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Merge pull request #41 from reactome:fix-2nd-layer-nav-links
Fix 2nd layer nav links
2 parents 694f5b0 + 8a0e98c commit 3e42608

37 files changed

Lines changed: 238 additions & 84 deletions

.github/workflows/deploy.yml

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name: Deploy to S3
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on:
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push:
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branches:
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- main
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- prod
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permissions:
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id-token: write
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contents: read
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-node@v4
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with:
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node-version: 20
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cache: npm
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- name: Determine version
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id: version
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run: |
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PROD_VERSION=$(curl -sf https://reactome.org/ContentService/data/database/version)
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echo "prod_version=$PROD_VERSION" >> "$GITHUB_OUTPUT"
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if [ "${{ github.ref_name }}" = "prod" ]; then
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VERSION=$PROD_VERSION
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else
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VERSION=$((PROD_VERSION + 1))
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fi
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echo "version=$VERSION" >> "$GITHUB_OUTPUT"
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echo "Deploying to version $VERSION"
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- name: Install dependencies
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run: npm ci
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- name: Build
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run: |
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npx ng build reactome-cytoscape-style
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npx ng build reactome --configuration production --base-href /${{ steps.version.outputs.version }}/website/
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- name: Configure AWS credentials
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uses: aws-actions/configure-aws-credentials@v4
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with:
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role-to-assume: ${{ vars.AWS_ROLE }}
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aws-region: us-east-1
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- name: Deploy to S3
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run: |
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aws s3 sync dist/reactome/browser/ \
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s3://${{ vars.S3_BUCKET }}/${{ steps.version.outputs.version }}/website/ \
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--delete
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- name: Invalidate CloudFront cache
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run: |
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aws cloudfront create-invalidation \
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--distribution-id E2WMIF8KN88WPK \
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--paths "/${{ steps.version.outputs.version }}/website/*"

angular.json

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},
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{
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"type": "anyComponentStyle",
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"maximumWarning": "4kB",
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"maximumError": "8kB"
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"maximumWarning": "8kB",
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"maximumError": "16kB"
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}
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],
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"outputHashing": "all"
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},
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{
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"type": "anyComponentStyle",
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"maximumWarning": "4kB",
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"maximumError": "8kB"
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"maximumWarning": "8kB",
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"maximumError": "16kB"
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}
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],
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"outputHashing": "all"

projects/pathway-browser/src/app/details/common/controller-tree/controller-tree.component.ts

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@@ -3,7 +3,7 @@ import {DatabaseObject} from "../../../model/graph/database-object.model";
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import {PageEvent} from "@angular/material/paginator";
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import {isArray, max} from "lodash";
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import {InDepth} from "../../../model/graph/in-depth.model";
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import {Relationship} from "../../../model/graph/relationship.model";
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import type {Relationship} from "../../../model/graph/relationship.model";
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import {MatPaginator} from "@angular/material/paginator";
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import {ObjectTreeComponent} from "../object-tree/object-tree.component";
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import {MatSlider, MatSliderThumb} from "@angular/material/slider";

projects/pathway-browser/src/app/details/common/molecular-process/molecular-process.component.ts

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import {Component, computed, input} from '@angular/core';
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import {CatalystActivityReference} from "../../../model/graph/control-reference/catalyst-activity-reference.model";
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import {CatalystActivity} from "../../../model/graph/catalyst-activity.model";
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import {Relationship} from "../../../model/graph/relationship.model";
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import type {Relationship} from "../../../model/graph/relationship.model";
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import {Regulation} from "../../../model/graph/Regulation/regulation.model";
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import {IconService} from "../../../services/icon.service";
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import {RegulationReference} from "../../../model/graph/control-reference/regulation-reference.model";
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isReplacedResidue
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} from "../../../services/utils";
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import {MolecularProcess} from "../../../model/graph/molecular-process.model";
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import HasModifiedResidue = Relationship.HasModifiedResidue;
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type HasModifiedResidue = Relationship.HasModifiedResidue;
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import {ObjectTreeComponent} from "../object-tree/object-tree.component";
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import {MatIcon} from "@angular/material/icon";
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import {MatTooltip} from "@angular/material/tooltip";

projects/pathway-browser/src/app/details/common/object-tree/object-tree.component.ts

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@@ -35,7 +35,7 @@ import {SchemaClasses} from "../../../constants/constants";
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import {IconService} from "../../../services/icon.service";
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import {EntityService} from "../../../services/entity.service";
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import {DataStateService} from "../../../services/data-state.service";
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import {Relationship} from "../../../model/graph/relationship.model";
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import type {Relationship} from "../../../model/graph/relationship.model";
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import {cloneDeep, isArray} from "lodash";
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import {UrlStateService} from "../../../services/url-state.service";
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import {NgClass} from "@angular/common";

projects/pathway-browser/src/app/details/tabs/description-tab/description-overview/description-overview.component.ts

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@@ -4,13 +4,13 @@ import {getProperty} from "../../../../services/utils";
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import {Anatomy} from "../../../../model/graph/external-ontology/anatomy.model";
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import {ReviewStatus} from "../../../../model/graph/review-status.model";
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import {DataKeys} from "../../../../constants/constants";
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import {Relationship} from "../../../../model/graph/relationship.model";
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import type {Relationship} from "../../../../model/graph/relationship.model";
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import {Disease} from "../../../../model/graph/external-ontology/disease.model";
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import {CellType} from "../../../../model/graph/external-ontology/cell-type.model";
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import {TitleCasePipe} from "@angular/common";
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import {OntologyTermComponent} from "../../../common/ontology-term/ontology-term.component";
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import {MatProgressSpinner} from "@angular/material/progress-spinner";
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import HasCompartment = Relationship.HasCompartment;
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type HasCompartment = Relationship.HasCompartment;
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@Component({

projects/pathway-browser/src/app/details/tabs/description-tab/description-tab.component.ts

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TemplateRef,
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viewChild
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} from '@angular/core';
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import {Analysis} from "../../../model/analysis.model";
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import type {Analysis} from "../../../model/analysis.model";
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import {IconService} from "../../../services/icon.service";
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import {
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getProperty,
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import {CatalystActivityReference} from "../../../model/graph/control-reference/catalyst-activity-reference.model";
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import {Regulation} from "../../../model/graph/Regulation/regulation.model";
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import {RegulationReference} from "../../../model/graph/control-reference/regulation-reference.model";
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import {Relationship} from "../../../model/graph/relationship.model";
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import type {Relationship} from "../../../model/graph/relationship.model";
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import {DatabaseIdentifier} from "../../../model/graph/database-identifier.model";
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import {
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EntityWithAccessionedSequence
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import {SpeciesService} from "../../../services/species.service";
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import {Summation} from "../../../model/graph/summation.model";
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import {FigureService} from "./figure/figure.service";
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import HasModifiedResidue = Relationship.HasModifiedResidue;
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type HasModifiedResidue = Relationship.HasModifiedResidue;
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import {KeyValuePipe, NgClass, NgTemplateOutlet} from "@angular/common";
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import {RouterLink} from "@angular/router";
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import {SortByTextPipe} from "../../../pipes/sort-by-text.pipe";
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import {IncludeRefPipe} from "../../../pipes/include-ref.pipe";
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import {AuthorshipDateFormatPipe} from "../../../pipes/authorship-date-format.pipe";
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import {KeyValuePipe, NgClass, NgTemplateOutlet} from "@angular/common";
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import {RouterLink} from "@angular/router";
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import {SortByTextPipe} from "../../../pipes/sort-by-text.pipe";

projects/pathway-browser/src/app/details/tabs/result-tab/found-table/found-table.component.ts

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import {MatTableDataSource, MatTableModule} from "@angular/material/table";
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import {TypeSafeMatCellDef} from "../../../../utils/type-safe-mat-cell-def.directive";
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import {TypeSafeMatRowDef} from "../../../../utils/type-safe-mat-row-def.directive";
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import {Analysis} from "../../../../model/analysis.model";
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import type {Analysis} from "../../../../model/analysis.model";
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import {AnalysisService} from "../../../../services/analysis.service";
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import {rxResource} from "@angular/core/rxjs-interop";
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import {of} from "rxjs";

projects/pathway-browser/src/app/details/tabs/result-tab/not-found-table/not-found-table.component.ts

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import {MatTooltipModule} from "@angular/material/tooltip";
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import {TypeSafeMatCellDef} from "../../../../utils/type-safe-mat-cell-def.directive";
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import {TypeSafeMatRowDef} from "../../../../utils/type-safe-mat-row-def.directive";
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import {Analysis} from "../../../../model/analysis.model";
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import type {Analysis} from "../../../../model/analysis.model";
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import {AnalysisService} from "../../../../services/analysis.service";
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import {MatProgressSpinner} from "@angular/material/progress-spinner";
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import {UrlStateService} from "../../../../services/url-state.service";

projects/pathway-browser/src/app/details/tabs/result-tab/result-tab.component.ts

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} from '@angular/core';
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import {AnalysisService} from "../../../services/analysis.service";
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import {MatTableDataSource, MatTableModule} from "@angular/material/table";
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import {Analysis} from "../../../model/analysis.model";
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import type {Analysis} from "../../../model/analysis.model";
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import {MatPaginator, MatPaginatorModule} from "@angular/material/paginator";
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import {MatSort, MatSortModule, Sort} from "@angular/material/sort";
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import {DecimalPipe} from "@angular/common";

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