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Merge pull request #137 from eastgenomics/IN-759-Fix-broken-unittests
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In 759 fix broken unittests (#137)
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@jethror1
jethror1 authored Sep 16, 2024
2 parents 4e83795 + 34b532c commit c490bf8
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Showing 3 changed files with 55 additions and 60 deletions.
8 changes: 4 additions & 4 deletions trendyqc/trend_monitoring/backend_utils/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -351,7 +351,7 @@ def format_data_for_plotly_js(plot_data: pd.DataFrame) -> tuple:

# get groups of assay and sequencer id
groups = build_groups(plot_data)
seen_groups = []
seen_groups = {}

# too many groups are possible
if sum([len(v) for v in colors.values()]) < len(groups):
Expand All @@ -376,7 +376,7 @@ def format_data_for_plotly_js(plot_data: pd.DataFrame) -> tuple:
if legend_name not in seen_groups:
assay_colors = colors[assay_name]
color_assay_sequencer = assay_colors.pop(0)
seen_groups.append(legend_name)
seen_groups[legend_name] = color_assay_sequencer
shown_legend = True
else:
shown_legend = False
Expand All @@ -393,8 +393,8 @@ def format_data_for_plotly_js(plot_data: pd.DataFrame) -> tuple:
args["First lane"]["columns"] = plot_data.columns[7:9]
args["Second lane"]["columns"] = plot_data.columns[9:11]

args["Combined"]["boxplot_color"] = color_assay_sequencer
args["Combined"]["boxplot_line_color"] = color_assay_sequencer
args["Combined"]["boxplot_color"] = seen_groups[legend_name]
args["Combined"]["boxplot_line_color"] = seen_groups[legend_name]
args["Combined"]["name"] = legend_name
args["Combined"]["offsetgroup"] = legend_name
args["Combined"]["legendgroup"] = legend_name
Expand Down
99 changes: 46 additions & 53 deletions trendyqc/trend_monitoring/tests/test_plotting.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
import datetime
import json
import random
from unittest.mock import Mock, patch

from django.test import TestCase
Expand Down Expand Up @@ -606,14 +605,12 @@ def test_format_data_for_plotly_js_normal_metric(self):
"sample_id": ["Sample1", "Sample2", "Sample3", "Sample4"],
"date": ["2024-06-24", "2024-06-24", "2024-06-24", "2024-06-24"],
"project_name": ["240624_Project1", "240624_Project1", "240624_Project2", "240624_Project2"],
"assay": ["Assay1", "Assay1", "Assay2", "Assay2"],
"assay": ["Cancer Endocrine Neurology", "Cancer Endocrine Neurology", "TruSight Oncology 500", "TruSight Oncology 500"],
"sequencer_id": ["Sequencer1", "Sequencer1", "Sequencer2", "Sequencer2"],
"verifybamid_data__freemix": [1, 2, 3, 4]
}
)

# set the seed to get expected results
random.seed(0)
test_output = format_data_for_plotly_js(test_input)
expected_output = (
json.dumps([
Expand All @@ -623,20 +620,20 @@ def test_format_data_for_plotly_js_normal_metric(self):
["240624_Project1", "240624_Project1"]
],
"y": [1.0, 2.0],
"name": "Assay1 - Sequencer1",
"name": "Cancer Endocrine Neurology - Sequencer1",
"type": "box",
"text": ["Sample1", "Sample2"],
"boxpoints": "suspectedoutliers",
"marker": {
"color": "#6600cc",
"color": "#FF0000",
},
"line": {
"color": "#6600cc"
"color": "#FF0000"
},
"fillcolor": "#6600cc80",
"fillcolor": "#FF000080",
"offsetgroup": "",
"legendgroup": "Assay1 - Sequencer1",
"legend": "Assay1 - Sequencer1",
"legendgroup": "Cancer Endocrine Neurology - Sequencer1",
"legend": "Cancer Endocrine Neurology - Sequencer1",
"visible": True,
"showlegend": True
},
Expand All @@ -646,20 +643,20 @@ def test_format_data_for_plotly_js_normal_metric(self):
["240624_Project2", "240624_Project2"]
],
"y": [3.0, 4.0],
"name": "Assay2 - Sequencer2",
"name": "TruSight Oncology 500 - Sequencer2",
"type": "box",
"text": ["Sample3", "Sample4"],
"boxpoints": "suspectedoutliers",
"marker": {
"color": "#6ddfff",
"color": "#7D8040",
},
"line": {
"color": "#6ddfff"
"color": "#7D8040"
},
"fillcolor": "#6ddfff80",
"fillcolor": "#7D804080",
"offsetgroup": "",
"legendgroup": "Assay2 - Sequencer2",
"legend": "Assay2 - Sequencer2",
"legendgroup": "TruSight Oncology 500 - Sequencer2",
"legend": "TruSight Oncology 500 - Sequencer2",
"visible": True,
"showlegend": True
},
Expand All @@ -679,7 +676,7 @@ def test_format_data_for_plotly_js_lane_metric(self):
"sample_id": ["Sample1", "Sample2", "Sample3", "Sample4", "Sample5"],
"date": ["2024-06-24", "2024-06-24", "2024-06-24", "2024-06-24", "2024-06-25"],
"project_name": ["240624_Project1", "240624_Project1", "240624_Project2", "240624_Project2", "240625_Project3"],
"assay": ["Assay1", "Assay1", "Assay2", "Assay2", "Assay1"],
"assay": ["TruSight Oncology 500", "TruSight Oncology 500", "Twist WES", "Twist WES", "TruSight Oncology 500"],
"sequencer_id": ["Sequencer1", "Sequencer1", "Sequencer2", "Sequencer2", "Sequencer1"],
"fastqc__read_data_1st_lane_R1__lane": ["L001", "L001", "L003", "L003", "L001"],
"fastqc__read_data_2nd_lane_R1__lane": ["L002", "L002", "L004", "L004", "L002"],
Expand All @@ -690,8 +687,6 @@ def test_format_data_for_plotly_js_lane_metric(self):
}
)

# set the seed to get expected results
random.seed(0)
test_output = format_data_for_plotly_js(test_input)
expected_output = (
json.dumps([
Expand All @@ -702,20 +697,20 @@ def test_format_data_for_plotly_js_lane_metric(self):
["240624_Project1", "240624_Project1"]
],
"y": [7.0, 8.0],
"name": "Assay1 - Sequencer1",
"name": "TruSight Oncology 500 - Sequencer1",
"type": "box",
"text": ["Sample1", "Sample2"],
"boxpoints": "suspectedoutliers",
"marker": {
"color": "#6600cc",
"color": "#7D8040",
},
"line": {
"color": "#6600cc"
"color": "#7D8040"
},
"fillcolor": "#6600cc80",
"offsetgroup": "Assay1 - Sequencer1",
"legendgroup": "Assay1 - Sequencer1",
"legend": "Assay1 - Sequencer1",
"fillcolor": "#7D804080",
"offsetgroup": "TruSight Oncology 500 - Sequencer1",
"legendgroup": "TruSight Oncology 500 - Sequencer1",
"legend": "TruSight Oncology 500 - Sequencer1",
"visible": True,
"showlegend": True
},
Expand Down Expand Up @@ -774,20 +769,20 @@ def test_format_data_for_plotly_js_lane_metric(self):
["240624_Project2", "240624_Project2"]
],
"y": [9.0, 10.0],
"name": "Assay2 - Sequencer2",
"name": "Twist WES - Sequencer2",
"type": "box",
"text": ["Sample3", "Sample4"],
"boxpoints": "suspectedoutliers",
"marker": {
"color": "#6ddfff",
"color": "#ff65ff",
},
"line": {
"color": "#6ddfff"
"color": "#ff65ff"
},
"fillcolor": "#6ddfff80",
"offsetgroup": "Assay2 - Sequencer2",
"legendgroup": "Assay2 - Sequencer2",
"legend": "Assay2 - Sequencer2",
"fillcolor": "#ff65ff80",
"offsetgroup": "Twist WES - Sequencer2",
"legendgroup": "Twist WES - Sequencer2",
"legend": "Twist WES - Sequencer2",
"visible": True,
"showlegend": True
},
Expand Down Expand Up @@ -846,20 +841,20 @@ def test_format_data_for_plotly_js_lane_metric(self):
["240625_Project3"]
],
"y": [2.0],
"name": "Assay1 - Sequencer1",
"name": "TruSight Oncology 500 - Sequencer1",
"type": "box",
"text": ["Sample5"],
"boxpoints": "suspectedoutliers",
"marker": {
"color": "#6600cc",
"color": "#7D8040",
},
"line": {
"color": "#6600cc"
"color": "#7D8040"
},
"fillcolor": "#6600cc80",
"offsetgroup": "Assay1 - Sequencer1",
"legendgroup": "Assay1 - Sequencer1",
"legend": "Assay1 - Sequencer1",
"fillcolor": "#7D804080",
"offsetgroup": "TruSight Oncology 500 - Sequencer1",
"legendgroup": "TruSight Oncology 500 - Sequencer1",
"legend": "TruSight Oncology 500 - Sequencer1",
"visible": True,
"showlegend": False
},
Expand Down Expand Up @@ -952,7 +947,7 @@ def test_create_trace(self):
"sample_id": ["Sample1", "Sample2", "Sample3"],
"date": ["2024-06-25", "2024-06-25", "2024-06-25"],
"project_name": ["240625_Project1", "240625_Project1", "240625_Project1"],
"assay": ["Assay1", "Assay1", "Assay1"],
"assay": ["Myeloid", "Myeloid", "Myeloid"],
"sequencer_id": ["Sequencer1", "Sequencer1", "Sequencer1"],
"metric": [1, 2, 3]
}
Expand All @@ -963,16 +958,14 @@ def test_create_trace(self):
"data_column": "metric",
"project_name": "240625_Project1",
"lane": None,
"name": "Assay1 - Project1",
"boxplot_color": "#6600cc",
"boxplot_line_color": "#6600cc",
"name": "Myeloid - Project1",
"boxplot_color": "#FF7800",
"boxplot_line_color": "#FF7800",
"offsetgroup": "",
"legendgroup": "Assay1 - Project1",
"legendgroup": "Myeloid - Project1",
"showlegend": True
}

# set the seed to get expected results
random.seed(0)
test_output = create_trace(**test_input)

expected_output = {
Expand All @@ -983,13 +976,13 @@ def test_create_trace(self):
"type": "box",
"text": ["Sample1", "Sample2", "Sample3"],
"boxpoints": "suspectedoutliers",
"marker": {"color": "#6600cc"},
"line": {"color": "#6600cc"},
"fillcolor": "#6600cc80",
"name": "Assay1 - Project1",
"marker": {"color": "#FF7800"},
"line": {"color": "#FF7800"},
"fillcolor": "#FF780080",
"name": "Myeloid - Project1",
"offsetgroup": "",
"legendgroup": "Assay1 - Project1",
"legend": "Assay1 - Project1",
"legendgroup": "Myeloid - Project1",
"legend": "Myeloid - Project1",
"visible": True,
"showlegend": True
}
Expand Down
8 changes: 5 additions & 3 deletions trendyqc/trend_monitoring/tests/test_views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
from unittest.mock import patch

from trend_monitoring.models.filters import Filter
from trend_monitoring.models.metadata import Report
from trend_monitoring.tables import ReportTable


class TestDashboard(TestCase):
Expand Down Expand Up @@ -36,7 +38,7 @@ def test_dashboard_get(self, mock_context_data):

mock_context_data.return_value = {
"assays": ["CEN", "TSO500"],
"tables": [],
"tables": [ReportTable(Report.objects.all())],
"project_names": ["Project1", "Project2"],
"sequencer_ids": ["Sequencer1", "Sequencer2"],
"metrics": ["Metric1", "Metric2"]
Expand Down Expand Up @@ -127,8 +129,8 @@ def test_dashboard_post_save_filter(self):
self.assertEqual(created_filter_id.content, json.dumps(
{
'assay_select': ['Cancer Endocrine Neurology'],
'date_start': '2024-08-20',
'date_end': '2024-08-23',
'date_start': ['2024-08-20'],
'date_end': ['2024-08-23'],
'metrics_y': ['read_data|avg_length'],
}
))
Expand Down

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