def get_r_doc(image_dir):
raw_r_doc = utils.docker_exec(
image_dir,
"sh -c \"echo 'ip <- as.data.frame(installed.packages()[,c(1,3:4)]) \n rownames(ip) <- NULL \n ip <- ip[is.na(ip\$Priority),1:2,drop=FALSE] \n print(ip, row.names=FALSE)' > temp.r; Rscript temp.r; rm temp.r\""
)
packages = raw_r_doc.strip().split("\n")
r_version_output = utils.docker_exec(image_dir, "R --version | head -1")
try:
r_version = re.search("(\d+\.)(\d+\.)(\*|\d+)",
r_version_output).group(0)
except AttributeError as e:
raise ValueError(
"the R has produced output with an improperly formatted version. Something has likely gone wrong with this script, ensure that the output has a version properly parsed by the regex in the function write_r_doc.\n\tOutput: "
+ r_version_output)
package_json = [{"r": r_version}]
for package in packages[1:]:
processed_tuple = re.sub(' +', ' ', package.strip()).split(' ')
assert len(processed_tuple
) == 2, "Asserting format for {} is correct".format(package)
json = {processed_tuple[0]: processed_tuple[1]}
package_json.append(json)
return package_json
def get_python_doc(params):
image_dir = params.image_dir
python_version_output = utils.docker_exec(image_dir, "python3 --version")
raw_python_doc = utils.docker_exec(image_dir, "pip list --format=json")
try:
python_version = re.search("(\d+\.)(\d+\.)(\*|\d+)", python_version_output).group(0)
except AttributeError as e:
raise ValueError("the python command has produced output with an improperly formatted version. Something has likely gone wrong with this script, ensure that the output has a version properly parsed by the regex in the function write_python_doc. \n\tOutput: " + python_version_output)
json_python_doc = json.loads(raw_python_doc)
json_python_doc = list(map(lambda package: { package["name"]: package["version"] }, json_python_doc))
json_python_doc.append({"python": python_version})
return json_python_doc
def get_gatk_doc(image_dir):
cmd = "ls /etc/ | grep gatk | tr '-' ' ' | awk '{print $2}'"
gatk_version = utils.docker_exec(image_dir, cmd)
return [{"gatk": gatk_version}]