avro.gel_participant_6_2_0.ClinicalReport.avdl Maven / Gradle / Ivy

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@namespace("org.gel.models.report.avro")

protocol ClinicalReports {

    import idl "CommonInterpreted.avdl";
    import idl "ReportVersionControl.avdl";

    /**
    A panel of genes and the specific disease that it assesses
    */
    record AdditionalAnalysisPanel {
        /*
        The specific disease
        */
        string specificDisease;
        /*
        The panel of genes
        */
        GenePanel panel;
    }

    /**
    A clinical report. This holds the list of reported variants by an expert together with all
    the relevant information that identify the case and how these conclusions were reached.
    */
    record ClinicalReport {
        /**
        This is the interpretation request identifier (i.e.: first number in 123-1)
        */
        string interpretationRequestId;

        /**
        This is the version of the interpretation request identifier (i.e.: second number in 123-1)
        */
        int interpretationRequestVersion;

        /**
        Date of this report in format YYYY-MM-DD
        */
        string reportingDate;

        /**
        Author of this report
        */
        string user;

        /**
        List of small reported variants
        */
        union {null, array} variants;

        /**
        List of simple structural reported variants (duplications, deletions, insertions, inversions, CNVs)
        */
        union {null, array} structuralVariants;

        /**
        List of complex structural reported variants (chomosomal rearrangement)
        */
        union {null, array} chromosomalRearrangements;

        /**
        List of short tandem repeat variants
        */
        union {null, array} shortTandemRepeats;

        /**
        List of uniparental disomies across all the individuals in this report
        */
        union {null, array} uniparentalDisomies;

        /**
        List of inferred karyotypes across all the individuals in this report
        */
        union {null, array} karyotypes;

        /**
        Summary of the interpretation, this should reflect the positive conclusions of this interpretation
        */
        string genomicInterpretation;

        /**
        The list of panels analysed to generate this report
        */
        union {null, array} additionalAnalysisPanels;

        /**
        Supporting evidence (pubmed identifiers)
        */
        union {null, array} references;

        /**
        This map contains the versions of the different databases used in the process, being the database names the
        keys and the versions the values.
        */
        map referenceDatabasesVersions;

        /**
        This map contains the versions of the different software systems used in the process, being the software
        names the keys and the versions the values.
        */
        map softwareVersions;
    }

    /*
    -------------------------------------------------
    ADDITIONAL FINDINGS CLINICAL REPORT
    -------------------------------------------------
    */

    record AdditionalFindingsClinicalReport{
        /**
        This is the unique identifier (i.e.: in case of additionalFindings can be participantId)
        */
        string participantId;

        /**
        Date of this report in format YYYY-MM-DD
        */
        string reportingDate;

        /**
        Author of this report
        */
        string user;

        /**
        List of small reported variants
        */
        union {null, array} variants;

        /**
        List of simple structural reported variants (duplications, deletions, insertions, inversions, CNVs)
        */
        union {null, array} structuralVariants;

        /**
        List of complex structural reported variants (chomosomal rearrangement)
        */
        union {null, array} chromosomalRearrangements;

        /**
        List of short tandem repeat variants
        */
        union {null, array} shortTandemRepeats;

        /**
        List of uniparental disomies across all the individuals in this report
        */
        union {null, array} uniparentalDisomies;

        /**
        List of inferred karyotypes across all the individuals in this report
        */
        union {null, array} karyotypes;

        /**
        Summary of the interpretation, this should reflect the positive conclusions of this interpretation
        */
        string genomicInterpretation;

        /**
        The list of panels analysed to generate this report
        */
        union {null, array} additionalAnalysisPanels;

        /**
        Supporting evidence (pubmed identifiers)
        */
        union {null, array} references;

        /**
        This map contains the versions of the different databases used in the process, being the database names the
        keys and the versions the values.
        */
        map referenceDatabasesVersions;

        /**
        This map contains the versions of the different software systems used in the process, being the software
        names the keys and the versions the values.
        */
        map softwareVersions;
    }
}