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Description: Allow tests to be run using pre-downloaded data files
allow passing --datadir to pytest to use local data files without
attempting a download.
Author: Afif Elghraoui <afif@debian.org>
Forwarded: https://github.com/konstantint/intervaltree-bio/pull/2
Last-Update: 2016-12-10
--- python-intervaltree-bio.orig/tests/genomeintervaltree_test.py
+++ python-intervaltree-bio/tests/genomeintervaltree_test.py
@@ -13,11 +13,9 @@
from intervaltree_bio import GenomeIntervalTree, UCSCTable
-def test_knownGene():
+def test_knownGene(base_url):
# To speed up testing, we'll download the file and reuse the downloaded copy
- knownGene_url = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/knownGene.txt.gz'
- # Mirror. Slightly faster and more stable, I believe:
- knownGene_url = 'http://kt.era.ee/distribute/pyintervaltree/knownGene.txt.gz'
+ knownGene_url = base_url + 'knownGene.txt.gz'
# To speed up testing, we'll download the file and reuse the downloaded copy
knownGene_file, headers = urlretrieve(knownGene_url)
@@ -39,16 +37,14 @@
assert len(result) == 3
assert result[0].data == result[1].data and result[0].data == result[2].data
-def test_ensGene():
+def test_ensGene(base_url):
# Smoke-test we can at least read ensGene.
- ensGene_url = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/ensGene.txt.gz'
- ensGene_url = 'http://kt.era.ee/distribute/pyintervaltree/ensGene.txt.gz'
+ ensGene_url = base_url + 'ensGene.txt.gz'
ensGene = GenomeIntervalTree.from_table(url=ensGene_url, mode='cds', parser=UCSCTable.ENS_GENE)
assert len(ensGene) == 204940
-def test_refGene():
+def test_refGene(base_url):
# Smoke-test for refGene
- refGene_url = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz'
- refGene_url = 'http://kt.era.ee/distribute/pyintervaltree/refGene.txt.gz'
+ refGene_url = base_url + 'refGene.txt.gz'
refGene = GenomeIntervalTree.from_table(url=refGene_url, mode='tx', parser=UCSCTable.REF_GENE)
assert len(refGene) == 52350 # NB: Some time ago it was 50919, hence it seems the table data changes on UCSC and eventually the mirror and UCSC won't be the same.
--- /dev/null
+++ python-intervaltree-bio/conftest.py
@@ -0,0 +1,20 @@
+import os
+
+import pytest
+
+def pytest_addoption(parser):
+ parser.addoption("--datadir",
+ help="path to data files")
+
+def pytest_generate_tests(metafunc):
+ if 'base_url' in metafunc.fixturenames:
+ if metafunc.config.option.datadir:
+ base_url = ('file://'
+ + os.path.abspath(metafunc.config.option.datadir)
+ + os.sep)
+ else:
+ base_url = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/'
+ # Mirror. Slightly faster and more stable, I believe -KT
+
+ base_url = 'http://kt.era.ee/distribute/pyintervaltree/'
+ metafunc.parametrize('base_url',[base_url])
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