatus", - "releaseStatus", - "clinicalSignificance", - "observedIn", - "conditionSet" - ], - "properties": { - "assertionCriteria": { - "type": "object", - "required": [ - "method", - "citation" - ], - "properties": { - "citation": { - "type": "object", - "description": "\"Assertion criteria\" refers to documentation of the criteria that your organization uses to classify variants. It can be provided as a database identifier, like a PubMed ID, or a file that is submitted to ClinVar, but not both. Only one document may be provided for assertion criteria. These fields are equivalent to the \"Assertion method citation\" column in the spreadsheet.", - "properties": { - "db": { - "type": "string", - "enum": [ - "PubMed", - "BookShelf", - "DOI", - "pmc" - ] - }, - "id": { - "type": "string" - }, - "url": { - "type": "string", - "description": "The URL for a file that you have already submitted to ClinVar as assertion criteria.", - "errors": { - "pattern": "The URL for assertion criteria must be the URL provided by ClinVar. Contact clinvar@ncbi.nlm.nih.gov if you need to find this URL or if you need to submit new assertion criteria." - }, - "pattern": "^https://[qd]?submit.ncbi.nlm.nih.gov/ft/byid/.*" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "url" - ] - }, - { - "required": [ - "db", - "id" - ] - } - ] - }, - "method": { - "type": "string", - "description": "A name for your assertion criteria is required. We'll use the file name if a file is cited so the submitter does not need to provide a separate name. The submitter must provide a name if a database identifier is cited. This field is equivalent to the \"Assertion method\" column in the spreadsheet." - } - }, - "additionalProperties": false - }, - "clinicalSignificance": { - "type": "object", - "description": "Clinical significance", - "required": [ - "clinicalSignificanceDescription" - ], - "properties": { - "citation": { - "type": "array", - "items": { - "type": "object", - "description": "Citations that were used by the submitter to evaluate the clinical significance of the variant. More than one citation may be provided. Each citation can be provided as a database identifier, like a PubMed ID, or a URL, but not both.", - "properties": { - "db": { - "type": "string", - "enum": [ - "PubMed", - "BookShelf", - "DOI", - "pmc" - ] - }, - "id": { - "type": "string" - }, - "url": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "db", - "id" - ] - }, - { - "required": [ - "url" - ] - } - ] - } - }, - "clinicalSignificanceDescription": { - "type": "string", - "description": "The interpretation, or clinical significance, of the variant for the submitted condition, equivalent to Clinical significance in the submission spreadsheet.", - "enum": [ - "Pathogenic", - "Likely pathogenic", - "Uncertain significance", - "Likely benign", - "Benign", - "Pathogenic, low penetrance", - "Uncertain risk allele", - "Likely pathogenic, low penetrance", - "Established risk allele", - "Likely risk allele", - "affects", - "association", - "drug response", - "confers sensitivity", - "protective", - "other", - "not provided" - ] - }, - "comment": { - "type": "string", - "description": "Optional, but highly encouraged. Free text describing the rationale for the clinical significance." - }, - "customAssertionScore": { - "type": "number", - "description": "The final score, or point value, calculated when the assertion method uses a point-based scoring system, e.g. ACMG/ClinGen CNV Guidelines, 2019 (PMID: 31690835). The assertion method must also be provided. " - }, - "dateLastEvaluated": { - "type": "string", - "description": "The date that the clinical significance was last evaluated by the submitter (not the date the phenotype of the patient was evaluated), equivalent to Date last evaluated in the submission spreadsheet. Use the format yyyy-mm-dd. If only month/year is known, use the first day of the month. If only year is known, use Jan. 1.", - "pattern": "^[1-9][0-9][0-9][0-9]-[0-1][0-9]-[0-3][0-9]$" - }, - "explanationOfDrugResponse": { - "type": "string", - "description": "Required for a record with clinical significance of 'drug response'. Please provide a value describing the drug response, e.g. 'likely responsive'. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." - }, - "explanationOfOtherClinicalSignificance": { - "type": "string", - "description": "Required if 'other' is selected for clinical significance. Please provide the new value for clinical significance, e.g. pseudodeficiency allele. This value must be short for display purposes. A longer explanation should be provided in the 'Comment on clinical significance'." - }, - "modeOfInheritance": { - "type": "string", - "description": "The mode of inheritance specific to the variant-disease pair, not generally for the disease.", - "enum": [ - "Autosomal dominant inheritance", - "Autosomal recessive inheritance", - "Mitochondrial inheritance", - "Somatic mutation", - "Genetic anticipation", - "Sporadic", - "Sex-limited autosomal dominant", - "X-linked recessive inheritance", - "X-linked dominant inheritance", - "Y-linked inheritance", - "Other", - "X-linked inheritance", - "Codominant", - "Semidominant inheritance", - "Autosomal unknown", - "Autosomal dominant inheritance with maternal imprinting", - "Autosomal dominant inheritance with paternal imprinting", - "Multifactorial inheritance", - "Unknown mechanism", - "Oligogenic inheritance" - ] - } - }, - "additionalProperties": false - }, - "clinvarAccession": { - "type": "string", - "description": "Required for updated records and for novel records if accession numbers were reserved. Provide the SCV number for your submitted record (not the RCV number). For novel records without reserved accessions: the SCV accession number will be returned to you after your submission file is processed. You should provide that accession number back to ClinVar when you update your SCV record. " - }, - "compoundHeterozygoteSet": { - "$ref": "#/definitions/compoundHeterozygoteSetType" - }, - "conditionSet": { - "type": "object", - "description": "The condition for which the variant is interpreted. Detailed information about reporting condition is available at https://www.ncbi.nlm.nih.gov/clinvar/docs/faq_submitters/#pheno If multiple conditions are submitted for a variant, this indicates that the variant was interpreted for the combination of conditions in the same individual(s). i.e. this variant causes both condition A and condition B in the same individual. This scenario is most common for a new disease or syndrome that does not yet have a name and is described by several clinical features. If you want to indicate that the variant has been interpreted for more than one condition, please submit these as separate records. i.e. this variant causes condition A in some individuals and causes disease B in other individuals. Provide only one name or identifier for a condition; do not provide multiple names or identifiers for the same condition.", - "properties": { - "condition": { - "description": "The condition must be provided as either a database identifier or a name, but not both. A database identifier is preferred by ClinVar; a name should be provided only if there is no database identifier available.", - "$ref": "#/definitions/conditionType" - }, - "drugResponse": { - "description": "The drug Response evaluated specified by database ID or drug name, but not both", - "$ref": "#/definitions/drugResponseType" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "condition" - ] - }, - { - "required": [ - "drugResponse" - ] - } - ] - }, - "diplotypeSet": { - "$ref": "#/definitions/diplotypeSetType" - }, - "distinctChromosomesSet": { - "$ref": "#/definitions/distinctChromosomesSetType" - }, - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - }, - "localID": { - "type": "string", - "description": "Optional, but highly recommended. The stable unique identifier your organization uses to identifiy this variant. This identifier will be public so should not include protected health information." - }, - "localKey": { - "type": "string", - "description": "Your unique local identifier for the variant-condition pair, equivalent to the Linking ID in the submission spreadsheet." - }, - "observedIn": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "required": [ - "alleleOrigin", - "affectedStatus", - "collectionMethod" - ], - "properties": { - "affectedStatus": { - "type": "string", - "description": "Indicates whether or not the individual(s) in each observation were affected by the condition for the interpretation", - "enum": [ - "yes", - "no", - "unknown", - "not provided", - "not applicable" - ] - }, - "alleleOrigin": { - "type": "string", - "description": "The genetic origin of the variant for individuals in each aggregate observation. For de novo variants, please indicate 'de novo', not the origin of the chromosome.", - "enum": [ - "germline", - "somatic", - "de novo", - "unknown", - "inherited", - "maternal", - "paternal", - "biparental", - "not applicable" - ] - }, - "clinicalFeatures": { - "type": "array", - "items": { - "type": "object", - "description": "Clinical features that were observed by the submitter in an individual with the variant. More than one feature may be provided. Each clinical feature may be described by a database identifier or by a name, but not both. These fields are equivalent to the \"Clinical features\" column in the spreadsheet.", - "required": [ - "clinicalFeaturesAffectedStatus" - ], - "properties": { - "clinicalFeaturesAffectedStatus": { - "type": "string", - "description": "To indicate whether each clinical feature was present, absent, or not tested in the individual(s) observed. ", - "enum": [ - "present", - "absent", - "not tested" - ] - }, - "db": { - "type": "string", - "enum": [ - "HP" - ] - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "name" - ] - } - ] - } - }, - "clinicalFeaturesComment": { - "type": "string", - "description": "To provide a free text explanation of clinical features provided in the previous column, e.g. to describe the progression of disease or diagnosis. Please use this comment to expand on the information in 'clinicalFeatures'" - }, - "collectionMethod": { - "type": "string", - "description": "The method used to collect the data for each observation, e.g. clinical testing or research. See https://www.ncbi.nlm.nih.gov/clinvar/docs/spreadsheet/#collection", - "enum": [ - "curation", - "literature only", - "reference population", - "provider interpretation", - "phenotyping only", - "case-control", - "clinical testing", - "in vitro", - "in vivo", - "research", - "not provided" - ] - }, - "numberOfIndividuals": { - "type": "integer", - "description": "The total number of individuals with the variant observed by the submitter.", - "minimum": 0 - }, - "structVarMethodType": { - "type": "string", - "description": "The method and type of analysis used to identify a structural variant, i.e. any variant >50 nt, equivalent to \"Structural variant method/analysis type\" in the submission spreadsheet. Allowed values are enumerated in the schema. Although optional in the JSON, this field is required for variants that are >50 nt (and in scope for dbVar).", - "enum": [ - "SNP array", - "Oligo array", - "Read depth", - "Paired-end mapping", - "One end anchored assembly", - "Sequence alignment", - "Optical mapping", - "Curated,PCR" - ] - } - }, - "additionalProperties": false - } - }, - "phaseUnknownSet": { - "$ref": "#/definitions/phaseUnknownSetType" - }, - "recordStatus": { - "type": "string", - "description": "If you include SCV accessions for 'clinvarAccession', you must indicate whether each record is novel (and accessions were reserved prior to submission) or is an update to an existing SCV record.", - "enum": [ - "novel", - "update" - ] - }, - "releaseStatus": { - "type": "string", - "description": "\"hold until published\" allows a temporary hold on data being presented publicly. If no value is provided, the default is public.", - "enum": [ - "public", - "hold until published" - ] - }, - "variantSet": { - "$ref": "#/definitions/variantSetType" - } - }, - "additionalProperties": false, - "else": { - "properties": { - "conditionSet": { - "required": [ - "condition" - ], - "errors": { - "required": "conditionSet.drugResponse is allowed only when clinicalSignificanceDescription is \"drug response\"" - } - } - } - }, - "if": { - "properties": { - "clinicalSignificance": { - "properties": { - "clinicalSignificanceDescription": { - "const": "drug response" - } - } - } - } - }, - "oneOf": [ - { - "required": [ - "variantSet" - ] - }, - { - "required": [ - "haplotypeSet" - ] - }, - { - "required": [ - "haplotypeSingleVariantSet" - ] - }, - { - "required": [ - "phaseUnknownSet" - ] - }, - { - "required": [ - "distinctChromosomesSet" - ] - }, - { - "required": [ - "diplotypeSet" - ] - }, - { - "required": [ - "compoundHeterozygoteSet" - ] - } - ], - "then": { - "properties": { - "conditionSet": { - "required": [ - "drugResponse" - ], - "errors": { - "required": "when clinicalSignificanceDescription is \"drug response\", conditionSet.drugResponse is a required property" - } - } - } - } - } - }, - "submissionName": { - "type": "string", - "description": "Optional. The name for this submission. If not provided, it will be the submission id." - } - }, - "additionalProperties": false, - "anyOf": [ - { - "required": [ - "clinvarSubmission" - ] - }, - { - "required": [ - "clinvarDeletion" - ] - } - ], - "definitions": { - "compoundHeterozygoteSetType": { - "type": "object", - "description": "Complex variants on different chromosomes, affecting multiple polypeptide chains.", - "required": [ - "hgvs", - "variantSets" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression" - }, - "variantSets": { - "type": "array", - "description": "Sets of variants grouped by chromosome", - "minItems": 2, - "maxItems": 2, - "items": { - "type": "object", - "properties": { - "variantSet": { - "$ref": "#/definitions/variantSetType" - } - }, - "additionalProperties": false - }, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - } - }, - "additionalProperties": false - }, - "conditionType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "id": { - "type": "string" - }, - "name": { - "type": "string" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "name" - ] - } - ] - }, - "errors": { - "minItems": "Empty condition not allowed" - } - }, - "diplotypeSetType": { - "type": "object", - "description": "A genotype consisting of two haplotypes.", - "required": [ - "hgvs", - "haplotypeSets" - ], - "properties": { - "haplotypeSets": { - "type": "array", - "description": "A container for a combination of exactly two sets, which may be any combination of haplotypeSet and/or haplotypeSingleVariantSet", - "minItems": 2, - "maxItems": 2, - "items": { - "type": "object", - "properties": { - "haplotypeSet": { - "$ref": "#/definitions/haplotypeSetType" - }, - "haplotypeSingleVariantSet": { - "$ref": "#/definitions/haplotypeSingleVariantSetType" - } - }, - "additionalProperties": false - }, - "errors": { - "minItems": "Only allow exactly two sets of variants.", - "maxItems": "Only allow exactly two sets of variants." - } - }, - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the diplotype." - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the diplotype" - } - }, - "additionalProperties": false - }, - "distinctChromosomesSetType": { - "type": "object", - "description": "Linked variant data from more than one chromosome", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "Set level HGVS" - }, - "variants": { - "type": "array", - "description": "The linked variants from more than one chromosome", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "drugResponseType": { - "type": "array", - "minItems": 1, - "items": { - "type": "object", - "properties": { - "condition": { - "description": "The conditions for which the drug is used specified by database ID or name, but not both.", - "$ref": "#/definitions/conditionType" - }, - "db": { - "type": "string", - "enum": [ - "OMIM", - "MedGen", - "Orphanet", - "MeSH", - "HP", - "MONDO" - ] - }, - "drugName": { - "type": "string", - "description": "Name of the drug for which the response is evaluated." - }, - "id": { - "type": "string", - "description": "The identifier for the drug response" - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id", - "db" - ] - }, - { - "required": [ - "drugName" - ] - } - ] - }, - "errors": { - "minItems": "Empty drugResponse not allowed" - } - }, - "haplotypeSetType": { - "type": "object", - "description": "A set of two or more variants on the same chromosome, typically in the same gene, that were classified together.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "The star allele name for the haplotype." - }, - "variants": { - "type": "array", - "description": "List of variants that make up the haplotype", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "haplotypeSingleVariantSetType": { - "type": "object", - "description": "A haplotype that is defined by a single variant; likely only expected for pharmacogenomic genes where a single variant may represent the haplotype across an entire gene.", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the haplotype." - }, - "starAlleleName": { - "type": "string", - "description": "Star allele name for haplotype." - }, - "variants": { - "type": "array", - "description": "The variant that makes up the haplotype", - "minItems": 1, - "maxItems": 1, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "phaseUnknownSetType": { - "type": "object", - "description": "A set of two or more variants that were classified together, but the phasing has not been established", - "required": [ - "hgvs", - "variants" - ], - "properties": { - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression." - }, - "variants": { - "type": "array", - "description": "The linked variants with unknown phase", - "minItems": 2, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "At least two variants are required." - } - } - }, - "additionalProperties": false - }, - "variantSetType": { - "type": "object", - "description": "A single variant that was classified; this is the most common type of set for variants in ClinVar. The interpreted variant must be described either by HGVS or by chromosome coordinates, but not both.", - "required": [ - "variant" - ], - "properties": { - "variant": { - "type": "array", - "minItems": 1, - "maxItems": 1, - "items": { - "$ref": "#/definitions/variantType" - }, - "errors": { - "minItems": "Only allow exact one variant", - "maxItems": "Only allow exact one variant" - } - } - }, - "additionalProperties": false - }, - "variantType": { - "type": "object", - "description": "type of variant", - "properties": { - "chromosomeCoordinates": { - "type": "object", - "description": "The location of the variant in chromosome coordinates. Use only 1-based coordinates, not 0-based. For large variants (> 50 nt.), if the exact coordinates (to basepair resolution) of the variant call are known, provide only the start and stop coordinates. Otherwise, use outer_start (lower value) and inner_start (upper value) to define the interval in which the call begins. Likewise, use inner_stop (lower value) and outer_stop (upper value) to define the interval in which the call ends. If only the minimal region is known, use inner_start and inner_stop. If only the maximum region is known, use outer_start and outer_stop. You must provide either one set of coordinates (start and stop, outers only, or inners only) or two sets of coordinates (inners and outers).", - "properties": { - "accession": { - "type": "string" - }, - "alternateAllele": { - "type": "string", - "description": "The alternate allele for the submitted variant. This is used only for small variants (up to 50 nt.)" - }, - "assembly": { - "type": "string", - "description": "The genome assembly that was used to call the variant.", - "enum": [ - "GRCh38", - "hg38", - "GRCh37", - "hg19", - "NCBI36", - "hg18" - ] - }, - "chromosome": { - "type": "string", - "description": "The chromosome for the location of the variant. Values are 1-22, X, Y, and MT. If the location is pseudoautosomal, submit on X and ClinVar will calculate the Y location.", - "enum": [ - "1", - "2", - "3", - "4", - "5", - "6", - "7", - "8", - "9", - "10", - "11", - "12", - "13", - "14", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "X", - "Y", - "MT" - ] - }, - "innerStart": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "innerStop": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "outerStart": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "outerStop": { - "type": "integer", - "description": "Indicate imprecise locations for structural variants. This is used only for large variants (more than 50 nt.)", - "minimum": 0 - }, - "referenceAllele": { - "type": "string", - "description": "The reference allele for the submitted variant. This is used only for small variants (up to 50 nt.)" - }, - "start": { - "type": "integer", - "description": "The start location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", - "minimum": 0 - }, - "stop": { - "type": "integer", - "description": "The stop location for the reference allele in chromosome coordinates. If only start is provided for the location, stop will be presumed to be the same coordinate.", - "minimum": 0 - }, - "variantLength": { - "type": "integer", - "description": "Required for structural variants if outer start/stop is provided but inner start/stop is not provided", - "minimum": 0 - } - }, - "additionalProperties": false, - "anyOf": [ - { - "required": [ - "assembly", - "chromosome" - ] - }, - { - "required": [ - "accession" - ] - } - ] - }, - "copyNumber": { - "type": "string", - "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The observed copy number is a string, to allow for cases where the copy number is ambiguous and a range is provided, e.g. 3,4." - }, - "gene": { - "type": "array", - "items": { - "type": "object", - "description": "Gene symbol should be provided only to indicate the gene-disease relationship supporting the variant interpretation. Gene symbol is not expected for CNVs or cytogenetic variants, except to make a statement that a specific gene within the variant has a relationship to the interpreted condition. Gene symbol can be provided as either the HGNC official symbol or as the NCBI Gene ID, but not both.", - "properties": { - "id": { - "type": "integer", - "description": "NCBI Gene ID", - "minimum": 0 - }, - "symbol": { - "type": "string", - "description": "HGNC official gene symbol." - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "id" - ] - }, - { - "required": [ - "symbol" - ] - } - ] - } - }, - "hgvs": { - "type": "string", - "description": "A single, valid HGVS expression to describe the variant on a nucleotide sequence." - }, - "referenceCopyNumber": { - "type": "integer", - "description": "For copy number variants, both the reference copy number and the observed copy number can be provided. The reference copy number is an integer and is typically \"2\", as most genes and variants are on autosomes.", - "minimum": 0 - }, - "variantType": { - "type": "string", - "description": "The type of variant; provided for larger variants instead of reference and alternate alleles. Required for any variant for which the reference and alternate alleles are not specified. In practice, this will occur for structural variants and for deletions or duplications described only by genomic coordinates.", - "enum": [ - "Insertion", - "Deletion", - "Duplication", - "Tandem duplication", - "copy number loss", - "copy number gain", - "Inversion", - "Translocation", - "Complex" - ] - } - }, - "additionalProperties": false, - "oneOf": [ - { - "required": [ - "chromosomeCoordinates" - ] - }, - { - "required": [ - "hgvs" - ] - } - ] - } - } -} \ No newline at end of file From 887e51f2d60fabad560f7320aa1318c59de6ac12 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 09:40:09 +0100 Subject: [PATCH 8/9] Change inheritance mechanism of demo variant --- preClinVar/demo/Variant_sv_range_coords.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/preClinVar/demo/Variant_sv_range_coords.csv b/preClinVar/demo/Variant_sv_range_coords.csv index 87fbcc1..8bf5bf7 100644 --- a/preClinVar/demo/Variant_sv_range_coords.csv +++ b/preClinVar/demo/Variant_sv_range_coords.csv @@ -1,2 +1,2 @@ "##Local ID","Linking ID","Chromosome","Reference allele","Alternate allele","Variant type","Copy number","Reference copy number","Outer start","Inner start","Inner stop","Outer stop","Condition ID type","Condition ID value","Clinical significance","Date last evaluated","Mode of inheritance" -"77d69d4d78a8e272365bdabe4f607327","77d69d4d78a8e272365bdabe4f607327","15","TAAGAATGTTGTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA","T","Deletion","1","2","66633800","66633900","66634100","66634200","HPO","HP:0001298;HP:0001250","Likely pathogenic","2022-12-07","Somatic mutation" +"77d69d4d78a8e272365bdabe4f607327","77d69d4d78a8e272365bdabe4f607327","15","TAAGAATGTTGTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA","T","Deletion","1","2","66633800","66633900","66634100","66634200","HPO","HP:0001298;HP:0001250","Likely pathogenic","2022-12-07","Unknown mechanism" From 5a30214c9cb74c09e1b8477fbe25587172f4c3fe Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Thu, 1 Feb 2024 09:43:25 +0100 Subject: [PATCH 9/9] Updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e2d83d1..947536e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,7 @@ ### Changed - Updated version of external images in GitHub actions - Updated API submission schema to the latest +- Dmo variant to take care of "Somatic mutation" no longer available among Mode of inheritance choices ### Fixed - Bump certifi from 2022.12.7 to 2023.7.22 - Description of the response returned by dry run endpoint in README file