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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.participant.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public class ReferralTest 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\":\"ReferralTest\",\"namespace\":\"org.gel.models.participant.avro\",\"fields\":[{\"name\":\"referralTestId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Test UID\"},{\"name\":\"referralTestOrderingDate\",\"type\":[\"null\",{\"type\":\"record\",\"name\":\"Date\",\"doc\":\"This defines a date record\",\"fields\":[{\"name\":\"year\",\"type\":\"int\",\"doc\":\"Format YYYY\"},{\"name\":\"month\",\"type\":[\"null\",\"int\"],\"doc\":\"Format MM. e.g June is 06\"},{\"name\":\"day\",\"type\":[\"null\",\"int\"],\"doc\":\"Format DD e.g. 12th of October is 12\"}]}],\"doc\":\"The date of which the referralTest was sent to Bioinformatics\"},{\"name\":\"clinicalIndicationTest\",\"type\":{\"type\":\"record\",\"name\":\"ClinicalIndicationTest\",\"fields\":[{\"name\":\"clinicalIndicationTestTypeId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Clinical indication Test type ID\"},{\"name\":\"clinicalIndicationTestTypeCode\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Clinical indication Test code (e.g. R13-1)\"},{\"name\":\"testTypeId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Test Type Id\"},{\"name\":\"testTypeName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Test Type Name\"},{\"name\":\"technology\",\"type\":{\"type\":\"record\",\"name\":\"Technology\",\"fields\":[{\"name\":\"testTechnologyId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Technology unique identifier\"},{\"name\":\"testTechnologyDescription\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Technology description\"}]},\"doc\":\"Technology used in ClinicalIndicationTest\"}]},\"doc\":\"Clinical indication test\"},{\"name\":\"tumourSamples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"TumourSample\",\"doc\":\"A tumour sample\",\"fields\":[{\"name\":\"sampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample identifier (e.g, LP00012645_5GH))\"},{\"name\":\"labSampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Lab sample identifier\"},{\"name\":\"LDPCode\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"LDP Code (Local Delivery Partner)\"},{\"name\":\"tumourId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"This is the ID of the tumour from which this tumour sample was taken from\"},{\"name\":\"programmePhase\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Genomics England programme phase\"},{\"name\":\"diseaseType\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"diseaseType\",\"symbols\":[\"ADULT_GLIOMA\",\"BLADDER\",\"BREAST\",\"CARCINOMA_OF_UNKNOWN_PRIMARY\",\"CHILDHOOD\",\"COLORECTAL\",\"ENDOCRINE\",\"ENDOMETRIAL_CARCINOMA\",\"HAEMONC\",\"HEPATOPANCREATOBILIARY\",\"LUNG\",\"MALIGNANT_MELANOMA\",\"NASOPHARYNGEAL\",\"ORAL_OROPHARYNGEAL\",\"OVARIAN\",\"PROSTATE\",\"RENAL\",\"SARCOMA\",\"SINONASAL\",\"TESTICULAR_GERM_CELL_TUMOURS\",\"UPPER_GASTROINTESTINAL\",\"OTHER\",\"NON_HODGKINS_B_CELL_LYMPHOMA_LOW_MOD_GRADE\",\"CLASSICAL_HODGKINS\",\"NODULAR_LYMPHOCYTE_PREDOMINANT_HODGKINS\",\"T_CELL_LYMPHOMA\"]}],\"doc\":\"Disease type.\\n NOTE: Deprecated in GMS\"},{\"name\":\"diseaseSubType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Disease subtype.\\n NOTE: Deprecated in GMS\"},{\"name\":\"haematologicalCancer\",\"type\":[\"null\",\"boolean\"],\"doc\":\"True or false if this sample is of type: Haematological Cancer\"},{\"name\":\"haematologicalCancerLineage\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"HaematologicalCancerLineage\",\"symbols\":[\"MYELOID\",\"LYMPHOID\",\"UNKNOWN\"]}],\"doc\":\"This is the Haematological cancer lineage of the tumourSample if this sample is from a haematological cancer\"},{\"name\":\"clinicalSampleDateTime\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The time when the sample was received. In the format YYYY-MM-DDTHH:MM:SS+0000\"},{\"name\":\"tumourType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Tumor type.\\n NOTE: Deprecated in GMS in tumourSample but available in tumour record\"},{\"name\":\"tumourContent\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"TumourContent\",\"symbols\":[\"High\",\"Medium\",\"Low\"]}],\"doc\":\"This is the tumour content\"},{\"name\":\"tumourContentPercentage\",\"type\":[\"null\",\"float\"],\"doc\":\"This is the tumour content percentage\"},{\"name\":\"source\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"SampleSource\",\"doc\":\"The source of the sample\\n NOTE: IN GMS, BONE_MARROW_ASPIRATE_TUMOUR_CELLS and BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS are deprecated as they have been separated into their respective biotypes\",\"symbols\":[\"AMNIOTIC_FLUID\",\"BLOOD\",\"BONE_MARROW\",\"BONE_MARROW_ASPIRATE_TUMOUR_CELLS\",\"BONE_MARROW_ASPIRATE_TUMOUR_SORTED_CELLS\",\"BUCCAL_SWAB\",\"CHORIONIC_VILLUS_SAMPLE\",\"FIBROBLAST\",\"FLUID\",\"FRESH_TISSUE_IN_CULTURE_MEDIUM\",\"OTHER\",\"SALIVA\",\"TISSUE\",\"TUMOUR\",\"URINE\"]}],\"doc\":\"Source of the sample\"},{\"name\":\"preparationMethod\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"PreparationMethod\",\"doc\":\"In 100K, preparation Method of sample\\n NOTE: In GMS, this field is deprecated in favour of StorageMedium and Method\",\"symbols\":[\"ASPIRATE\",\"CD128_SORTED_CELLS\",\"CD138_SORTED_CELLS\",\"EDTA\",\"FF\",\"FFPE\",\"LI_HEP\",\"ORAGENE\"]}],\"doc\":\"The preparation method of the sample\\n NOTE: Deprecated in GMS in replace of Method and storageMedium record\"},{\"name\":\"tissueSource\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The tissue source of the sample.\\n NOTE: DEPRECATED IN GMS in replace of method record\"},{\"name\":\"product\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Product\",\"symbols\":[\"DNA\",\"RNA\"]}],\"doc\":\"Product of the sample\"},{\"name\":\"sampleMorphologies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Morphology\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)\"},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term name\"},{\"name\":\"value\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Optional value for the ontology term, the type of the value is not checked\\n (i.e.: we could set the pvalue term to \\\"significant\\\" or to \\\"0.0001\\\")\"},{\"name\":\"version\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Ontology version\"}]}}],\"doc\":\"Morphology according to the sample taken\"},{\"name\":\"sampleTopographies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"Topography\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)\"},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term name\"},{\"name\":\"value\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Optional value for the ontology term, the type of the value is not checked\\n (i.e.: we could set the pvalue term to \\\"significant\\\" or to \\\"0.0001\\\")\"},{\"name\":\"version\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Ontology version\"}]}}],\"doc\":\"Topography according to the sample taken\"},{\"name\":\"sampleUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the GUID of the sample\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Participant Id of the sample\"},{\"name\":\"participantUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Participant UId of the sample\"},{\"name\":\"maskedPid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the maskedPID\"},{\"name\":\"method\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"Method\",\"doc\":\"In GMS, Method is defined as how the sample was taken directly from the patient\",\"symbols\":[\"ASPIRATE\",\"BIOPSY\",\"NOT_APPLICABLE\",\"RESECTION\",\"SORTED_OTHER\",\"UNKNOWN\",\"UNSORTED\",\"CD138_SORTED\"]}],\"doc\":\"In GMS, this is how the sample was extracted from the participant\"},{\"name\":\"storageMedium\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"StorageMedium\",\"doc\":\"In GMS, storage medium of sample\",\"symbols\":[\"EDTA\",\"FF\",\"LI_HEP\",\"ORAGENE\",\"FFPE\"]}],\"doc\":\"In GMS, this is what solvent/medium the sample was stored in\"},","{\"name\":\"sampleType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleType as entered by the clinician in TOMs\"},{\"name\":\"sampleState\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleState as entered by the clinician in TOMs\"}]}}],\"doc\":\"List of all somatic samples applicable to this test\"},{\"name\":\"germlineSamples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"GermlineSample\",\"doc\":\"A germline sample\",\"fields\":[{\"name\":\"sampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Sample identifier (e.g, LP00012645_5GH))\"},{\"name\":\"labSampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Lab sample identifier\"},{\"name\":\"LDPCode\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"LDP Code (Local Delivery Partner)\"},{\"name\":\"source\",\"type\":[\"null\",\"SampleSource\"],\"doc\":\"Source of the sample\"},{\"name\":\"product\",\"type\":[\"null\",\"Product\"],\"doc\":\"Product of the sample\"},{\"name\":\"preparationMethod\",\"type\":[\"null\",\"PreparationMethod\"],\"doc\":\"Preparation method\\n NOTE: In GMS, this has been deprecated in favour of Method and storageMedium\"},{\"name\":\"programmePhase\",\"type\":[\"null\",{\"type\":\"enum\",\"name\":\"ProgrammePhase\",\"symbols\":[\"CRUK\",\"OXFORD\",\"CLL\",\"IIP\",\"MAIN\",\"EXPT\"]}],\"doc\":\"Genomics England programme phase\"},{\"name\":\"clinicalSampleDateTime\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The time when the sample was received. In the format YYYY-MM-DDTHH:MM:SS+0000\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"participantUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Participant UId of the sample\"},{\"name\":\"sampleUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"maskedPid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"method\",\"type\":[\"null\",\"Method\"],\"doc\":\"In GMS, this is how the sample was extracted from the participant\"},{\"name\":\"storageMedium\",\"type\":[\"null\",\"StorageMedium\"],\"doc\":\"In GMS, this is what solvent/medium the sample was stored in\"},{\"name\":\"sampleType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleType as entered by the clinician in TOMs\"},{\"name\":\"sampleState\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"In GMS, this is the sampleState as entered by the clinician in TOMs\"}]}}],\"doc\":\"List of all germline samples aplicable to this test\"},{\"name\":\"analysisPanels\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"AnalysisPanel\",\"doc\":\"An analysis panel\",\"fields\":[{\"name\":\"specificDisease\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The specific disease that a panel tests\"},{\"name\":\"panelName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The name of the panel\"},{\"name\":\"panelId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Id of the panel\"},{\"name\":\"panelVersion\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The version of the panel\"},{\"name\":\"reviewOutcome\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Deprecated\"},{\"name\":\"multipleGeneticOrigins\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Deprecated\"}]}}],\"doc\":\"List of Analysis panels\"},{\"name\":\"interpreter\",\"type\":{\"type\":\"record\",\"name\":\"OrganisationNgis\",\"fields\":[{\"name\":\"organisationId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Organisation Id\"},{\"name\":\"organisationCode\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Ods code\"},{\"name\":\"organisationName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Organisation Name\"},{\"name\":\"organisationNationalGroupingId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"National Grouping (GLH) Id\"},{\"name\":\"organisationNationalGroupingName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"National Grouping (GLH) Name\"}]},\"doc\":\"Organisation assigned for the interpretation of this test\"},{\"name\":\"processingLab\",\"type\":\"OrganisationNgis\",\"doc\":\"Organisation assigned for the processing of the test\"},{\"name\":\"priority\",\"type\":{\"type\":\"enum\",\"name\":\"Priority\",\"doc\":\"Transformed from TOMs from routine=medium, and urgent=high\",\"symbols\":[\"low\",\"routine\",\"urgent\"]},\"doc\":\"Priority\"},{\"name\":\"pipelineStartDate\",\"type\":[\"null\",\"Date\"],\"doc\":\"Date of ordering. NOTE: this field is not required from upstream\\n and will be generated by Bioinformatics when all sample data and all\\n required clinical data is received for the first time\"},{\"name\":\"diseasePenetrances\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"DiseasePenetrance\",\"doc\":\"A disease penetrance definition\",\"fields\":[{\"name\":\"specificDisease\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"The disease to which the penetrance applies\"},{\"name\":\"penetrance\",\"type\":{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetrance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]},\"doc\":\"The penetrance\"}]}}],\"doc\":\"Disease Penetrance applied for that referralTest\"},{\"name\":\"matchedSamples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"record\",\"name\":\"MatchedSamples\",\"doc\":\"This defines a pair of germline and tumor, this pair should/must be analyzed together\",\"fields\":[{\"name\":\"germlineSampleId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Sample identifier (e.g, LP00012645_5GH)) for the germline\"},{\"name\":\"tumourSampleId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Sample identifier (e.g, LP00012643_7JS)) for the tumor\"}]}}],\"doc\":\"List of matched samples (i.e.: pairs tumour-germline)\"}]}");
public static org.apache.avro.Schema getClassSchema() { return SCHEMA$; }
/** Test UID */
private java.lang.String referralTestId;
/** The date of which the referralTest was sent to Bioinformatics */
private org.gel.models.participant.avro.Date referralTestOrderingDate;
/** Clinical indication test */
private org.gel.models.participant.avro.ClinicalIndicationTest clinicalIndicationTest;
/** List of all somatic samples applicable to this test */
private java.util.List tumourSamples;
/** List of all germline samples aplicable to this test */
private java.util.List germlineSamples;
/** List of Analysis panels */
private java.util.List analysisPanels;
/** Organisation assigned for the interpretation of this test */
private org.gel.models.participant.avro.OrganisationNgis interpreter;
/** Organisation assigned for the processing of the test */
private org.gel.models.participant.avro.OrganisationNgis processingLab;
/** Priority */
private org.gel.models.participant.avro.Priority priority;
/** Date of ordering. NOTE: this field is not required from upstream
and will be generated by Bioinformatics when all sample data and all
required clinical data is received for the first time */
private org.gel.models.participant.avro.Date pipelineStartDate;
/** Disease Penetrance applied for that referralTest */
private java.util.List diseasePenetrances;
/** List of matched samples (i.e.: pairs tumour-germline) */
private java.util.List matchedSamples;
/**
* 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 ReferralTest() {}
/**
* All-args constructor.
*/
public ReferralTest(java.lang.String referralTestId, org.gel.models.participant.avro.Date referralTestOrderingDate, org.gel.models.participant.avro.ClinicalIndicationTest clinicalIndicationTest, java.util.List tumourSamples, java.util.List germlineSamples, java.util.List analysisPanels, org.gel.models.participant.avro.OrganisationNgis interpreter, org.gel.models.participant.avro.OrganisationNgis processingLab, org.gel.models.participant.avro.Priority priority, org.gel.models.participant.avro.Date pipelineStartDate, java.util.List diseasePenetrances, java.util.List matchedSamples) {
this.referralTestId = referralTestId;
this.referralTestOrderingDate = referralTestOrderingDate;
this.clinicalIndicationTest = clinicalIndicationTest;
this.tumourSamples = tumourSamples;
this.germlineSamples = germlineSamples;
this.analysisPanels = analysisPanels;
this.interpreter = interpreter;
this.processingLab = processingLab;
this.priority = priority;
this.pipelineStartDate = pipelineStartDate;
this.diseasePenetrances = diseasePenetrances;
this.matchedSamples = matchedSamples;
}
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 referralTestId;
case 1: return referralTestOrderingDate;
case 2: return clinicalIndicationTest;
case 3: return tumourSamples;
case 4: return germlineSamples;
case 5: return analysisPanels;
case 6: return interpreter;
case 7: return processingLab;
case 8: return priority;
case 9: return pipelineStartDate;
case 10: return diseasePenetrances;
case 11: return matchedSamples;
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$) {
case 0: referralTestId = (java.lang.String)value$; break;
case 1: referralTestOrderingDate = (org.gel.models.participant.avro.Date)value$; break;
case 2: clinicalIndicationTest = (org.gel.models.participant.avro.ClinicalIndicationTest)value$; break;
case 3: tumourSamples = (java.util.List)value$; break;
case 4: germlineSamples = (java.util.List)value$; break;
case 5: analysisPanels = (java.util.List)value$; break;
case 6: interpreter = (org.gel.models.participant.avro.OrganisationNgis)value$; break;
case 7: processingLab = (org.gel.models.participant.avro.OrganisationNgis)value$; break;
case 8: priority = (org.gel.models.participant.avro.Priority)value$; break;
case 9: pipelineStartDate = (org.gel.models.participant.avro.Date)value$; break;
case 10: diseasePenetrances = (java.util.List)value$; break;
case 11: matchedSamples = (java.util.List)value$; break;
default: throw new org.apache.avro.AvroRuntimeException("Bad index");
}
}
/**
* Gets the value of the 'referralTestId' field.
* Test UID */
public java.lang.String getReferralTestId() {
return referralTestId;
}
/**
* Sets the value of the 'referralTestId' field.
* Test UID * @param value the value to set.
*/
public void setReferralTestId(java.lang.String value) {
this.referralTestId = value;
}
/**
* Gets the value of the 'referralTestOrderingDate' field.
* The date of which the referralTest was sent to Bioinformatics */
public org.gel.models.participant.avro.Date getReferralTestOrderingDate() {
return referralTestOrderingDate;
}
/**
* Sets the value of the 'referralTestOrderingDate' field.
* The date of which the referralTest was sent to Bioinformatics * @param value the value to set.
*/
public void setReferralTestOrderingDate(org.gel.models.participant.avro.Date value) {
this.referralTestOrderingDate = value;
}
/**
* Gets the value of the 'clinicalIndicationTest' field.
* Clinical indication test */
public org.gel.models.participant.avro.ClinicalIndicationTest getClinicalIndicationTest() {
return clinicalIndicationTest;
}
/**
* Sets the value of the 'clinicalIndicationTest' field.
* Clinical indication test * @param value the value to set.
*/
public void setClinicalIndicationTest(org.gel.models.participant.avro.ClinicalIndicationTest value) {
this.clinicalIndicationTest = value;
}
/**
* Gets the value of the 'tumourSamples' field.
* List of all somatic samples applicable to this test */
public java.util.List getTumourSamples() {
return tumourSamples;
}
/**
* Sets the value of the 'tumourSamples' field.
* List of all somatic samples applicable to this test * @param value the value to set.
*/
public void setTumourSamples(java.util.List value) {
this.tumourSamples = value;
}
/**
* Gets the value of the 'germlineSamples' field.
* List of all germline samples aplicable to this test */
public java.util.List getGermlineSamples() {
return germlineSamples;
}
/**
* Sets the value of the 'germlineSamples' field.
* List of all germline samples aplicable to this test * @param value the value to set.
*/
public void setGermlineSamples(java.util.List value) {
this.germlineSamples = value;
}
/**
* Gets the value of the 'analysisPanels' field.
* List of Analysis panels */
public java.util.List getAnalysisPanels() {
return analysisPanels;
}
/**
* Sets the value of the 'analysisPanels' field.
* List of Analysis panels * @param value the value to set.
*/
public void setAnalysisPanels(java.util.List value) {
this.analysisPanels = value;
}
/**
* Gets the value of the 'interpreter' field.
* Organisation assigned for the interpretation of this test */
public org.gel.models.participant.avro.OrganisationNgis getInterpreter() {
return interpreter;
}
/**
* Sets the value of the 'interpreter' field.
* Organisation assigned for the interpretation of this test * @param value the value to set.
*/
public void setInterpreter(org.gel.models.participant.avro.OrganisationNgis value) {
this.interpreter = value;
}
/**
* Gets the value of the 'processingLab' field.
* Organisation assigned for the processing of the test */
public org.gel.models.participant.avro.OrganisationNgis getProcessingLab() {
return processingLab;
}
/**
* Sets the value of the 'processingLab' field.
* Organisation assigned for the processing of the test * @param value the value to set.
*/
public void setProcessingLab(org.gel.models.participant.avro.OrganisationNgis value) {
this.processingLab = value;
}
/**
* Gets the value of the 'priority' field.
* Priority */
public org.gel.models.participant.avro.Priority getPriority() {
return priority;
}
/**
* Sets the value of the 'priority' field.
* Priority * @param value the value to set.
*/
public void setPriority(org.gel.models.participant.avro.Priority value) {
this.priority = value;
}
/**
* Gets the value of the 'pipelineStartDate' field.
* Date of ordering. NOTE: this field is not required from upstream
and will be generated by Bioinformatics when all sample data and all
required clinical data is received for the first time */
public org.gel.models.participant.avro.Date getPipelineStartDate() {
return pipelineStartDate;
}
/**
* Sets the value of the 'pipelineStartDate' field.
* Date of ordering. NOTE: this field is not required from upstream
and will be generated by Bioinformatics when all sample data and all
required clinical data is received for the first time * @param value the value to set.
*/
public void setPipelineStartDate(org.gel.models.participant.avro.Date value) {
this.pipelineStartDate = value;
}
/**
* Gets the value of the 'diseasePenetrances' field.
* Disease Penetrance applied for that referralTest */
public java.util.List getDiseasePenetrances() {
return diseasePenetrances;
}
/**
* Sets the value of the 'diseasePenetrances' field.
* Disease Penetrance applied for that referralTest * @param value the value to set.
*/
public void setDiseasePenetrances(java.util.List value) {
this.diseasePenetrances = value;
}
/**
* Gets the value of the 'matchedSamples' field.
* List of matched samples (i.e.: pairs tumour-germline) */
public java.util.List getMatchedSamples() {
return matchedSamples;
}
/**
* Sets the value of the 'matchedSamples' field.
* List of matched samples (i.e.: pairs tumour-germline) * @param value the value to set.
*/
public void setMatchedSamples(java.util.List value) {
this.matchedSamples = value;
}
/** Creates a new ReferralTest RecordBuilder */
public static org.gel.models.participant.avro.ReferralTest.Builder newBuilder() {
return new org.gel.models.participant.avro.ReferralTest.Builder();
}
/** Creates a new ReferralTest RecordBuilder by copying an existing Builder */
public static org.gel.models.participant.avro.ReferralTest.Builder newBuilder(org.gel.models.participant.avro.ReferralTest.Builder other) {
return new org.gel.models.participant.avro.ReferralTest.Builder(other);
}
/** Creates a new ReferralTest RecordBuilder by copying an existing ReferralTest instance */
public static org.gel.models.participant.avro.ReferralTest.Builder newBuilder(org.gel.models.participant.avro.ReferralTest other) {
return new org.gel.models.participant.avro.ReferralTest.Builder(other);
}
/**
* RecordBuilder for ReferralTest instances.
*/
public static class Builder extends org.apache.avro.specific.SpecificRecordBuilderBase
implements org.apache.avro.data.RecordBuilder {
private java.lang.String referralTestId;
private org.gel.models.participant.avro.Date referralTestOrderingDate;
private org.gel.models.participant.avro.ClinicalIndicationTest clinicalIndicationTest;
private java.util.List tumourSamples;
private java.util.List germlineSamples;
private java.util.List analysisPanels;
private org.gel.models.participant.avro.OrganisationNgis interpreter;
private org.gel.models.participant.avro.OrganisationNgis processingLab;
private org.gel.models.participant.avro.Priority priority;
private org.gel.models.participant.avro.Date pipelineStartDate;
private java.util.List diseasePenetrances;
private java.util.List matchedSamples;
/** Creates a new Builder */
private Builder() {
super(org.gel.models.participant.avro.ReferralTest.SCHEMA$);
}
/** Creates a Builder by copying an existing Builder */
private Builder(org.gel.models.participant.avro.ReferralTest.Builder other) {
super(other);
if (isValidValue(fields()[0], other.referralTestId)) {
this.referralTestId = data().deepCopy(fields()[0].schema(), other.referralTestId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.referralTestOrderingDate)) {
this.referralTestOrderingDate = data().deepCopy(fields()[1].schema(), other.referralTestOrderingDate);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.clinicalIndicationTest)) {
this.clinicalIndicationTest = data().deepCopy(fields()[2].schema(), other.clinicalIndicationTest);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.tumourSamples)) {
this.tumourSamples = data().deepCopy(fields()[3].schema(), other.tumourSamples);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.germlineSamples)) {
this.germlineSamples = data().deepCopy(fields()[4].schema(), other.germlineSamples);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.analysisPanels)) {
this.analysisPanels = data().deepCopy(fields()[5].schema(), other.analysisPanels);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.interpreter)) {
this.interpreter = data().deepCopy(fields()[6].schema(), other.interpreter);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.processingLab)) {
this.processingLab = data().deepCopy(fields()[7].schema(), other.processingLab);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.priority)) {
this.priority = data().deepCopy(fields()[8].schema(), other.priority);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.pipelineStartDate)) {
this.pipelineStartDate = data().deepCopy(fields()[9].schema(), other.pipelineStartDate);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.diseasePenetrances)) {
this.diseasePenetrances = data().deepCopy(fields()[10].schema(), other.diseasePenetrances);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.matchedSamples)) {
this.matchedSamples = data().deepCopy(fields()[11].schema(), other.matchedSamples);
fieldSetFlags()[11] = true;
}
}
/** Creates a Builder by copying an existing ReferralTest instance */
private Builder(org.gel.models.participant.avro.ReferralTest other) {
super(org.gel.models.participant.avro.ReferralTest.SCHEMA$);
if (isValidValue(fields()[0], other.referralTestId)) {
this.referralTestId = data().deepCopy(fields()[0].schema(), other.referralTestId);
fieldSetFlags()[0] = true;
}
if (isValidValue(fields()[1], other.referralTestOrderingDate)) {
this.referralTestOrderingDate = data().deepCopy(fields()[1].schema(), other.referralTestOrderingDate);
fieldSetFlags()[1] = true;
}
if (isValidValue(fields()[2], other.clinicalIndicationTest)) {
this.clinicalIndicationTest = data().deepCopy(fields()[2].schema(), other.clinicalIndicationTest);
fieldSetFlags()[2] = true;
}
if (isValidValue(fields()[3], other.tumourSamples)) {
this.tumourSamples = data().deepCopy(fields()[3].schema(), other.tumourSamples);
fieldSetFlags()[3] = true;
}
if (isValidValue(fields()[4], other.germlineSamples)) {
this.germlineSamples = data().deepCopy(fields()[4].schema(), other.germlineSamples);
fieldSetFlags()[4] = true;
}
if (isValidValue(fields()[5], other.analysisPanels)) {
this.analysisPanels = data().deepCopy(fields()[5].schema(), other.analysisPanels);
fieldSetFlags()[5] = true;
}
if (isValidValue(fields()[6], other.interpreter)) {
this.interpreter = data().deepCopy(fields()[6].schema(), other.interpreter);
fieldSetFlags()[6] = true;
}
if (isValidValue(fields()[7], other.processingLab)) {
this.processingLab = data().deepCopy(fields()[7].schema(), other.processingLab);
fieldSetFlags()[7] = true;
}
if (isValidValue(fields()[8], other.priority)) {
this.priority = data().deepCopy(fields()[8].schema(), other.priority);
fieldSetFlags()[8] = true;
}
if (isValidValue(fields()[9], other.pipelineStartDate)) {
this.pipelineStartDate = data().deepCopy(fields()[9].schema(), other.pipelineStartDate);
fieldSetFlags()[9] = true;
}
if (isValidValue(fields()[10], other.diseasePenetrances)) {
this.diseasePenetrances = data().deepCopy(fields()[10].schema(), other.diseasePenetrances);
fieldSetFlags()[10] = true;
}
if (isValidValue(fields()[11], other.matchedSamples)) {
this.matchedSamples = data().deepCopy(fields()[11].schema(), other.matchedSamples);
fieldSetFlags()[11] = true;
}
}
/** Gets the value of the 'referralTestId' field */
public java.lang.String getReferralTestId() {
return referralTestId;
}
/** Sets the value of the 'referralTestId' field */
public org.gel.models.participant.avro.ReferralTest.Builder setReferralTestId(java.lang.String value) {
validate(fields()[0], value);
this.referralTestId = value;
fieldSetFlags()[0] = true;
return this;
}
/** Checks whether the 'referralTestId' field has been set */
public boolean hasReferralTestId() {
return fieldSetFlags()[0];
}
/** Clears the value of the 'referralTestId' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearReferralTestId() {
referralTestId = null;
fieldSetFlags()[0] = false;
return this;
}
/** Gets the value of the 'referralTestOrderingDate' field */
public org.gel.models.participant.avro.Date getReferralTestOrderingDate() {
return referralTestOrderingDate;
}
/** Sets the value of the 'referralTestOrderingDate' field */
public org.gel.models.participant.avro.ReferralTest.Builder setReferralTestOrderingDate(org.gel.models.participant.avro.Date value) {
validate(fields()[1], value);
this.referralTestOrderingDate = value;
fieldSetFlags()[1] = true;
return this;
}
/** Checks whether the 'referralTestOrderingDate' field has been set */
public boolean hasReferralTestOrderingDate() {
return fieldSetFlags()[1];
}
/** Clears the value of the 'referralTestOrderingDate' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearReferralTestOrderingDate() {
referralTestOrderingDate = null;
fieldSetFlags()[1] = false;
return this;
}
/** Gets the value of the 'clinicalIndicationTest' field */
public org.gel.models.participant.avro.ClinicalIndicationTest getClinicalIndicationTest() {
return clinicalIndicationTest;
}
/** Sets the value of the 'clinicalIndicationTest' field */
public org.gel.models.participant.avro.ReferralTest.Builder setClinicalIndicationTest(org.gel.models.participant.avro.ClinicalIndicationTest value) {
validate(fields()[2], value);
this.clinicalIndicationTest = value;
fieldSetFlags()[2] = true;
return this;
}
/** Checks whether the 'clinicalIndicationTest' field has been set */
public boolean hasClinicalIndicationTest() {
return fieldSetFlags()[2];
}
/** Clears the value of the 'clinicalIndicationTest' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearClinicalIndicationTest() {
clinicalIndicationTest = null;
fieldSetFlags()[2] = false;
return this;
}
/** Gets the value of the 'tumourSamples' field */
public java.util.List getTumourSamples() {
return tumourSamples;
}
/** Sets the value of the 'tumourSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder setTumourSamples(java.util.List value) {
validate(fields()[3], value);
this.tumourSamples = value;
fieldSetFlags()[3] = true;
return this;
}
/** Checks whether the 'tumourSamples' field has been set */
public boolean hasTumourSamples() {
return fieldSetFlags()[3];
}
/** Clears the value of the 'tumourSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearTumourSamples() {
tumourSamples = null;
fieldSetFlags()[3] = false;
return this;
}
/** Gets the value of the 'germlineSamples' field */
public java.util.List getGermlineSamples() {
return germlineSamples;
}
/** Sets the value of the 'germlineSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder setGermlineSamples(java.util.List value) {
validate(fields()[4], value);
this.germlineSamples = value;
fieldSetFlags()[4] = true;
return this;
}
/** Checks whether the 'germlineSamples' field has been set */
public boolean hasGermlineSamples() {
return fieldSetFlags()[4];
}
/** Clears the value of the 'germlineSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearGermlineSamples() {
germlineSamples = null;
fieldSetFlags()[4] = false;
return this;
}
/** Gets the value of the 'analysisPanels' field */
public java.util.List getAnalysisPanels() {
return analysisPanels;
}
/** Sets the value of the 'analysisPanels' field */
public org.gel.models.participant.avro.ReferralTest.Builder setAnalysisPanels(java.util.List value) {
validate(fields()[5], value);
this.analysisPanels = value;
fieldSetFlags()[5] = true;
return this;
}
/** Checks whether the 'analysisPanels' field has been set */
public boolean hasAnalysisPanels() {
return fieldSetFlags()[5];
}
/** Clears the value of the 'analysisPanels' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearAnalysisPanels() {
analysisPanels = null;
fieldSetFlags()[5] = false;
return this;
}
/** Gets the value of the 'interpreter' field */
public org.gel.models.participant.avro.OrganisationNgis getInterpreter() {
return interpreter;
}
/** Sets the value of the 'interpreter' field */
public org.gel.models.participant.avro.ReferralTest.Builder setInterpreter(org.gel.models.participant.avro.OrganisationNgis value) {
validate(fields()[6], value);
this.interpreter = value;
fieldSetFlags()[6] = true;
return this;
}
/** Checks whether the 'interpreter' field has been set */
public boolean hasInterpreter() {
return fieldSetFlags()[6];
}
/** Clears the value of the 'interpreter' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearInterpreter() {
interpreter = null;
fieldSetFlags()[6] = false;
return this;
}
/** Gets the value of the 'processingLab' field */
public org.gel.models.participant.avro.OrganisationNgis getProcessingLab() {
return processingLab;
}
/** Sets the value of the 'processingLab' field */
public org.gel.models.participant.avro.ReferralTest.Builder setProcessingLab(org.gel.models.participant.avro.OrganisationNgis value) {
validate(fields()[7], value);
this.processingLab = value;
fieldSetFlags()[7] = true;
return this;
}
/** Checks whether the 'processingLab' field has been set */
public boolean hasProcessingLab() {
return fieldSetFlags()[7];
}
/** Clears the value of the 'processingLab' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearProcessingLab() {
processingLab = null;
fieldSetFlags()[7] = false;
return this;
}
/** Gets the value of the 'priority' field */
public org.gel.models.participant.avro.Priority getPriority() {
return priority;
}
/** Sets the value of the 'priority' field */
public org.gel.models.participant.avro.ReferralTest.Builder setPriority(org.gel.models.participant.avro.Priority value) {
validate(fields()[8], value);
this.priority = value;
fieldSetFlags()[8] = true;
return this;
}
/** Checks whether the 'priority' field has been set */
public boolean hasPriority() {
return fieldSetFlags()[8];
}
/** Clears the value of the 'priority' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearPriority() {
priority = null;
fieldSetFlags()[8] = false;
return this;
}
/** Gets the value of the 'pipelineStartDate' field */
public org.gel.models.participant.avro.Date getPipelineStartDate() {
return pipelineStartDate;
}
/** Sets the value of the 'pipelineStartDate' field */
public org.gel.models.participant.avro.ReferralTest.Builder setPipelineStartDate(org.gel.models.participant.avro.Date value) {
validate(fields()[9], value);
this.pipelineStartDate = value;
fieldSetFlags()[9] = true;
return this;
}
/** Checks whether the 'pipelineStartDate' field has been set */
public boolean hasPipelineStartDate() {
return fieldSetFlags()[9];
}
/** Clears the value of the 'pipelineStartDate' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearPipelineStartDate() {
pipelineStartDate = null;
fieldSetFlags()[9] = false;
return this;
}
/** Gets the value of the 'diseasePenetrances' field */
public java.util.List getDiseasePenetrances() {
return diseasePenetrances;
}
/** Sets the value of the 'diseasePenetrances' field */
public org.gel.models.participant.avro.ReferralTest.Builder setDiseasePenetrances(java.util.List value) {
validate(fields()[10], value);
this.diseasePenetrances = value;
fieldSetFlags()[10] = true;
return this;
}
/** Checks whether the 'diseasePenetrances' field has been set */
public boolean hasDiseasePenetrances() {
return fieldSetFlags()[10];
}
/** Clears the value of the 'diseasePenetrances' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearDiseasePenetrances() {
diseasePenetrances = null;
fieldSetFlags()[10] = false;
return this;
}
/** Gets the value of the 'matchedSamples' field */
public java.util.List getMatchedSamples() {
return matchedSamples;
}
/** Sets the value of the 'matchedSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder setMatchedSamples(java.util.List value) {
validate(fields()[11], value);
this.matchedSamples = value;
fieldSetFlags()[11] = true;
return this;
}
/** Checks whether the 'matchedSamples' field has been set */
public boolean hasMatchedSamples() {
return fieldSetFlags()[11];
}
/** Clears the value of the 'matchedSamples' field */
public org.gel.models.participant.avro.ReferralTest.Builder clearMatchedSamples() {
matchedSamples = null;
fieldSetFlags()[11] = false;
return this;
}
@Override
public ReferralTest build() {
try {
ReferralTest record = new ReferralTest();
record.referralTestId = fieldSetFlags()[0] ? this.referralTestId : (java.lang.String) defaultValue(fields()[0]);
record.referralTestOrderingDate = fieldSetFlags()[1] ? this.referralTestOrderingDate : (org.gel.models.participant.avro.Date) defaultValue(fields()[1]);
record.clinicalIndicationTest = fieldSetFlags()[2] ? this.clinicalIndicationTest : (org.gel.models.participant.avro.ClinicalIndicationTest) defaultValue(fields()[2]);
record.tumourSamples = fieldSetFlags()[3] ? this.tumourSamples : (java.util.List) defaultValue(fields()[3]);
record.germlineSamples = fieldSetFlags()[4] ? this.germlineSamples : (java.util.List) defaultValue(fields()[4]);
record.analysisPanels = fieldSetFlags()[5] ? this.analysisPanels : (java.util.List) defaultValue(fields()[5]);
record.interpreter = fieldSetFlags()[6] ? this.interpreter : (org.gel.models.participant.avro.OrganisationNgis) defaultValue(fields()[6]);
record.processingLab = fieldSetFlags()[7] ? this.processingLab : (org.gel.models.participant.avro.OrganisationNgis) defaultValue(fields()[7]);
record.priority = fieldSetFlags()[8] ? this.priority : (org.gel.models.participant.avro.Priority) defaultValue(fields()[8]);
record.pipelineStartDate = fieldSetFlags()[9] ? this.pipelineStartDate : (org.gel.models.participant.avro.Date) defaultValue(fields()[9]);
record.diseasePenetrances = fieldSetFlags()[10] ? this.diseasePenetrances : (java.util.List) defaultValue(fields()[10]);
record.matchedSamples = fieldSetFlags()[11] ? this.matchedSamples : (java.util.List) defaultValue(fields()[11]);
return record;
} catch (Exception e) {
throw new org.apache.avro.AvroRuntimeException(e);
}
}
}
}
