app_needleplot loading data improvements #51

Bachibouzouk · 2018-11-28T17:09:51Z

Dash Bio pull request

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I am adding a feature to an existing component

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-added a dcc.Store to share data between the callbacks
-added the option to load protein domains independently from the mutation data, the user can now download the protein domain from UniProt/PFAM database and load their own mutation data on top of it (the protein domains can also be loaded from an individual file as well)
-documented the callbacks and the code
-deleted sample data files which weren't used anymore for needleplot app

addresses #56 and #64

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…d component or from a file

…om the mutation data and thus another dcc.Upload component in the Upload file option

…data loading and whether or not the user wants to load the protein domains independently. Also added a dcc.Store to share data between callbacks.

… component larger

shammamah-zz

Really cool! It would be nice to do the same with other database APIs for some of the other components.

tests/dash/app_needleplot.py

tests/dash/utils/needle_plot_parser.py

assets/needleplot-style.css

…in filename. Implemented Sham's code styling comments

…fixed a typo in needle_plot_parser.py

…d from UniProt, now getting the mutations labels and the multi-site mutations as well

… choose the demo option

…oss callbacks

…rot downloaded data sets

… independent loading option

Conflicts: tests/dash/app_needle_plot.py Solved it :)

shammamah-zz

Some minor suggestions. Other than that it looks good!

shammamah-zz · 2018-12-03T17:38:39Z

tests/dash/app_needle_plot.py

 import dash_core_components as dcc
 import dash_html_components as html
 from dash.dependencies import Input, Output, State
 import dash_bio
+
 from .utils.needle_plot_parser import UniprotQueryBuilder, extract_mutations, EMPTY_MUT_DATA,\


I was wondering why this is in utils for tests/dash? It might belong in dash_bio/utils, and that way other apps can use it too.

Yes it starts to become big enough for that, some of it is specific to needleplot data parser though, should I still separate the functions that can be used by other apps while moving the sharable code to dash_bio/utils?

@Bachibouzouk I just reviewed your current solution and it looks great :)

tests/dash/app_needle_plot.py

shammamah-zz · 2018-12-03T17:44:38Z

tests/dash/app_needle_plot.py

-        else:
-            return ''
+
+        div = []


You might not have to initialize this; at the end you can put return [] instead of return div and then on line 476 have

return html.Div( [....] )

Thanks for the suggestion :)

shammamah-zz · 2018-12-03T17:45:36Z

tests/dash/app_needle_plot.py

@@ -430,15 +514,36 @@ def toggle_individual_domain_loading_in_upload(domains_opt, div_style):
    @app.callback(
        Output('needle-domain-query-info-div', 'style'),
        [Input('needle-protein-domains-select-checklist', 'values')],
-        [State('needle-domain-query-info-div', 'value')]
+        [


Maybe put these on the same line?

[State('needle-domain-query-info-div', 'value'), State('needle-dataset-select-radio', 'value')]

…ecify the color of the protein domains

…load them from local file instead

…the tabs

shammamah-zz

Some minor changes

shammamah-zz · 2018-12-04T14:32:15Z

dash_bio/utils/uniprotDatabaseTools.py

@@ -1,63 +1,15 @@
-import base64


Cool! It'll be nice to have all of these tools together for other people to use as well :)

shammamah-zz · 2018-12-04T14:33:30Z

tests/dash/app_needle_plot.py

@@ -88,6 +89,14 @@ def description():
    Also known under the lollipop plot name.'


+def header_colors():
+    return {
+        'bg_color': '#00cc96',


The logo is a bit difficult to see on this color, could you maybe choose something with more contrast?

default header looks good : ) maybe we could leave it like that as it seems to look good on all apps

@VeraZab I thought it would be nice to use different colours for all of our headers, since right now my Clustergram app is the only one with a different colour.

I guess that's not on dds, I don't see it, thought Pierre's was the only one using a different one. I'll let you guys decide.

shammamah-zz · 2018-12-04T14:36:56Z

tests/dash/app_needle_plot.py

+                                        html.Div(
+                                            id='needle-dataset-select-div',
+                                            title='"Demo dataset" choice will allow you to play with the options.\n'
+                                                  '"UniProt dataset" choice will retrieve protein domain '


Use \ to break multiline strings

When I use \ it leaves a bunch of trailing whitespaces in the hover text, so I prefer not to

shammamah-zz · 2018-12-04T14:37:07Z

tests/dash/app_needle_plot.py

+                                        ),
+                                        html.Div(
+                                            id='needle-protein-domains-select-div',
+                                            title='If checked, it will allow the user to load mutation data such '


Same as above

shammamah-zz · 2018-12-04T16:45:30Z

Everything looks great :) 💃

Bachibouzouk added 9 commits November 27, 2018 14:40

add a store component

69f67a0

Merge branch 'needle_app_fix_css' into needle_plot_store_app

8195b5f

use a dcc.Store to share the data between callbacks

a8cef59

Merge branch 'master' into needle_plot_store_app

cf1e78a

Merge branch 'master' into needle_plot_store_app

abd6d4d

reused a function to format the mutation data loaded from a dcc.Uploa…

4090bc2

…d component or from a file

Added a section to choose to load the protein domain independently fr…

4494aa3

…om the mutation data and thus another dcc.Upload component in the Upload file option

added callback to change the layout depending on the user choice for …

407f6e1

…data loading and whether or not the user wants to load the protein domains independently. Also added a dcc.Store to share data between callbacks.

cleant the data files not needed anymore and made the margin of a css…

7231ea1

… component larger

mtwichan temporarily deployed to dash-bio-test-pr-51 November 28, 2018 17:10 Inactive

Bachibouzouk requested review from VeraZab, wilzbach and shammamah-zz November 28, 2018 17:11

shammamah-zz suggested changes Nov 28, 2018

View reviewed changes

VeraZab reviewed Nov 28, 2018

View reviewed changes

assets/needleplot-style.css Outdated Show resolved Hide resolved

Bachibouzouk added 11 commits November 28, 2018 19:25

removed commented lines in the .css file. Better identify .json file …

d4f162f

…in filename. Implemented Sham's code styling comments

added a download data button using a link and saving a file locally, …

e83ae53

…fixed a typo in needle_plot_parser.py

implemented json testing of the mutation and protein domain data

9b1dcf4

added a parser to extrat the mutations data from a gff file downloade…

a0b348b

…d from UniProt, now getting the mutations labels and the multi-site mutations as well

added a jsonschema used it to parse the protein domains json files

d2b746e

disabled the view of the protein domain loading options when the user…

cad5c72

… choose the demo option

replaced the argument name method by load_choice to be consistent acr…

8253cb5

…oss callbacks

managed the appearance of a div displaying information about the Unip…

9d06fd5

…rot downloaded data sets

managed the appearance of a div with the information about the domain…

850212c

… independent loading option

added hover information on the upload divs

c031fa3

Merge branch 'master' into needle_plot_store_app

5006d00

Conflicts: tests/dash/app_needle_plot.py Solved it :)

Bachibouzouk mentioned this pull request Dec 1, 2018

Dash Bio apps - initial impressions #64

Closed

20 tasks

shammamah-zz suggested changes Dec 3, 2018

View reviewed changes

Bachibouzouk added 2 commits December 3, 2018 20:28

moved the data parser into dash-bio/utils

f7c6a32

implemented style changes as required by jack, added the option to sp…

fbf5312

…ecify the color of the protein domains

mtwichan temporarily deployed to dash-bio-test-pr-51 December 3, 2018 19:34 Inactive

Bachibouzouk added 3 commits December 3, 2018 21:20

Merge branch 'master' into needle_plot_store_app

ceca336

deleted the function to extract the demo data from a github repo and …

dbdc545

…load them from local file instead

changed the color of the header and modified the overflow option for …

5273504

…the tabs

mtwichan temporarily deployed to dash-bio-test-pr-51 December 3, 2018 21:00 Inactive

shammamah-zz suggested changes Dec 4, 2018

View reviewed changes

changed the header color

cc0b19f

mtwichan deployed to dash-bio-test-pr-51 December 4, 2018 16:22 View deployment

shammamah-zz approved these changes Dec 4, 2018

View reviewed changes

Bachibouzouk merged commit 034dc55 into master Dec 4, 2018

Bachibouzouk deleted the needle_plot_store_app branch February 1, 2019 09:28

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app_needleplot loading data improvements #51

app_needleplot loading data improvements #51

Bachibouzouk commented Nov 28, 2018 •

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shammamah-zz commented Dec 4, 2018

app_needleplot loading data improvements #51

app_needleplot loading data improvements #51

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Bachibouzouk commented Nov 28, 2018 • edited Loading

Dash Bio pull request

Name and description of your component

Before asking for a review

PR merging checklist

DDS Deployment

DDS Deployment Debugging

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shammamah-zz commented Dec 4, 2018

Bachibouzouk commented Nov 28, 2018 •

edited

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