grnsight 6.0.4 → 6.0.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1197) hide show
  1. package/database/README.md +40 -16
  2. package/database/expression-database/README.md +2 -2
  3. package/database/expression-database/schema.sql +14 -14
  4. package/database/expression-database/scripts/loader.py +6 -6
  5. package/database/network-database/README.md +36 -4
  6. package/database/network-database/schema.sql +7 -7
  7. package/database/network-database/scripts/filter_genes.py +1 -1
  8. package/database/network-database/scripts/generate_network.py +1 -1
  9. package/database/network-database/scripts/generate_new_network_version.py +223 -0
  10. package/database/network-database/scripts/loader.py +3 -3
  11. package/database/network-database/scripts/loader_updates.py +99 -0
  12. package/package.json +2 -2
  13. package/server/controllers/custom-workbook-controller.js +4 -3
  14. package/server/dals/expression-dal.js +8 -7
  15. package/server/dals/network-dal.js +3 -3
  16. package/web-client/public/js/api/grnsight-api.js +56 -55
  17. package/web-client/public/js/generateNetwork.js +15 -7
  18. package/web-client/public/js/setup-load-and-import-handlers.js +171 -170
  19. package/web-client/public/js/upload.js +74 -95
  20. package/.bundle/config +0 -3
  21. package/GRNsight - Beta.html +0 -194
  22. package/Gemfile.lock +0 -259
  23. package/_gh_pages/about.html +0 -807
  24. package/_gh_pages/assets/css/bootstrap.min.css +0 -10
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214
- <a name='L166'></a><a href='#L166'>166</a>
215
- <a name='L167'></a><a href='#L167'>167</a>
216
- <a name='L168'></a><a href='#L168'>168</a>
217
- <a name='L169'></a><a href='#L169'>169</a>
218
- <a name='L170'></a><a href='#L170'>170</a>
219
- <a name='L171'></a><a href='#L171'>171</a>
220
- <a name='L172'></a><a href='#L172'>172</a>
221
- <a name='L173'></a><a href='#L173'>173</a>
222
- <a name='L174'></a><a href='#L174'>174</a>
223
- <a name='L175'></a><a href='#L175'>175</a>
224
- <a name='L176'></a><a href='#L176'>176</a>
225
- <a name='L177'></a><a href='#L177'>177</a>
226
- <a name='L178'></a><a href='#L178'>178</a>
227
- <a name='L179'></a><a href='#L179'>179</a>
228
- <a name='L180'></a><a href='#L180'>180</a>
229
- <a name='L181'></a><a href='#L181'>181</a>
230
- <a name='L182'></a><a href='#L182'>182</a>
231
- <a name='L183'></a><a href='#L183'>183</a>
232
- <a name='L184'></a><a href='#L184'>184</a>
233
- <a name='L185'></a><a href='#L185'>185</a>
234
- <a name='L186'></a><a href='#L186'>186</a>
235
- <a name='L187'></a><a href='#L187'>187</a>
236
- <a name='L188'></a><a href='#L188'>188</a>
237
- <a name='L189'></a><a href='#L189'>189</a>
238
- <a name='L190'></a><a href='#L190'>190</a>
239
- <a name='L191'></a><a href='#L191'>191</a>
240
- <a name='L192'></a><a href='#L192'>192</a>
241
- <a name='L193'></a><a href='#L193'>193</a>
242
- <a name='L194'></a><a href='#L194'>194</a>
243
- <a name='L195'></a><a href='#L195'>195</a>
244
- <a name='L196'></a><a href='#L196'>196</a>
245
- <a name='L197'></a><a href='#L197'>197</a>
246
- <a name='L198'></a><a href='#L198'>198</a>
247
- <a name='L199'></a><a href='#L199'>199</a>
248
- <a name='L200'></a><a href='#L200'>200</a>
249
- <a name='L201'></a><a href='#L201'>201</a>
250
- <a name='L202'></a><a href='#L202'>202</a>
251
- <a name='L203'></a><a href='#L203'>203</a>
252
- <a name='L204'></a><a href='#L204'>204</a>
253
- <a name='L205'></a><a href='#L205'>205</a>
254
- <a name='L206'></a><a href='#L206'>206</a>
255
- <a name='L207'></a><a href='#L207'>207</a>
256
- <a name='L208'></a><a href='#L208'>208</a>
257
- <a name='L209'></a><a href='#L209'>209</a>
258
- <a name='L210'></a><a href='#L210'>210</a>
259
- <a name='L211'></a><a href='#L211'>211</a>
260
- <a name='L212'></a><a href='#L212'>212</a>
261
- <a name='L213'></a><a href='#L213'>213</a>
262
- <a name='L214'></a><a href='#L214'>214</a>
263
- <a name='L215'></a><a href='#L215'>215</a>
264
- <a name='L216'></a><a href='#L216'>216</a>
265
- <a name='L217'></a><a href='#L217'>217</a>
266
- <a name='L218'></a><a href='#L218'>218</a>
267
- <a name='L219'></a><a href='#L219'>219</a>
268
- <a name='L220'></a><a href='#L220'>220</a>
269
- <a name='L221'></a><a href='#L221'>221</a>
270
- <a name='L222'></a><a href='#L222'>222</a>
271
- <a name='L223'></a><a href='#L223'>223</a>
272
- <a name='L224'></a><a href='#L224'>224</a>
273
- <a name='L225'></a><a href='#L225'>225</a>
274
- <a name='L226'></a><a href='#L226'>226</a>
275
- <a name='L227'></a><a href='#L227'>227</a>
276
- <a name='L228'></a><a href='#L228'>228</a>
277
- <a name='L229'></a><a href='#L229'>229</a>
278
- <a name='L230'></a><a href='#L230'>230</a>
279
- <a name='L231'></a><a href='#L231'>231</a>
280
- <a name='L232'></a><a href='#L232'>232</a>
281
- <a name='L233'></a><a href='#L233'>233</a>
282
- <a name='L234'></a><a href='#L234'>234</a>
283
- <a name='L235'></a><a href='#L235'>235</a>
284
- <a name='L236'></a><a href='#L236'>236</a>
285
- <a name='L237'></a><a href='#L237'>237</a>
286
- <a name='L238'></a><a href='#L238'>238</a>
287
- <a name='L239'></a><a href='#L239'>239</a>
288
- <a name='L240'></a><a href='#L240'>240</a>
289
- <a name='L241'></a><a href='#L241'>241</a>
290
- <a name='L242'></a><a href='#L242'>242</a>
291
- <a name='L243'></a><a href='#L243'>243</a>
292
- <a name='L244'></a><a href='#L244'>244</a>
293
- <a name='L245'></a><a href='#L245'>245</a>
294
- <a name='L246'></a><a href='#L246'>246</a>
295
- <a name='L247'></a><a href='#L247'>247</a>
296
- <a name='L248'></a><a href='#L248'>248</a>
297
- <a name='L249'></a><a href='#L249'>249</a>
298
- <a name='L250'></a><a href='#L250'>250</a>
299
- <a name='L251'></a><a href='#L251'>251</a>
300
- <a name='L252'></a><a href='#L252'>252</a>
301
- <a name='L253'></a><a href='#L253'>253</a>
302
- <a name='L254'></a><a href='#L254'>254</a>
303
- <a name='L255'></a><a href='#L255'>255</a>
304
- <a name='L256'></a><a href='#L256'>256</a>
305
- <a name='L257'></a><a href='#L257'>257</a>
306
- <a name='L258'></a><a href='#L258'>258</a>
307
- <a name='L259'></a><a href='#L259'>259</a>
308
- <a name='L260'></a><a href='#L260'>260</a>
309
- <a name='L261'></a><a href='#L261'>261</a>
310
- <a name='L262'></a><a href='#L262'>262</a>
311
- <a name='L263'></a><a href='#L263'>263</a>
312
- <a name='L264'></a><a href='#L264'>264</a>
313
- <a name='L265'></a><a href='#L265'>265</a>
314
- <a name='L266'></a><a href='#L266'>266</a>
315
- <a name='L267'></a><a href='#L267'>267</a>
316
- <a name='L268'></a><a href='#L268'>268</a>
317
- <a name='L269'></a><a href='#L269'>269</a>
318
- <a name='L270'></a><a href='#L270'>270</a>
319
- <a name='L271'></a><a href='#L271'>271</a>
320
- <a name='L272'></a><a href='#L272'>272</a>
321
- <a name='L273'></a><a href='#L273'>273</a>
322
- <a name='L274'></a><a href='#L274'>274</a>
323
- <a name='L275'></a><a href='#L275'>275</a>
324
- <a name='L276'></a><a href='#L276'>276</a>
325
- <a name='L277'></a><a href='#L277'>277</a>
326
- <a name='L278'></a><a href='#L278'>278</a>
327
- <a name='L279'></a><a href='#L279'>279</a>
328
- <a name='L280'></a><a href='#L280'>280</a>
329
- <a name='L281'></a><a href='#L281'>281</a>
330
- <a name='L282'></a><a href='#L282'>282</a>
331
- <a name='L283'></a><a href='#L283'>283</a>
332
- <a name='L284'></a><a href='#L284'>284</a>
333
- <a name='L285'></a><a href='#L285'>285</a>
334
- <a name='L286'></a><a href='#L286'>286</a>
335
- <a name='L287'></a><a href='#L287'>287</a>
336
- <a name='L288'></a><a href='#L288'>288</a>
337
- <a name='L289'></a><a href='#L289'>289</a>
338
- <a name='L290'></a><a href='#L290'>290</a>
339
- <a name='L291'></a><a href='#L291'>291</a>
340
- <a name='L292'></a><a href='#L292'>292</a>
341
- <a name='L293'></a><a href='#L293'>293</a>
342
- <a name='L294'></a><a href='#L294'>294</a>
343
- <a name='L295'></a><a href='#L295'>295</a>
344
- <a name='L296'></a><a href='#L296'>296</a>
345
- <a name='L297'></a><a href='#L297'>297</a>
346
- <a name='L298'></a><a href='#L298'>298</a>
347
- <a name='L299'></a><a href='#L299'>299</a>
348
- <a name='L300'></a><a href='#L300'>300</a>
349
- <a name='L301'></a><a href='#L301'>301</a>
350
- <a name='L302'></a><a href='#L302'>302</a>
351
- <a name='L303'></a><a href='#L303'>303</a>
352
- <a name='L304'></a><a href='#L304'>304</a>
353
- <a name='L305'></a><a href='#L305'>305</a>
354
- <a name='L306'></a><a href='#L306'>306</a>
355
- <a name='L307'></a><a href='#L307'>307</a>
356
- <a name='L308'></a><a href='#L308'>308</a>
357
- <a name='L309'></a><a href='#L309'>309</a>
358
- <a name='L310'></a><a href='#L310'>310</a>
359
- <a name='L311'></a><a href='#L311'>311</a>
360
- <a name='L312'></a><a href='#L312'>312</a>
361
- <a name='L313'></a><a href='#L313'>313</a>
362
- <a name='L314'></a><a href='#L314'>314</a>
363
- <a name='L315'></a><a href='#L315'>315</a>
364
- <a name='L316'></a><a href='#L316'>316</a>
365
- <a name='L317'></a><a href='#L317'>317</a>
366
- <a name='L318'></a><a href='#L318'>318</a>
367
- <a name='L319'></a><a href='#L319'>319</a>
368
- <a name='L320'></a><a href='#L320'>320</a>
369
- <a name='L321'></a><a href='#L321'>321</a>
370
- <a name='L322'></a><a href='#L322'>322</a>
371
- <a name='L323'></a><a href='#L323'>323</a>
372
- <a name='L324'></a><a href='#L324'>324</a>
373
- <a name='L325'></a><a href='#L325'>325</a>
374
- <a name='L326'></a><a href='#L326'>326</a>
375
- <a name='L327'></a><a href='#L327'>327</a>
376
- <a name='L328'></a><a href='#L328'>328</a>
377
- <a name='L329'></a><a href='#L329'>329</a>
378
- <a name='L330'></a><a href='#L330'>330</a>
379
- <a name='L331'></a><a href='#L331'>331</a>
380
- <a name='L332'></a><a href='#L332'>332</a>
381
- <a name='L333'></a><a href='#L333'>333</a>
382
- <a name='L334'></a><a href='#L334'>334</a>
383
- <a name='L335'></a><a href='#L335'>335</a>
384
- <a name='L336'></a><a href='#L336'>336</a>
385
- <a name='L337'></a><a href='#L337'>337</a>
386
- <a name='L338'></a><a href='#L338'>338</a>
387
- <a name='L339'></a><a href='#L339'>339</a>
388
- <a name='L340'></a><a href='#L340'>340</a>
389
- <a name='L341'></a><a href='#L341'>341</a>
390
- <a name='L342'></a><a href='#L342'>342</a>
391
- <a name='L343'></a><a href='#L343'>343</a>
392
- <a name='L344'></a><a href='#L344'>344</a>
393
- <a name='L345'></a><a href='#L345'>345</a>
394
- <a name='L346'></a><a href='#L346'>346</a>
395
- <a name='L347'></a><a href='#L347'>347</a>
396
- <a name='L348'></a><a href='#L348'>348</a>
397
- <a name='L349'></a><a href='#L349'>349</a>
398
- <a name='L350'></a><a href='#L350'>350</a>
399
- <a name='L351'></a><a href='#L351'>351</a>
400
- <a name='L352'></a><a href='#L352'>352</a>
401
- <a name='L353'></a><a href='#L353'>353</a>
402
- <a name='L354'></a><a href='#L354'>354</a>
403
- <a name='L355'></a><a href='#L355'>355</a>
404
- <a name='L356'></a><a href='#L356'>356</a>
405
- <a name='L357'></a><a href='#L357'>357</a>
406
- <a name='L358'></a><a href='#L358'>358</a>
407
- <a name='L359'></a><a href='#L359'>359</a>
408
- <a name='L360'></a><a href='#L360'>360</a>
409
- <a name='L361'></a><a href='#L361'>361</a>
410
- <a name='L362'></a><a href='#L362'>362</a>
411
- <a name='L363'></a><a href='#L363'>363</a>
412
- <a name='L364'></a><a href='#L364'>364</a>
413
- <a name='L365'></a><a href='#L365'>365</a>
414
- <a name='L366'></a><a href='#L366'>366</a>
415
- <a name='L367'></a><a href='#L367'>367</a>
416
- <a name='L368'></a><a href='#L368'>368</a>
417
- <a name='L369'></a><a href='#L369'>369</a>
418
- <a name='L370'></a><a href='#L370'>370</a>
419
- <a name='L371'></a><a href='#L371'>371</a>
420
- <a name='L372'></a><a href='#L372'>372</a>
421
- <a name='L373'></a><a href='#L373'>373</a>
422
- <a name='L374'></a><a href='#L374'>374</a>
423
- <a name='L375'></a><a href='#L375'>375</a>
424
- <a name='L376'></a><a href='#L376'>376</a>
425
- <a name='L377'></a><a href='#L377'>377</a>
426
- <a name='L378'></a><a href='#L378'>378</a>
427
- <a name='L379'></a><a href='#L379'>379</a>
428
- <a name='L380'></a><a href='#L380'>380</a>
429
- <a name='L381'></a><a href='#L381'>381</a>
430
- <a name='L382'></a><a href='#L382'>382</a>
431
- <a name='L383'></a><a href='#L383'>383</a>
432
- <a name='L384'></a><a href='#L384'>384</a>
433
- <a name='L385'></a><a href='#L385'>385</a>
434
- <a name='L386'></a><a href='#L386'>386</a>
435
- <a name='L387'></a><a href='#L387'>387</a>
436
- <a name='L388'></a><a href='#L388'>388</a>
437
- <a name='L389'></a><a href='#L389'>389</a>
438
- <a name='L390'></a><a href='#L390'>390</a>
439
- <a name='L391'></a><a href='#L391'>391</a>
440
- <a name='L392'></a><a href='#L392'>392</a>
441
- <a name='L393'></a><a href='#L393'>393</a>
442
- <a name='L394'></a><a href='#L394'>394</a>
443
- <a name='L395'></a><a href='#L395'>395</a>
444
- <a name='L396'></a><a href='#L396'>396</a>
445
- <a name='L397'></a><a href='#L397'>397</a>
446
- <a name='L398'></a><a href='#L398'>398</a>
447
- <a name='L399'></a><a href='#L399'>399</a>
448
- <a name='L400'></a><a href='#L400'>400</a>
449
- <a name='L401'></a><a href='#L401'>401</a>
450
- <a name='L402'></a><a href='#L402'>402</a>
451
- <a name='L403'></a><a href='#L403'>403</a>
452
- <a name='L404'></a><a href='#L404'>404</a>
453
- <a name='L405'></a><a href='#L405'>405</a>
454
- <a name='L406'></a><a href='#L406'>406</a>
455
- <a name='L407'></a><a href='#L407'>407</a>
456
- <a name='L408'></a><a href='#L408'>408</a>
457
- <a name='L409'></a><a href='#L409'>409</a>
458
- <a name='L410'></a><a href='#L410'>410</a>
459
- <a name='L411'></a><a href='#L411'>411</a>
460
- <a name='L412'></a><a href='#L412'>412</a>
461
- <a name='L413'></a><a href='#L413'>413</a>
462
- <a name='L414'></a><a href='#L414'>414</a>
463
- <a name='L415'></a><a href='#L415'>415</a>
464
- <a name='L416'></a><a href='#L416'>416</a>
465
- <a name='L417'></a><a href='#L417'>417</a>
466
- <a name='L418'></a><a href='#L418'>418</a>
467
- <a name='L419'></a><a href='#L419'>419</a>
468
- <a name='L420'></a><a href='#L420'>420</a>
469
- <a name='L421'></a><a href='#L421'>421</a>
470
- <a name='L422'></a><a href='#L422'>422</a>
471
- <a name='L423'></a><a href='#L423'>423</a>
472
- <a name='L424'></a><a href='#L424'>424</a>
473
- <a name='L425'></a><a href='#L425'>425</a>
474
- <a name='L426'></a><a href='#L426'>426</a>
475
- <a name='L427'></a><a href='#L427'>427</a>
476
- <a name='L428'></a><a href='#L428'>428</a>
477
- <a name='L429'></a><a href='#L429'>429</a>
478
- <a name='L430'></a><a href='#L430'>430</a>
479
- <a name='L431'></a><a href='#L431'>431</a>
480
- <a name='L432'></a><a href='#L432'>432</a>
481
- <a name='L433'></a><a href='#L433'>433</a>
482
- <a name='L434'></a><a href='#L434'>434</a>
483
- <a name='L435'></a><a href='#L435'>435</a>
484
- <a name='L436'></a><a href='#L436'>436</a>
485
- <a name='L437'></a><a href='#L437'>437</a>
486
- <a name='L438'></a><a href='#L438'>438</a>
487
- <a name='L439'></a><a href='#L439'>439</a>
488
- <a name='L440'></a><a href='#L440'>440</a>
489
- <a name='L441'></a><a href='#L441'>441</a>
490
- <a name='L442'></a><a href='#L442'>442</a>
491
- <a name='L443'></a><a href='#L443'>443</a>
492
- <a name='L444'></a><a href='#L444'>444</a>
493
- <a name='L445'></a><a href='#L445'>445</a>
494
- <a name='L446'></a><a href='#L446'>446</a>
495
- <a name='L447'></a><a href='#L447'>447</a>
496
- <a name='L448'></a><a href='#L448'>448</a>
497
- <a name='L449'></a><a href='#L449'>449</a>
498
- <a name='L450'></a><a href='#L450'>450</a>
499
- <a name='L451'></a><a href='#L451'>451</a>
500
- <a name='L452'></a><a href='#L452'>452</a>
501
- <a name='L453'></a><a href='#L453'>453</a>
502
- <a name='L454'></a><a href='#L454'>454</a>
503
- <a name='L455'></a><a href='#L455'>455</a>
504
- <a name='L456'></a><a href='#L456'>456</a>
505
- <a name='L457'></a><a href='#L457'>457</a>
506
- <a name='L458'></a><a href='#L458'>458</a>
507
- <a name='L459'></a><a href='#L459'>459</a>
508
- <a name='L460'></a><a href='#L460'>460</a>
509
- <a name='L461'></a><a href='#L461'>461</a>
510
- <a name='L462'></a><a href='#L462'>462</a>
511
- <a name='L463'></a><a href='#L463'>463</a>
512
- <a name='L464'></a><a href='#L464'>464</a>
513
- <a name='L465'></a><a href='#L465'>465</a>
514
- <a name='L466'></a><a href='#L466'>466</a>
515
- <a name='L467'></a><a href='#L467'>467</a>
516
- <a name='L468'></a><a href='#L468'>468</a>
517
- <a name='L469'></a><a href='#L469'>469</a>
518
- <a name='L470'></a><a href='#L470'>470</a>
519
- <a name='L471'></a><a href='#L471'>471</a>
520
- <a name='L472'></a><a href='#L472'>472</a>
521
- <a name='L473'></a><a href='#L473'>473</a>
522
- <a name='L474'></a><a href='#L474'>474</a>
523
- <a name='L475'></a><a href='#L475'>475</a>
524
- <a name='L476'></a><a href='#L476'>476</a>
525
- <a name='L477'></a><a href='#L477'>477</a>
526
- <a name='L478'></a><a href='#L478'>478</a>
527
- <a name='L479'></a><a href='#L479'>479</a>
528
- <a name='L480'></a><a href='#L480'>480</a>
529
- <a name='L481'></a><a href='#L481'>481</a>
530
- <a name='L482'></a><a href='#L482'>482</a>
531
- <a name='L483'></a><a href='#L483'>483</a>
532
- <a name='L484'></a><a href='#L484'>484</a>
533
- <a name='L485'></a><a href='#L485'>485</a>
534
- <a name='L486'></a><a href='#L486'>486</a>
535
- <a name='L487'></a><a href='#L487'>487</a>
536
- <a name='L488'></a><a href='#L488'>488</a>
537
- <a name='L489'></a><a href='#L489'>489</a>
538
- <a name='L490'></a><a href='#L490'>490</a>
539
- <a name='L491'></a><a href='#L491'>491</a>
540
- <a name='L492'></a><a href='#L492'>492</a>
541
- <a name='L493'></a><a href='#L493'>493</a>
542
- <a name='L494'></a><a href='#L494'>494</a>
543
- <a name='L495'></a><a href='#L495'>495</a>
544
- <a name='L496'></a><a href='#L496'>496</a>
545
- <a name='L497'></a><a href='#L497'>497</a>
546
- <a name='L498'></a><a href='#L498'>498</a>
547
- <a name='L499'></a><a href='#L499'>499</a>
548
- <a name='L500'></a><a href='#L500'>500</a>
549
- <a name='L501'></a><a href='#L501'>501</a>
550
- <a name='L502'></a><a href='#L502'>502</a>
551
- <a name='L503'></a><a href='#L503'>503</a>
552
- <a name='L504'></a><a href='#L504'>504</a>
553
- <a name='L505'></a><a href='#L505'>505</a>
554
- <a name='L506'></a><a href='#L506'>506</a>
555
- <a name='L507'></a><a href='#L507'>507</a>
556
- <a name='L508'></a><a href='#L508'>508</a>
557
- <a name='L509'></a><a href='#L509'>509</a>
558
- <a name='L510'></a><a href='#L510'>510</a>
559
- <a name='L511'></a><a href='#L511'>511</a>
560
- <a name='L512'></a><a href='#L512'>512</a>
561
- <a name='L513'></a><a href='#L513'>513</a>
562
- <a name='L514'></a><a href='#L514'>514</a>
563
- <a name='L515'></a><a href='#L515'>515</a>
564
- <a name='L516'></a><a href='#L516'>516</a>
565
- <a name='L517'></a><a href='#L517'>517</a>
566
- <a name='L518'></a><a href='#L518'>518</a>
567
- <a name='L519'></a><a href='#L519'>519</a>
568
- <a name='L520'></a><a href='#L520'>520</a>
569
- <a name='L521'></a><a href='#L521'>521</a>
570
- <a name='L522'></a><a href='#L522'>522</a>
571
- <a name='L523'></a><a href='#L523'>523</a>
572
- <a name='L524'></a><a href='#L524'>524</a>
573
- <a name='L525'></a><a href='#L525'>525</a>
574
- <a name='L526'></a><a href='#L526'>526</a>
575
- <a name='L527'></a><a href='#L527'>527</a>
576
- <a name='L528'></a><a href='#L528'>528</a>
577
- <a name='L529'></a><a href='#L529'>529</a>
578
- <a name='L530'></a><a href='#L530'>530</a>
579
- <a name='L531'></a><a href='#L531'>531</a>
580
- <a name='L532'></a><a href='#L532'>532</a>
581
- <a name='L533'></a><a href='#L533'>533</a>
582
- <a name='L534'></a><a href='#L534'>534</a>
583
- <a name='L535'></a><a href='#L535'>535</a>
584
- <a name='L536'></a><a href='#L536'>536</a>
585
- <a name='L537'></a><a href='#L537'>537</a>
586
- <a name='L538'></a><a href='#L538'>538</a>
587
- <a name='L539'></a><a href='#L539'>539</a>
588
- <a name='L540'></a><a href='#L540'>540</a>
589
- <a name='L541'></a><a href='#L541'>541</a>
590
- <a name='L542'></a><a href='#L542'>542</a>
591
- <a name='L543'></a><a href='#L543'>543</a>
592
- <a name='L544'></a><a href='#L544'>544</a>
593
- <a name='L545'></a><a href='#L545'>545</a>
594
- <a name='L546'></a><a href='#L546'>546</a>
595
- <a name='L547'></a><a href='#L547'>547</a>
596
- <a name='L548'></a><a href='#L548'>548</a>
597
- <a name='L549'></a><a href='#L549'>549</a>
598
- <a name='L550'></a><a href='#L550'>550</a>
599
- <a name='L551'></a><a href='#L551'>551</a>
600
- <a name='L552'></a><a href='#L552'>552</a>
601
- <a name='L553'></a><a href='#L553'>553</a>
602
- <a name='L554'></a><a href='#L554'>554</a>
603
- <a name='L555'></a><a href='#L555'>555</a>
604
- <a name='L556'></a><a href='#L556'>556</a>
605
- <a name='L557'></a><a href='#L557'>557</a>
606
- <a name='L558'></a><a href='#L558'>558</a>
607
- <a name='L559'></a><a href='#L559'>559</a>
608
- <a name='L560'></a><a href='#L560'>560</a>
609
- <a name='L561'></a><a href='#L561'>561</a>
610
- <a name='L562'></a><a href='#L562'>562</a>
611
- <a name='L563'></a><a href='#L563'>563</a>
612
- <a name='L564'></a><a href='#L564'>564</a>
613
- <a name='L565'></a><a href='#L565'>565</a>
614
- <a name='L566'></a><a href='#L566'>566</a>
615
- <a name='L567'></a><a href='#L567'>567</a>
616
- <a name='L568'></a><a href='#L568'>568</a>
617
- <a name='L569'></a><a href='#L569'>569</a>
618
- <a name='L570'></a><a href='#L570'>570</a>
619
- <a name='L571'></a><a href='#L571'>571</a></td><td class="line-coverage quiet"><span class="cline-any cline-yes">1x</span>
620
- <span class="cline-any cline-yes">1x</span>
621
- <span class="cline-any cline-neutral">&nbsp;</span>
622
- <span class="cline-any cline-yes">1x</span>
623
- <span class="cline-any cline-yes">1x</span>
624
- <span class="cline-any cline-neutral">&nbsp;</span>
625
- <span class="cline-any cline-neutral">&nbsp;</span>
626
- <span class="cline-any cline-yes">1x</span>
627
- <span class="cline-any cline-neutral">&nbsp;</span>
628
- <span class="cline-any cline-yes">1x</span>
629
- <span class="cline-any cline-neutral">&nbsp;</span>
630
- <span class="cline-any cline-neutral">&nbsp;</span>
631
- <span class="cline-any cline-yes">1x</span>
632
- <span class="cline-any cline-neutral">&nbsp;</span>
633
- <span class="cline-any cline-neutral">&nbsp;</span>
634
- <span class="cline-any cline-neutral">&nbsp;</span>
635
- <span class="cline-any cline-neutral">&nbsp;</span>
636
- <span class="cline-any cline-neutral">&nbsp;</span>
637
- <span class="cline-any cline-neutral">&nbsp;</span>
638
- <span class="cline-any cline-neutral">&nbsp;</span>
639
- <span class="cline-any cline-neutral">&nbsp;</span>
640
- <span class="cline-any cline-neutral">&nbsp;</span>
641
- <span class="cline-any cline-neutral">&nbsp;</span>
642
- <span class="cline-any cline-yes">1x</span>
643
- <span class="cline-any cline-neutral">&nbsp;</span>
644
- <span class="cline-any cline-neutral">&nbsp;</span>
645
- <span class="cline-any cline-neutral">&nbsp;</span>
646
- <span class="cline-any cline-neutral">&nbsp;</span>
647
- <span class="cline-any cline-neutral">&nbsp;</span>
648
- <span class="cline-any cline-neutral">&nbsp;</span>
649
- <span class="cline-any cline-neutral">&nbsp;</span>
650
- <span class="cline-any cline-neutral">&nbsp;</span>
651
- <span class="cline-any cline-neutral">&nbsp;</span>
652
- <span class="cline-any cline-no">&nbsp;</span>
653
- <span class="cline-any cline-no">&nbsp;</span>
654
- <span class="cline-any cline-no">&nbsp;</span>
655
- <span class="cline-any cline-neutral">&nbsp;</span>
656
- <span class="cline-any cline-neutral">&nbsp;</span>
657
- <span class="cline-any cline-neutral">&nbsp;</span>
658
- <span class="cline-any cline-neutral">&nbsp;</span>
659
- <span class="cline-any cline-neutral">&nbsp;</span>
660
- <span class="cline-any cline-neutral">&nbsp;</span>
661
- <span class="cline-any cline-neutral">&nbsp;</span>
662
- <span class="cline-any cline-no">&nbsp;</span>
663
- <span class="cline-any cline-no">&nbsp;</span>
664
- <span class="cline-any cline-no">&nbsp;</span>
665
- <span class="cline-any cline-neutral">&nbsp;</span>
666
- <span class="cline-any cline-neutral">&nbsp;</span>
667
- <span class="cline-any cline-neutral">&nbsp;</span>
668
- <span class="cline-any cline-neutral">&nbsp;</span>
669
- <span class="cline-any cline-neutral">&nbsp;</span>
670
- <span class="cline-any cline-neutral">&nbsp;</span>
671
- <span class="cline-any cline-neutral">&nbsp;</span>
672
- <span class="cline-any cline-neutral">&nbsp;</span>
673
- <span class="cline-any cline-yes">16x</span>
674
- <span class="cline-any cline-neutral">&nbsp;</span>
675
- <span class="cline-any cline-neutral">&nbsp;</span>
676
- <span class="cline-any cline-neutral">&nbsp;</span>
677
- <span class="cline-any cline-neutral">&nbsp;</span>
678
- <span class="cline-any cline-neutral">&nbsp;</span>
679
- <span class="cline-any cline-neutral">&nbsp;</span>
680
- <span class="cline-any cline-neutral">&nbsp;</span>
681
- <span class="cline-any cline-yes">2x</span>
682
- <span class="cline-any cline-yes">2x</span>
683
- <span class="cline-any cline-yes">2x</span>
684
- <span class="cline-any cline-neutral">&nbsp;</span>
685
- <span class="cline-any cline-neutral">&nbsp;</span>
686
- <span class="cline-any cline-neutral">&nbsp;</span>
687
- <span class="cline-any cline-neutral">&nbsp;</span>
688
- <span class="cline-any cline-neutral">&nbsp;</span>
689
- <span class="cline-any cline-neutral">&nbsp;</span>
690
- <span class="cline-any cline-neutral">&nbsp;</span>
691
- <span class="cline-any cline-yes">168x</span>
692
- <span class="cline-any cline-yes">168x</span>
693
- <span class="cline-any cline-neutral">&nbsp;</span>
694
- <span class="cline-any cline-neutral">&nbsp;</span>
695
- <span class="cline-any cline-neutral">&nbsp;</span>
696
- <span class="cline-any cline-neutral">&nbsp;</span>
697
- <span class="cline-any cline-neutral">&nbsp;</span>
698
- <span class="cline-any cline-neutral">&nbsp;</span>
699
- <span class="cline-any cline-neutral">&nbsp;</span>
700
- <span class="cline-any cline-neutral">&nbsp;</span>
701
- <span class="cline-any cline-neutral">&nbsp;</span>
702
- <span class="cline-any cline-no">&nbsp;</span>
703
- <span class="cline-any cline-no">&nbsp;</span>
704
- <span class="cline-any cline-no">&nbsp;</span>
705
- <span class="cline-any cline-neutral">&nbsp;</span>
706
- <span class="cline-any cline-neutral">&nbsp;</span>
707
- <span class="cline-any cline-neutral">&nbsp;</span>
708
- <span class="cline-any cline-neutral">&nbsp;</span>
709
- <span class="cline-any cline-neutral">&nbsp;</span>
710
- <span class="cline-any cline-neutral">&nbsp;</span>
711
- <span class="cline-any cline-neutral">&nbsp;</span>
712
- <span class="cline-any cline-neutral">&nbsp;</span>
713
- <span class="cline-any cline-neutral">&nbsp;</span>
714
- <span class="cline-any cline-neutral">&nbsp;</span>
715
- <span class="cline-any cline-neutral">&nbsp;</span>
716
- <span class="cline-any cline-neutral">&nbsp;</span>
717
- <span class="cline-any cline-neutral">&nbsp;</span>
718
- <span class="cline-any cline-neutral">&nbsp;</span>
719
- <span class="cline-any cline-neutral">&nbsp;</span>
720
- <span class="cline-any cline-neutral">&nbsp;</span>
721
- <span class="cline-any cline-neutral">&nbsp;</span>
722
- <span class="cline-any cline-neutral">&nbsp;</span>
723
- <span class="cline-any cline-neutral">&nbsp;</span>
724
- <span class="cline-any cline-neutral">&nbsp;</span>
725
- <span class="cline-any cline-neutral">&nbsp;</span>
726
- <span class="cline-any cline-neutral">&nbsp;</span>
727
- <span class="cline-any cline-neutral">&nbsp;</span>
728
- <span class="cline-any cline-neutral">&nbsp;</span>
729
- <span class="cline-any cline-neutral">&nbsp;</span>
730
- <span class="cline-any cline-neutral">&nbsp;</span>
731
- <span class="cline-any cline-neutral">&nbsp;</span>
732
- <span class="cline-any cline-neutral">&nbsp;</span>
733
- <span class="cline-any cline-neutral">&nbsp;</span>
734
- <span class="cline-any cline-neutral">&nbsp;</span>
735
- <span class="cline-any cline-neutral">&nbsp;</span>
736
- <span class="cline-any cline-neutral">&nbsp;</span>
737
- <span class="cline-any cline-neutral">&nbsp;</span>
738
- <span class="cline-any cline-neutral">&nbsp;</span>
739
- <span class="cline-any cline-neutral">&nbsp;</span>
740
- <span class="cline-any cline-neutral">&nbsp;</span>
741
- <span class="cline-any cline-neutral">&nbsp;</span>
742
- <span class="cline-any cline-yes">1x</span>
743
- <span class="cline-any cline-neutral">&nbsp;</span>
744
- <span class="cline-any cline-yes">20x</span>
745
- <span class="cline-any cline-yes">20x</span>
746
- <span class="cline-any cline-yes">20x</span>
747
- <span class="cline-any cline-neutral">&nbsp;</span>
748
- <span class="cline-any cline-neutral">&nbsp;</span>
749
- <span class="cline-any cline-neutral">&nbsp;</span>
750
- <span class="cline-any cline-neutral">&nbsp;</span>
751
- <span class="cline-any cline-neutral">&nbsp;</span>
752
- <span class="cline-any cline-neutral">&nbsp;</span>
753
- <span class="cline-any cline-yes">28x</span>
754
- <span class="cline-any cline-yes">28x</span>
755
- <span class="cline-any cline-yes">28x</span>
756
- <span class="cline-any cline-neutral">&nbsp;</span>
757
- <span class="cline-any cline-neutral">&nbsp;</span>
758
- <span class="cline-any cline-neutral">&nbsp;</span>
759
- <span class="cline-any cline-neutral">&nbsp;</span>
760
- <span class="cline-any cline-neutral">&nbsp;</span>
761
- <span class="cline-any cline-neutral">&nbsp;</span>
762
- <span class="cline-any cline-yes">98398x</span>
763
- <span class="cline-any cline-yes">98398x</span>
764
- <span class="cline-any cline-yes">98398x</span>
765
- <span class="cline-any cline-neutral">&nbsp;</span>
766
- <span class="cline-any cline-neutral">&nbsp;</span>
767
- <span class="cline-any cline-neutral">&nbsp;</span>
768
- <span class="cline-any cline-neutral">&nbsp;</span>
769
- <span class="cline-any cline-neutral">&nbsp;</span>
770
- <span class="cline-any cline-neutral">&nbsp;</span>
771
- <span class="cline-any cline-yes">43x</span>
772
- <span class="cline-any cline-yes">43x</span>
773
- <span class="cline-any cline-yes">43x</span>
774
- <span class="cline-any cline-neutral">&nbsp;</span>
775
- <span class="cline-any cline-neutral">&nbsp;</span>
776
- <span class="cline-any cline-neutral">&nbsp;</span>
777
- <span class="cline-any cline-neutral">&nbsp;</span>
778
- <span class="cline-any cline-neutral">&nbsp;</span>
779
- <span class="cline-any cline-neutral">&nbsp;</span>
780
- <span class="cline-any cline-neutral">&nbsp;</span>
781
- <span class="cline-any cline-no">&nbsp;</span>
782
- <span class="cline-any cline-no">&nbsp;</span>
783
- <span class="cline-any cline-neutral">&nbsp;</span>
784
- <span class="cline-any cline-neutral">&nbsp;</span>
785
- <span class="cline-any cline-neutral">&nbsp;</span>
786
- <span class="cline-any cline-neutral">&nbsp;</span>
787
- <span class="cline-any cline-neutral">&nbsp;</span>
788
- <span class="cline-any cline-neutral">&nbsp;</span>
789
- <span class="cline-any cline-no">&nbsp;</span>
790
- <span class="cline-any cline-neutral">&nbsp;</span>
791
- <span class="cline-any cline-neutral">&nbsp;</span>
792
- <span class="cline-any cline-neutral">&nbsp;</span>
793
- <span class="cline-any cline-neutral">&nbsp;</span>
794
- <span class="cline-any cline-neutral">&nbsp;</span>
795
- <span class="cline-any cline-neutral">&nbsp;</span>
796
- <span class="cline-any cline-neutral">&nbsp;</span>
797
- <span class="cline-any cline-yes">63x</span>
798
- <span class="cline-any cline-neutral">&nbsp;</span>
799
- <span class="cline-any cline-neutral">&nbsp;</span>
800
- <span class="cline-any cline-neutral">&nbsp;</span>
801
- <span class="cline-any cline-neutral">&nbsp;</span>
802
- <span class="cline-any cline-neutral">&nbsp;</span>
803
- <span class="cline-any cline-neutral">&nbsp;</span>
804
- <span class="cline-any cline-neutral">&nbsp;</span>
805
- <span class="cline-any cline-neutral">&nbsp;</span>
806
- <span class="cline-any cline-neutral">&nbsp;</span>
807
- <span class="cline-any cline-yes">1x</span>
808
- <span class="cline-any cline-yes">98724x</span>
809
- <span class="cline-any cline-neutral">&nbsp;</span>
810
- <span class="cline-any cline-neutral">&nbsp;</span>
811
- <span class="cline-any cline-yes">1x</span>
812
- <span class="cline-any cline-yes">98552x</span>
813
- <span class="cline-any cline-yes">98552x</span>
814
- <span class="cline-any cline-yes">98552x</span>
815
- <span class="cline-any cline-yes">428x</span>
816
- <span class="cline-any cline-neutral">&nbsp;</span>
817
- <span class="cline-any cline-yes">98124x</span>
818
- <span class="cline-any cline-yes">98124x</span>
819
- <span class="cline-any cline-neutral">&nbsp;</span>
820
- <span class="cline-any cline-neutral">&nbsp;</span>
821
- <span class="cline-any cline-neutral">&nbsp;</span>
822
- <span class="cline-any cline-yes">1x</span>
823
- <span class="cline-any cline-yes">172x</span>
824
- <span class="cline-any cline-yes">172x</span>
825
- <span class="cline-any cline-yes">172x</span>
826
- <span class="cline-any cline-yes">168x</span>
827
- <span class="cline-any cline-neutral">&nbsp;</span>
828
- <span class="cline-any cline-yes">4x</span>
829
- <span class="cline-any cline-yes">4x</span>
830
- <span class="cline-any cline-neutral">&nbsp;</span>
831
- <span class="cline-any cline-neutral">&nbsp;</span>
832
- <span class="cline-any cline-neutral">&nbsp;</span>
833
- <span class="cline-any cline-yes">1x</span>
834
- <span class="cline-any cline-neutral">&nbsp;</span>
835
- <span class="cline-any cline-yes">405x</span>
836
- <span class="cline-any cline-yes">5722x</span>
837
- <span class="cline-any cline-yes">8x</span>
838
- <span class="cline-any cline-neutral">&nbsp;</span>
839
- <span class="cline-any cline-neutral">&nbsp;</span>
840
- <span class="cline-any cline-neutral">&nbsp;</span>
841
- <span class="cline-any cline-yes">405x</span>
842
- <span class="cline-any cline-yes">5721x</span>
843
- <span class="cline-any cline-yes">8x</span>
844
- <span class="cline-any cline-neutral">&nbsp;</span>
845
- <span class="cline-any cline-neutral">&nbsp;</span>
846
- <span class="cline-any cline-neutral">&nbsp;</span>
847
- <span class="cline-any cline-neutral">&nbsp;</span>
848
- <span class="cline-any cline-yes">1x</span>
849
- <span class="cline-any cline-neutral">&nbsp;</span>
850
- <span class="cline-any cline-yes">413x</span>
851
- <span class="cline-any cline-neutral">&nbsp;</span>
852
- <span class="cline-any cline-neutral">&nbsp;</span>
853
- <span class="cline-any cline-neutral">&nbsp;</span>
854
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- <span class="cline-any cline-neutral">&nbsp;</span></td><td class="text"><pre class="prettyprint lang-js">var multiparty = require("multiparty");
1190
- var xlsx = require("node-xlsx");
1191
- // var util = require("util");
1192
- var path = require("path");
1193
- var parseAdditionalSheets = require(__dirname + "/additional-sheet-parser");
1194
- // var cytoscape = require("cytoscape"); //NOTE: Commented out for issue #474
1195
- &nbsp;
1196
- var helpers = require(__dirname + "/helpers");
1197
- &nbsp;
1198
- var semanticChecker = require(__dirname + "/semantic-checker");
1199
- &nbsp;
1200
- // Currently only going to number 76 because currently the network errors out at 75+ genes.
1201
- var numbersToLetters = {0:"A", 1:"B", 2:"C", 3:"D", 4:"E", 5:"F", 6:"G", 7:"H", 8: "I", 9:"J", 10:"K", 11:"L",
1202
- 12:"M", 13:"N", 14:"O", 15:"P", 16:"Q", 17:"R", 18:"S", 19:"T", 20:"U", 21:"V", 22:"W", 23:"X", 24:"Y",
1203
- 25:"Z", 26:"AA", 27:"AB", 28:"AC", 29:"AD", 30:"AE", 31:"AF", 32:"AG", 33:"AH", 34:"AI", 35:"AJ", 36:"AK",
1204
- 37:"AL", 38:"AM", 39:"AN", 40:"AO", 41:"AP", 42:"AQ", 43:"AR", 44:"AS", 45:"AT", 46:"AU", 47:"AV", 48:"AW",
1205
- 49:"AX", 51:"AY", 52:"AZ", 53:"BA", 54:"BB", 55:"BC", 56:"BD", 57:"BE", 58:"BF", 59:"BG", 60:"BH", 61:"BI",
1206
- 62:"BJ", 63:"BK", 64:"BL", 65:"BM", 66:"BN", 67:"BO", 68:"BP", 69:"BQ", 70:"BR", 71:"BS", 72:"BT", 73:"BU",
1207
- 74:"BV", 75:"BW", 76:"BX"};
1208
- &nbsp;
1209
- // TODO: Put this and the warnings list into helpers.
1210
- // This is the massive list of errors. Yay!
1211
- // The graph will not load if an error is detected.
1212
- var errorList = {
1213
- missingNetworkError: {
1214
- errorCode: "MISSING_NETWORK",
1215
- possibleCause: "This file does not have a 'network' sheet or a 'network_optimized_weights' sheet.",
1216
- suggestedFix: "Please select another file, or rename the sheet containing the adjacency matrix accordingly. \
1217
- Please refer to the " + "&lt;a href='http://dondi.github.io/GRNsight/documentation.html#section1' \
1218
- target='_blank'&gt;Documentation page&lt;/a&gt; for more information."
1219
- },
1220
- &nbsp;
1221
- corruptGeneError: <span class="fstat-no" title="function not covered" >function (</span>row, column) {
1222
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1223
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1224
- <span class="cstat-no" title="statement not covered" > return {</span>
1225
- errorCode: "CORRUPT_GENE",
1226
- possibleCause: "The gene name in cell " + colLetter + rowNum + " appears to be invalid.",
1227
- suggestedFix: "Please fix the error and try uploading again."
1228
- };
1229
- },
1230
- &nbsp;
1231
- missingValueError: <span class="fstat-no" title="function not covered" >function (</span>row, column) {
1232
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1233
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1234
- <span class="cstat-no" title="statement not covered" > return {</span>
1235
- errorCode: "MISSING_VALUE",
1236
- possibleCause: "The value in the cell " + colLetter + rowNum +
1237
- " in the adjacency matrix appears to have a missing value.",
1238
- suggestedFix: "Please ensure that all cells have a value, then upload the file again."
1239
- };
1240
- },
1241
- &nbsp;
1242
- duplicateGeneError: function (geneType, geneName) {
1243
- return {
1244
- errorCode: "DUPLICATE_GENE",
1245
- possibleCause: "There exists a duplicate for " + geneType + " gene " + geneName + ".",
1246
- suggestedFix: "Please remove the duplicate gene and submit again."
1247
- };
1248
- },
1249
- &nbsp;
1250
- dataTypeError: function (row, column) {
1251
- var colLetter = numbersToLetters[column];
1252
- var rowNum = row + 1;
1253
- return {
1254
- errorCode: "INVALID_CELL_DATA_TYPE",
1255
- possibleCause: "The value in cell " + colLetter + rowNum + " is not a number.",
1256
- suggestedFix: "Please ensure all values in the data matrix are numbers and try again."
1257
- };
1258
- },
1259
- &nbsp;
1260
- emptyRowError: function (row) {
1261
- var rowNum = row + 1;
1262
- return {
1263
- errorCode: "EMPTY_ROW",
1264
- possibleCause: "Row " + rowNum + " does not contain any data.",
1265
- suggestedFix: "Please ensure all rows contain data and all empty rows are removed. " +
1266
- "Also, please ensure that no extraneous data is outside of the matrix, " +
1267
- "as this may cause this error."
1268
- };
1269
- },
1270
- &nbsp;
1271
- outsideCellError: <span class="fstat-no" title="function not covered" >function (</span>row, column) {
1272
- var colLetter = <span class="cstat-no" title="statement not covered" >numbersToLetters[column];</span>
1273
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1274
- <span class="cstat-no" title="statement not covered" > return {</span>
1275
- errorCode: "EMPTY_CELL",
1276
- possibleCause: "The cell at " + colLetter + rowNum + " contains data that is outside the matrix.",
1277
- suggestedFix: "Please remove all extraneous data from outside the matrix and ensure" +
1278
- " the matrix is "
1279
- };
1280
- },
1281
- &nbsp;
1282
- errorsCountError: {
1283
- errorCode: "ERRORS_OVERLOAD",
1284
- possibleCause: "This network has over 20 errors.",
1285
- suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
1286
- "Documentation page and try again. If you fix these errors and try to upload again, there may be " +
1287
- "further errors detected. As a general approach for fixing the errors, consider copying and " +
1288
- "pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
1289
- },
1290
- &nbsp;
1291
- warningsCountError: {
1292
- errorCode: "WARNINGS_OVERLOAD",
1293
- possibleCause: "This network has over 75 warnings.",
1294
- suggestedFix: "Please check the format of your spreadsheet with the guidlines outlined on the" +
1295
- " Documentation page and try again. If you fix these errors and try to upload again, there may be " +
1296
- " further errors detected. As a general approach for fixing the errors, consider copying and " +
1297
- " pasting just your adjacency matrix into a fresh Excel Workbook and saving it."
1298
- },
1299
- &nbsp;
1300
- unknownError: {
1301
- errorCode: "UNKNOWN_ERROR",
1302
- possibleCause: "An unexpected error occurred.",
1303
- suggestedFix: "Please contact the GRNsight team at kdahlquist@lmu.edu, \
1304
- and attach the spreadsheet you attempted to upload."
1305
- }
1306
- &nbsp;
1307
- };
1308
- &nbsp;
1309
- &nbsp;
1310
- // This is the list of warnings.
1311
- // The graph will still load if warnings are detected, but these will be reported to the user.
1312
- var warningsList = {
1313
- missingSourceGeneWarning: function (row, column) {
1314
- var colLetter = numbersToLetters[column];
1315
- var rowNum = row + 1;
1316
- return {
1317
- warningCode: "MISSING_SOURCE",
1318
- errorDescription: "A source gene name is missing in cell " + colLetter + rowNum + "."
1319
- };
1320
- },
1321
- &nbsp;
1322
- missingTargetGeneWarning: function (row, column) {
1323
- var colLetter = numbersToLetters[column];
1324
- var rowNum = row + 1;
1325
- return {
1326
- warningCode: "MISSING_TARGET",
1327
- errorDescription: "A target gene name is missing in cell " + colLetter + rowNum + "."
1328
- };
1329
- },
1330
- &nbsp;
1331
- invalidMatrixDataWarning: function (row, column) {
1332
- var colLetter = numbersToLetters[column];
1333
- var rowNum = row + 1;
1334
- return {
1335
- warningCode: "INVALID_DATA",
1336
- errorDescription: "The value in cell " + colLetter + rowNum + ", is undefined."
1337
- };
1338
- },
1339
- &nbsp;
1340
- randomDataWarning: function (type, row, column) {
1341
- var colLetter = numbersToLetters[column];
1342
- var rowNum = row + 1;
1343
- return {
1344
- warningCode: "RANDOM_DATA",
1345
- errorDescription: "The value in cell " + colLetter + rowNum +
1346
- ", has a corresponding source and/or target gene that is detected as " + type + "."
1347
- };
1348
- },
1349
- &nbsp;
1350
- emptyRowWarning: <span class="fstat-no" title="function not covered" >function (</span>row) {
1351
- var rowNum = <span class="cstat-no" title="statement not covered" >row + 1;</span>
1352
- <span class="cstat-no" title="statement not covered" > return {</span>
1353
- warningCode: "EMPTY_ROW",
1354
- errorDescription: "Row " + rowNum + " was found to contain no data."
1355
- };
1356
- },
1357
- &nbsp;
1358
- networkSizeWarning: <span class="fstat-no" title="function not covered" >function (</span>genesLength, edgesLength) {
1359
- <span class="cstat-no" title="statement not covered" > return {</span>
1360
- warningCode: "INVALID_NETWORK_SIZE",
1361
- errorDescription: "Your network has " + genesLength + " genes, and " + edgesLength +
1362
- " edges. Please note that networks are recommended to have less than 50 genes and 100 edges."
1363
- };
1364
- },
1365
- &nbsp;
1366
- incorrectlyNamedSheetWarning: function () {
1367
- return {
1368
- warningCode: "INCORRECTLY_NAMED_SHEET",
1369
- errorDescription: "The uploaded file appears to contain a weighted network, but contains no \
1370
- 'network_optimized_weights' sheet. A weighted network must be contained in a sheet called \
1371
- 'network_optimized_weights' in order to be drawn as a weighted graph. \
1372
- Please check if the sheet(s) in the uploaded spreadsheet have been named properly."
1373
- };
1374
- }
1375
- };
1376
- &nbsp;
1377
- var addMessageToArray = function (messageArray, message) {
1378
- messageArray.push(message);
1379
- };
1380
- &nbsp;
1381
- var addWarning = function (network, message) {
1382
- var warningsCount = network.warnings.length;
1383
- var MAX_WARNINGS = 75;
1384
- if (warningsCount &lt; MAX_WARNINGS) {
1385
- addMessageToArray(network.warnings, message);
1386
- } else {
1387
- addMessageToArray(network.errors, errorList.warningsCountError);
1388
- return false;
1389
- }
1390
- };
1391
- &nbsp;
1392
- var addError = function (network, message) {
1393
- var errorsCount = network.errors.length;
1394
- var MAX_ERRORS = 20;
1395
- if (errorsCount &lt; MAX_ERRORS) {
1396
- addMessageToArray(network.errors, message);
1397
- } else {
1398
- addMessageToArray(network.errors, errorList.errorsCountError);
1399
- return false;
1400
- }
1401
- };
1402
- &nbsp;
1403
- var checkDuplicates = function (errorArray, sourceGenes, targetGenes) {
1404
- // Run through the source genes and check if the gene in slot i is the same as the one next to it
1405
- for (var i = 0; i &lt; sourceGenes.length - 1; i++) {
1406
- if (sourceGenes[i] === sourceGenes[i + 1]) {
1407
- errorArray.push(errorList.duplicateGeneError("source", sourceGenes[i]));
1408
- }
1409
- }
1410
- // Run through the target genes and check if the gene in slot j is the same as the one next to it
1411
- for (var j = 0; j &lt; targetGenes.length - 1; j++) {
1412
- if (targetGenes[j] === targetGenes[j + 1]) {
1413
- errorArray.push(errorList.duplicateGeneError("target", targetGenes[j]));
1414
- }
1415
- }
1416
- };
1417
- &nbsp;
1418
- var parseSheet = function (sheet) {
1419
- var currentSheet;
1420
- var network = {
1421
- genes: [],
1422
- links: [],
1423
- errors: [],
1424
- warnings: [],
1425
- positiveWeights: [],
1426
- negativeWeights: [],
1427
- sheetType: "unweighted",
1428
- };
1429
- var currentLink;
1430
- var currentGene;
1431
- var sourceGene;
1432
- var targetGene;
1433
- var sourceGeneNumber;
1434
- var targetGeneNumber;
1435
- var genesList = []; // This will contain all of the genes in upper case for use in error checking
1436
- var sourceGenes = [];
1437
- var targetGenes = [];
1438
- &nbsp;
1439
- // Look for the worksheet containing the network data
1440
- for (var i = 0; i &lt; sheet.length; i++) {
1441
- if (sheet[i].name === "network") {
1442
- // Here we have found a sheet containing simple data. We keep looking
1443
- // in case there is also a sheet with optimized weights
1444
- currentSheet = sheet[i];
1445
- } else if (sheet[i].name === "network_optimized_weights") {
1446
- // We found a sheet with optimized weights, which is the ideal data source.
1447
- // So we stop looking.
1448
- currentSheet = sheet[i];
1449
- network.sheetType = "weighted";
1450
- break;
1451
- }
1452
- }
1453
- &nbsp;
1454
- // If it didn't find a network/network_optimized_weights sheet
1455
- // TODO For expediency, we are wrapping every `return network` statement in `semanticChecker`.
1456
- // Some refactoring may be desirable to prevent excessive repetition.
1457
- if (currentSheet === undefined) {
1458
- addError(network, errorList.missingNetworkError);
1459
- return network;
1460
- }
1461
- &nbsp;
1462
- for (var row = 0, column = 1; row &lt; currentSheet.data.length; row++) {
1463
- if (currentSheet.data[row].length === 0) { // if the current row is empty
1464
- if (addError(network, errorList.emptyRowError(row)) === false) {
1465
- return network;
1466
- }
1467
- } else { // if the row has data...
1468
- // Genes found when row = 0 are targets. Genes found when column = 0 are source genes.
1469
- // We set column = 1 in the for loop so it skips row 0 column 0, since that contains no matrix data.
1470
- // Yes, the rows and columns use array numbering. That is, they start at 0, not 1.
1471
- try { // This prevents the server from crashing if something goes wrong anywhere in here
1472
- while (column &lt; currentSheet.data[row].length) {
1473
- // While we haven't gone through all of the columns in this row...
1474
- if (row === 0) { // If we are at the top of a new column...
1475
- // These genes are the source genes
1476
- try {
1477
- currentGene = {name: currentSheet.data[0][column]};
1478
- // ie: Cin5 is the same as cin5
1479
- if (currentGene.name === undefined) {
1480
- addWarning(network, warningsList.missingSourceGeneWarning(row, column));
1481
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {
1482
- <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingSourceGeneWarning(row, column));</span>
1483
- } else {
1484
- // set currentGeneName to a String so toUpperCase doesn't mess up
1485
- currentGene.name = currentGene.name.toString();
1486
- sourceGenes.push(String(currentGene.name.toUpperCase()));
1487
- genesList.push(String(currentGene.name.toUpperCase()));
1488
- network.genes.push(currentGene);
1489
- }
1490
- } catch (err) {
1491
- <span class="cstat-no" title="statement not covered" > addError(network, errorList.corruptGeneError(row, column));</span>
1492
- <span class="cstat-no" title="statement not covered" > return network;</span>
1493
- }
1494
- } else if (column === 0) { // If we are at the far left of a new row...
1495
- // These genes are the target genes
1496
- try {
1497
- currentGene = {name: currentSheet.data[row][0]};
1498
- if (currentGene.name === undefined) {
1499
- addWarning(network, warningsList.missingTargetGeneWarning(row, column));
1500
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if (isNaN(currentGene.name) &amp;&amp; typeof currentGene.name !== "string") {
1501
- <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.missingTargetGeneWarning(row, column));</span>
1502
- } else {
1503
- // set currentGeneName to a String so toUpperCase doesn't mess up
1504
- currentGene.name = currentGene.name.toString();
1505
- targetGenes.push(String(currentGene.name.toUpperCase()));
1506
- // Here we check to see if we've already seen the gene name that we're about to store
1507
- // Genes may or may not be present due to asymmetry or unorderedness
1508
- // If it's in the genesList, it will return a number &gt; 0, so we won't store it
1509
- // If it's not there, it will return -1, so we add it.
1510
- if (genesList.indexOf(String(currentGene.name.toUpperCase())) === -1) {
1511
- genesList.push(String(currentGene.name.toUpperCase()));
1512
- network.genes.push(currentGene);
1513
- }
1514
- }
1515
- } catch (err) {
1516
- <span class="cstat-no" title="statement not covered" > sourceGene = currentSheet.data[0][column];</span>
1517
- <span class="cstat-no" title="statement not covered" > targetGene = currentSheet.data[row][0];</span>
1518
- <span class="cstat-no" title="statement not covered" > addError(network, errorList.corruptGeneError(row, column));</span>
1519
- <span class="cstat-no" title="statement not covered" > return network;</span>
1520
- }
1521
- } else { // If we're within the matrix and lookin' at the data...
1522
- try {
1523
- if (currentSheet.data[row][column] === undefined) {
1524
- // SHOULD BE: addError(network, errorList.missingValueError(row, column));
1525
- addWarning(network, warningsList.invalidMatrixDataWarning(row, column));
1526
- } else if (isNaN(+("" + currentSheet.data[row][column])) ||
1527
- typeof currentSheet.data[row][column] !== "number") {
1528
- addError(network, errorList.dataTypeError(row, column));
1529
- return network;
1530
- } else {
1531
- if (currentSheet.data[row][column] !== 0) { // We only care about non-zero values
1532
- // Grab the source and target genes' names
1533
- sourceGene = currentSheet.data[0][column];
1534
- targetGene = currentSheet.data[row][0];
1535
- if (sourceGene === undefined || targetGene === undefined) {
1536
- addWarning(network, warningsList.randomDataWarning("undefined", row, column));
1537
- } else <span class="missing-if-branch" title="if path not taken" >I</span>if ((isNaN(sourceGene) &amp;&amp; typeof sourceGene !== "string") ||
1538
- (isNaN(targetGene) &amp;&amp; typeof targetGene !== "string")) {
1539
- <span class="cstat-no" title="statement not covered" > addWarning(network, warningsList.randomDataWarning("NaN", row, column));</span>
1540
- } else {
1541
- // Grab the source and target genes' numbers
1542
- sourceGeneNumber = genesList.indexOf(sourceGene.toString().toUpperCase());
1543
- targetGeneNumber = genesList.indexOf(targetGene.toString().toUpperCase());
1544
- currentLink = {source: sourceGeneNumber, target: targetGeneNumber,
1545
- value: currentSheet.data[row][column]};
1546
- // Here we set the properties of the current link
1547
- // before we push them to the network
1548
- if (network.sheetType === "weighted") {
1549
- if (currentLink.value &gt; 0) {
1550
- // If it's a positive number, mark it as an activator
1551
- currentLink.type = "arrowhead";
1552
- // GRNsight v1 magenta edge color
1553
- // currentLink.stroke = "MediumVioletRed";
1554
- // Node coloring-consistent red edge color
1555
- currentLink.stroke = "rgb(195, 61, 61)";
1556
- network.positiveWeights.push(currentLink.value);
1557
- } else { // if it's a negative number, mark it as a repressor
1558
- currentLink.type = "repressor";
1559
- // currentLink.stroke = "DarkTurquoise"; // GRNsight v1 cyan edge color
1560
- // Node coloring-consistent blue edge color
1561
- currentLink.stroke = "rgb(51, 124, 183)";
1562
- network.negativeWeights.push(currentLink.value);
1563
- }
1564
- } else <span class="missing-if-branch" title="else path not taken" >E</span>if (network.sheetType === "unweighted") {
1565
- currentLink.type = "arrowhead";
1566
- currentLink.stroke = "black";
1567
- if (currentLink.value !== 1) {
1568
- addWarning(network, warningsList.incorrectlyNamedSheetWarning());
1569
- currentLink.value = 1;
1570
- }
1571
- network.positiveWeights.push(currentLink.value);
1572
- }
1573
- network.links.push(currentLink);
1574
- }
1575
- }
1576
- }
1577
- &nbsp;
1578
- } catch (err) {
1579
- <span class="cstat-no" title="statement not covered" > addError(network, errorList.missingValueError(row, column));</span>
1580
- // SHOULD BE: addError(network, errorList.unknownFileError);
1581
- <span class="cstat-no" title="statement not covered" > return network;</span>
1582
- }
1583
- }
1584
- column++; // Let's move on to the next column!
1585
- } // Once we finish with the current row...
1586
- column = 0; // let's go back to column 0 on the next row!
1587
- } catch (err) {
1588
- // We only get here if something goes drastically wrong. We don't want to get here.
1589
- <span class="cstat-no" title="statement not covered" > addError(network, errorList.unknownError);</span>
1590
- <span class="cstat-no" title="statement not covered" > return network;</span>
1591
- }
1592
- }
1593
- }
1594
- &nbsp;
1595
- // Move on to semanticChecker.
1596
- &nbsp;
1597
- &nbsp;
1598
- // We sort them here because gene order is not relevant before this point
1599
- // Sorting them now means duplicates will be right next to each other
1600
- sourceGenes.sort();
1601
- targetGenes.sort();
1602
- &nbsp;
1603
- // syntactic duplicate checker for both columns and rows
1604
- checkDuplicates(network.errors, sourceGenes, targetGenes);
1605
- &nbsp;
1606
- // NOTE: Temporarily commented out pending resolution of #474, and other related issues
1607
- // try {
1608
- // network.graphStatisticsReport = graphStatisticsReport(network);
1609
- // } catch (err) {
1610
- // console.log ("Graph statistics report failed to be complete.");
1611
- // }
1612
- return semanticChecker(network);
1613
- };
1614
- &nbsp;
1615
- var <span class="fstat-no" title="function not covered" >processGRNmap = f</span>unction (path, res, app) {
1616
- var sheet;
1617
- var network;
1618
- &nbsp;
1619
- <span class="cstat-no" title="statement not covered" > helpers.attachCorsHeader(res, app);</span>
1620
- &nbsp;
1621
- <span class="cstat-no" title="statement not covered" > try {</span>
1622
- <span class="cstat-no" title="statement not covered" > sheet = xlsx.parse(path);</span>
1623
- } catch (err) {
1624
- <span class="cstat-no" title="statement not covered" > return res.json(400, "Unable to read input. The file may be corrupt.");</span>
1625
- }
1626
- &nbsp;
1627
- <span class="cstat-no" title="statement not covered" > helpers.attachFileHeaders(res, path);</span>
1628
- <span class="cstat-no" title="statement not covered" > network = parseSheet(sheet);</span>
1629
- &nbsp;
1630
- // Parse expression and 2-column data, then add to network object
1631
- var additionalData = <span class="cstat-no" title="statement not covered" >parseAdditionalSheets(sheet);</span>
1632
- <span class="cstat-no" title="statement not covered" > Object.assign(network, additionalData);</span>
1633
- &nbsp;
1634
- <span class="cstat-no" title="statement not covered" > return (network.errors.length === 0) ?</span>
1635
- // If all looks well, return the network with an all clear
1636
- res.json(network) :
1637
- // If all does not look well, return the network with an error 400
1638
- res.status(400).json(network);
1639
- };
1640
- &nbsp;
1641
- var <span class="fstat-no" title="function not covered" >grnSightToCytoscape = f</span>unction (network) {
1642
- var result = <span class="cstat-no" title="statement not covered" >[];</span>
1643
- <span class="cstat-no" title="statement not covered" > network.genes.forEach(<span class="fstat-no" title="function not covered" >function (</span>gene) {</span>
1644
- <span class="cstat-no" title="statement not covered" > result.push({</span>
1645
- data: {
1646
- id: gene.name
1647
- }
1648
- });
1649
- });
1650
- &nbsp;
1651
- <span class="cstat-no" title="statement not covered" > network.links.forEach(<span class="fstat-no" title="function not covered" >function (</span>link) {</span>
1652
- var sourceGene = <span class="cstat-no" title="statement not covered" >network.genes[link.source];</span>
1653
- var targetGene = <span class="cstat-no" title="statement not covered" >network.genes[link.target];</span>
1654
- <span class="cstat-no" title="statement not covered" > result.push({</span>
1655
- data: {
1656
- id: sourceGene.name + targetGene.name,
1657
- source: sourceGene.name,
1658
- target: targetGene.name
1659
- }
1660
- });
1661
- });
1662
- &nbsp;
1663
- <span class="cstat-no" title="statement not covered" > return result;</span>
1664
- };
1665
- &nbsp;
1666
- /* NOTE: See above. Commented out until resolution of #474
1667
- var graphStatisticsReport = function(network) {
1668
- var betweennessCentrality = [];
1669
- var shortestPath = [];
1670
- var cytoscapeElements = grnSightToCytoscape(network);
1671
- &nbsp;
1672
- var cy = cytoscape({
1673
- headless: true,
1674
- elements: cytoscapeElements
1675
- });
1676
- &nbsp;
1677
- for (var i = 0; i &lt; network.genes.length; i++) {
1678
- var bc = cy.$().bc();
1679
- betweennessCentrality.push({
1680
- gene: network.genes[i],
1681
- betweennessCentrality: bc.betweenness("#" + network.genes[i].name, null, true)
1682
- });
1683
- &nbsp;
1684
- var dijkstra = cy.elements().dijkstra("#" + network.genes[i].name, null, true);
1685
- &nbsp;
1686
- for (var j = 0; j &lt; network.genes.length; j++) {
1687
- shortestPath.push({
1688
- source: network.genes[i].name,
1689
- pathData: {
1690
- target: network.genes[j].name,
1691
- shortestPath: dijkstra.distanceTo("#" + network.genes[j].name, null, true)
1692
- }
1693
- });
1694
- }
1695
- }
1696
- return {
1697
- betweennessCentrality: betweennessCentrality,
1698
- shortestPath: shortestPath
1699
- };
1700
- };
1701
- */
1702
- &nbsp;
1703
- module.exports = function (app) {
1704
- <span class="missing-if-branch" title="if path not taken" >I</span>if (app) {
1705
- &nbsp;
1706
- // parse the incoming form data, then parse the spreadsheet. Finally, send back json.
1707
- <span class="cstat-no" title="statement not covered" > app.post("/upload", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
1708
- // TODO: Add file validation
1709
- (<span class="cstat-no" title="statement not covered" >new multiparty.Form()).parse(req, <span class="fstat-no" title="function not covered" >function (</span>err, fields, files) {</span>
1710
- <span class="cstat-no" title="statement not covered" > if (err) {</span>
1711
- <span class="cstat-no" title="statement not covered" > return res.json(400, "There was a problem uploading your file. Please try again.");</span>
1712
- }
1713
- var input;
1714
- <span class="cstat-no" title="statement not covered" > try {</span>
1715
- <span class="cstat-no" title="statement not covered" > input = files.file[0].path;</span>
1716
- } catch (err) {
1717
- <span class="cstat-no" title="statement not covered" > return res.json(400, "No upload file selected.");</span>
1718
- }
1719
- &nbsp;
1720
- <span class="cstat-no" title="statement not covered" > if (path.extname(input) !== ".xlsx") {</span>
1721
- <span class="cstat-no" title="statement not covered" > return res.json(400, "This file cannot be loaded because:&lt;br&gt;&lt;br&gt; The file is \</span>
1722
- not in a format GRNsight can read." + "&lt;br&gt;Please select an Excel Workbook \
1723
- (.xlsx) file. Note that Excel 97-2003 Workbook (.xls) files are not " +
1724
- " able to be read by GRNsight. &lt;br&gt;&lt;br&gt;SIF and GraphML files can be loaded \
1725
- using the importer under File &gt; Import." + " Additional information about file \
1726
- types that GRNsight supports is in the Documentation.");
1727
- }
1728
- &nbsp;
1729
- <span class="cstat-no" title="statement not covered" > return processGRNmap(input, res, app);</span>
1730
- });
1731
- });
1732
- &nbsp;
1733
- // Load the demos
1734
- <span class="cstat-no" title="statement not covered" > app.get("/demo/unweighted", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
1735
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_input.xlsx", res, app);</span>
1736
- });
1737
- &nbsp;
1738
- <span class="cstat-no" title="statement not covered" > app.get("/demo/weighted", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
1739
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/15-genes_28-edges_db5_Dahlquist-data_estimation_output.xlsx",</span>
1740
- res, app);
1741
- });
1742
- &nbsp;
1743
- <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeInput", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
1744
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_31-edges_Schade-data_input.xlsx", res, app);</span>
1745
- });
1746
- &nbsp;
1747
- <span class="cstat-no" title="statement not covered" > app.get("/demo/schadeOutput", <span class="fstat-no" title="function not covered" >function (</span>req, res) {</span>
1748
- <span class="cstat-no" title="statement not covered" > return processGRNmap("test-files/demo-files/21-genes_31-edges_Schade-data_estimation_output.xlsx",</span>
1749
- res, app);
1750
- });
1751
- }
1752
- &nbsp;
1753
- // exporting parseSheet for use in testing. Do not remove!
1754
- return {
1755
- parseSheet: parseSheet,
1756
- grnSightToCytoscape: grnSightToCytoscape
1757
- };
1758
- };
1759
- &nbsp;</pre></td></tr>
1760
- </table></pre>
1761
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1763
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1764
- Code coverage
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1770
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