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@derBlaumond
derBlaumond committed Dec 18, 2022
1 parent aac9abb commit 80dd223
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Showing 2 changed files with 262 additions and 61 deletions.
8 changes: 7 additions & 1 deletion app.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,13 @@
html.Img(
src=r"assets/rki_logo.png",
alt="Img_RKI",
style={"float": "right", "height": "10%", "width": "10%"},
style={
"float": "right",
"height": "10%",
"width": "10%",
"margin-top": "50px",
"margin-right": "20px",
},
className="responsive",
),
html.Img(
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315 changes: 255 additions & 60 deletions example.app.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
import argparse
import os

from dash import Dash
from dash import dash_table
Expand All @@ -8,81 +9,273 @@
from dash import Output
from dash import State
import dash_bootstrap_components as dbc
from dotenv import load_dotenv
from flask import Flask

from pages.app_controller import get_freq_mutation
from pages.app_controller import match_controller
from pages.app_controller import sonarBasicsChild
from pages.libs.mpxsonar.src.mpxsonar.sonar import parse_args

load_dotenv()
# stylesheet with the .dbc class
dbc_css = "https://cdn.jsdelivr.net/gh/AnnMarieW/dash-bootstrap-templates/dbc.min.css"
app = Dash(__name__, external_stylesheets=[dbc.themes.BOOTSTRAP, dbc_css])
flask_server = Flask(__name__)
app = Dash(
__name__, server=flask_server, external_stylesheets=[dbc.themes.BOOTSTRAP, dbc_css]
)
custom_cmd_cards = html.Div(
[
dbc.Card(
[
dbc.CardHeader([html.H3("MPXsonar command!")]),
dbc.CardHeader(
[
html.H3(
[
"MPXSonar command!",
dbc.Badge(
"Alpha-Test", className="ms-1", color="warning"
),
]
)
]
),
dbc.CardBody(
dbc.Row(
[
dbc.Col(
[
html.Div(
[
"sonar: ",
dcc.Input(
id="my-input",
value="match --count",
type="text",
size="100",
),
]
),
html.Br(),
html.Label("MPXSonar command:"),
html.Div(id="my-command", children=""),
]
),
dbc.Col(
[
html.Div(
dbc.Button(
id="submit-button-state",
n_clicks=0,
children="Submit",
color="primary",
className="mb-2",
[
dbc.Row(
[
dbc.Col(
[
html.Div(
[
dcc.Input(
id="my-input",
value="match --count",
type="text",
size="100",
),
dbc.FormText(
"type the sonar command here and press submit (no need to put sonar at the begining)",
color="secondary",
),
html.Br(),
dbc.Row(
[
dbc.Col([]),
] # row
),
]
),
),
]
),
]
),
),
],
className="mb-3",
),
dbc.Card(
[
html.Label("Output:"),
html.Div(id="my-output", children=""),
html.Div(
]
),
dbc.Col(
[
html.Div(
[
dbc.Button(
id="submit-button-state",
n_clicks=0,
children="Submit",
color="primary",
className="mb-2",
),
]
),
]
),
]
), # end row
dbc.Row(
[
dbc.Col(
[
dbc.Toast(
[
html.Div(id="my-command", children=""),
html.P(
"-------",
className="mb-0",
),
html.P(
"",
className="mb-0",
),
],
header="Translate into Sonar command",
style={"margin-top": "15px"},
),
],
width=3,
),
dbc.Col(
[
dbc.Accordion(
[
dbc.AccordionItem(
[
html.Ul(
"1.The output will be showed in the below section."
),
html.Ul(
"2. Available reference: NC_063383.1, NC_003310.1, ON563414.3, MN648051.1, MT903344.1, ON585033.1, and ON568298.1 "
),
],
title="Note>",
),
dbc.AccordionItem(
[
html.P(
"Currenlty we allow only 'match' and 'list-prop' commands."
),
dbc.Badge(
"match -r NC_063383.1 --COUNTRY USA",
color="white",
text_color="primary",
className="border me-1",
id="cmd-1",
),
dbc.Badge(
"match --profile del:1-60",
color="white",
text_color="primary",
className="border me-1",
id="cmd-3",
),
dbc.Badge(
"match --profile ^C162331T",
color="white",
text_color="primary",
className="border me-1",
id="cmd-4",
),
dbc.Badge(
"match --profile OPG188:L246F --profile MPXV-UK_P2-164:L246F ",
color="white",
text_color="primary",
className="border me-1",
id="cmd-5",
),
dbc.Badge(
"match --profile A151461C del:=1-=6",
color="white",
text_color="primary",
className="border me-1",
id="cmd-8",
),
dbc.Badge(
"match --LENGTH >197120 <197200",
color="white",
text_color="primary",
className="border me-1",
id="cmd-2",
),
dbc.Badge(
"match --sample ON585033.1",
color="white",
text_color="primary",
className="border me-1",
id="cmd-9",
),
dbc.Badge(
"list-prop",
color="white",
text_color="secondary",
className="border me-1",
id="cmd-7",
),
dbc.Tooltip(
"Select all samples from reference 'NC_063383.1' and in USA",
target="cmd-1",
),
dbc.Tooltip(
"Select all samples from sequence length in a range between 197120 and 197200 bp",
target="cmd-2",
),
dbc.Tooltip(
"List all properties",
target="cmd-7",
),
dbc.Tooltip(
"Select all samples that have or in range 1-60 deletion mutation (e.g., del:1-60, del:1-6, del:11-20)",
target="cmd-3",
),
dbc.Tooltip(
"Select all samples except samples contain C162331T mutation (^ = exclude)",
target="cmd-4",
),
dbc.Tooltip(
"Combine with 'OR'; for example, get all samples that have mutation at 'OPG188:L246F' OR 'MPXV-UK_P2-164:L246F' (format, GENE/TAG:protien mutation)",
target="cmd-5",
),
dbc.Tooltip(
"Get all samples ",
target="cmd-6",
),
dbc.Tooltip(
"'AND' operation; for example, get all samples that have mutation at A151461C and exact 1-6 deletion",
target="cmd-8",
),
dbc.Tooltip(
"Get sample by name",
target="cmd-9",
),
],
title="Example commands...",
),
dbc.AccordionItem(
html.Label(
[
"We are currently working to resolve bugs :)..Thank you for your understanding and patience while we work on solutions! "
"Please visit ",
html.A(
"MPXSonar",
href="https://github.com/rki-mf1/covsonar/tree/dev/cov2_mpire",
),
" for more usage and detail.",
]
),
title="FMI",
),
],
style={"margin-top": "15px"},
)
],
width=8,
),
]
), # end row
]
), # end card body
dbc.Card( # Output
[
dash_table.DataTable(
id="my-output-df",
page_current=0,
page_size=10,
style_data={
"whiteSpace": "normal",
"height": "auto",
},
style_table={"overflowX": "auto"},
export_format="csv",
html.H4("Output:"),
html.Hr(),
html.Div(id="my-output", children=""),
html.Div(
[
dash_table.DataTable(
id="my-output-df",
page_current=0,
page_size=10,
style_data={
"whiteSpace": "normal",
"height": "auto",
# all three widths are needed
"minWidth": "300px",
"width": "300px",
"maxWidth": "300px",
},
style_table={"overflowX": "auto"},
export_format="csv",
),
]
),
]
),
],
body=True,
className="mx-1 my-1",
), # end of Output
],
body=True,
className="mb-3",
),
]
)
Expand Down Expand Up @@ -143,8 +336,8 @@ def update_output_sonar(n_clicks, commands):
elif args.tool == "dev":
get_freq_mutation(args)
else:

output = "This command is not available."

except argparse.ArgumentError as exc:
output = exc.message
except SystemExit:
Expand All @@ -153,4 +346,6 @@ def update_output_sonar(n_clicks, commands):


if __name__ == "__main__":
app.run_server(debug=True, host="127.0.0.1")
app.run_server(
debug=os.getenv("DEBUG"), host=os.getenv("SERVER"), port=os.getenv("PORT")
)

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