test_igv.py

import requests
import dash
import dash_bio
import dash_html_components as html

from common_features import simple_app_layout
from selenium.webdriver.support.ui import WebDriverWait

_COMPONENT_ID = 'myigv'

igvStyle = dict(
    paddingTop='10px',
    paddingBottom='10px',
    margin='8px',
    border='1px solid lightgray'
)


def test_dbigv001_ASM985889v3(dash_duo):
    app = dash.Dash(__name__)

    try:
        requests.get('https://www.google.com/').status_code
        data_path = 'https://s3.amazonaws.com/igv.org.genomes/'
    except requests.exceptions.ConnectionError:
        print("Running test with local datasets")
        data_path = app.get_asset_url('')

    app.layout = html.Div(simple_app_layout(
        dash_bio.Igv(
            id=_COMPONENT_ID,
            reference={
                "id": "ASM985889v3",
                "name": "Sars-CoV-2 (ASM985889v3)",
                "fastaURL": data_path + "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
                "indexURL": data_path +
                        "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
                "order": 1000000,
                "tracks": [
                    {
                        "name": "Annotations",
                        "url": data_path +
                        "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
                        "displayMode": "EXPANDED",
                        "nameField": "gene",
                        "height": 150
                    }
                ]

            },
            minimumBases=100,
            style=igvStyle
        ),
    ))

    dash_duo.start_server(app)

    # Check that the genome loaded
    dash_duo.wait_for_text_to_equal('.igv-current-genome', 'ASM985889v3')

    # Check that track(s) loaded
    tracks = dash_duo.find_elements('.igv-track-label')
    assert len(tracks) == 1
    assert tracks[0].text == 'Annotations'


def test_dbigv002_ASM985889v3_tracks(dash_duo):
    app = dash.Dash(__name__)

    try:
        requests.get('https://www.google.com/').status_code
        data_path = 'https://s3.amazonaws.com/igv.org.genomes/'
    except requests.exceptions.ConnectionError:
        print("Running test with local datasets")
        data_path = app.get_asset_url('')

    app.layout = html.Div(simple_app_layout(
        dash_bio.Igv(
            id=_COMPONENT_ID,
            reference={
                "id": "ASM985889v3",
                "name": "Sars-CoV-2 (ASM985889v3)",
                "fastaURL": data_path + "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna",
                "indexURL": data_path +
                        "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.fai",
                "order": 1000000,
                "tracks": [
                    {
                        "name": "Annotations",
                        "url": data_path +
                        "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
                        "displayMode": "EXPANDED",
                        "nameField": "gene",
                        "height": 150
                    }
                ]

            },
            tracks=[
                {  # normally, tracks listed here would not duplicate those already present above

                    "name": "Genes",
                    "type": "annotation",
                    "url": data_path +
                    "covid_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz",
                    "displayMode": "EXPANDED"

                }],
            minimumBases=100,
            style=igvStyle
        ),
    ))

    dash_duo.start_server(app)

    # Check that the genome loaded
    dash_duo.wait_for_text_to_equal('.igv-current-genome', 'ASM985889v3')

    WebDriverWait(dash_duo.driver, 5).until(
        lambda _:
        len(dash_duo.find_elements('.igv-track-label')) >= 2,
        "Can't find second track"
    )

    # Check that track(s) loaded
    tracks = dash_duo.find_elements('.igv-track-label')
    assert tracks[0].text == 'Annotations'
    dash_duo.percy_snapshot('test-igv_tracks', convert_canvases=True)


def test_dbigv003_sacCer3(dash_duo):
    app = dash.Dash(__name__)

    try:
        requests.get('https://www.google.com/').status_code
        data_path = 'https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/'
    except requests.exceptions.ConnectionError:
        print("Running test with local datasets")
        data_path = app.get_asset_url('')

    app.layout = html.Div(simple_app_layout(
        dash_bio.Igv(
            id=_COMPONENT_ID,
            reference={
                "id": "sacCer3",
                "name": "S. cerevisiae (sacCer3)",
                "fastaURL": data_path + "sacCer3/sacCer3.fa",
                "indexURL": data_path + "sacCer3/sacCer3.fa.fai",
                "tracks": [
                    {
                        "name": "Ensembl Genes",
                        "type": "annotation",
                        "format": "ensgene",
                        "displayMode": "EXPANDED",
                        "url": data_path + "sacCer3/ensGene.txt.gz",
                        "indexed": False,
                        "supportsWholeGenome": False
                    }
                ]
            },
            minimumBases=100,
            style=igvStyle
        ),
    ))

    dash_duo.start_server(app)

    # Check that the genome loaded
    dash_duo.wait_for_text_to_equal('.igv-current-genome', 'sacCer3')

    # Check that track(s) loaded
    tracks = dash_duo.find_elements('.igv-track-label')
    assert len(tracks) == 1
    assert tracks[0].text == 'Ensembl Genes'