org.gel.models.report.avro.RareDiseaseExitQuestionnaire Maven / Gradle / Ivy
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.report.avro;
@SuppressWarnings("all")
/** The rare disease program exit questionnaire */
@org.apache.avro.specific.AvroGenerated
public class RareDiseaseExitQuestionnaire extends org.apache.avro.specific.SpecificRecordBase implements org.apache.avro.specific.SpecificRecord {
public static final org.apache.avro.Schema SCHEMA$ = new org.apache.avro.Schema.Parser().parse("{\"type\":\"record\",\"name\":\"RareDiseaseExitQuestionnaire\",\"namespace\":\"org.gel.models.report.avro\",\"doc\":\"The rare disease program exit questionnaire\",\"fields\":[{\"name\":\"eventDate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The date when the questionnaire was submitted\"},{\"name\":\"reporter\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The person that submitted the questionnaire\"},{\"name\":\"familyLevelQuestions\",\"type\":{\"type\":\"record\",\"name\":\"FamilyLevelQuestions\",\"doc\":\"The family level questions\",\"fields\":[{\"name\":\"caseSolvedFamily\",\"type\":{\"type\":\"enum\",\"name\":\"CaseSolvedFamily\",\"symbols\":[\"yes\",\"no\",\"partially\",\"unknown\"]},\"doc\":\"Have the results reported here explained the genetic basis of the family’s presenting phenotype(s)?\"},{\"name\":\"segregationQuestion\",\"type\":{\"type\":\"enum\",\"name\":\"SegregationQuestion\",\"symbols\":[\"yes\",\"no\"]},\"doc\":\"Have you done any segregation testing in non-participating family members?\"},{\"name\":\"additionalComments\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Comments regarding report\"}]},\"doc\":\"The set of questions at family level\"},{\"name\":\"variantGroupLevelQuestions\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantGroupLevelQuestions\",\"doc\":\"The variant group level questions\",\"fields\":[{\"name\":\"variantGroup\",\"type\":\"int\",\"doc\":\"This value groups variants that together could explain the phenotype according to the mode of inheritance used.\\n (e.g.: compound heterozygous). All the variants in the same report sharing the same value will be considered in\\n the same group (i.e.: reported together). This value is an integer unique in the whole report.\\n These values are only relevant within the same report.\"},{\"name\":\"variantLevelQuestions\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"VariantLevelQuestions\",\"doc\":\"The variant level questions\",\"fields\":[{\"name\":\"variantCoordinates\",\"type\":{\"type\":\"record\",\"name\":\"VariantCoordinates\",\"doc\":\"The variant coordinates representing uniquely a small variant.\\n No multi-allelic variant supported, alternate only represents one alternate allele.\",\"fields\":[{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"position\",\"type\":\"int\",\"doc\":\"Genomic position\"},{\"name\":\"reference\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The reference bases.\"},{\"name\":\"alternate\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The alternate bases\"},{\"name\":\"assembly\",\"type\":{\"type\":\"enum\",\"name\":\"Assembly\",\"doc\":\"The reference genome assembly\",\"symbols\":[\"GRCh38\",\"GRCh37\"]},\"doc\":\"The assembly to which this variant corresponds\"}]},\"doc\":\"Variant coordinates\"},{\"name\":\"confirmationDecision\",\"type\":{\"type\":\"enum\",\"name\":\"ConfirmationDecision\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did you carry out technical confirmation of this variant via an alternative test?\"},{\"name\":\"confirmationOutcome\",\"type\":{\"type\":\"enum\",\"name\":\"ConfirmationOutcome\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did the test confirm that the variant is present?\"},{\"name\":\"reportingQuestion\",\"type\":{\"type\":\"enum\",\"name\":\"ReportingQuestion\",\"symbols\":[\"yes\",\"no\",\"na\"]},\"doc\":\"Did you include the variant in your report to the clinician?\"},{\"name\":\"acmgClassification\",\"type\":{\"type\":\"enum\",\"name\":\"ACMGClassification\",\"symbols\":[\"pathogenic_variant\",\"likely_pathogenic_variant\",\"variant_of_unknown_clinical_significance\",\"likely_benign_variant\",\"benign_variant\",\"not_assessed\",\"na\"]},\"doc\":\"What ACMG pathogenicity score (1-5) did you assign to this variant?\"},{\"name\":\"publications\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers\"}]}}],\"doc\":\"Variant level questions for each of the variants in the group\"},{\"name\":\"shortTandemRepeatLevelQuestions\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"ShortTandemRepeatLevelQuestions\",\"doc\":\"The variant level questions\",\"fields\":[{\"name\":\"coordinates\",\"type\":{\"type\":\"record\",\"name\":\"Coordinates\",\"fields\":[{\"name\":\"assembly\",\"type\":\"Assembly\",\"doc\":\"The assembly to which this variant corresponds\"},{\"name\":\"chromosome\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Chromosome without \\\"chr\\\" prefix (e.g. X rather than chrX)\"},{\"name\":\"start\",\"type\":\"int\",\"doc\":\"Start genomic position for variant (1-based)\"},{\"name\":\"end\",\"type\":\"int\",\"doc\":\"End genomic position for variant\"},{\"name\":\"ciStart\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"ConfidenceInterval\",\"fields\":[{\"name\":\"left\",\"type\":\"int\"},{\"name\":\"right\",\"type\":\"int\"}]}]},{\"name\":\"ciEnd\",\"type\":[\"null\",\"ConfidenceInterval\"]}]},\"doc\":\"Variant coordinates\"},{\"name\":\"confirmationDecision\",\"type\":\"ConfirmationDecision\",\"doc\":\"Did you carry out technical confirmation of this variant via an alternative test?\"},{\"name\":\"confirmationOutcome\",\"type\":\"ConfirmationOutcome\",\"doc\":\"Did the test confirm that the variant is present?\"},{\"name\":\"reportingQuestion\",\"type\":\"ReportingQuestion\",\"doc\":\"Did you include the variant in your report to the clinician?\"},{\"name\":\"acmgClassification\",\"type\":\"ACMGClassification\",\"doc\":\"What ACMG pathogenicity score (1-5) did you assign to this variant?\"},{\"name\":\"publications\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers\"}]}}],\"doc\":\"STR level questions for each of the variants in the group\"},{\"name\":\"structuralVariantLevelQuestions\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"StructuralVariantLevelQuestions\",\"doc\":\"Structural variant level questions\",\"fields\":[{\"name\":\"variantType\",\"type\":{\"type\":\"enum\",\"name\":\"StructuralVariantType\",\"symbols\":[\"ins\",\"dup\",\"inv\",\"amplification\",\"deletion\",\"dup_tandem\",\"del_me\",\"ins_me\"]},\"doc\":\"Structural variant type\"},{\"name\":\"coordinates\",\"type\":\"Coordinates\",\"doc\":\"Variant coordinates\"},{\"name\":\"confirmationDecision\",\"type\":\"ConfirmationDecision\",\"doc\":\"Did you carry out technical confirmation of this variant via an alternative test?\"},{\"name\":\"confirmationOutcome\",\"type\":\"ConfirmationOutcome\",\"doc\":\"Did the test confirm that the variant is present?\"},{\"name\":\"reportingQuestion\",\"type\":\"ReportingQuestion\",\"doc\":\"Did you include the variant in your report to the clinician?\"},{\"name\":\"acmgClassification\",\"type\":\"ACMGClassification\",\"doc\":\"What ACMG pathogenicity score (1-5) did you assign to this variant?\"},{\"name\":\"publications\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Please provide PMIDs for papers which you have used to inform your assessment for this variant, separated by a `;` for multiple papers\"}]}}],\"doc\":\"Structural level questions for each of the variants in the group\"},{\"name\":\"actionability\",\"type\":{\"type\":\"enum\",\"name\":\"Actionability\",\"symbols\":[\"yes\",\"no\",\"not_yet\",\"na\"]},\"doc\":\"Is evidence for this variant/variant pair sufficient to use it for clinical purposes such as prenatal diagnosis or predictive testing?\"},{\"name\":\"clinicalUtility\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"enum\",\"name\":\"ClinicalUtility\",\"symbols\":[\"none\",\"change_in_medication\",\"surgical_option\",\"additional_surveillance_for_proband_or_relatives\",\"clinical_trial_eligibility\",\"informs_reproductive_choice\",\"unknown\",\"other\"]}},\"doc\":\"Has the clinical team identified any changes to clinical care which could potentially arise as a result of this variant/variant pair?\"},{\"name\":\"phenotypesSolved\",\"type\":{\"type\":\"enum\",\"name\":\"PhenotypesSolved\",\"symbols\":[\"yes\",\"no\",\"partially\",\"unknown\"]},\"doc\":\"Did you report the variant(s) as being partially or completely causative of the family's presenting phenotype(s)?\"},{\"name\":\"phenotypesExplained\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"If you indicated that the variant(s) only partially explained the family’s presenting phenotypes, please indicate which HPO terms you are confident that they DO explain\"}]}},\"doc\":\"The list of variant g","roup level variants (ungrouped variants are to be set in single variant group)\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** The date when the questionnaire was submitted */
private java.lang.String eventDate;
/** The person that submitted the questionnaire */
private java.lang.String reporter;
/** The set of questions at family level */
private org.gel.models.report.avro.FamilyLevelQuestions familyLevelQuestions;
/** The list of variant group level variants (ungrouped variants are to be set in single variant group) */
private java.util.List variantGroupLevelQuestions;
/**
* Default constructor. Note that this does not initialize fields
* to their default values from the schema. If that is desired then
* one should use newBuilder().
*/
public RareDiseaseExitQuestionnaire() {}
/**
* All-args constructor.
*/
public RareDiseaseExitQuestionnaire(java.lang.String eventDate, java.lang.String reporter, org.gel.models.report.avro.FamilyLevelQuestions familyLevelQuestions, java.util.List variantGroupLevelQuestions) {
this.eventDate = eventDate;
this.reporter = reporter;
this.familyLevelQuestions = familyLevelQuestions;
this.variantGroupLevelQuestions = variantGroupLevelQuestions;
}
public org.apache.avro.Schema getSchema() { return SCHEMA$; }
// Used by DatumWriter. Applications should not call.
public java.lang.Object get(int field$) {
switch (field$) {
case 0: return eventDate;
case 1: return reporter;
case 2: return familyLevelQuestions;
case 3: return variantGroupLevelQuestions;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
// Used by DatumReader. Applications should not call.
@SuppressWarnings(value="unchecked")
public void put(int field$, java.lang.Object value$) {
switch (field$) {
case 0: eventDate = (java.lang.String)value$; break;
case 1: reporter = (java.lang.String)value$; break;
case 2: familyLevelQuestions = (org.gel.models.report.avro.FamilyLevelQuestions)value$; break;
case 3: variantGroupLevelQuestions = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'eventDate' field.
* The date when the questionnaire was submitted */
public java.lang.String getEventDate() {
return eventDate;
}
/**
* Sets the value of the 'eventDate' field.
* The date when the questionnaire was submitted * @param value the value to set.
*/
public void setEventDate(java.lang.String value) {
this.eventDate = value;
}
/**
* Gets the value of the 'reporter' field.
* The person that submitted the questionnaire */
public java.lang.String getReporter() {
return reporter;
}
/**
* Sets the value of the 'reporter' field.
* The person that submitted the questionnaire * @param value the value to set.
*/
public void setReporter(java.lang.String value) {
this.reporter = value;
}
/**
* Gets the value of the 'familyLevelQuestions' field.
* The set of questions at family level */
public org.gel.models.report.avro.FamilyLevelQuestions getFamilyLevelQuestions() {
return familyLevelQuestions;
}
/**
* Sets the value of the 'familyLevelQuestions' field.
* The set of questions at family level * @param value the value to set.
*/
public void setFamilyLevelQuestions(org.gel.models.report.avro.FamilyLevelQuestions value) {
this.familyLevelQuestions = value;
}
/**
* Gets the value of the 'variantGroupLevelQuestions' field.
* The list of variant group level variants (ungrouped variants are to be set in single variant group) */
public java.util.List getVariantGroupLevelQuestions() {
return variantGroupLevelQuestions;
}
/**
* Sets the value of the 'variantGroupLevelQuestions' field.
* The list of variant group level variants (ungrouped variants are to be set in single variant group) * @param value the value to set.
*/
public void setVariantGroupLevelQuestions(java.util.List value) {
this.variantGroupLevelQuestions = value;
}
/** Creates a new RareDiseaseExitQuestionnaire RecordBuilder */
public static org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder newBuilder() {
return new org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder();
}
/** Creates a new RareDiseaseExitQuestionnaire RecordBuilder by copying an existing Builder */
public static org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder newBuilder(org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder other) {
return new org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder(other);
}
/** Creates a new RareDiseaseExitQuestionnaire RecordBuilder by copying an existing RareDiseaseExitQuestionnaire instance */
public static org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder newBuilder(org.gel.models.report.avro.RareDiseaseExitQuestionnaire other) {
return new org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder(other);
}
/**
* RecordBuilder for RareDiseaseExitQuestionnaire instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String eventDate;
private java.lang.String reporter;
private org.gel.models.report.avro.FamilyLevelQuestions familyLevelQuestions;
private java.util.List variantGroupLevelQuestions;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.report.avro.RareDiseaseExitQuestionnaire.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder other) {
super(other);
if (isValidValue(fields()[0], other.eventDate)) {
this.eventDate = data().deepCopy(fields()[0].schema(), other.eventDate);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.reporter)) {
this.reporter = data().deepCopy(fields()[1].schema(), other.reporter);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.familyLevelQuestions)) {
this.familyLevelQuestions = data().deepCopy(fields()[2].schema(), other.familyLevelQuestions);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.variantGroupLevelQuestions)) {
this.variantGroupLevelQuestions = data().deepCopy(fields()[3].schema(), other.variantGroupLevelQuestions);
fieldSetFlags()[3] = true;
}
}
/** Creates a Builder by copying an existing RareDiseaseExitQuestionnaire instance */
private Builder(org.gel.models.report.avro.RareDiseaseExitQuestionnaire other) {
super(org.gel.models.report.avro.RareDiseaseExitQuestionnaire.SCHEMA$);
if (isValidValue(fields()[0], other.eventDate)) {
this.eventDate = data().deepCopy(fields()[0].schema(), other.eventDate);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.reporter)) {
this.reporter = data().deepCopy(fields()[1].schema(), other.reporter);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.familyLevelQuestions)) {
this.familyLevelQuestions = data().deepCopy(fields()[2].schema(), other.familyLevelQuestions);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.variantGroupLevelQuestions)) {
this.variantGroupLevelQuestions = data().deepCopy(fields()[3].schema(), other.variantGroupLevelQuestions);
fieldSetFlags()[3] = true;
}
}
/** Gets the value of the 'eventDate' field */
public java.lang.String getEventDate() {
return eventDate;
}
/** Sets the value of the 'eventDate' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder setEventDate(java.lang.String value) {
validate(fields()[0], value);
this.eventDate = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'eventDate' field has been set */
public boolean hasEventDate() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'eventDate' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder clearEventDate() {
eventDate = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'reporter' field */
public java.lang.String getReporter() {
return reporter;
}
/** Sets the value of the 'reporter' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder setReporter(java.lang.String value) {
validate(fields()[1], value);
this.reporter = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'reporter' field has been set */
public boolean hasReporter() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'reporter' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder clearReporter() {
reporter = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'familyLevelQuestions' field */
public org.gel.models.report.avro.FamilyLevelQuestions getFamilyLevelQuestions() {
return familyLevelQuestions;
}
/** Sets the value of the 'familyLevelQuestions' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder setFamilyLevelQuestions(org.gel.models.report.avro.FamilyLevelQuestions value) {
validate(fields()[2], value);
this.familyLevelQuestions = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'familyLevelQuestions' field has been set */
public boolean hasFamilyLevelQuestions() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'familyLevelQuestions' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder clearFamilyLevelQuestions() {
familyLevelQuestions = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'variantGroupLevelQuestions' field */
public java.util.List getVariantGroupLevelQuestions() {
return variantGroupLevelQuestions;
}
/** Sets the value of the 'variantGroupLevelQuestions' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder setVariantGroupLevelQuestions(java.util.List value) {
validate(fields()[3], value);
this.variantGroupLevelQuestions = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'variantGroupLevelQuestions' field has been set */
public boolean hasVariantGroupLevelQuestions() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'variantGroupLevelQuestions' field */
public org.gel.models.report.avro.RareDiseaseExitQuestionnaire.Builder clearVariantGroupLevelQuestions() {
variantGroupLevelQuestions = null;
fieldSetFlags()[3] = false;
return this;
}
@Override
public RareDiseaseExitQuestionnaire build() {
try {
RareDiseaseExitQuestionnaire record = new RareDiseaseExitQuestionnaire();
record.eventDate = fieldSetFlags()[0] ? this.eventDate : (java.lang.String) defaultValue(fields()[0]);
record.reporter = fieldSetFlags()[1] ? this.reporter : (java.lang.String) defaultValue(fields()[1]);
record.familyLevelQuestions = fieldSetFlags()[2] ? this.familyLevelQuestions : (org.gel.models.report.avro.FamilyLevelQuestions) defaultValue(fields()[2]);
record.variantGroupLevelQuestions = fieldSetFlags()[3] ? this.variantGroupLevelQuestions : (java.util.List) defaultValue(fields()[3]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
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