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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} "...

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