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How to use partial_resolve method in lisa

Best Python code snippet using lisa_python

resolve_layouts.py

Source:resolve_layouts.py

1#!/usr/bin/env python2from __future__ import print_function3from __future__ import division4import re5import sys6from collections import defaultdict7import argparse8gaf_path_pattern=re.compile(r"[<>][\w\-\_]+")9def transform_from_gaf(s):10    if s[0] == '>':11        return s[1:] + '+'12    elif s[0] == '<':13        return s[1:] + '-'14    assert(false)15def transform_to_gaf(s):16    if s[-1] == '+':17        return '>' + s[:-1]18    elif s[-1] == '-':19        return '<' + s[:-1]20    assert(false)21def process_path(l):22    if l[0] == '>' or l[0] == '<':23        return [transform_from_gaf(t) for t in gaf_path_pattern.findall(l)]24    else:25        return [t.strip() for t in l.split(',')]26parser = argparse.ArgumentParser(description="Recursive resolution of the layouts")27parser.add_argument("fragment_names", help="File with names of the fragments to resolve OR layout file OR .gfa file -- segment names will be extracted")28parser.add_argument("composition", help="File specifying composition of intermediate fragments")29parser.add_argument("--resolved-marker", help="String marking the nodes that got duplicated during repeat resolution (e.g. '_i'). Part of the name past the marker will be ignored.")30parser.add_argument("--partial-resolve", action="store_true", help="Allow 'partial' resolving of layout. By default fails if can't resolve down to path of <resolved-prefix>.* fragments")31parser.add_argument("--gaf-paths", action="store_true", help="Use GAF path format ([<>]-prefix instead of [+-]-suffix)")32parser.add_argument("--miniasm", help="File with miniasm layout via 'a' lines")33parser.add_argument("--resolved-prefix", default='read', help="Prefix of completely resolved elements")34args = parser.parse_args()35mapping=defaultdict(list)36usage=defaultdict(int)37if args.miniasm:38    print("Loading miniasm layout", file=sys.stderr)39    with open(args.miniasm, 'r') as miniasm_layout:40        for l in miniasm_layout:41            if not l.startswith('a'):42                continue43            s = l.split()44            assert s[0] == 'a'45            mapping[s[1]].append(s[3] + s[4])46    print("Loaded", file=sys.stderr)47print("Loading compression mappings", file=sys.stderr)48with open(args.composition, 'r') as compress_mapping:49    for l in compress_mapping:50        s = l.split()51        assert s[0] not in mapping52        mapping[s[0]] = process_path(s[1])53print("Loaded", file=sys.stderr)54names = []55if args.fragment_names.endswith('.gfa'):56    print("Loading fragment names from GFA file", file=sys.stderr)57    with open(args.fragment_names, 'r') as gfa_fn:58        for l in gfa_fn:59            if not l.startswith('S'):60                continue61            #TODO optimize for GFA with sequences62            s = l.split()63            assert s[0] == 'S'64            names.append(s[1])65    print("Loaded", file=sys.stderr)66else:67    print("Loading fragment info from text file", file=sys.stderr)68    with open(args.fragment_names, 'r') as fragment_handle:69        for l in fragment_handle:70            s = l.strip().split()71            names.append(s[0].strip())72            if len(s) > 1:73                mapping[s[0]] = process_path(s[1])74    print("Loaded", file=sys.stderr)75def opposite_sign(o):76    if o == '+':77        return '-'78    elif o == '-':79        return '+'80    assert False81def swap_sign(n_o):82    return n_o[:-1] + opposite_sign(n_o[-1])83def need_swap(n_o):84    if n_o[-1] == '+':85        return False86    elif n_o[-1] == '-':87        return True88    assert False89def resolve(n_o, resolved):90    if n_o.startswith(args.resolved_prefix):91        resolved.append(n_o)92        return93    name = n_o[:-1]94    if args.resolved_marker:95        pos=name.find(args.resolved_marker)96        assert pos != 097        if pos > 0:98            name=name[:pos]99    if not args.partial_resolve and name not in mapping:100        print("Problem with ", name, file=sys.stderr)101    assert args.partial_resolve or name in mapping102    if usage[name] > 0:103        print(name, "used multiple times", file=sys.stderr)104    usage[name] += 1105    if name not in mapping and args.partial_resolve:106        resolved.append(name + n_o[-1])107        return108    parts = mapping[name]109    if need_swap(n_o):110        for i in range(len(parts),0,-1):111            p = parts[i - 1]112            resolve(swap_sign(p), resolved)113    else:114        for p in parts:115            resolve(p, resolved)116print("Resolving segment composition", file=sys.stderr)117for s in names:118    resolved = []119    resolve(s + '+', resolved)120    if args.gaf_paths:121        print(s, ''.join([transform_to_gaf(s) for s in resolved]))122    else:123        print(s, ','.join(resolved))...

commands.py

Source:commands.py

...15_get_init_logger = functools.partial(get_logger, "init")16def run(args: Namespace) -> int:17    enable_console_timestamp()18    builder = RunbookBuilder.from_path(args.runbook, args.variables)19    notifier_data = builder.partial_resolve(constants.NOTIFIER)20    if notifier_data:21        notifier_runbook = schema.load_by_type_many(schema.Notifier, notifier_data)22        notifier.initialize(runbooks=notifier_runbook)23    run_message = messages.TestRunMessage(24        runbook_name=builder.partial_resolve(constants.NAME),25        test_project=builder.partial_resolve(constants.TEST_PROJECT),26        test_pass=builder.partial_resolve(constants.TEST_PASS),27        run_name=constants.RUN_NAME,28        tags=builder.partial_resolve(constants.TAGS),29    )30    notifier.notify(run_message)31    run_status = messages.TestRunStatus.FAILED32    run_timer = create_timer()33    run_error_message = ""34    try:35        runner = RootRunner(runbook_builder=builder)36        asyncio.run(runner.start())37        run_status = messages.TestRunStatus.SUCCESS38    except Exception as identifier:39        run_error_message = str(identifier)40        raise identifier41    finally:42        run_message.status = run_status43        run_message.elapsed = run_timer.elapsed()44        run_message.message = run_error_message45        notifier.notify(run_message)46        notifier.finalize()47        run_finalize()48    return runner.exit_code49def run_finalize() -> None:50    try:51        plugin_manager.hook.on_run_finalize()52    except Exception as exception:53        log = _get_init_logger("run_finalize")54        log.info(f"run_finalize failed with error {exception}")55# check runbook56def check(args: Namespace) -> int:57    RunbookBuilder.from_path(args.runbook, args.variables)58    return 059def list_start(args: Namespace) -> int:60    builder = RunbookBuilder.from_path(args.runbook, args.variables)61    list_all = cast(Optional[bool], args.list_all)62    log = _get_init_logger("list")63    if args.type == constants.LIST_CASE:64        if list_all:65            cases: Iterable[TestCaseRuntimeData] = select_testcases()66        else:67            cases = select_testcases(builder.partial_resolve(constants.TESTCASE))68        for case_data in cases:69            log.info(70                f"case: {case_data.name}, suite: {case_data.metadata.suite.name}, "71                f"area: {case_data.suite.area}, "72                f"category: {case_data.suite.category}, "73                f"tags: {','.join(case_data.suite.tags)}, "74                f"priority: {case_data.priority}"75            )76    else:77        raise LisaException(f"unknown list type '{args.type}'")78    log.info("list information here")79    return 080class CommandHookSpec:81    @hookspec...

plot.py

Source:plot.py

1#!/usr/bin/python32import numpy as np3import matplotlib.pyplot as plt4resolve = np.genfromtxt('resolve', delimiter=',', names=['size', 'time'])5plt.plot(resolve['size'], resolve['time'], label='Execution time for resolve_indirect_jumps on synthetic BIR programs')6plt.xlabel('Program size (middle blocks)')7plt.ylabel('Time (seconds)')8plt.title('Experiment 1')9plt.legend()10plt.savefig('resolve.png')11plt.figure()12partial_resolve = np.genfromtxt('partial_resolve', delimiter=',', names=['size', 'time'])13plt.plot(partial_resolve['size'], partial_resolve['time'], label='Execution time for resolve_indirect_jumps on synthetic BIR programs')14plt.xlabel('Program size (middle blocks)')15plt.ylabel('Time (seconds)')16plt.title('Experiment 2')17plt.legend()18plt.savefig('partial_resolve.png')19plt.figure()20constant_resolve = np.genfromtxt('constant_resolve', delimiter=',', names=['size', 'time'])21plt.plot(constant_resolve['size'], constant_resolve['time'], label='Execution time for resolve_indirect_jumps on synthetic BIR programs')22plt.xlabel('Program size (middle blocks)')23plt.ylabel('Time (seconds)')24plt.title('Experiment 3')25plt.legend()26plt.savefig('constant_resolve.png')27plt.figure()28transfer = np.genfromtxt('transfer', delimiter=',', names=['size', 'time'])29plt.plot(transfer['size'], transfer['time'], label='Execution time for transfer_contract on synthetic BIR programs')30plt.xlabel('Program size (middle blocks)')31plt.ylabel('Time (seconds)')32plt.title('Experiment 4')33plt.legend()34plt.savefig('transfer.png')...

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