Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.gel.models.participant.avro;
@SuppressWarnings("all")
/** This protocol defines the `CancerParticipant` */
@org.apache.avro.specific.AvroGenerated
public interface CancerParticipants {
public static final org.apache.avro.Protocol PROTOCOL = org.apache.avro.Protocol.parse("{\"protocol\":\"CancerParticipants\",\"namespace\":\"org.gel.models.participant.avro\",\"doc\":\"This protocol defines the `CancerParticipant`\",\"types\":[{\"type\":\"enum\",\"name\":\"TissueSource\",\"symbols\":[\"BMA_TUMOUR_SORTED_CELLS\",\"CT_GUIDED_BIOPSY\",\"ENDOSCOPIC_BIOPSY\",\"ENDOSCOPIC_ULTRASOUND_GUIDED_BIOPSY\",\"ENDOSCOPIC_ULTRASOUND_GUIDED_FNA\",\"LAPAROSCOPIC_BIOPSY\",\"LAPAROSCOPIC_EXCISION\",\"MRI_GUIDED_BIOPSY\",\"NON_GUIDED_BIOPSY\",\"SURGICAL_RESECTION\",\"STEREOTACTICALLY_GUIDED_BIOPSY\",\"USS_GUIDED_BIOPSY\",\"NON_STANDARD_BIOPSY\",\"NOT_SPECIFIED\"]},{\"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\"]},{\"type\":\"enum\",\"name\":\"TumourType\",\"doc\":\"NOTE: This has been changed completely, the previous tumour type has been split into TumourPresentation and PrimaryOrMetastatic\",\"symbols\":[\"BRAIN_TUMOUR\",\"HAEMATOLOGICAL_MALIGNANCY_SOLID_SAMPLE\",\"HAEMATOLOGICAL_MALIGNANCY_LIQUID_SAMPLE\",\"SOLID_TUMOUR_METASTATIC\",\"SOLID_TUMOUR_PRIMARY\",\"SOLID_TUMOUR\",\"UNKNOWN\"]},{\"type\":\"enum\",\"name\":\"ProgrammePhase\",\"symbols\":[\"CRUK\",\"OXFORD\",\"CLL\",\"IIP\",\"MAIN\",\"EXPT\"]},{\"type\":\"enum\",\"name\":\"Product\",\"symbols\":[\"DNA\",\"RNA\"]},{\"type\":\"enum\",\"name\":\"TumourContent\",\"symbols\":[\"High\",\"Medium\",\"Low\"]},{\"type\":\"enum\",\"name\":\"HaematologicalCancerLineage\",\"symbols\":[\"MYELOID\",\"LYMPHOID\",\"UNKNOWN\"]},{\"type\":\"enum\",\"name\":\"TumourPresentation\",\"symbols\":[\"FIRST_PRESENTATION\",\"RECURRENCE\",\"UNKNOWN\"]},{\"type\":\"enum\",\"name\":\"PrimaryOrMetastatic\",\"symbols\":[\"PRIMARY\",\"METASTATIC\",\"UNKNOWN\",\"NOT_APPLICABLE\"]},{\"type\":\"enum\",\"name\":\"Sex\",\"doc\":\"Sex\",\"symbols\":[\"MALE\",\"FEMALE\",\"UNKNOWN\"]},{\"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\"]},{\"type\":\"enum\",\"name\":\"PersonKaryotipicSex\",\"doc\":\"Karyotipic Sex\",\"symbols\":[\"UNKNOWN\",\"XX\",\"XY\",\"XO\",\"XXY\",\"XXX\",\"XXYY\",\"XXXY\",\"XXXX\",\"XYY\",\"OTHER\"]},{\"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\"]},{\"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\"]},{\"type\":\"enum\",\"name\":\"StorageMedium\",\"doc\":\"In GMS, storage medium of sample\",\"symbols\":[\"EDTA\",\"FF\",\"LI_HEP\",\"ORAGENE\",\"FFPE\"]},{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetrance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]},{\"type\":\"enum\",\"name\":\"TernaryOption\",\"doc\":\"This defines a yes/no/unknown case\",\"symbols\":[\"yes\",\"no\",\"unknown\"]},{\"type\":\"enum\",\"name\":\"EthnicCategory\",\"doc\":\"This is the list of ethnicities in ONS16\\n\\n * `D`: Mixed: White and Black Caribbean\\n * `E`: Mixed: White and Black African\\n * `F`: Mixed: White and Asian\\n * `G`: Mixed: Any other mixed background\\n * `A`: White: British\\n * `B`: White: Irish\\n * `C`: White: Any other White background\\n * `L`: Asian or Asian British: Any other Asian background\\n * `M`: Black or Black British: Caribbean\\n * `N`: Black or Black British: African\\n * `H`: Asian or Asian British: Indian\\n * `J`: Asian or Asian British: Pakistani\\n * `K`: Asian or Asian British: Bangladeshi\\n * `P`: Black or Black British: Any other Black background\\n * `S`: Other Ethnic Groups: Any other ethnic group\\n * `R`: Other Ethnic Groups: Chinese\\n * `Z`: Not stated\",\"symbols\":[\"D\",\"E\",\"F\",\"G\",\"A\",\"B\",\"C\",\"L\",\"M\",\"N\",\"H\",\"J\",\"K\",\"P\",\"S\",\"R\",\"Z\"]},{\"type\":\"enum\",\"name\":\"ClinicalEthnicity\",\"doc\":\"* A British, Mixed British\\n * B Irish\\n * C Any other White background\\n * C2 Northern Irish\\n * C3 Other white, white unspecified\\n * CA English\\n * CB Scottish\\n * CC Welsh\\n * CD Cornish\\n * CE Cypriot (part not stated)\\n * CF Greek\\n * CG Greek Cypriot\\n * CH Turkish\\n * CJ Turkish Cypriot\\n * CK Italian\\n * CL Irish Traveller\\n * CM Traveller\\n * CN Gypsy/Romany\\n * CP Polish\\n * CQ All republics which made up the former USSR\\n * CR Kosovan\\n * CS Albanian\\n * CT Bosnian\\n * CU Croatian\\n * CV Serbian\\n * CW Other republics which made up the former Yugoslavia\\n * CX Mixed white\\n * CY Other white European, European unspecified, European mixed\\n * D White and Black Caribbean\\n * E White and Black African\\n * F White and Asian\\n * G Any other mixed background\\n * GA Black and Asian\\n * GB Black and Chinese\\n * GC Black and White\\n * GD Chinese and White\\n * GE Asian and Chinese\\n * GF Other Mixed, Mixed Unspecified\\n * H Indian or British Indian\\n * J Pakistani or British Pakistani\\n * K Bangladeshi or British Bangladeshi\\n * L Any other Asian background\\n * LA Mixed Asian\\n * LB Punjabi\\n * LC Kashmiri\\n * LD East African Asian\\n * LE Sri Lanka\\n * LF Tamil\\n * LG Sinhalese\\n * LH British Asian\\n * LJ Caribbean Asian\\n * LK Other Asian, Asian unspecified\\n * M Caribbean\\n * N African\\n * P Any other Black background\\n * PA Somali\\n * PB Mixed Black\\n * PC Nigerian\\n * PD Black British\\n * PE Other Black, Black unspecified\\n * R Chinese\\n * S Any other ethnic group\\n * S1 Ashkenazi\\n * S2 Sephardi\\n * SA Vietnamese\\n * SB Japanese\\n * SC Filipino\\n * SD Malaysian\\n * SE Any Other Group\\n * Z Not stated\",\"symbols\":[\"A\",\"B\",\"C\",\"C2\",\"C3\",\"CA\",\"CB\",\"CC\",\"CD\",\"CE\",\"CF\",\"CG\",\"CH\",\"CJ\",\"CK\",\"CL\",\"CM\",\"CN\",\"CP\",\"CQ\",\"CR\",\"CS\",\"CT\",\"CU\",\"CV\",\"CW\",\"CX\",\"CY\",\"D\",\"E\",\"F\",\"G\",\"GA\",\"GB\",\"GC\",\"GD\",\"GE\",\"GF\",\"H\",\"J\",\"K\",\"L\",\"LA\",\"LB\",\"LC\",\"LD\",\"LE\",\"LF\",\"LG\",\"LH\",\"LJ\",\"LK\",\"M\",\"N\",\"P\",\"PA\",\"PB\",\"PC\",\"PD\",\"PE\",\"R\",\"S\",\"S1\",\"S2\",\"SA\",\"SB\",\"SC\",\"SD\",\"SE\",\"Z\"]},{\"type\":\"enum\",\"name\":\"KgPopCategory\",\"doc\":\"1K Genomes project populations\",\"symbols\":[\"ACB\",\"ASW\",\"BEB\",\"CDX\",\"CEU\",\"CHB\",\"CHS\",\"CLM\",\"ESN\",\"FIN\",\"GBR\",\"GIH\",\"GWD\",\"IBS\",\"ITU\",\"JPT\",\"KHV\",\"LWK\",\"MSL\",\"MXL\",\"PEL\",\"PJL\",\"PUR\",\"STU\",\"TSI\",\"YRI\"]},{\"type\":\"enum\",\"name\":\"KgSuperPopCategory\",\"doc\":\"1K Genomes project super populations\",\"symbols\":[\"AFR\",\"AMR\",\"EAS\",\"EUR\",\"SAS\"]},{\"type\":\"record\",\"name\":\"ChiSquare1KGenomesPhase3Pop\",\"doc\":\"Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations\",\"fields\":[{\"name\":\"kgSuperPopCategory\",\"type\":\"KgSuperPopCategory\",\"doc\":\"1K Super Population\"},{\"name\":\"kgPopCategory\",\"type\":[\"null\",\"KgPopCategory\"],\"doc\":\"1K Population\"},{\"name\":\"chiSquare\",\"type\":\"double\",\"doc\":\"Chi-square test for goodness of fit of this sample to this 1000 Genomes Phase 3 population\"}]},{\"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\"}]},{\"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\"}]},{\"type\":\"record\",\"name\":\"Ancestries\",\"doc\":\"Ancestries, defined as Ethnic category(ies) and Chi-square test\",\"fields\":[{\"name\":\"mothersEthnicOrigin\",\"type\":[\"null\",\"EthnicCategory\"],\"doc\":\"Mother's Ethnic Origin\"},{\"name\":\"mothersOtherRelevantAncestry\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Mother's Ethnic Origin Description\"},{\"name\":\"fathersEthnicOrigin\",\"type\":[\"null\",\"EthnicCategory\"],\"doc\":\"Father's Ethnic Origin\"},{\"name\":\"fathersOtherRelevantAncestry\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Father's Ethnic Origin Description\"},{\"name\":\"chiSquare1KGenomesPhase3Pop\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"ChiSquare1KGenomesPhase3Pop\"}],\"doc\":\"Chi-square test for goodness of fit of this sample to 1000 Genomes Phase 3 populations\"}]},{\"type\":\"enum\",\"name\":\"GenericConsent\",\"doc\":\"clinicalEthnicities supersedes Ancestries in GMS\",\"symbols\":[\"yes\",\"no\",\"undefined\",\"not_applicable\"]},{\"type\":\"record\",\"name\":\"GmsConsentStatus\",\"doc\":\"Consent Status for GMS\",\"fields\":[{\"name\":\"programmeConsent\",\"type\":\"GenericConsent\",\"doc\":\"Is this individual consented to the programme? It could simply be a family member that is not consented\\n but for whom affection status is known\"},{\"name\":\"primaryFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for feedback of primary findings?\\n RD: Primary Findings\\n Cancer: PrimaryFindings is somatic + pertinent germline findings\"},{\"name\":\"researchConsent\",\"type\":\"GenericConsent\",\"doc\":\"Research Consent\"},{\"name\":\"healthRelatedFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for secondary health related findings?\"},{\"name\":\"carrierStatusConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for carrier status check?\"},{\"name\":\"pharmacogenomicsFindingConsent\",\"type\":\"GenericConsent\",\"doc\":\"Consent for pharmacogenomics consent as secondary findings?\"}]},{\"type\":\"record\",\"name\":\"ConsentStatus\",\"doc\":\"Consent Status for 100k program\",\"fields\":[{\"name\":\"programmeConsent\",\"type\":\"boolean\",\"doc\":\"Is this individual consented to the programme?\\n It could simply be a family member that is not consented but for whom affection status is known\",\"default\":false},{\"name\":\"primaryFindingConsent\",\"type\":\"boolean\",\"doc\":\"Consent for feedback of primary findings?\",\"default\":false},{\"name\":\"secondaryFindingConsent\",\"type\":\"boolean\",\"doc\":\"Consent for secondary finding lookup\",\"default\":false},{\"name\":\"carrierStatusConsent\",\"type\":\"boolean\",\"doc\":\"Consent for carrier status check?\",\"default\":false}]},{\"type\":\"record\",\"name\":\"InbreedingCoefficient\",\"doc\":\"Inbreeding coefficient\",\"fields\":[{\"name\":\"sampleId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"This is the sample id against which the coefficient was estimated\"},{\"name\":\"program\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Name of program used to calculate the coefficient\"},{\"name\":\"version\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Version of the programme\"},{\"name\":\"estimationMethod\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Where various methods for estimation exist, which method was used.\"},{\"name\":\"coefficient\",\"type\":\"double\",\"doc\":\"Inbreeding coefficient ideally a real number in [0,1]\"},{\"name\":\"standardError\",\"type\":[\"null\",\"double\"],\"doc\":\"Standard error of the Inbreeding coefficient\"}]},{\"type\":\"enum\",\"name\":\"FamiliarRelationship\",\"doc\":\"Familiar relationship from pedrigree\",\"symbols\":[\"TwinsMonozygous\",\"TwinsDizygous\",\"TwinsUnknown\",\"FullSibling\",\"FullSiblingF\",\"FullSiblingM\",\"Mother\",\"Father\",\"Son\",\"Daughter\",\"ChildOfUnknownSex\",\"MaternalAunt\",\"MaternalUncle\",\"MaternalUncleOrAunt\",\"PaternalAunt\",\"PaternalUncle\",\"PaternalUncleOrAunt\",\"MaternalGrandmother\",\"PaternalGrandmother\",\"MaternalGrandfather\",\"PaternalGrandfather\",\"DoubleFirstCousin\",\"MaternalCousinSister\",\"PaternalCousinSister\",\"MaternalCousinBrother\",\"PaternalCousinBrother\",\"Cousin\",\"Spouse\",\"Other\",\"RelationIsNotClear\",\"Unrelated\",\"Unknown\"]},{\"type\":\"record\",\"name\":\"PreviousTreatment\",\"doc\":\"In GMS, Previous Treatment of Patient\",\"fields\":[{\"name\":\"previousTreatmentType\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"previousTreatmentName\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}]},{\"name\":\"previousTreatmentDate\",\"type\":[\"null\",\"Date\"]}]},{\"type\":\"record\",\"name\":\"ClinicalIndication\",\"fields\":[{\"name\":\"clinicalIndicationUid\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"GUID of Clinical Indication for the Referral\"},{\"name\":\"clinicalIndicationCode\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Code of Clinical Indication, e.g. (RT-13)\"},{\"name\":\"clinicalIndicationFullName\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Clinical Indication Full Name\"},{\"name\":\"clinicalIndicationVersionNumber\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Clinical Indication version number\"}]},{\"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\"}]},{\"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\"}]},{\"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\",\"ProgrammePhase\"],\"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\"}]},{\"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\",\"diseaseType\"],\"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\",\"HaematologicalCancerLineage\"],\"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\",\"TumourContent\"],\"doc\":\"This is the tumour content\"},{\"name\":\"tumourContentPercentage\",\"type\":[\"null\",\"float\"],\"doc\":\"This is the tumour content percentage\"},{\"name\":\"source\",\"type\":[\"null\",\"SampleSource\"],\"doc\":\"Source of the sample\"},{\"name\":\"preparationMethod\",\"type\":[\"null\",\"PreparationMethod\"],\"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\",\"Product\"],\"doc\":\"Product of the sample\"},{\"name\":\"sampleMorphologies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Morphology\"}],\"doc\":\"Morphology according to the sample taken\"},{\"name\":\"sampleTopographies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Topography\"}],\"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\",\"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\"}]},{\"type\":\"record\",\"name\":\"VersionControl\",\"fields\":[{\"name\":\"GitVersionControl\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"This is the version for the entire set of data models as referred to the Git release tag\",\"default\":\"1.3.0\"}]},{\"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\"}]},{\"type\":\"record\",\"name\":\"Tumour\",\"fields\":[{\"name\":\"tumourId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"TumourId in GMS\"},{\"name\":\"tumourLocalId\",\"type\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"doc\":\"Local hospital tumour ID from the GLH Laboratory Information Management System (LIMS) in GMS\"},{\"name\":\"tumourType\",\"type\":\"TumourType\",\"doc\":\"tumourType\"},{\"name\":\"tumourParentId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Parent Tumour UID if this tumour is metastatic\"},{\"name\":\"tumourDiagnosisDate\",\"type\":[\"null\",\"Date\"],\"doc\":\"Date of Diagnosis of the specific tumour\"},{\"name\":\"tumourDescription\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Description of the tumour\"},{\"name\":\"tumourMorphologies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Morphology\"}],\"doc\":\"Morphology of the tumour\"},{\"name\":\"tumourTopographies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Topography\"}],\"doc\":\"Topography of the tumour\"},{\"name\":\"tumourPrimaryTopographies\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Topography\"}],\"doc\":\"Associated primary topography for metastatic tumours\"},{\"name\":\"tumourGrade\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Grade of the Tumour\"},{\"name\":\"tumourStage\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Stage of the Tumour\"},{\"name\":\"tumourPrognosticScore\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Prognostic Score of the Tumour\"},{\"name\":\"tumourPresentation\",\"type\":[\"null\",\"TumourPresentation\"],\"doc\":\"In GMS, tumour presentation\"},{\"name\":\"primaryOrMetastatic\",\"type\":[\"null\",\"PrimaryOrMetastatic\"],\"doc\":\"In GMS, primary or metastatic\"}]},{\"type\":\"record\",\"name\":\"CancerParticipant\",\"doc\":\"This defines a Cancer Participant\",\"fields\":[{\"name\":\"yearOfBirth\",\"type\":[\"null\",\"int\"],\"doc\":\"Year of birth for the cancer participant\"},{\"name\":\"morphology\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"Morphology of any tumours\\n NOTE: In GMS, this field is deprecated as morphology will be in sample or with respect to a tumour record\"},{\"name\":\"readyForAnalysis\",\"type\":\"boolean\",\"doc\":\"Flag indicating if the participant is ready for analysis\\n NOTE: In GMS, this will default to true\"},{\"name\":\"consentStatus\",\"type\":[\"null\",\"ConsentStatus\"],\"doc\":\"What has this participant consented to?\\n A participant that has been consented to the programme should also have sequence data associated with them; however\\n this needs to be programmatically checked\"},{\"name\":\"testConsentStatus\",\"type\":[\"null\",\"GmsConsentStatus\"],\"doc\":\"What has this participant consented in the context of a Genomic Test?\"},{\"name\":\"center\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Center\\n NOTE: In GMS, this will be taken from the ReferralTest and duplicated here\"},{\"name\":\"individualId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.ja","va.string\":\"String\"}],\"doc\":\"Individual identifier\"},{\"name\":\"participantId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"This is a human readable participant ID\"},{\"name\":\"primaryDiagnosisDisease\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"This should be an enumeration when it is well defined\\n blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.\\n In GMS, this field is deprecated\"},{\"name\":\"primaryDiagnosisSubDisease\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"This should be an enumeration when it is well defined\\n blood, breast, prostate, colorectal, cll, aml, renal, ovarian, skin, lymphNode, bone, saliva //for individual - there could be more than I have listed here, in fact there definitely will.\\n In GMS, this field is deprecated\"},{\"name\":\"sex\",\"type\":\"Sex\",\"doc\":\"Sex\"},{\"name\":\"additionalInformation\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"We could add a map here to store additional information for example URIs to images, ECGs, etc\"},{\"name\":\"assignedICD10\",\"type\":[\"null\",{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}}],\"doc\":\"assigned ICD10 code\\n IN GMS, this is deprecated\"},{\"name\":\"tumourSamples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"TumourSample\"}],\"doc\":\"List of tumour samples\\n IN GMS, this is deprecated and moved to ReferralTest\"},{\"name\":\"germlineSamples\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"GermlineSample\"}],\"doc\":\"List of germline samples\\n IN GMS, this is deprecated and moved to ReferralTest\"},{\"name\":\"versionControl\",\"type\":[\"null\",\"VersionControl\"],\"doc\":\"Model version number\"},{\"name\":\"participantUid\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Individual UID in GMS\"},{\"name\":\"tumours\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"Tumour\"}],\"doc\":\"In GMS, for all tumours for the CancerParticipant, independent of any samples\"},{\"name\":\"previousTreatment\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"PreviousTreatment\"}],\"doc\":\"In GMS, any previous treatment recorded in TOMs\"}]}],\"messages\":{}}");
@SuppressWarnings("all")
/** This protocol defines the `CancerParticipant` */
public interface Callback extends CancerParticipants {
public static final org.apache.avro.Protocol PROTOCOL = org.gel.models.participant.avro.CancerParticipants.PROTOCOL;
}
}
