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Inactivate all code that tries to set paths based on the installed pa…
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…th of microSALT via CONDA_PREFIX
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@samuell
samuell committed Jul 4, 2024
1 parent 920a88e commit 68a7efd
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Showing 6 changed files with 33 additions and 33 deletions.
24 changes: 12 additions & 12 deletions tests/test_commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,9 +25,9 @@
def unpack_db_json(filename):
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/{}'.format(filename)))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down Expand Up @@ -65,27 +65,27 @@ def runner():
def config():
config = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'configExample.json'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
config = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/configExample.json'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# config = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/configExample.json'))
return config

@pytest.fixture
def path_testdata():
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/sampleinfo_samples.json'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
return testdata

@pytest.fixture
def path_testproject():
testproject = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/AAA1234_2000.1.2_3.4.5'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testproject = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testproject/AAA1234_2000.1.2_3.4.5'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testproject = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testproject/AAA1234_2000.1.2_3.4.5'))
return testproject


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6 changes: 3 additions & 3 deletions tests/test_database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,9 @@
def unpack_db_json(filename):
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/{}'.format(filename)))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down
6 changes: 3 additions & 3 deletions tests/test_jobcreator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,9 @@
def testdata():
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/sampleinfo_samples.json'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down
6 changes: 3 additions & 3 deletions tests/test_reporter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@
def unpack_db_json(filename):
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/{}'.format(filename)))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down
12 changes: 6 additions & 6 deletions tests/test_scraper.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,18 +18,18 @@
def testdata_prefix():
test_path = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
test_path = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# test_path = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/'))
return test_path

@pytest.fixture
def testdata():
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/sampleinfo_samples.json'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down
12 changes: 6 additions & 6 deletions tests/test_webserver.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,9 +22,9 @@
def unpack_db_json(filename):
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/{}'.format(filename)))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/{}'.format(filename)))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand All @@ -51,9 +51,9 @@ def mock_db():
def testdata():
testdata = os.path.abspath(os.path.join(pathlib.Path(__file__).parent.parent, 'tests/testdata/sampleinfo_samples.json'))
#Check if release install exists
for entry in os.listdir(get_python_lib()):
if 'microSALT-' in entry:
testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
#for entry in os.listdir(get_python_lib()):
# if 'microSALT-' in entry:
# testdata = os.path.abspath(os.path.join(os.path.expandvars('$CONDA_PREFIX'), 'testdata/sampleinfo_samples.json'))
with open(testdata) as json_file:
data = json.load(json_file)
return data
Expand Down

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