Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add IHC report and Therapies #4

Merged
merged 1 commit into from
Dec 24, 2024
Merged

Add IHC report and Therapies #4

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
140 changes: 115 additions & 25 deletions mtb.go
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ type Mtb struct {
GuidelineProcedures []OncoProdecure `json:"guidelineProcedures,omitempty"`
GuidelineTherapies []GuidelineTherapyElement `json:"guidelineTherapies,omitempty"`
HistologyReports []HistologyReport `json:"histologyReports,omitempty"`
IhcReports []IHCReport `json:"ihcReports,omitempty"`
MolecularTherapies []MolecularTherapy `json:"molecularTherapies,omitempty"`
NgsReports []SomaticNGSReport `json:"ngsReports,omitempty"`
Patient MtbPatient `json:"patient"`
Expand All @@ -31,6 +32,7 @@ type Mtb struct {
Responses []Response `json:"responses,omitempty"`
Specimens []SpecimenElement `json:"specimens,omitempty"`
StudyInclusionRequests []StudyEnrollmentRecommendation `json:"studyInclusionRequests,omitempty"`
Therapies []Therapy `json:"therapies,omitempty"`
}

type MTBCarePlan struct {
Expand Down Expand Up @@ -267,7 +269,7 @@ type CodingTherapyStatusReason struct {
}

type GuidelineTherapyElement struct {
BasedOn *string `json:"basedOn,omitempty"`
BasedOn *Reference `json:"basedOn,omitempty"`
Diagnosis *string `json:"diagnosis,omitempty"`
ID string `json:"id"`
Indication *Reference `json:"indication,omitempty"`
Expand Down Expand Up @@ -331,6 +333,63 @@ type HistologyReportSpecimen struct {
Type SpecimenType `json:"type"`
}

type IHCReport struct {
BlockID ExternalID `json:"blockId"`
Date string `json:"date"`
ID string `json:"id"`
JournalID ExternalID `json:"journalId"`
MSIMmrResults []MSIMmrResult `json:"msiMmrResults"`
Patient Reference `json:"patient"`
ProteinExpressionResults []ProteinExpressionResult `json:"proteinExpressionResults"`
Specimen Reference `json:"specimen"`
}

type ExternalID struct {
System *string `json:"system,omitempty"`
Value string `json:"value"`
}

type MSIMmrResult struct {
ICScore *CodingProteinExpressionICScore `json:"icScore,omitempty"`
ID string `json:"id"`
Patient Reference `json:"patient"`
Protein Coding `json:"protein"`
TcScore *CodingProteinExpressionTCScore `json:"tcScore,omitempty"`
TpsScore *int64 `json:"tpsScore,omitempty"`
Value CodingProteinExpressionResult `json:"value"`
}

type CodingProteinExpressionICScore struct {
Code ICScoreCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
}

type CodingProteinExpressionTCScore struct {
Code TcScoreCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
}

type CodingProteinExpressionResult struct {
Code ProteinExpressionResultCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
}

type ProteinExpressionResult struct {
ICScore *CodingProteinExpressionICScore `json:"icScore,omitempty"`
ID string `json:"id"`
Patient Reference `json:"patient"`
Protein Coding `json:"protein"`
TcScore *CodingProteinExpressionTCScore `json:"tcScore,omitempty"`
TpsScore *int64 `json:"tpsScore,omitempty"`
Value CodingProteinExpressionResult `json:"value"`
}

type MolecularTherapy struct {
History []GuidelineTherapyElement `json:"history"`
}
Expand Down Expand Up @@ -522,11 +581,6 @@ type Snv struct {
TranscriptID *ExternalID `json:"transcriptId,omitempty"`
}

type ExternalID struct {
System *string `json:"system,omitempty"`
Value string `json:"value"`
}

type Position struct {
End *float64 `json:"end,omitempty"`
Start float64 `json:"start"`
Expand Down Expand Up @@ -597,10 +651,10 @@ type PerformanceStatus struct {
}

type CodingECOG struct {
Code PurpleCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
Code EcogCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
}

type Response struct {
Expand All @@ -617,7 +671,7 @@ type ResponseTherapy struct {
}

type CodingRECIST struct {
Code FluffyCode `json:"code"`
Code RecistCode `json:"code"`
Display *string `json:"display,omitempty"`
System *string `json:"system,omitempty"`
Version *string `json:"version,omitempty"`
Expand Down Expand Up @@ -660,6 +714,10 @@ type CodingTumorSpecimenType struct {
System *string `json:"system,omitempty"`
}

type Therapy struct {
History []GuidelineTherapyElement `json:"history"`
}

type PatientType string

const (
Expand Down Expand Up @@ -795,6 +853,38 @@ const (
TumorSpecimen SpecimenType = "TumorSpecimen"
)

type ICScoreCode string

const (
ICScoreCode0 ICScoreCode = "0"
ICScoreCode1 ICScoreCode = "1"
ICScoreCode2 ICScoreCode = "2"
ICScoreCode3 ICScoreCode = "3"
)

type TcScoreCode string

const (
TcScoreCode0 TcScoreCode = "0"
TcScoreCode1 TcScoreCode = "1"
TcScoreCode2 TcScoreCode = "2"
TcScoreCode3 TcScoreCode = "3"
TcScoreCode4 TcScoreCode = "4"
TcScoreCode5 TcScoreCode = "5"
TcScoreCode6 TcScoreCode = "6"
)

type ProteinExpressionResultCode string

const (
Exp ProteinExpressionResultCode = "exp"
NotExp ProteinExpressionResultCode = "not-exp"
TentacledUnknown ProteinExpressionResultCode = "unknown"
ProteinExpressionResultCode1Plus ProteinExpressionResultCode = "1+"
ProteinExpressionResultCode2Plus ProteinExpressionResultCode = "2+"
ProteinExpressionResultCode3Plus ProteinExpressionResultCode = "3+"
)

type ChromosomeCode string

const (
Expand Down Expand Up @@ -879,14 +969,14 @@ const (
Deceased VitalStatusCode = "deceased"
)

type PurpleCode string
type EcogCode string

const (
Code1 PurpleCode = "1"
Code2 PurpleCode = "2"
Code3 PurpleCode = "3"
Code4 PurpleCode = "4"
Code0 PurpleCode = "0"
EcogCode0 EcogCode = "0"
EcogCode1 EcogCode = "1"
EcogCode2 EcogCode = "2"
EcogCode3 EcogCode = "3"
EcogCode4 EcogCode = "4"
)

type ResponseTherapyType string
Expand All @@ -895,16 +985,16 @@ const (
MTBMedicationTherapy ResponseTherapyType = "MTBMedicationTherapy"
)

type FluffyCode string
type RecistCode string

const (
CR FluffyCode = "CR"
Mr FluffyCode = "MR"
Na FluffyCode = "NA"
Nya FluffyCode = "NYA"
PD FluffyCode = "PD"
PR FluffyCode = "PR"
SD FluffyCode = "SD"
CR RecistCode = "CR"
Mr RecistCode = "MR"
Na RecistCode = "NA"
Nya RecistCode = "NYA"
PD RecistCode = "PD"
PR RecistCode = "PR"
SD RecistCode = "SD"
)

type TumorSpecimenCollectionLocalization string
Expand Down
Loading