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Remove dead code (#44)
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@lvreynoso
lvreynoso authored Feb 2, 2021
1 parent 15e03c8 commit 875d0c2
Showing 1 changed file with 4 additions and 174 deletions.
178 changes: 4 additions & 174 deletions src/ts/src/upload/index.tsx
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Original file line number Diff line number Diff line change
@@ -1,24 +1,11 @@
import { Step } from "./types";

import React, { useState } from "react";
import cx from "classnames";
import { get, without, flow, omit, set, find } from "lodash/fp";

import UploadHeader from "./UploadHeader";
// import UploadSampleStep from "./UploadSampleStep";
// import UploadMetadataStep from "./UploadMetadataStep";
// import UploadReviewStep from "./UploadReviewStep";

import style from "./index.module.scss";

// See HOST_GENOME_SYNONYMS in MetadataField
const HOST_GENOME_SYNONYMS = [
"host_genome",
"Host Genome",
"host_organism",
"Host Organism",
];

interface IProps {
csrf?: string;
hostGenomes?: Array<HostGenome>;
Expand All @@ -30,178 +17,21 @@ interface IProps {

export default function Upload(_props: IProps): JSX.Element {
const [currentStep, setCurrentStep] = useState<Step>(Step.UploadSamples);
// eslint-disable-next-line @typescript-eslint/no-unused-vars
const [samples, setSamples] = useState<Array<Sample>>([]);
const [uploadType, setUploadType] = useState<string>("");
// eslint-disable-next-line @typescript-eslint/no-unused-vars
const [project, setProject] = useState<Project | undefined>(undefined);
const [sampleNamesToFiles, setSampleNamesToFiles] = useState<any>(null);
const [metadata, setMetadata] = useState<any>(null);
const [metadataIssues, setMetadataIssues] = useState<any>(null);
// eslint-disable-next-line @typescript-eslint/no-unused-vars
const [stepsEnabled, setStepsEnabled] = useState({
uploadSamples: true,
uploadMetadata: false,
review: false,
});
const [hostGenomes, setHostGenomes] = useState<Array<HostGenome>>([]);
const [workflows, setWorkflows] = useState(new Set());
const [wetlabProtocol, setWetlabProtocol] = useState<any>(null);

window.onbeforeunload = () =>
"Are you sure you want to leave? All data will be lost.";

const onUploadComplete = (): void => {
window.onbeforeunload = null;
};

const handleUploadSamples = ({
samples,
project,
uploadType,
sampleNamesToFiles,
workflows,
wetlabProtocol,
}: Record<string, any>): void => {
const newStepsEnabled = set("uploadMetadata", true, stepsEnabled);

setCurrentStep(Step.UploadMetadata);
setProject(project);
setSampleNamesToFiles(sampleNamesToFiles);
setStepsEnabled(newStepsEnabled);
setUploadType(uploadType);
setWetlabProtocol(wetlabProtocol);
setWorkflows(workflows);
};

const handleUploadMetadata = ({
metadata,
issues,
newHostGenomes,
}: Record<string, any>): void => {
const currentHostGenomes: Array<HostGenome> = hostGenomes ?? [];
const updatedHostGenomes = currentHostGenomes.concat(newHostGenomes);

// Populate host_genome_id in sample using metadata.
const newSamples: Array<any> = [];
samples.forEach((sample) => {
const metadataRow = find(
(row) =>
get("sample_name", row) === sample.name ||
get("Sample Name", row) === sample.name,
metadata.rows
);
const hostGenomeName: string = HOST_GENOME_SYNONYMS.reduce(
(match, name) => metadataRow[name] || match,
""
);
const hostGenomeId =
find(
// Lowercase to allow for 'human' to match 'Human'. The same logic
// is replicated in MetadataHelper.
(hg) => {
return (
hg.name.toLowerCase() ===
hostGenomeName.toLowerCase()
);
},
updatedHostGenomes
)?.id ?? null;

newSamples.push({
...sample,
// Set the host_genome_id and name so it is available in review
host_genome_id: hostGenomeId,
host_genome_name: hostGenomeName,
});
});

// Remove host_genome from metadata.
const newMetadata = flow(
set("rows", metadata.rows.map(omit(HOST_GENOME_SYNONYMS))),
set("headers", without(HOST_GENOME_SYNONYMS, metadata.headers))
)(metadata);

setSamples(newSamples);
setMetadata(newMetadata);
setMetadataIssues(issues);
setCurrentStep(Step.Review);
// setStepsEnabled(set("review", true, this.state.stepsEnabled));
setHostGenomes(updatedHostGenomes);
};

const samplesChanged = (): void => {
setStepsEnabled({
uploadSamples: true,
uploadMetadata: false,
review: false,
});
};

const metadataChanged = (): void => {
setStepsEnabled({
uploadSamples: true,
uploadMetadata: true,
review: false,
});
};

const handleStepSelect = (step: Step): void => {
setCurrentStep(step);
};

const onUploadStatusChange = (uploadStatus: any): void => {
setStepsEnabled({
uploadSamples: !uploadStatus,
uploadMetadata: !uploadStatus,
review: !uploadStatus,
});
};

// Uncomment function when child components are converted to Typscript/functional components
// Original IDSeq comment:
// SLIGHT HACK: Keep steps mounted, so user can return to them if needed.
// The internal state of some steps is difficult to recover if they are unmounted.
// const renderSteps = (): JSX.Element => {
// return (
// <div>
// <UploadSampleStep
// onDirty={samplesChanged}
// onUploadSamples={handleUploadSamples}
// visible={currentStep === Step.UploadSamples}
// basespaceClientId={props.basespaceClientId}
// basespaceOauthRedirectUri={props.basespaceOauthRedirectUri}
// admin={props.admin}
// biohubS3UploadEnabled={props.biohubS3UploadEnabled}
// />
// {samples && (
// <UploadMetadataStep
// onUploadMetadata={handleUploadMetadata}
// samples={samples}
// project={project}
// visible={currentStep === Step.UploadMetadata}
// onDirty={metadataChanged}
// workflows={workflows}
// />
// )}
// {samples && metadata && (
// <UploadReviewStep
// hostGenomes={hostGenomes}
// metadata={metadata}
// onStepSelect={handleStepSelect}
// onUploadComplete={onUploadComplete}
// onUploadStatusChange={onUploadStatusChange}
// originalHostGenomes={props.hostGenomes}
// project={project}
// sampleNamesToFiles={sampleNamesToFiles}
// samples={samples}
// uploadType={uploadType}
// visible={currentStep === Step.Review}
// wetlabProtocol={wetlabProtocol}
// workflows={workflows}
// />
// )}
// </div>
// );
// };

return (
<div>
<UploadHeader
Expand All @@ -211,7 +41,7 @@ export default function Upload(_props: IProps): JSX.Element {
onStepSelect={handleStepSelect}
stepsEnabled={stepsEnabled}
/>
<div className={cx(style.sampleUploadFlow)}>
<div className={style.sampleUploadFlow}>
<div className={style.inner}>{"Steps go here."}</div>
</div>
</div>
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