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update tests for all orgaisms
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@davidsmejia
davidsmejia committed Sep 27, 2023
1 parent 4213147 commit bada128
Showing 1 changed file with 47 additions and 118 deletions.
165 changes: 47 additions & 118 deletions foreman/tests/surveyor/test_transcriptome_index.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
import urllib
from unittest.mock import call, patch

from django.test import TestCase
Expand All @@ -8,6 +7,7 @@
from data_refinery_common.enums import Downloaders
from data_refinery_common.models import DownloaderJob, Organism, SurveyJob, SurveyJobKeyValue
from data_refinery_foreman.surveyor.transcriptome_index import TranscriptomeIndexSurveyor
from data_refinery_foreman.surveyor.utils import requests_has_content_length


class SurveyTestCase(TestCase):
Expand All @@ -33,123 +33,52 @@ def test_survey(self, mock_send_job):

mock_send_job.assert_has_calls(send_job_calls)

@vcr.use_cassette(
"/home/user/data_store/cassettes/surveyor.transcriptome.correct_index_location.yaml"
)
def test_correct_index_location(self):
"""Tests that the files returned actually exist.
Uses an organism in the main division.
def test_all_correct_index_location(self):
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="ensembl_division", value="Ensembl"
)
key_value_pair.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="organism_name", value="Danio rerio"
)
key_value_pair.save()

surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]

# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="DANIO_RERIO")

for file in files:
urllib.request.urlopen(file.source_url)

@vcr.use_cassette(
"/home/user/data_store/cassettes/surveyor.transcriptome.correct_location_metazoa.yaml"
)
def test_correct_index_location_metazoa(self):
"""Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
Tests one organism from all supported Ensembl divisions.
Fungi and Bacteria organisms have mappings defined
in config/organism_strain_mapping.csv
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="ensembl_division", value="EnsemblMetazoa"
)
key_value_pair.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="organism_name", value="Octopus bimaculoides"
)
key_value_pair.save()

surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]

for file in files:
urllib.request.urlopen(file.source_url)

# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="OCTOPUS_BIMACULOIDES")

@vcr.use_cassette("/home/user/data_store/cassettes/surveyor.transcriptome.single_plant.yaml")
def test_single_plant(self):
"""Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="ensembl_division", value="EnsemblPlants"
)
key_value_pair.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="organism_name", value="Arabidopsis thaliana"
)
key_value_pair.save()

surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]

for file in files:
urllib.request.urlopen(file.source_url)

# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name="ARABIDOPSIS_THALIANA")

@vcr.use_cassette(
"/home/user/data_store/cassettes/surveyor.transcriptome.correct_location_protist.yaml"
)
def test_correct_index_location_protist(self):
"""Tests that the files returned actually exist.
Tests the Metazoa division instead of the main division.
"""
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="ensembl_division", value="EnsemblProtists"
)
key_value_pair.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="organism_name", value="Leishmania major"
)
key_value_pair.save()

surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]

for file in files:
urllib.request.urlopen(file.source_url)
test_organisms = [
{"division": "Ensembl", "name": "Danio rerio"},
{"division": "EnsemblMetazoa", "name": "Octopus bimaculoides"},
{"division": "EnsemblPlants", "name": "Arabidopsis thaliana"},
{"division": "EnsemblProtists", "name": "Leishmania major"},
{"division": "EnsemblFungi", "name": "Candida albicans"},
{"division": "EnsemblBacteria", "name": "Pseudomonas aeruginosa"},
]

for organism in test_organisms:
scientific_name = organism["name"].upper().replace(" ", "_")
# Break up cassettes into multiple files.
with vcr.use_cassette(
f"/home/user/data_store/cassettes/surveyor.transcriptome.correct_index_location_{scientific_name.lower()}.yaml"
):
survey_job = SurveyJob(source_type="TRANSCRIPTOME_INDEX")
survey_job.save()
key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="ensembl_division", value=organism["division"]
)
key_value_pair.save()

key_value_pair = SurveyJobKeyValue(
survey_job=survey_job, key="organism_name", value=organism["name"]
)
key_value_pair.save()

surveyor = TranscriptomeIndexSurveyor(survey_job)
files = surveyor.discover_species()[0]
# Make sure the organism object got created by making sure
# this doesn't raise an exception.
Organism.objects.get(name=scientific_name)

# Assert that both Fasta and GTF files are found.
self.assertEqual(len(files), 2)

# Ensure that the file exists at the location by performing
# a HEAD request and reading the content-length header.
checks = [requests_has_content_length(file.source_url) for file in files]
self.assertTrue(all(checks))

@vcr.use_cassette("/home/user/data_store/cassettes/surveyor.transcriptome.survey_fungi.yaml")
@patch("data_refinery_foreman.surveyor.external_source.send_job")
Expand Down Expand Up @@ -209,8 +138,8 @@ def test_survey_bacteria(self, mock_send_job):

mock_send_job.assert_has_calls(send_job_calls)

# Make sure the organism object got created with the correct
# taxonomy id by making sure this doesn't raise an exception.
# Make sure the organism object was created with the correct
# species taxonomy id by making sure this doesn't raise an exception.
Organism.objects.get(name="PSEUDOMONAS_AERUGINOSA", taxonomy_id=287)

@vcr.use_cassette(
Expand Down

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