started upload process

[nathandunn]

fixes #631

https://www.geeksforgeeks.org/file-uploading-in-react-js/

• [x] remove extra line for doing test1.gmt analysis
• [ ] validate test-data/hallmark.gmt
• [x] clean out logging, etc.
• [x] handle error on bad GMT file
• [x] handle duplicate GMT file name
• [x] seems to be mismatching both names and scores test1.gmt

---

• [x] when editing gene sets, it should bring up the cached scores
• [x] trigger find on upload with diff selected and uploaded after upload (or at least setting to the uploaded geneset)

---

FROM

A: [ data ], data[i]: { X: <golabel (go:id)> , <sample 1>: <value 1>, , <sample N>: <value N> } B: TSV data, <golabel1>\t<goid1>\t<gene1>\t<gene2>\t<geneN>\n

INTO

C: [ data ] : data[i] = { goid: <goid> ,golabel: <golabel>, gene: [ genes in set], firstGeneExpressionPathwayActivity, secondGeneExpressionPathwayActivity }

• Note, the activity is the mean activity across all of the gene + samples

---

• [x] sorting similarity scores don't work
• [x] add loading during analysis while grayed out (or just gray out button)
• [x] when changing sorting, defaults to DefaultGeneSet, have to change genesets to get bakc the original one
• [x] write Service to format output:
  1. [x] make await methods async
  2. [x] make sure we can store the analyized output properly
  3. [x] store scores locally in cache (not necessary to cache on server I think)

---

1. [x] get service to submit properly with the loaded gmt and the tpm for the cohort
2. [x] validate caching
3. [x] fix analysis output (regulon, etc.) <simpleError: There are no regulons with size of at least 2 targets.> by comparing to the curl data
4. [x] submit analysis to server for each cohort
5. [x] store analysis locally and load on demand, or pull (from the right source), I think this is "probes", as we are trying to get gene expression
6. [x] run analysis after fetch in handleUploadFile?
7. [x] create analysis service

---

1. [x] verify submit GMT data

2. [x] get tpm data on the server side

3. [x] cache tpm file on servder

4. [x] do analysis for EACH cohort

5. [x] fixed server submit CORS issue

6. [x] upload geneset / GMT

7. [x] cache geneset / GMT

8. [x] get it to fetch properly (dropping or not storing GMT files properly)

9. [x] should close and change selected on fetch completion

10. [x] filter for gmt filename

[nathandunn]

To get TPM data, we use this query:

https://xenago.xenahubs.net/download/expr_tpm/TCGA-CHOL_tpm_tab.tsv.gz

this is:

defaultCohortDatasetForGetSet.host + '/download/'+ defaultCohortDatasetForGetSet.dataset + '.gz'

We have 3 options:

1. call on the client before sending in
2. call on the server with the provided URL
3. store all of these on the client

[nathandunn]

Going to opt for (2) for now.

[nathandunn]

So the differential is the exact opposite of this one, but is weird as it doesn't really capture the diff, just the ascending sort of the left to right diff.

However, that is probably correct, as we are filtering by least different first and then filtering by left to right afterwards. So I filter 3 out I get the most similar and then filterdd form

And the the scores are ascending (-0.4, +0.2, +0.4, etc.) so this is correct.