Bulk Scan Updates by raginirai553 · Pull Request #94 · biocore/microsetta-admin

raginirai553 · 2023-02-14T02:04:34Z

No description provided.

cassidysymons · 2023-02-21T20:52:30Z

@ragini7913 It looks like bulk_scan.html is missing, can you please upload that and address the lint errors?

microsetta_admin/server.py

cassidysymons · 2023-03-07T05:12:03Z

microsetta_admin/server.py

+                        code = [random.choice(hex) for i in range(6)]
+                        color_code = ['#' + ''.join(code)]
+                        while color_code[0] in dict:
+                            code = [random.choice(hex) for i in range(6)]
+                            color_code = ['#' + ''.join(code)]
+                        dict[obj["values"][val]] = color_code[0]


Two issues here:

This code is essentially repeated twice below. Please decompose it into a function that only handles the task of generating a dictionary of colors.

The code can produce colors that are very similar, which somewhat defeats the purpose of color-coding. Can you consider alternatives that would do a better job of ensuring visual clarity?

Created a function to generate random color code. The logic to generate color codes is adjusted so that produced colors are not very similar. The code is further simplified

It's still generating very similar colors, see below.

microsetta_admin/server.py

microsetta_admin/templates/bulk_scan.html

microsetta_admin/server.py

cassidysymons · 2023-03-30T18:59:56Z

microsetta_admin/server.py

+                            while color_code in dict:
+                                color_code = _get_color_code()
+                            dict[obj["values"][val]] = color_code
+


Should the function return an error if it's called with an invalid criteria?

In case the function is called with an invalid criteria, it will return an empty dictionary.

It looks like there's nothing checking that between the function and the UI. Should there be a check and explicit exception if the result is an empty dictionary, rather than letting the UI silently fail?

In case of invalid criteria, visualization must show all samples to "None" legend for provided criteria. I have updated code to return the legend dictionary to at least return "None" as value for every sorting criteria.

microsetta_admin/server.py

cassidysymons · 2023-04-06T17:21:49Z

microsetta_admin/server.py

+                            color_code = _get_color_code()
+
+                        if color_code is not None:
+                            while color_code in dict.values():


It looks like this has the potential to go into an infinite loop if the supply of defined colors is exhausted. Can that be handled more gracefully?

cassidysymons · 2023-04-06T17:24:04Z

microsetta_admin/server.py

+                            while color_code in dict:
+                                color_code = _get_color_code()
+                            dict[obj["values"][val]] = color_code
+


It looks like there's nothing checking that between the function and the UI. Should there be a check and explicit exception if the result is an empty dictionary, rather than letting the UI silently fail?

microsetta_admin/templates/bulk_scan.html

microsetta_admin/server.py

cassidysymons · 2023-04-27T16:46:53Z

Hi @raginirai553 please see the below comments/issues:

When I upload a file and choose Sort by Project, I get the following exception:

File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "microsetta_admin/server.py", line 994, in bulk_scan
    return _visualize_scans()
  File "microsetta_admin/server.py", line 897, in _visualize_scans
    table=_compose_table(legends, criteria),
  File "microsetta_admin/server.py", line 864, in _compose_table
    current_cols.append([rec[5], legends[val], proj, status, src])
KeyError: 'THDMI - Spain (Main)'

I'm seeing the following in the logs, so I think you'll need to find a more efficient way to pass data around than using the session scope. It's safe to use session for a few specific options, but not large amounts of data:

/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/werkzeug/wrappers/base_response.py:468: UserWarning: The "b'session-microsetta-admin'" cookie is too large: the value was 5326 bytes but the header required 43 extra bytes. The final size was 5369 bytes but the limit is 4093 bytes. Browsers may silently ignore cookies larger than this.

It would be good to add the Sort By dropdown to the upload screen so that there's not an extra step when first viewing a file.

microsetta_admin/server.py

cassidysymons · 2023-05-11T17:20:06Z

microsetta_admin/server.py

+                    break
                else:
                    obj["location_col"] = str(int(rec[3]))
                if math.isnan(rec[4]):


This isnan check needs to be removed, rec[4] will never be a number. Also, the error message strategy as written doesn't work - when it hits the isnan block, it throws an internal server error, meaning the user will never see the error.

Resolved the issued! As per the revised flow, samples without row or column numbers are ignored during bulk scan. Further, appropriate errors are displayed for such samples.

cassidysymons · 2023-05-16T16:03:41Z

@raginirai553 There are a couple of significant issues with the Bulk Scan function that I'm experiencing in testing:

When I sort by Sample Project, I receive the following exception:

[2023-05-16 08:49:59,572] ERROR in app: Exception on /scan-bulk [POST]
Traceback (most recent call last):
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 2447, in wsgi_app
    response = self.full_dispatch_request()
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1952, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1821, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/_compat.py", line 39, in reraise
    raise value
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1950, in full_dispatch_request
    rv = self.dispatch_request()
  File "/Users/api_user/miniconda3/envs/microsetta-admin/lib/python3.8/site-packages/flask/app.py", line 1936, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "microsetta_admin/server.py", line 1024, in bulk_scan
    return _visualize_scans()
  File "microsetta_admin/server.py", line 905, in _visualize_scans
    table=_compose_table(legends, criteria),
  File "microsetta_admin/server.py", line 872, in _compose_table
    curr_cols.append([code, legends[val], proj, status, src])
KeyError: 'PROJECT NAME REDACTED - XXXXX (XXXXX)'

When I sort by Sample Status or Sample Type, the first sample in the upload file renders 96 times in a single row:

Are you experiencing either of these issues in your local development environment?

microsetta_admin/server.py

ragini7913 added 2 commits February 9, 2023 20:31

bul scan updates

7599651

Merge https://github.com/raginirai553/microsetta-admin

e95159d

ragini7913 added 4 commits February 23, 2023 22:22

add misisng bulk_scan.html

01504b8

fix lint errors

dd03544

testing workflow

d95529c

removing test change

cd9b609

cassidysymons requested changes Mar 7, 2023

View reviewed changes

ragini7913 added 3 commits March 9, 2023 08:18

address PR comments

24bc3cc

DB changes for barcode bulk_scan

006d59b

fix lint errors

041a037

cassidysymons reviewed Mar 30, 2023

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cassidysymons reviewed Mar 30, 2023

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ragini7913 added 2 commits April 3, 2023 11:21

fix color coding and PR feedback

7d2454b

fix lints

b22181d

cassidysymons requested changes Apr 6, 2023

View reviewed changes

ragini7913 added 2 commits April 11, 2023 14:48

modify color code logic

c2193e2

fix code loop

886c4fa

ragini7913 added 2 commits May 4, 2023 13:12

admin change for db retrieve

f2958d1

fix lint

bc1045b

cassidysymons requested changes May 9, 2023

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address PR comments

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cassidysymons reviewed May 11, 2023

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ragini7913 added 2 commits May 12, 2023 09:51

fix isnan code block

b6217c0

fix lint

a409836

ragini7913 added 2 commits May 16, 2023 15:43

fix sample sorting

e5c2bb7

fix lint errors

128d511

ragini7913 added 2 commits May 16, 2023 16:10

fix lint

030bd52

fix project sorting

9e4bd75

cassidysymons requested changes May 30, 2023

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ragini7913 added 3 commits June 1, 2023 13:40

PR feedbaxck

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PR feedback

aa64cb5

fix lint

8a24ed3

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raginirai553 commented Feb 14, 2023

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cassidysymons commented Feb 21, 2023

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cassidysymons commented Apr 27, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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cassidysymons commented May 16, 2023

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cassidysymons commented Apr 27, 2023 •

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