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[major changes] data transformed on the server
* Server now stores all the data and sends only the data necessary to view. Should allow for a much more responsive client. * Communication now through sockets in preparation for eventual move to electron * viz completely broken * sidebar UI * config can be changed through the GUI (buggy)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,7 @@ | ||
| { | ||
| "extends": "react-app" | ||
| "extends": "react-app", | ||
| "plugins": ["import"], | ||
| "rules": { | ||
| "import/no-unresolved": 2 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,45 +1,22 @@ | ||
| const server = require("./server/server"); | ||
| const { parser } = require("./server/args"); | ||
| const { parseConfig } = require("./server/config"); | ||
| const Deque = require("collections/deque"); | ||
| const { mapper } = require("./server/mapper"); | ||
| const { demuxer } = require("./server/demuxer"); | ||
| const getInitialConfig = require("./server/config").getInitialConfig; | ||
| const { startUp } = require("./server/startUp"); | ||
| const { startGuppyWatcher } = require("./server/guppyWatcher"); | ||
| const { sleep } = require("./server/utils"); | ||
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|
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| /* make some globals available everywhere */ | ||
| global.args = parser.parseArgs(); | ||
| global.config = parseConfig(global.args); | ||
| const args = parser.parseArgs(); | ||
| if (args.verbose) global.VERBOSE = true; | ||
| if (args.mockFailures) global.MOCK_FAILURES = true; | ||
| global.io = undefined; | ||
| global.config = getInitialConfig(args) | ||
| global.datastore = {}; | ||
| global.barcodesSeen = new Set(); | ||
| global.haveBeenSeen = new Set(); | ||
| global.demuxQueue = new Deque(); | ||
| global.mappingQueue = new Deque(); | ||
| global.mappingResults = new Deque(); | ||
| global.timeMap = new Map(); | ||
| global.epochMap = new Map(); | ||
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| const startWatchers = () => { | ||
| /* as things get pushed onto the deques, we want to spawn the | ||
| appropriate processes (e.g. guppy, porechop). | ||
| As things are processed, they are shifted off one deque and pushed | ||
| onto another! */ | ||
| global.demuxQueue.addRangeChangeListener(() => demuxer()); | ||
| global.mappingQueue.addRangeChangeListener(() => mapper()); | ||
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| // start watchers | ||
| demuxer(); | ||
| mapper(); | ||
| startGuppyWatcher(); | ||
| } | ||
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| const main = async () => { | ||
| await startUp(); /* block until we've read the appropriate files */ | ||
| /* Listen on localhost and process requests from the client */ | ||
| const app = server.run({}); // eslint-disable-line | ||
| await sleep(200); | ||
| startWatchers(); | ||
| await startUp({emptyDemuxed: args.emptyDemuxed}); /* block until we've read the appropriate files */ | ||
| const app = await server.run({devClient: args.devClient}); // eslint-disable-line | ||
| } | ||
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| main(); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,71 +1,128 @@ | ||
| const fs = require('fs') | ||
| const path = require('path') | ||
| const chalk = require('chalk'); | ||
| const { getAbsolutePath } = require("./utils"); | ||
| const { getAbsolutePath, verbose, log, warn } = require("./utils"); | ||
| const { mapper } = require("./mapper"); | ||
|
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| const ensurePathExists = (p, {make=false}={}) => { | ||
| if (!fs.existsSync(p)) { | ||
| if (make) { | ||
| console.log(chalk.yellowBright("Path", p, "created")); | ||
| log(`Creating path ${p}`); | ||
| fs.mkdirSync(p, {recursive: true}) | ||
| } else { | ||
| console.log("ERROR. Path", p, "doesn't exist."); | ||
| process.exit(1); | ||
| throw new Error(`ERROR. Path ${p} doesn't exist.`); | ||
| } | ||
| } | ||
| } | ||
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| const parseConfig = (args) => { | ||
| const configDir = path.dirname(getAbsolutePath(args.config)); | ||
| let config = JSON.parse(fs.readFileSync(getAbsolutePath(args.config))); | ||
| const getReferenceNames = (referencePanelPath) => { | ||
| return fs.readFileSync(referencePanelPath, "utf8") | ||
| .split("\n") | ||
| .filter((l) => l.startsWith(">")) | ||
| .map((n) => { | ||
| if (n.indexOf(" ") > 0) { | ||
| return { | ||
| "name": n.substring(1, n.indexOf(" ")), // fasta name is up until the first space | ||
| "description": n.substring(n.indexOf(" ")) // fasta description is the rest | ||
| }; | ||
| } else { | ||
| return { | ||
| "name": n.substring(1), | ||
| "description": "" | ||
| }; | ||
| } | ||
| }); | ||
| } | ||
|
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| /* check config file has the appropriate fields... */ | ||
| /** | ||
| * Create initial config file from command line arguments | ||
| */ | ||
| const getInitialConfig = (args) => { | ||
| const barcodes = [ | ||
| "BC01", "BC02", "BC03", "BC04", "BC05", "BC06", "BC07", "BC08", "BC09", "BC10", "BC11", "BC12" | ||
| ]; | ||
|
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| /* sort out paths */ | ||
| config.referenceConfigPath = getAbsolutePath(config.referenceConfigPath, {relativeTo: configDir}); | ||
| config.referencePanelPath = getAbsolutePath(config.referencePanelPath, {relativeTo: configDir}); | ||
| const config = { | ||
| title: args.title ? args.title : "", | ||
| barcodeToName: {}, | ||
| barcodes, | ||
| basecalledPath: "", | ||
| demuxedPath: "", | ||
| referenceConfigPath: "", | ||
| referencePanelPath: "", | ||
| referencePanel: [], | ||
| reference: undefined, | ||
| relaxedDemuxing: args.relaxedDemuxing, | ||
| }; | ||
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| if (args.basecalledDir) { | ||
| config.basecalledPath = getAbsolutePath(args.basecalledDir, {relativeTo: process.cwd()}); | ||
| console.log("BC:", config.basecalledPath) | ||
| } else { | ||
| config.basecalledPath = getAbsolutePath(config.basecalledPath, {relativeTo: configDir}); | ||
| } | ||
| config.demuxedPath = getAbsolutePath(config.demuxedPath, {relativeTo: configDir}); | ||
| /* most options _can_ be specified on the command line, but may also be specified in the client */ | ||
| barcodes.forEach((bc) => { | ||
| config.barcodeToName[bc] = undefined; | ||
| }) | ||
| if (args.barcodeNames) { | ||
| args.barcodeNames.forEach((raw) => { | ||
| const [bc, name] = raw.split('='); | ||
| if (!barcodes.includes(bc)) { | ||
| throw new Error(`Invalid barcode ${bc}`) | ||
| } | ||
| config.barcodeToName[bc] = name; | ||
| }); | ||
| } | ||
|
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| /* check if paths exist (perhaps we could make them if they don't) */ | ||
| ensurePathExists(config.referenceConfigPath); | ||
| ensurePathExists(config.referencePanelPath); | ||
| if (args.basecalledDir !== "") { | ||
| config.basecalledPath = getAbsolutePath(args.basecalledDir, {relativeTo: process.cwd()}); | ||
| } | ||
| if (args.demuxedDir !== "") { | ||
| config.demuxedPath = getAbsolutePath(args.demuxedDir, {relativeTo: process.cwd()}); | ||
| ensurePathExists(config.demuxedPath, {make: true}); | ||
| } | ||
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| if (args.referencePanelPath) { | ||
| ensurePathExists(args.referencePanelPath); | ||
| config.referencePanelPath = getAbsolutePath(args.referencePanelPath, {relativeTo: process.cwd()}); | ||
| config.referencePanel = getReferenceNames(config.referencePanelPath); | ||
| } | ||
|
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| if (args.referenceConfigPath) { | ||
| ensurePathExists(args.referenceConfigPath); | ||
| config.referenceConfigPath = getAbsolutePath(args.referenceConfigPath, {relativeTo: process.cwd()}); | ||
|
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| /* parse the "main reference" configuration file (e.g. primers, genes, ref seq etc) */ | ||
| const secondConfig = JSON.parse(fs.readFileSync(config.referenceConfigPath)); | ||
| config = {...config, ...secondConfig}; | ||
|
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| /* get the names of the sequences in the reference panel */ | ||
| config.referencePanel = fs.readFileSync(config.referencePanelPath, "utf8") | ||
| .split("\n") | ||
| .filter((l) => l.startsWith(">")) | ||
| .map((n) => { | ||
| if (n.indexOf(" ") > 0) { | ||
| return { | ||
| "name": n.substring(1, n.indexOf(" ")), // fasta name is up until the first space | ||
| "description": n.substring(n.indexOf(" ")) // fasta description is the rest | ||
| }; | ||
| } else { | ||
| return { | ||
| "name": n.substring(1), | ||
| "description": "" | ||
| }; | ||
| } | ||
| }); // remove the > character | ||
|
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| /* things that may be put into the config JSON in the future */ | ||
| config.maxMappingFilesPerRequest = 100; | ||
|
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| return config; | ||
| const reference = JSON.parse(fs.readFileSync(config.referenceConfigPath)).reference; | ||
| config.reference = reference; | ||
|
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| } | ||
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| return config; | ||
| }; | ||
|
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| /** | ||
| * update the config file via GUI provided data | ||
| */ | ||
| const modifyConfig = (newConfig) => { | ||
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| global.config.barcodeToName = newConfig.barcodeToName; | ||
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| if (!global.config.referencePanelPath && newConfig.referencePanelPath) { | ||
| try { | ||
| ensurePathExists(newConfig.referencePanelPath); | ||
| // take approprieate action? | ||
| } catch (err) { | ||
| warn(err.message); | ||
| newConfig.referencePanelPath = ""; | ||
| } | ||
| } | ||
|
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| global.config = Object.assign({}, global.config, newConfig); | ||
|
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| /* try to start the mapper, which may not be running due to insufficent | ||
| config information. It will exit gracefully if required */ | ||
| mapper(); | ||
|
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| } | ||
|
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| module.exports = { | ||
| parseConfig | ||
| getInitialConfig, | ||
| modifyConfig | ||
| }; |
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