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Feature/clinical options columns #52

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merged 6 commits into from
Sep 12, 2024
Merged

Feature/clinical options columns #52

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ced067f
fix survivalTuplesForm
juanNH Sep 5, 2024
059e608
fix surivalTuplesForm
juanNH Sep 5, 2024
01550ca
Merge branch 'v5.0.0' of https://github.com/omics-datascience/multiom…
juanNH Sep 5, 2024
573fdcc
fix code legebility
juanNH Sep 8, 2024
e875d3a
Merge branch 'v5.0.0' of https://github.com/omics-datascience/multiom…
juanNH Sep 8, 2024
fd7c2f8
fix error message getting samples in common
juanNH Sep 10, 2024
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8 changes: 4 additions & 4 deletions src/api_service/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -478,13 +478,13 @@ def get_number_samples_in_common_action(request):
@login_required
def get_number_samples_in_common_clinical_validation_source(request):
json_request_data = json.loads(request.body)
headers_in_front: Optional[List[str]] = json_request_data.get('headersColumnsNames')
clinical_data: Optional[List[str]] = json_request_data.get('clinicalData')
mrna_source_id = json_request_data.get('mRNASourceId')
mrna_source_type = json_request_data.get('mRNASourceType')

gem_source_id = json_request_data.get('gemSourceId')
gem_source_type = json_request_data.get('gemSourceType')
if None in [mrna_source_id, gem_source_id, mrna_source_type, gem_source_type, json_request_data, headers_in_front]:
if None in [mrna_source_id, gem_source_id, mrna_source_type, gem_source_type, json_request_data, clinical_data]:
response = {
'status': ResponseStatus(
ResponseCode.ERROR,
Expand Down Expand Up @@ -518,13 +518,13 @@ def get_number_samples_in_common_clinical_validation_source(request):
)
# Gets intersection
if response is None:
intersection = get_intersection_clinical(samples_list_mrna, samples_list_gem, headers_in_front)
intersection = get_intersection_clinical(samples_list_mrna, samples_list_gem, clinical_data)
response = {
'status': ResponseStatus(ResponseCode.SUCCESS),
'data': {
'number_samples_mrna': len(samples_list_mrna) if samples_list_mrna is not None else 0,
'number_samples_gem': len(samples_list_gem) if samples_list_gem is not None else 0,
'number_samples_clinical': len(headers_in_front) if headers_in_front is not None else 0,
'number_samples_clinical': len(clinical_data) if clinical_data is not None else 0,
'number_samples_in_common': intersection.size
}
}
Expand Down
15 changes: 9 additions & 6 deletions src/frontend/static/frontend/src/components/files-manager/FilesManager.tsx
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Expand Up @@ -3,7 +3,7 @@ import { Base } from '../Base'
import { Grid, Header, Button, Modal, DropdownItemProps, Table, Icon } from 'semantic-ui-react'
import { DjangoTag, DjangoUserFile, TagType, DjangoInstitution, DjangoMethylationPlatform, DjangoResponseUploadUserFileError, DjangoUserFileUploadErrorInternalCode, DjangoSurvivalColumnsTupleSimple, RowHeader } from '../../utils/django_interfaces'
import ky from 'ky'
import { getDjangoHeader, alertGeneralError, getFileTypeSelectOptions, getDefaultNewTag, copyObject, formatDateLocale, getFileTypeName } from '../../utils/util_functions'
import { getDjangoHeader, alertGeneralError, getFileTypeSelectOptions, getDefaultNewTag, copyObject, formatDateLocale, getFileTypeName, getInputFileCSVColumns } from '../../utils/util_functions'
import { TagsPanel } from './TagsPanel'
import { FileType, Nullable } from '../../utils/interfaces'
import { NewFileForm } from './NewFileForm'
Expand Down Expand Up @@ -65,6 +65,8 @@ interface FilesManagerState {
addingTag: boolean,
uploadPercentage: number,
uploadState: Nullable<UploadState>
/** posibles values for survival tuple */
survivalTuplesPossiblesValues: string[],
}

/**
Expand Down Expand Up @@ -94,7 +96,8 @@ class FilesManager extends React.Component<{}, FilesManagerState> {
newFile: this.getDefaultNewFile(),
addingTag: false,
uploadPercentage: 0,
uploadState: null
uploadState: null,
survivalTuplesPossiblesValues: []
}
}

Expand All @@ -121,19 +124,18 @@ class FilesManager extends React.Component<{}, FilesManagerState> {
*/
fileChange = () => {
const newFileForm = this.state.newFile

// Get Filename if file was selected
const newFile = this.newFileInputRef.current
const newFileName = (newFile && newFile.files.length > 0) ? newFile.files[0].name : FILE_INPUT_LABEL

// If there wasn't a File name written by the user, loads the filename in the input
const newFileNameUser = (newFileForm.newFileNameUser.trim().length > 0) ? newFileForm.newFileNameUser : newFileName

// Sets the new field values
newFileForm.newFileName = newFileName
newFileForm.newFileNameUser = newFileNameUser

this.setState({ newFile: newFileForm })
getInputFileCSVColumns(newFile.files[0]).then((headersColumnsNames) => {
this.setState({ newFile: newFileForm, survivalTuplesPossiblesValues: headersColumnsNames })
})
}

/**
Expand Down Expand Up @@ -764,6 +766,7 @@ class FilesManager extends React.Component<{}, FilesManagerState> {
handleSurvivalFormDatasetChanges={this.handleSurvivalFormDatasetChanges}
addSurvivalFormTuple={this.addSurvivalFormTuple}
removeSurvivalFormTuple={this.removeSurvivalFormTuple}
survivalTuplesPossiblesValues={this.state.survivalTuplesPossiblesValues}
/>

<TagsPanel
Expand Down
6 changes: 4 additions & 2 deletions src/frontend/static/frontend/src/components/files-manager/NewFileForm.tsx
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Expand Up @@ -60,12 +60,13 @@ interface NewFileFormProps {
isEditing: boolean,
uploadState: Nullable<UploadState>
uploadFile: () => void,
fileChange: (e: any) => void,
fileChange: any, // (e: any) => void
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Sacar el comentario

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JAJAJA, recuerdo poner ese any, para probar sin problemas. Ahi lo vuelvo como estaba antes, un (e:any)=> void. Porque recibe almenos un metodo que va a recibir el evento, no un cualquier cosa

handleAddFileInputsChange: (name: string, value: any) => void,
resetNewFileForm: () => void,
handleSurvivalFormDatasetChanges: (idx: number, name: string, value) => void,
addSurvivalFormTuple: () => void,
removeSurvivalFormTuple: (idx: number) => void
removeSurvivalFormTuple: (idx: number) => void,
survivalTuplesPossiblesValues: string[],
}

/**
Expand Down Expand Up @@ -297,6 +298,7 @@ export const NewFileForm = (props: NewFileFormProps) => {
addSurvivalFormTuple={props.addSurvivalFormTuple}
removeSurvivalFormTuple={props.removeSurvivalFormTuple}
disabled={props.uploadingFile}
survivalTuplesPossiblesValues={props.survivalTuplesPossiblesValues}
/>
}
</Grid>
Expand Down
58 changes: 34 additions & 24 deletions ...tend/static/frontend/src/components/pipeline/all-experiments-view/ClinicalSourcePopup.tsx
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Expand Up @@ -3,7 +3,7 @@ import React from 'react'
import { Button, Grid, Icon, Label, Popup } from 'semantic-ui-react'
import { DjangoCGDSStudy, DjangoCommonResponse, DjangoExperiment, DjangoExperimentClinicalSource, DjangoExperimentSource, DjangoNumberSamplesInCommonClinicalValidationResult, DjangoResponseCode, DjangoSurvivalColumnsTupleSimple, DjangoUserFile, ExperimentState } from '../../../utils/django_interfaces'
import { CustomAlert, CustomAlertTypes, FileType, KySearchParams, Nullable, Source, SourceType } from '../../../utils/interfaces'
import { alertGeneralError, cleanRef, experimentSourceIsValid, getDefaultSource, getDjangoHeader, getFilenameFromSource, getFileSizeInMB, getInputFileCSVColumns, makeSourceAndAppend } from '../../../utils/util_functions'
import { alertGeneralError, cleanRef, experimentSourceIsValid, getDefaultSource, getDjangoHeader, getFilenameFromSource, getFileSizeInMB, getInputFileCSVColumns, getInputFileCSVFirstColumnAllRows, makeSourceAndAppend } from '../../../utils/util_functions'
import { SurvivalTuplesForm } from '../../survival/SurvivalTuplesForm'
import { SourceForm } from '../SourceForm'
import { BiomarkerState, InferenceExperimentForTable } from '../../biomarkers/types'
Expand Down Expand Up @@ -71,6 +71,8 @@ interface ClinicalSourceState {
cgdsStudyName: Nullable<string>,
/** alert interface */
alert: CustomAlert,
/** posibles values for survival tuple */
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Por consistencia, arrancá los comentarios en mayúscula hdp!

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Vos sabes que nunca me di cuenta ajajaj. Dale ahora lo tomo para toda la documentacion que vaya a hacer. Gracias!

survivalTuplesPossiblesValues: string[],
}

/**
Expand All @@ -89,7 +91,8 @@ export class ClinicalSourcePopup extends React.Component<PopupClinicalSourceProp
gettingSourceData: false,
unlinkingSource: false,
cgdsStudyName: null,
alert: this.getDefaultAlertProps()
alert: this.getDefaultAlertProps(),
survivalTuplesPossiblesValues: []
}
}

Expand Down Expand Up @@ -168,32 +171,37 @@ export class ClinicalSourcePopup extends React.Component<PopupClinicalSourceProp

if (fileSizeInMB < MAX_FILE_SIZE_IN_MB_WARN) {
const file = clinicalSource.newUploadedFileRef.current.files[0]
getInputFileCSVColumns(file, undefined, FileType.CLINICAL).then((headersColumnsNames) => {
// Sets the Request's Headers
const myHeaders = getDjangoHeader()
// Sends an array of headers to compare in server
const jsonData = {
headersColumnsNames,
mRNASourceId,
mRNASourceType: SourceType.UPLOADED_DATASETS,
gemSourceId,
gemSourceType: SourceType.UPLOADED_DATASETS
}
getInputFileCSVFirstColumnAllRows(file, undefined).then((firstColumnAllRows) => {
getInputFileCSVColumns(file, undefined).then((headersColumnsNames) => {
// Sets the Request's Headers
const myHeaders = getDjangoHeader()
// Sends an array of headers to compare in server
const jsonData = {
clinicalData: firstColumnAllRows,
mRNASourceId,
mRNASourceType: SourceType.UPLOADED_DATASETS,
gemSourceId,
gemSourceType: SourceType.UPLOADED_DATASETS
}

ky.post(urlGetCommonSamplesClinicalSource, { json: jsonData, headers: myHeaders }).then((response) => {
response.json().then((jsonResponse: DjangoNumberSamplesInCommonClinicalValidationResult) => {
if (jsonResponse.status.code === DjangoResponseCode.SUCCESS) {
if (jsonResponse.data.number_samples_in_common > 0) {
this.setState({ clinicalSource })
} else {
this.clinicalSourceVoid()
ky.post(urlGetCommonSamplesClinicalSource, { json: jsonData, headers: myHeaders }).then((response) => {
response.json().then((jsonResponse: DjangoNumberSamplesInCommonClinicalValidationResult) => {
if (jsonResponse.status.code === DjangoResponseCode.SUCCESS) {
if (jsonResponse.data.number_samples_in_common > 0) {
this.setState({
clinicalSource,
survivalTuplesPossiblesValues: headersColumnsNames
})
} else {
this.clinicalSourceVoid()
}
}
}
}).catch((err) => {
console.log('Error parsing JSON ->', err)
})
}).catch((err) => {
console.log('Error parsing JSON ->', err)
console.log('Error getting user experiments', err)
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@Genarito Genarito Sep 5, 2024 •
edited
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Ya que estamos, corregir el mensaje de error. Acá no está trayendo los experimentos del usuario

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Dejar el comentario que editaste como estaba antes 'Error parsing JSON ->'. Ese estaba bien! Lo que está mal es el de abajo que dice "Error getting user experiments" cuando en realidad choca contra un endpoint que compara los Samples en común. Debería decir algo como "Error getting samples in common"

})
}).catch((err) => {
console.log('Error getting user experiments', err)
})
})
}
Expand Down Expand Up @@ -510,6 +518,7 @@ export class ClinicalSourcePopup extends React.Component<PopupClinicalSourceProp
} else {
clinicalIsDisabled = experiment.state !== BiomarkerState.COMPLETED
}

const survColumnsAreComplete = !this.validateSurvivalsColumnsComplete()
const iconExtraClassNames = this.props.iconExtraClassNames ?? ''
const clinicalButtonClassName = clinicalIsDisabled
Expand Down Expand Up @@ -584,6 +593,7 @@ export class ClinicalSourcePopup extends React.Component<PopupClinicalSourceProp
handleSurvivalFormDatasetChanges={this.handleSurvivalFormDatasetChanges}
addSurvivalFormTuple={this.addSurvivalFormTuple}
removeSurvivalFormTuple={this.removeSurvivalFormTuple}
survivalTuplesPossiblesValues={this.state.survivalTuplesPossiblesValues}
/>
</Grid.Column>
}
Expand Down
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