Issues/247 Remove Seperation of Datapath and Filename in Requests #339
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src/components/TrackFilePicker.js
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| <div data-testid={testID}> | ||
| <Input | ||
| type="file" | ||
| className="customDataUpload form-control-file" | ||
| accept={acceptedExtensions} | ||
| innerRef={uploadFileInput} | ||
| onChange={uploadOnChange} | ||
| /> |
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This part doesn't actually work yet in this branch, right? But also it's not displayed yet?
src/config.json
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| @@ -4,19 +4,19 @@ | |||
| { | |||
| "name": "snp1kg-BRCA1", | |||
| "tracks": [ | |||
| {"trackFile": "snp1kg-BRCA1.vg.xg", "trackType": "graph", "trackColorSettings": {"mainPalette": "greys", "auxPalette": "ygreys"}}, | |||
| {"trackFile": "NA12878-BRCA1.sorted.gam", "trackType": "read"} | |||
| {"trackFile": "./exampleData/internal/snp1kg-BRCA1.vg.xg", "trackType": "graph", "trackColorSettings": {"mainPalette": "greys", "auxPalette": "ygreys"}}, | |||
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All the leading ./es are redundant; I think exampleData/whatever ought to work fine.
src/server.mjs
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| fs.readdirSync(MOUNTED_DATA_PATH).forEach((file) => { | ||
| if (endsWithExtensions(file, GRAPH_EXTENSIONS)) { | ||
| result.files.push({"trackFile": file, "trackType": "graph"}); | ||
| result.files.push({"trackFile": path.resolve(config.dataPath, file), "trackType": "graph"}); |
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We're looping over the contents of MOUNTED_DATA_PATH, but resolving the absolute paths with config.dataPath. Those should really both be the same expression to ensure we actually end up pointing to the files we are looking at.
We might want to have a const absPath = path.resolve(config.dataPath, file) outside all the conditionals, also. Instead of repeating it so much.
src/components/TrackFilePicker.js
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| const fileTypeToExtensions = { | ||
| "graph": ".xg,.vg,.hg,.gbz,.pg", | ||
| "read": ".gbwt,.gbz", | ||
| "haplotype": ".gam", | ||
| } |
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I think read and haplotype are swapped here.
Can we make these come from the same constants used on the server, like HAPLOTYPE_EXTENSIONS, by moving the strings to a common file?
| @@ -310,20 +307,20 @@ class HeaderForm extends Component { | |||
| } else { | |||
| json.bedFiles.unshift("none"); | |||
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| if (this.state.dataPath === "mounted") { | |||
| if (this.state.dataType === dataTypes.MOUNTED_FILES) { | |||
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Should we rename MOUNTED_FILES to maybe CUSTOM?
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