Merge pull request #54 from omics-datascience/feature/datasets_experiments

Genarito · web-flow · commit 9349e91b543e · 2024-10-02T08:22:35.000-03:00
Feature/datasets experiments
diff --git a/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/BiomarkerTrainedModelsTable.tsx b/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/BiomarkerTrainedModelsTable.tsx
@@ -12,6 +12,7 @@ import { TrainedModelStateLabel } from '../labels/TrainedModelStateLabel'
 import ky from 'ky'
 import { StopExperimentButton } from '../../pipeline/all-experiments-view/StopExperimentButton'
 import { DeleteExperimentButton } from '../../pipeline/all-experiments-view/DeleteExperimentButton'
+import { TableCellSources } from '../../common/TableCellSources'
 
 declare const urlBiomarkerTrainedModels: string
 declare const urlStopTrainedModel: string
@@ -213,6 +214,7 @@ export const BiomarkerTrainedModelsTable = (props: BiomarkerTrainedModelsPanelPr
                     { name: 'Date', serverCodeToSort: 'created' },
                     { name: 'Metric', serverCodeToSort: 'fitness_metric' },
                     { name: 'Best CV metric', serverCodeToSort: 'best_fitness_value' },
+                    { name: 'Datasets' },
                     ...actionColumn
                 ]}
                 defaultSortProp={{ sortField: 'created', sortOrderAscendant: false }}
@@ -271,6 +273,15 @@ export const BiomarkerTrainedModelsTable = (props: BiomarkerTrainedModelsPanelPr
                             <TableCellWithTitle value={formatDateLocale(trainedModel.created as string, 'L')} />
                             <Table.Cell>{trainedModel.fitness_metric ?? '-'}</Table.Cell>
                             <Table.Cell>{trainedModel.best_fitness_value ? trainedModel.best_fitness_value.toFixed(4) : '-'}</Table.Cell>
+                            <Table.Cell>
+                                <TableCellSources
+                                    clinical_source={trainedModel.clinical_source}
+                                    methylation_source={trainedModel.mrna_source}
+                                    mrna_source={trainedModel.mirna_source}
+                                    cna_source={trainedModel.cna_source}
+                                    mirna_source={trainedModel.methylation_source}
+                                />
+                            </Table.Cell>
 
                             {/* Actions column */}
                             {props.allowFullManagement &&
diff --git a/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/inference/InferenceExperimentsTable.tsx b/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/inference/InferenceExperimentsTable.tsx
@@ -10,6 +10,7 @@ import ky from 'ky'
 import { Nullable } from '../../../../utils/interfaces'
 import { StopExperimentButton } from '../../../pipeline/all-experiments-view/StopExperimentButton'
 import { DeleteExperimentButton } from '../../../pipeline/all-experiments-view/DeleteExperimentButton'
+import { TableCellSources } from '../../../common/TableCellSources'
 
 declare const urlBiomarkerInferenceExperiments: string
 declare const urlStopInferenceExperiment: string
@@ -171,6 +172,7 @@ export const InferenceExperimentsTable = (props: InferenceExperimentsTableProps)
                     { name: 'State', serverCodeToSort: 'state', textAlign: 'center' },
                     { name: 'Model', serverCodeToSort: 'model', width: 1 },
                     { name: 'Date', serverCodeToSort: 'created' },
+                    { name: 'Datasets' },
                     { name: 'Actions' }
                 ]}
                 queryParams={{ biomarker_pk: props.selectedBiomarker.id }}
@@ -201,6 +203,15 @@ export const InferenceExperimentsTable = (props: InferenceExperimentsTableProps)
                             </Table.Cell>
                             <Table.Cell><FitnessFunctionLabel fitnessFunction={inferenceExperiment.model} /></Table.Cell>
                             <TableCellWithTitle value={formatDateLocale(inferenceExperiment.created as string, 'L')} />
+                            <Table.Cell>
+                                <TableCellSources
+                                    clinical_source={inferenceExperiment.clinical_source}
+                                    methylation_source={inferenceExperiment.mrna_source}
+                                    mrna_source={inferenceExperiment.mirna_source}
+                                    cna_source={inferenceExperiment.cna_source}
+                                    mirna_source={inferenceExperiment.methylation_source}
+                                />
+                            </Table.Cell>
                             <Table.Cell width={1}>
                                 {inferenceExperiment.state === BiomarkerState.COMPLETED &&
                                     <Icon
diff --git a/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/stat-validations/StatisticalValidationsTable.tsx b/src/frontend/static/frontend/src/components/biomarkers/biomarker-details-modal/stat-validations/StatisticalValidationsTable.tsx
@@ -10,6 +10,7 @@ import ky from 'ky'
 import { StopExperimentButton } from '../../../pipeline/all-experiments-view/StopExperimentButton'
 import { Nullable } from '../../../../utils/interfaces'
 import { DeleteExperimentButton } from '../../../pipeline/all-experiments-view/DeleteExperimentButton'
+import { TableCellSources } from '../../../common/TableCellSources'
 
 declare const urlBiomarkerStatisticalValidations: string
 declare const urlStopStatisticalValidation: string
@@ -173,6 +174,7 @@ export const StatisticalValidationsTable = (props: StatisticalValidationsTablePr
                     { name: 'State', serverCodeToSort: 'state', textAlign: 'center' },
                     { name: 'Model', textAlign: 'center', width: 2 },
                     { name: 'Date', serverCodeToSort: 'created' },
+                    { name: 'Datasets' },
                     { name: 'Actions' }
                 ]}
                 queryParams={{ biomarker_pk: props.selectedBiomarker.id }}
@@ -205,6 +207,15 @@ export const StatisticalValidationsTable = (props: StatisticalValidationsTablePr
                                 <FitnessFunctionLabel fitnessFunction={statisticalValidation.fitness_function} />
                             </Table.Cell>
                             <TableCellWithTitle value={formatDateLocale(statisticalValidation.created as string, 'L')} />
+                            <Table.Cell>
+                                <TableCellSources
+                                    clinical_source={statisticalValidation.clinical_source}
+                                    methylation_source={statisticalValidation.mrna_source}
+                                    mrna_source={statisticalValidation.mirna_source}
+                                    cna_source={statisticalValidation.cna_source}
+                                    mirna_source={statisticalValidation.methylation_source}
+                                />
+                            </Table.Cell>
                             <Table.Cell width={1}>
                                 {statisticalValidation.state === BiomarkerState.COMPLETED &&
                                     <Icon
diff --git a/src/frontend/static/frontend/src/components/biomarkers/labels/MoleculeTypeLabel.tsx b/src/frontend/static/frontend/src/components/biomarkers/labels/MoleculeTypeLabel.tsx
@@ -1,6 +1,6 @@
 import React from 'react'
 import { Label, SemanticCOLORS } from 'semantic-ui-react'
-import { MoleculeType } from '../../../utils/interfaces'
+import { GenesColors, MoleculeType } from '../../../utils/interfaces'
 
 /** MoleculeTypeLabel props. */
 interface MoleculeTypeLabelProps {
@@ -23,19 +23,19 @@ export const MoleculeTypeLabel = (props: MoleculeTypeLabelProps) => {
 
     switch (props.moleculeType) {
         case MoleculeType.MRNA:
-            color = 'blue'
+            color = GenesColors.MRNA
             description = 'mRNA'
             break
         case MoleculeType.MIRNA:
-            color = 'orange'
+            color = GenesColors.MIRNA
             description = 'miRNA'
             break
         case MoleculeType.CNA:
-            color = 'yellow'
+            color = GenesColors.CNA
             description = 'CNA'
             break
         case MoleculeType.METHYLATION:
-            color = 'olive'
+            color = GenesColors.METHYLATION
             description = 'Methylation'
             break
         default:
diff --git a/src/frontend/static/frontend/src/components/biomarkers/types.ts b/src/frontend/static/frontend/src/components/biomarkers/types.ts
@@ -1,4 +1,4 @@
-import { DjangoTag } from '../../utils/django_interfaces'
+import { DjangoExperimentSource, DjangoTag } from '../../utils/django_interfaces'
 import { MoleculeType, Nullable, Source } from '../../utils/interfaces'
 import { KaplanMeierData } from '../pipeline/experiment-result/gene-gem-details/survival-analysis/KaplanMeierUtils'
 
@@ -407,6 +407,11 @@ interface TrainedModelForTable {
     cv_folds_modified: boolean,
     created: string,
     can_be_deleted: boolean,
+    clinical_source: DjangoExperimentSource,
+    methylation_source: Nullable<DjangoExperimentSource>,
+    mrna_source: Nullable<DjangoExperimentSource>,
+    cna_source: Nullable<DjangoExperimentSource>,
+    mirna_source: Nullable<DjangoExperimentSource>,
     fitness_metric: Nullable<string>,
     best_fitness_value: Nullable<number>
 }
@@ -437,6 +442,11 @@ interface BasicStatisticalValidation {
 interface StatisticalValidationForTable extends BasicStatisticalValidation {
     fitness_function: FitnessFunction,
     trained_model: Nullable<number>,
+    clinical_source: Nullable<DjangoExperimentSource>,
+    methylation_source: Nullable<DjangoExperimentSource>,
+    mrna_source: Nullable<DjangoExperimentSource>,
+    cna_source: Nullable<DjangoExperimentSource>,
+    mirna_source: Nullable<DjangoExperimentSource>,
 }
 
 /** A statistical validation of a Biomarker. */
@@ -467,6 +477,11 @@ interface InferenceExperimentForTable {
     trained_model: Nullable<number>,
     clinical_source_id: Nullable<number>
     created: string
+    clinical_source: Nullable<DjangoExperimentSource>,
+    methylation_source: Nullable<DjangoExperimentSource>,
+    mrna_source: Nullable<DjangoExperimentSource>,
+    cna_source: Nullable<DjangoExperimentSource>,
+    mirna_source: Nullable<DjangoExperimentSource>,
 }
 
 /** Django MoleculeWithCoefficient model. */
diff --git a/src/frontend/static/frontend/src/components/common/TableCellSources.tsx b/src/frontend/static/frontend/src/components/common/TableCellSources.tsx
@@ -0,0 +1,73 @@
+import React from 'react'
+import { SourcePopup } from '../pipeline/all-experiments-view/SourcePopup'
+import { DjangoExperimentSource } from '../../utils/django_interfaces'
+import { GenesColors, Nullable } from '../../utils/interfaces'
+
+/**
+ * Component to show sourcePopups if files provides
+ * @returns component
+ */
+interface Props {
+    clinical_source: Nullable<DjangoExperimentSource>,
+    methylation_source: Nullable<DjangoExperimentSource>,
+    mrna_source: Nullable<DjangoExperimentSource>,
+    cna_source: Nullable<DjangoExperimentSource>,
+    mirna_source: Nullable<DjangoExperimentSource>,
+}
+
+export const TableCellSources = (props: Props) => {
+    return (
+        <>
+            {
+                /* Download clinical file */
+                props.clinical_source &&
+                <SourcePopup
+                    source={props.clinical_source}
+                    iconName='file'
+                    iconColor={GenesColors.CLINICAL}
+                    downloadButtonTitle='Download source clinical file'
+                />
+            }
+            {
+                /* Download mRna file */
+                props.mrna_source &&
+                <SourcePopup
+                    source={props.mrna_source}
+                    iconName='file alternate'
+                    iconColor={GenesColors.MRNA}
+                    downloadButtonTitle='Download source mRna file'
+                />
+            }
+            {
+                /* Download mirna file */
+                props.mirna_source &&
+                <SourcePopup
+                    source={props.mirna_source}
+                    iconName='file alternate'
+                    iconColor={GenesColors.MIRNA}
+                    downloadButtonTitle='Download source mirna file'
+                />
+            }
+            {
+                /* Download cna file */
+                props.cna_source &&
+                <SourcePopup
+                    source={props.cna_source}
+                    iconName='file alternate'
+                    iconColor={GenesColors.CNA}
+                    downloadButtonTitle='Download source cna file'
+                />
+            }
+            {
+                /* Download methylation file */
+                props.methylation_source &&
+                <SourcePopup
+                    source={props.methylation_source}
+                    iconName='file alternate'
+                    iconColor={GenesColors.METHYLATION}
+                    downloadButtonTitle='Download source methylation file'
+                />
+            }
+        </>
+    )
+}
diff --git a/src/frontend/static/frontend/src/components/files-manager/FilesManager.tsx b/src/frontend/static/frontend/src/components/files-manager/FilesManager.tsx
@@ -29,6 +29,7 @@ declare const urlUserInstitutions: string
 declare const urlChunkUpload: string
 declare const urlChunkUploadComplete: string
 declare const downloadFileURL: string
+declare const downloadFileHeaders: string
 
 /**
  * New File Form fields
@@ -612,21 +613,49 @@ class FilesManager extends React.Component<{}, FilesManagerState> {
      * @param fileToEdit Selected file to edit
      */
     editFile = (fileToEdit: DjangoUserFile) => {
-        this.setState({
-            newFile: {
-                id: fileToEdit.id,
-                newFileName: fileToEdit.name,
-                newFileNameUser: fileToEdit.name,
-                newFileType: fileToEdit.file_type,
-                newFileDescription: fileToEdit.description ?? '',
-                newTag: fileToEdit.tag ? fileToEdit.tag.id : null,
-                isCpGSiteId: fileToEdit.is_cpg_site_id,
-                platform: fileToEdit.platform ? fileToEdit.platform : DjangoMethylationPlatform.PLATFORM_450,
-                // We only need the IDs
-                institutions: fileToEdit.institutions.map((institution) => institution.id),
-                survivalColumns: fileToEdit.survival_columns ?? []
-            }
-        })
+        if (fileToEdit.file_type === FileType.CLINICAL) {
+            ky.get(`${downloadFileHeaders}${fileToEdit.id}`, { signal: this.abortController.signal }).then((response) => {
+                response.json().then((fileHeaders: string[]) => {
+                    // Recieve file separates by , to get array of headers
+                    const survivalTuplesPossiblesValues = fileHeaders
+                    this.setState({
+                        survivalTuplesPossiblesValues,
+                        newFile: {
+                            id: fileToEdit.id,
+                            newFileName: fileToEdit.name,
+                            newFileNameUser: fileToEdit.name,
+                            newFileType: fileToEdit.file_type,
+                            newFileDescription: fileToEdit.description ?? '',
+                            newTag: fileToEdit.tag ? fileToEdit.tag.id : null,
+                            isCpGSiteId: fileToEdit.is_cpg_site_id,
+                            platform: fileToEdit.platform ? fileToEdit.platform : DjangoMethylationPlatform.PLATFORM_450,
+                            institutions: fileToEdit.institutions.map((institution) => institution.id),
+                            survivalColumns: fileToEdit.survival_columns ?? []
+                        }
+                    })
+                }).catch((err) => {
+                    console.log('Error parsing JSON ->', err)
+                })
+            }).catch((err) => {
+                console.log('Error getting file content ->', err)
+            })
+        } else {
+            this.setState({
+                survivalTuplesPossiblesValues: [],
+                newFile: {
+                    id: fileToEdit.id,
+                    newFileName: fileToEdit.name,
+                    newFileNameUser: fileToEdit.name,
+                    newFileType: fileToEdit.file_type,
+                    newFileDescription: fileToEdit.description ?? '',
+                    newTag: fileToEdit.tag ? fileToEdit.tag.id : null,
+                    isCpGSiteId: fileToEdit.is_cpg_site_id,
+                    platform: fileToEdit.platform ? fileToEdit.platform : DjangoMethylationPlatform.PLATFORM_450,
+                    institutions: fileToEdit.institutions.map((institution) => institution.id),
+                    survivalColumns: fileToEdit.survival_columns ?? []
+                }
+            })
+        }
     }
 
     /**
@@ -726,7 +755,6 @@ class FilesManager extends React.Component<{}, FilesManagerState> {
         const fileDeletionConfirmModal = this.getFileDeletionConfirmModals()
 
         const fileTypeOptions = getFileTypeSelectOptions(false)
-
         const tagOptions: DropdownItemProps[] = this.state.tags.map((tag) => {
             const id = tag.id as number
             return { key: id, value: id, text: tag.name }
diff --git a/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx b/src/frontend/static/frontend/src/components/pipeline/all-experiments-view/AllExperimentsView.tsx
@@ -1,6 +1,6 @@
 import React from 'react'
 import { Table, TableCell, Icon, DropdownItemProps } from 'semantic-ui-react'
-import { AllExperimentsTableControl, Nullable } from '../../../utils/interfaces'
+import { AllExperimentsTableControl, GenesColors, Nullable } from '../../../utils/interfaces'
 import { DjangoExperiment, DjangoTag, ExperimentState, ExperimentType, CorrelationMethod } from '../../../utils/django_interfaces'
 import { getExperimentTypeSelectOptions, getCorrelationMethodSelectOptions, formatDateLocale, getExperimentTypeObj, getExperimentCorrelationMethodInfo, getExperimentStateObj } from '../../../utils/util_functions'
 import { PaginatedTable, PaginationCustomFilter } from '../../common/PaginatedTable'
@@ -192,15 +192,15 @@ export class AllExperimentsView extends React.Component<AllExperimentsViewProps,
                                     <SourcePopup
                                         source={experiment.mRNA_source}
                                         iconName='file'
-                                        iconColor='blue'
+                                        iconColor={GenesColors.MRNA}
                                         downloadButtonTitle='Download source mRNA file'
                                     />
 
                                     {/* Download GEM file */}
                                     <SourcePopup
                                         source={experiment.gem_source}
                                         iconName='file alternate'
-                                        iconColor='teal'
+                                        iconColor={GenesColors.MIRNA}
                                         downloadButtonTitle={`Download ${getExperimentTypeObj(experiment.type, 'ExperimentType').description} source file`}
                                     />
                                 </TableCell>
diff --git a/src/frontend/static/frontend/src/components/survival/SurvivalTuplesForm.tsx b/src/frontend/static/frontend/src/components/survival/SurvivalTuplesForm.tsx
@@ -83,7 +83,6 @@ export const SurvivalTuplesForm = (props: SurvivalTuplesFormProps) => {
                 {props.survivalColumns?.map((survivalColumn, idx) => {
                     const checkedHandleSurvivalFormChanges = checkedValidityCallback(
                         (name, value) => {
-                            console.log(name, value)
                             const callback = props.handleSurvivalFormDatasetChanges
                             return callback(idx, name, value)
                         }
diff --git a/src/frontend/static/frontend/src/utils/interfaces.ts b/src/frontend/static/frontend/src/utils/interfaces.ts
@@ -122,11 +122,13 @@ interface GeneralTableControlWithoutSorting {
     // TODO: after big refactoring using only PaginatedTable.tsx, check if totalRowCount is optional
     totalRowCount?: number,
     // TODO: after big refactoring using only PaginatedTable.tsx, check if filters is optional
-    filters: { [key: string]: {
-        value: any,
-        /** Indicates if 0 as filter value is accepted */
-        allowZero?: boolean
-    } },
+    filters: {
+        [key: string]: {
+            value: any,
+            /** Indicates if 0 as filter value is accepted */
+            allowZero?: boolean
+        }
+    },
 }
 
 /**
@@ -308,7 +310,17 @@ type OkResponse = {
     ok: boolean
 }
 
+/** Types for genes colors */
+enum GenesColors {
+    MRNA = 'blue',
+    MIRNA = 'orange',
+    CNA = 'yellow',
+    METHYLATION = 'olive',
+    CLINICAL = 'teal'
+}
+
 export {
+    GenesColors,
     CustomAlertTypes,
     CustomAlert,
     Nullable,
diff --git a/src/frontend/templates/frontend/biomarkers.html b/src/frontend/templates/frontend/biomarkers.html
diff --git a/src/frontend/templates/frontend/datasets.html b/src/frontend/templates/frontend/datasets.html
diff --git a/src/user_files/urls.py b/src/user_files/urls.py
diff --git a/src/user_files/views.py b/src/user_files/views.py

Original file line number	Diff line number	Diff line change
`@@ -83,7 +83,6 @@ export const SurvivalTuplesForm = (props: SurvivalTuplesFormProps) => {`
`83`	`83`	`{props.survivalColumns?.map((survivalColumn, idx) => {`
`84`	`84`	`const checkedHandleSurvivalFormChanges = checkedValidityCallback(`
`85`	`85`	`(name, value) => {`
`86`		`- console.log(name, value)`
`87`	`86`	`const callback = props.handleSurvivalFormDatasetChanges`
`88`	`87`	`return callback(idx, name, value)`
`89`	`88`	`}`