How to use get_java_opts method in localstack

Best Python code snippet using localstack_python

cluster_information.py

Source:cluster_information.py

...21        22        self.config = parse(self.cluster_xml_file)23    def get_username(self):24        return get_tag_text(self.config, "username")25    def get_java_opts(self):26        return get_tag_text(self.config, "java_opts")27    def get_index_directory(self):28        return get_tag_text(self.config, "index_directory");29    def get_master_node_machine(self):30        master_node = self.config.getElementsByTagName("master_node")[0]31        id = NodeXmlReader.get_cluster_id(master_node)32        ip = NodeXmlReader.get_cluster_ip(master_node)33        client_ip = NodeXmlReader.get_client_ip(master_node)34        client_port = NodeXmlReader.get_client_port(master_node)35        java_opts = NodeXmlReader.get_java_opts(master_node)36        if java_opts is "":37            java_opts = self.get_java_opts()38        username = self.get_username()39        return Machine(id, ip, username, client_ip, client_port, java_opts)40    def get_node_machine_list(self):41        nodes = []42        username = self.get_username()43        for node in self.config.getElementsByTagName("node"):44            id = NodeXmlReader.get_cluster_id(node)45            ip = NodeXmlReader.get_cluster_ip(node)46            java_opts = NodeXmlReader.get_java_opts(node)47            if java_opts is "":48                java_opts = self.get_java_opts()49            nodes.append(Machine(id, ip, username, "", "", java_opts))50        return nodes51class NodeXmlReader(object):52    ''' --------------------------------------------------------------------------53     Node Specific Functions54    -------------------------------------------------------------------------- '''55    @staticmethod56    def get_cluster_id(node):57        return get_tag_text(node, "id")58    @staticmethod59    def get_cluster_ip(node):60        return get_tag_text(node, "cluster_ip")61    @staticmethod62    def get_client_ip(node):63        return get_tag_text(node, "client_ip")64    @staticmethod65    def get_client_port(node):66        return get_tag_text(node, "client_port")67    @staticmethod68    def get_java_opts(node):69        return get_tag_text(node, "java_opts")70def get_tag_text(xml_node, tag):71    values = xml_node.getElementsByTagName(tag)72    if len(values) > 0:73        return get_text(values[0])74    else:75        return ""76def get_text(xml_node):77    rc = []78    for node in xml_node.childNodes:79        if node.nodeType == node.TEXT_NODE:80            rc.append(node.data)81    return ''.join(rc)82class Machine:83    java_opts = ""84    log_path = ""85    port = ""86    87    def __init__(self, id, ip, username, client_ip="", client_port="", java_opts=""):88        self.id = id89        self.ip = ip90        self.username = username91        self.client_ip = client_ip92        self.client_port = client_port93        self.java_opts = java_opts94    95    def get_id(self):96        return self.id97    98    def get_ip(self):99        return self.ip100    101    def get_java_opts(self):102        return self.java_opts103    104    def get_client_ip(self):105        return self.client_ip106    107    def get_client_port(self):108        return self.client_port109    110    def get_username(self):111        return self.username112    113    def get_log_path(self):114        return self.log_path115    ...

genomicsdbimport.py

Source:genomicsdbimport.py

1import os2from snakemake.shell import shell3from snakemake_wrapper_utils.java import get_java_opts4extra = snakemake.params.get("extra", "")5java_opts = get_java_opts(snakemake)6gvcfs = list(map("--variant {}".format, snakemake.input.gvcfs))7db_action = snakemake.params.get("db_action", "create")8if db_action == "create":9    db_action = "--genomicsdb-workspace-path"10elif db_action == "update":11    db_action = "--genomicsdb-update-workspace-path"12else:13    raise ValueError(14        "invalid option provided to 'params.db_action'; please choose either 'create' or 'update'."15    )16log = snakemake.log_fmt_shell(stdout=True, stderr=True)17shell(18    "gatk --java-options '{java_opts}' GenomicsDBImport {extra} "19    "{gvcfs} "...

filter_by_info.py

Source:filter_by_info.py

...5__contact__ = "j.sendrowski18@gmail.com"6__date__ = "2022-05-31"7from snakemake.shell import shell8from snakemake_wrapper_utils.java import get_java_opts9java_opts = get_java_opts(snakemake)10vcf = snakemake.input.vcf11filter = snakemake.params.filter12out = snakemake.output[0]13shell(f"gatk --java-options '{java_opts}' SelectVariants -V {vcf} -O {out} "...

Automation Testing Tutorials

Learn to execute automation testing from scratch with LambdaTest Learning Hub. Right from setting up the prerequisites to run your first automation test, to following best practices and diving deeper into advanced test scenarios. LambdaTest Learning Hubs compile a list of step-by-step guides to help you be proficient with different test automation frameworks i.e. Selenium, Cypress, TestNG etc.