def test_make_bash_test_bad_genome_build():
"""
Test the main method of ggd make-recipe
"""
## test that make_bash fails when a bad genome build is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hg09', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS')
try:
temp_stderr = StringIO()
with redirect_stderr(temp_stderr):
make_bash.make_bash((),args)
except Exception as e:
os.rmdir("{}-{}-v{}".format("hg09","test-gaps","1"))
output = str(temp_stderr.getvalue().strip())
assert "ERROR: genome-build: hg09 not found in github repo for the Homo_sapiens species" in output
## test that make_bash fails when a bad genome build is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hgmm10', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS')
try:
temp_stderr = StringIO()
with redirect_stderr(temp_stderr):
make_bash.make_bash((),args)
except Exception as e:
os.rmdir("{}-{}-v{}".format("hgmm10","test-gaps","1"))
output = temp_stderr.getvalue().strip()
assert "ERROR: genome-build: hgmm10 not found in github repo for the Homo_sapiens species" in output
def test_make_bash_test_bad_name():
"""
Test the main method of ggd make-recipe
"""
## test that make_bash fails when a bad name is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name='', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS')
try:
assert make_bash.make_bash((),args)
except AssertionError as e:
## Correctly raises an assetion error due to the missing name
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a bad name is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name=' ', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS')
try:
assert make_bash.make_bash((),args)
except AssertionError as e:
## Correctly raises an assetion error due to the missing name
pass
except Exception as e:
print(e)
assert False
def test_make_bash_test_bad_genome_build():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
## test that make_bash fails when a bad genome build is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg09', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
temp_stderr = StringIO()
with redirect_stderr(temp_stderr):
make_bash.make_bash((),args)
except Exception as e:
os.rmdir("{}-{}-{}-v{}".format("hg09","test-gaps","ucsc","1"))
output = str(temp_stderr.getvalue().strip())
assert "ERROR: genome-build: hg09 not found in github repo for the Homo_sapiens species" in output
## test that make_bash fails when a bad genome build is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hgmm10', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
temp_stderr = StringIO()
with redirect_stderr(temp_stderr):
make_bash.make_bash((),args)
except Exception as e:
os.rmdir("{}-{}-{}-v{}".format("hgmm10","test-gaps","ucsc","1"))
output = temp_stderr.getvalue().strip()
assert "ERROR: genome-build: hgmm10 not found in github repo for the Homo_sapiens species" in output
def test_make_bash_test_bad_recipe():
"""
Test the main method of ggd make-recipe
"""
## test that make_bash fails when a bad recipe is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='bad-recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS')
with pytest.raises(SystemExit) as pytest_wrapped_e:
make_bash.make_bash((), args)
os.rmdir("{}-{}-v{}".format("hg19","test-gaps","1"))
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that SystemExit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## Check that the exit code is 1
def test_make_bash_test_bad_recipe():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
## test that make_bash fails when a bad recipe is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script='bad-recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
with pytest.raises(SystemExit) as pytest_wrapped_e:
make_bash.make_bash((), args)
os.rmdir("{}-{}-{}-v{}".format("hg19","test-gaps","ucsc","1"))
assert "SystemExit" in str(pytest_wrapped_e.exconly()) ## test that SystemExit was raised by sys.exit()
assert pytest_wrapped_e.match("1") ## Check that the exit code is 1
def test_make_bash_test_bad_name():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
## test that make_bash fails when a bad name is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing name
assert "The recipe name is required" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a bad name is provided
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name=' ', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing name
assert "The recipe name is required" in str(e)
pass
except Exception as e:
print(e)
assert False
def test_make_bash_meta_yaml_key_order():
"""
Test the main method of ggd make-recipe
"""
recipe = CreateRecipe(
"""
hg19-test-gaps3-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps3-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps3-v1"],"recipe.sh")
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=['vt','samtools','bedtools'], extra_file=['not.a.real.extra.file'], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps3', platform='none', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC')
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
## Test that the keys in the meta.yaml file are in the correct order.
## Conda-build requires a strict order: https://github.com/conda/conda-build/issues/3267
try:
ref_keys = ["build","extra","package","requirements","source","about"]
index = 0
with open(new_metayaml_file, "r") as mf:
for item in mf:
item = item.strip().replace(":","")
if item in ref_keys:
assert ref_keys[index] == item
ref_keys[index] = "Done"
index += 1
assert index-1 == 5 ## Index - 1 because an additional 1 was added at the end. (Only index 0-5 exists)
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.rmdir(ggd_package)
def test_make_bash_all_params():
"""
Test the main method of ggd make-recipe
"""
recipe = CreateRecipe(
"""
hg19-test-gaps2-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps2-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps2-v1"],"recipe.sh")
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=['vt','samtools','bedtools'], extra_file=['not.a.real.extra.file'], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps2', platform='none', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC')
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
## Test meta.yaml
try:
with open(new_metayaml_file, "r") as mf:
yamldict = yaml.safe_load(mf)
assert yamldict["build"]["number"] == 0
assert "noarch" not in yamldict["build"].keys()
assert yamldict["extra"]["authors"] == "me"
assert yamldict["extra"]["extra-files"] == ['{}.a.real.extra.file'.format(ggd_package)]
assert yamldict["package"]["name"] == ggd_package
assert yamldict["package"]["version"] == "1"
assert yamldict["requirements"]["build"] == ['bedtools', 'gsort', 'htslib', 'samtools', 'vt', 'zlib']
assert yamldict["requirements"]["run"] == ['bedtools', 'gsort', 'htslib', 'samtools', 'vt', 'zlib']
assert yamldict["source"]["path"] == "."
assert yamldict["about"]["identifiers"]["genome-build"] == "hg19"
assert yamldict["about"]["identifiers"]["species"] == "Homo_sapiens"
assert yamldict["about"]["keywords"] == ['gaps','region']
assert yamldict["about"]["summary"] == "Assembly gaps from UCSC"
assert yamldict["about"]["tags"]["data-version"] == "27-Apr-2009"
assert yamldict["about"]["tags"]["ggd-channel"] == "genomics"
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.rmdir(ggd_package)
def test_make_bash():
"""
Test the main method of ggd make-recipe
"""
recipe = CreateRecipe(
"""
hg19-test-gaps-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps-v1"],"recipe.sh")
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009',
dependency=[], extra_file=[], genome_build='hg19', ggd_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC')
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
## Test meta.yaml
try:
with open(new_metayaml_file, "r") as mf:
yamldict = yaml.safe_load(mf)
assert yamldict["build"]["noarch"] == "generic"
assert yamldict["build"]["number"] == 0
assert yamldict["extra"]["authors"] == "me"
assert yamldict["extra"]["extra-files"] == []
assert yamldict["package"]["name"] == ggd_package
assert yamldict["package"]["version"] == "1"
assert yamldict["requirements"]["build"] == ['gsort', 'htslib', 'zlib']
assert yamldict["requirements"]["run"] == ['gsort', 'htslib', 'zlib']
assert yamldict["source"]["path"] == "."
assert yamldict["about"]["identifiers"]["genome-build"] == "hg19"
assert yamldict["about"]["identifiers"]["species"] == "Homo_sapiens"
assert yamldict["about"]["keywords"] == ['gaps','region']
assert yamldict["about"]["summary"] == "Assembly gaps from UCSC"
assert yamldict["about"]["tags"]["data-version"] == "27-Apr-2009"
assert yamldict["about"]["tags"]["ggd-channel"] == "genomics"
except IOError as e:
print(e)
assert False
## Test post-link.sh
try:
with open(new_postlink_file, "r") as pf:
recipe_dir = False
pkd_dir = False
env_var = False
run_recipe_script = False
file_extention = False
rename_data = False
for line in pf:
### Check the assignment of RECIPE_DIR
if "RECIPE_DIR=" in line:
assert line.strip() == """export RECIPE_DIR=$CONDA_ROOT/share/ggd/Homo_sapiens/hg19/hg19-test-gaps-v1/1""" or line.strip() == """export RECIPE_DIR=$env_dir/share/ggd/Homo_sapiens/hg19/hg19-test-gaps-v1/1"""
recipe_dir = True
### Check the assigning of PKG_DIR to conform with proper file filtering for Linus and macOSX
if "PKG_DIR=" in line:
assert line.strip() == """PKG_DIR=`find "$CONDA_ROOT/pkgs/" -name "$PKG_NAME-$PKG_VERSION*" | grep -v ".tar.bz2" | grep "$PKG_VERSION.*$PKG_BUILDNUM$"`"""
pkd_dir = True
### Check enivornment variable setting
if "recipe_env_name=" in line:
assert line.strip() == """recipe_env_name="ggd_hg19-test-gaps-v1" """.strip() \
or line.strip() == """recipe_env_name="$(echo "$recipe_env_name" | sed 's/-/_/g')" """.strip() \
or line.strip() == """echo "export $recipe_env_name=$RECIPE_DIR" >> $activate_dir/env_vars.sh"""
env_var = True
#### Check that the recipe is being run
if "bash $PKG_DIR" in line:
assert line.strip() == """(cd $RECIPE_DIR && bash $PKG_DIR/info/recipe/recipe.sh)"""
run_recipe_script = True
### Check taht the extention for the data files is being extracted
if "ext=" in line:
assert line.strip() == """ext="${f#*.}" """.strip()
file_extention = True
### Check that the data file names are replaced with the ggd package name, but the extentions are kept
if "(mv $f" in line:
assert line.strip() == """(mv $f "hg19-test-gaps-v1.$ext")"""
rename_data = True
assert recipe_dir
assert pkd_dir
assert env_var
assert run_recipe_script
assert file_extention
assert rename_data
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.rmdir(ggd_package)
def test_make_bash_internet_free():
"""
Test the main method of ggd make-recipe in an internet free context
(make-recipe)
"""
## Check show-env in an internet free context
pytest_disable_socket()
### Check that there is no interent
assert utils.check_for_internet_connection() == False
recipe = CreateRecipe("""
hg19-test-gaps-ucsc-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""",
from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps-ucsc-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps-ucsc-v1"],
"recipe.sh")
args = Namespace(authors='me',
channel='genomics',
command='make-recipe',
data_version='27-Apr-2009',
data_provider="UCSC",
dependency=[],
extra_file=[],
genome_build='hg19',
package_version='1',
keyword=['gaps', 'region'],
name='test-gaps',
platform='noarch',
script=recipe_file,
species='Homo_sapiens',
summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive",
file_type=[],
final_file=[])
assert make_bash.make_bash((), args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
new_checksums_file = os.path.join("./", ggd_package, "checksums_file.txt")
assert os.path.exists(new_checksums_file)
assert os.path.isfile(new_checksums_file)
## Test meta.yaml
try:
with open(new_metayaml_file, "r") as mf:
yamldict = yaml.safe_load(mf)
assert yamldict["build"]["noarch"] == "generic"
assert yamldict["build"]["number"] == 0
assert yamldict["extra"]["authors"] == "me"
assert yamldict["extra"]["extra-files"] == []
assert yamldict["package"]["name"] == ggd_package
assert yamldict["package"]["version"] == "1"
assert yamldict["requirements"]["build"] == [
'gsort', 'htslib', 'zlib'
]
assert yamldict["requirements"]["run"] == [
'gsort', 'htslib', 'zlib'
]
assert yamldict["source"]["path"] == "."
assert yamldict["about"]["identifiers"]["genome-build"] == "hg19"
assert yamldict["about"]["identifiers"][
"species"] == "Homo_sapiens"
assert yamldict["about"]["keywords"] == ['gaps', 'region']
assert yamldict["about"]["summary"] == "Assembly gaps from UCSC"
assert yamldict["about"]["tags"][
"genomic-coordinate-base"] == "0-based-inclusive"
assert yamldict["about"]["tags"]["data-version"] == "27-Apr-2009"
assert yamldict["about"]["tags"]["data-provider"] == "UCSC"
assert yamldict["about"]["tags"]["file-type"] == []
assert yamldict["about"]["tags"]["final-files"] == []
assert yamldict["about"]["tags"]["final-file-sizes"] == {}
assert yamldict["about"]["tags"]["ggd-channel"] == "genomics"
except IOError as e:
print(e)
assert False
## Test post-link.sh
try:
with open(new_postlink_file, "r") as pf:
recipe_dir = False
pkd_dir = False
dir_env_var = False
file_env_var = False
run_recipe_script = False
file_extention = False
rename_data = False
for line in pf:
### Check the assignment of RECIPE_DIR
if "RECIPE_DIR=" in line:
assert line.strip(
) == """export RECIPE_DIR=$CONDA_ROOT/share/ggd/Homo_sapiens/hg19/hg19-test-gaps-ucsc-v1/1""" or line.strip(
) == """export RECIPE_DIR=$env_dir/share/ggd/Homo_sapiens/hg19/hg19-test-gaps-ucsc-v1/1"""
recipe_dir = True
### Check the assigning of PKG_DIR to conform with proper file filtering for Linus and macOSX
if "PKG_DIR=" in line:
assert line.strip(
) == """PKG_DIR=`find "$CONDA_SOURCE_PREFIX/pkgs/" -name "$PKG_NAME-$PKG_VERSION*" | grep -v ".tar.bz2" | grep "$PKG_VERSION.*$PKG_BUILDNUM$"`"""
pkd_dir = True
### Check enivornment variable setting
if "recipe_env_dir_name=" in line:
assert line.strip() == """recipe_env_dir_name="ggd_hg19-test-gaps-ucsc-v1_dir" """.strip() \
or line.strip() == """recipe_env_dir_name="$(echo "$recipe_env_dir_name" | sed 's/-/_/g' | sed 's/\./_/g')" """.strip() \
or line.strip() == """echo "export $recipe_env_dir_name=$RECIPE_DIR" >> $activate_dir/env_vars.sh"""
dir_env_var = True
if "recipe_env_file_name=" in line:
assert line.strip() == """recipe_env_file_name="ggd_hg19-test-gaps-ucsc-v1_file" """.strip() \
or line.strip() == """recipe_env_file_name="$(echo "$recipe_env_file_name" | sed 's/-/_/g' | sed 's/\./_/g')" """.strip() \
or line.strip() == """if [[ ! -z "${recipe_env_file_name:-}" ]] """.strip() \
or line.strip() == """echo "export $recipe_env_file_name=$file_path" >> $activate_dir/env_vars.sh"""
file_env_var = True
#### Check that the recipe is being run
if "bash $PKG_DIR" in line:
assert line.strip(
) == """(cd $RECIPE_DIR && bash $PKG_DIR/info/recipe/recipe.sh)"""
run_recipe_script = True
### Check taht the extention for the data files is being extracted
if "ext=" in line:
assert line.strip() == """ext="${f#*.}" """.strip()
file_extention = True
### Check that the data file names are replaced with the ggd package name, but the extentions are kept
if "(mv $f" in line:
assert line.strip(
) == """(mv $f "hg19-test-gaps-ucsc-v1.$ext")"""
rename_data = True
assert recipe_dir
assert pkd_dir
assert dir_env_var
assert file_env_var
assert run_recipe_script
assert file_extention
assert rename_data
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.remove(new_checksums_file)
os.rmdir(ggd_package)
def test_make_bash_meta_yaml_ggd_dependency():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
recipe = CreateRecipe(
"""
hg19-test-gaps4-ucsc-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps4-ucsc-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps4-ucsc-v1"],"recipe.sh")
## grch37-gene-features-ensembl-v1 as a dependency
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=['grch37-gene-features-ensembl-v1','hg38-chrom-mapping-ensembl2ucsc-ncbi-v1','vt','samtools','bedtools'], extra_file=['not.a.real.extra.file'], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps4', platform='none', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= ["Bed"], final_file=["hg19-test-gaps4-ucsc-v1.bed.gz", "hg19-test-gaps4-ucsc-v1.bed.gz.tbi"])
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
new_checksums_file = os.path.join("./", ggd_package, "checksums_file.txt")
assert os.path.exists(new_checksums_file)
assert os.path.isfile(new_checksums_file)
## Test meta.yaml has an ggd dependency in the run requirements and not the build requirements
try:
with open(new_metayaml_file, "r") as mf:
yamldict = yaml.safe_load(mf)
assert yamldict["requirements"]["build"] == ['bedtools', 'gsort', 'htslib', 'samtools', 'vt', 'zlib']
assert "grch37-gene-features-ensembl-v1" not in yamldict["requirements"]["build"]
assert "hg38-chrom-mapping-ensembl2ucsc-ncbi-v1" not in yamldict["requirements"]["build"]
assert yamldict["requirements"]["run"] == ['bedtools', 'grch37-gene-features-ensembl-v1', 'gsort', 'hg38-chrom-mapping-ensembl2ucsc-ncbi-v1', 'htslib', 'samtools', 'vt', 'zlib']
assert "grch37-gene-features-ensembl-v1" in yamldict["requirements"]["run"]
assert "hg38-chrom-mapping-ensembl2ucsc-ncbi-v1" in yamldict["requirements"]["run"]
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.remove(new_checksums_file)
os.rmdir(ggd_package)
def test_make_bash_meta_yaml_key_order():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
recipe = CreateRecipe(
"""
hg19-test-gaps3-ucsc-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps3-ucsc-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps3-ucsc-v1"],"recipe.sh")
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=['vt','samtools','bedtools'], extra_file=['not.a.real.extra.file'], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps3', platform='none', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= ["Bed"], final_file=["hg19-test-gaps3-ucsc-v1.bed.gz", "hg19-test-gaps3-ucsc-v1.bed.gz.tbi"])
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
new_checksums_file = os.path.join("./", ggd_package, "checksums_file.txt")
assert os.path.exists(new_checksums_file)
assert os.path.isfile(new_checksums_file)
## Test that the keys in the meta.yaml file are in the correct order.
## Conda-build requires a strict order: https://github.com/conda/conda-build/issues/3267
try:
ref_keys = ["build","extra","package","requirements","source","about"]
index = 0
with open(new_metayaml_file, "r") as mf:
for item in mf:
item = item.strip().replace(":","")
if item in ref_keys:
assert ref_keys[index] == item
ref_keys[index] = "Done"
index += 1
assert index-1 == 5 ## Index - 1 because an additional 1 was added at the end. (Only index 0-5 exists)
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.remove(new_checksums_file)
os.rmdir(ggd_package)
def test_make_bash_all_params():
"""
Test the main method of ggd make-recipe
"""
pytest_enable_socket()
recipe = CreateRecipe(
"""
hg19-test-gaps2-ucsc-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps2-ucsc-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps2-ucsc-v1"],"recipe.sh")
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=['vt','samtools','bedtools'], extra_file=['not.a.real.extra.file'], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps2', platform='none', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="1-based-inclusive", file_type= [],final_file=[])
assert make_bash.make_bash((),args)
new_recipe_file = os.path.join("./", ggd_package, "recipe.sh")
assert os.path.exists(new_recipe_file)
assert os.path.isfile(new_recipe_file)
new_metayaml_file = os.path.join("./", ggd_package, "meta.yaml")
assert os.path.exists(new_metayaml_file)
assert os.path.isfile(new_metayaml_file)
new_postlink_file = os.path.join("./", ggd_package, "post-link.sh")
assert os.path.exists(new_postlink_file)
assert os.path.isfile(new_postlink_file)
new_checksums_file = os.path.join("./", ggd_package, "checksums_file.txt")
assert os.path.exists(new_checksums_file)
assert os.path.isfile(new_checksums_file)
## Test meta.yaml
try:
with open(new_metayaml_file, "r") as mf:
yamldict = yaml.safe_load(mf)
assert yamldict["build"]["number"] == 0
assert "noarch" not in yamldict["build"].keys()
assert yamldict["extra"]["authors"] == "me"
assert yamldict["extra"]["extra-files"] == ['{}.a.real.extra.file'.format(ggd_package)]
assert yamldict["package"]["name"] == ggd_package
assert yamldict["package"]["version"] == "1"
assert yamldict["requirements"]["build"] == ['bedtools', 'gsort', 'htslib', 'samtools', 'vt', 'zlib']
assert yamldict["requirements"]["run"] == ['bedtools', 'gsort', 'htslib', 'samtools', 'vt', 'zlib']
assert yamldict["source"]["path"] == "."
assert yamldict["about"]["identifiers"]["genome-build"] == "hg19"
assert yamldict["about"]["identifiers"]["species"] == "Homo_sapiens"
assert yamldict["about"]["keywords"] == ['gaps','region']
assert yamldict["about"]["summary"] == "Assembly gaps from UCSC"
assert yamldict["about"]["tags"]["genomic-coordinate-base"] == "1-based-inclusive"
assert yamldict["about"]["tags"]["data-version"] == "27-Apr-2009"
assert yamldict["about"]["tags"]["file-type"] == [] ## Should be converted to lower case
assert yamldict["about"]["tags"]["final-files"] == []
assert yamldict["about"]["tags"]["final-file-sizes"] == {}
assert yamldict["about"]["tags"]["ggd-channel"] == "genomics"
except IOError as e:
print(e)
assert False
os.remove(new_recipe_file)
os.remove(new_metayaml_file)
os.remove(new_postlink_file)
os.remove(new_checksums_file)
os.rmdir(ggd_package)
def test_make_bash_missing_tags():
"""
Test that there is an error when missing tags
"""
pytest_enable_socket()
recipe = CreateRecipe(
"""
hg19-test-gaps-ucsc-v1:
recipe.sh: |
genome=https://raw.githubusercontent.com/gogetdata/ggd-recipes/master/genomes/Homo_sapiens/hg19/hg19.genome
wget --quiet -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/gap.txt.gz \\
| gzip -dc \\
| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \\
| gsort /dev/stdin $genome \\
| bgzip -c > gaps.bed.gz
tabix gaps.bed.gz
""", from_string=True)
recipe.write_recipes()
ggd_package = "hg19-test-gaps-ucsc-v1"
recipe_file = os.path.join(recipe.recipe_dirs["hg19-test-gaps-ucsc-v1"],"recipe.sh")
## Bad coordinate
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="2-based-exclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
assert "2-based-exclusive is not an acceptable genomic coordinate base" in str(e)
pass
except Exception as e:
print(e)
assert False
## Emtpy data version
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
assert "Please provide the version of the data this recipe curates" in str(e)
pass
except Exception as e:
print(e)
assert False
## Empty data provider
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test-gaps', platform='noarch', script=recipe_file, species='Homo_sapiens', summary='Assembly gaps from USCS',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
assert "The data provider is required" in str(e)
pass
except Exception as e:
print(e)
assert False
def test_make_bash_test_wildcards():
"""
Test the main method of ggd make-recipe, make sure that a name with a wildcard raises and assertion error
"""
pytest_enable_socket()
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test.gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\".\" wildcard is not allowed in the recipe name" in str(e)
assert "hg19-test.gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test?gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"?\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test?gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test*gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"*\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test*gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test[gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"[\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test[gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test]gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"]\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test]gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test{gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"{\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test{gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test}gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"}\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test}gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test!gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"!\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test!gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test+gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"+\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test+gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test^gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"^\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test^gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test$gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"$\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test$gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test(gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\"(\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test(gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
## test that make_bash fails when a wild card is added to the name
args = Namespace(authors='me', channel='genomics', command='make-recipe', data_version='27-Apr-2009', data_provider="UCSC",
dependency=[], extra_file=[], genome_build='hg19', package_version='1', keyword=['gaps', 'region'],
name='test)gaps', platform='noarch', script='recipe.sh', species='Homo_sapiens', summary='Assembly gaps from UCSC',
coordinate_base="0-based-inclusive", file_type= [],final_file=[])
try:
assert make_bash.make_bash((),args)
assert False
except AssertionError as e:
## Correctly raises an assetion error due to the missing summary
assert "\")\" wildcard is not allowed in the recipe name. Please rename the recipe." in str(e)
assert "hg19-test)gaps-ucsc-v1" in str(e)
pass
except Exception as e:
print(e)
assert False
