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How to use start_container method in localstack
Best Python code snippet using localstack_python
service_test.py
Source:service_test.py 
...24 Service(name='foo', ports=['8000'])25 def test_containers(self):26 foo = self.create_service('foo')27 bar = self.create_service('bar')28 foo.start_container()29 self.assertEqual(len(foo.containers()), 1)30 self.assertEqual(foo.containers()[0].name, 'figtest_foo_1')31 self.assertEqual(len(bar.containers()), 0)32 bar.start_container()33 bar.start_container()34 self.assertEqual(len(foo.containers()), 1)35 self.assertEqual(len(bar.containers()), 2)36 names = [c.name for c in bar.containers()]37 self.assertIn('figtest_bar_1', names)38 self.assertIn('figtest_bar_2', names)39 def test_containers_one_off(self):40 db = self.create_service('db')41 container = db.create_container(one_off=True)42 self.assertEqual(db.containers(stopped=True), [])43 self.assertEqual(db.containers(one_off=True, stopped=True), [container])44 def test_project_is_added_to_container_name(self):45 service = self.create_service('web')46 service.start_container()47 self.assertEqual(service.containers()[0].name, 'figtest_web_1')48 def test_start_stop(self):49 service = self.create_service('scalingtest')50 self.assertEqual(len(service.containers(stopped=True)), 0)51 service.create_container()52 self.assertEqual(len(service.containers()), 0)53 self.assertEqual(len(service.containers(stopped=True)), 1)54 service.start()55 self.assertEqual(len(service.containers()), 1)56 self.assertEqual(len(service.containers(stopped=True)), 1)57 service.stop(timeout=1)58 self.assertEqual(len(service.containers()), 0)59 self.assertEqual(len(service.containers(stopped=True)), 1)60 service.stop(timeout=1)61 self.assertEqual(len(service.containers()), 0)62 self.assertEqual(len(service.containers(stopped=True)), 1)63 def test_kill_remove(self):64 service = self.create_service('scalingtest')65 service.start_container()66 self.assertEqual(len(service.containers()), 1)67 service.remove_stopped()68 self.assertEqual(len(service.containers()), 1)69 service.kill()70 self.assertEqual(len(service.containers()), 0)71 self.assertEqual(len(service.containers(stopped=True)), 1)72 service.remove_stopped()73 self.assertEqual(len(service.containers(stopped=True)), 0)74 def test_create_container_with_one_off(self):75 db = self.create_service('db')76 container = db.create_container(one_off=True)77 self.assertEqual(container.name, 'figtest_db_run_1')78 def test_create_container_with_one_off_when_existing_container_is_running(self):79 db = self.create_service('db')80 db.start()81 container = db.create_container(one_off=True)82 self.assertEqual(container.name, 'figtest_db_run_1')83 def test_create_container_with_unspecified_volume(self):84 service = self.create_service('db', volumes=['/var/db'])85 container = service.create_container()86 service.start_container(container)87 self.assertIn('/var/db', container.inspect()['Volumes'])88 def test_recreate_containers(self):89 service = self.create_service(90 'db',91 environment={'FOO': '1'},92 volumes=['/var/db'],93 entrypoint=['ps'],94 command=['ax']95 )96 old_container = service.create_container()97 self.assertEqual(old_container.dictionary['Config']['Entrypoint'], ['ps'])98 self.assertEqual(old_container.dictionary['Config']['Cmd'], ['ax'])99 self.assertIn('FOO=1', old_container.dictionary['Config']['Env'])100 self.assertEqual(old_container.name, 'figtest_db_1')101 service.start_container(old_container)102 volume_path = old_container.inspect()['Volumes']['/var/db']103 num_containers_before = len(self.client.containers(all=True))104 service.options['environment']['FOO'] = '2'105 (intermediate, new) = service.recreate_containers()106 self.assertEqual(len(intermediate), 1)107 self.assertEqual(len(new), 1)108 new_container = new[0]109 intermediate_container = intermediate[0]110 self.assertEqual(intermediate_container.dictionary['Config']['Entrypoint'], ['echo'])111 self.assertEqual(new_container.dictionary['Config']['Entrypoint'], ['ps'])112 self.assertEqual(new_container.dictionary['Config']['Cmd'], ['ax'])113 self.assertIn('FOO=2', new_container.dictionary['Config']['Env'])114 self.assertEqual(new_container.name, 'figtest_db_1')115 service.start_container(new_container)116 self.assertEqual(new_container.inspect()['Volumes']['/var/db'], volume_path)117 self.assertEqual(len(self.client.containers(all=True)), num_containers_before + 1)118 self.assertNotEqual(old_container.id, new_container.id)119 def test_start_container_passes_through_options(self):120 db = self.create_service('db')121 db.start_container(environment={'FOO': 'BAR'})122 self.assertEqual(db.containers()[0].environment['FOO'], 'BAR')123 def test_start_container_inherits_options_from_constructor(self):124 db = self.create_service('db', environment={'FOO': 'BAR'})125 db.start_container()126 self.assertEqual(db.containers()[0].environment['FOO'], 'BAR')127 def test_start_container_creates_links(self):128 db = self.create_service('db')129 web = self.create_service('web', links=[(db, None)])130 db.start_container()131 web.start_container()132 self.assertIn('figtest_db_1', web.containers()[0].links())133 self.assertIn('db_1', web.containers()[0].links())134 def test_start_container_creates_links_with_names(self):135 db = self.create_service('db')136 web = self.create_service('web', links=[(db, 'custom_link_name')])137 db.start_container()138 web.start_container()139 self.assertIn('custom_link_name', web.containers()[0].links())140 def test_start_normal_container_does_not_create_links_to_its_own_service(self):141 db = self.create_service('db')142 c1 = db.start_container()143 c2 = db.start_container()144 self.assertNotIn(c1.name, c2.links())145 def test_start_one_off_container_creates_links_to_its_own_service(self):146 db = self.create_service('db')147 c1 = db.start_container()148 c2 = db.start_container(one_off=True)149 self.assertIn(c1.name, c2.links())150 def test_start_container_builds_images(self):151 service = Service(152 name='test',153 client=self.client,154 build='tests/fixtures/simple-dockerfile',155 project='figtest',156 )157 container = service.start_container()158 container.wait()159 self.assertIn('success', container.logs())160 self.assertEqual(len(self.client.images(name='figtest_test')), 1)161 def test_start_container_uses_tagged_image_if_it_exists(self):162 self.client.build('tests/fixtures/simple-dockerfile', tag='figtest_test')163 service = Service(164 name='test',165 client=self.client,166 build='this/does/not/exist/and/will/throw/error',167 project='figtest',168 )169 container = service.start_container()170 container.wait()171 self.assertIn('success', container.logs())172 def test_start_container_creates_ports(self):173 service = self.create_service('web', ports=[8000])174 container = service.start_container().inspect()175 self.assertEqual(list(container['NetworkSettings']['Ports'].keys()), ['8000/tcp'])176 self.assertNotEqual(container['NetworkSettings']['Ports']['8000/tcp'][0]['HostPort'], '8000')177 def test_start_container_stays_unpriviliged(self):178 service = self.create_service('web')179 container = service.start_container().inspect()180 self.assertEqual(container['HostConfig']['Privileged'], False)181 def test_start_container_becomes_priviliged(self):182 service = self.create_service('web', privileged = True)183 container = service.start_container().inspect()184 self.assertEqual(container['HostConfig']['Privileged'], True)185 def test_expose_does_not_publish_ports(self):186 service = self.create_service('web', expose=[8000])187 container = service.start_container().inspect()188 self.assertEqual(container['NetworkSettings']['Ports'], {'8000/tcp': None})189 def test_start_container_creates_port_with_explicit_protocol(self):190 service = self.create_service('web', ports=['8000/udp'])191 container = service.start_container().inspect()192 self.assertEqual(list(container['NetworkSettings']['Ports'].keys()), ['8000/udp'])193 def test_start_container_creates_fixed_external_ports(self):194 service = self.create_service('web', ports=['8000:8000'])195 container = service.start_container().inspect()196 self.assertIn('8000/tcp', container['NetworkSettings']['Ports'])197 self.assertEqual(container['NetworkSettings']['Ports']['8000/tcp'][0]['HostPort'], '8000')198 def test_start_container_creates_fixed_external_ports_when_it_is_different_to_internal_port(self):199 service = self.create_service('web', ports=['8001:8000'])200 container = service.start_container().inspect()201 self.assertIn('8000/tcp', container['NetworkSettings']['Ports'])202 self.assertEqual(container['NetworkSettings']['Ports']['8000/tcp'][0]['HostPort'], '8001')203 def test_scale(self):204 service = self.create_service('web')205 service.scale(1)206 self.assertEqual(len(service.containers()), 1)207 service.scale(3)208 self.assertEqual(len(service.containers()), 3)209 service.scale(1)210 self.assertEqual(len(service.containers()), 1)211 service.scale(0)212 self.assertEqual(len(service.containers()), 0)213 def test_scale_on_service_that_cannot_be_scaled(self):214 service = self.create_service('web', ports=['8000:8000'])...
test_run_data_managers.py
Source:test_run_data_managers.py
1#!/usr/bin/env python2# Stop pylint complaining from things that are necessary3# for pytest to work.4# pylint: disable=no-self-use,unused-import5import sys6import time7import pytest8import yaml9from docker_for_galaxy import GALAXY_ADMIN_KEY, GALAXY_ADMIN_PASSWORD, GALAXY_ADMIN_USER, start_container # noqa: F401 prevent unused error10from ephemeris import run_data_managers11from ephemeris.run_data_managers import DataManagers12from ephemeris.shed_tools import InstallRepositoryManager13from ephemeris.sleep import galaxy_wait14AUTH_BY = "key"15class TestRunDataManagers(object):16 """This class tests run-data-managers"""17 def test_install_data_managers(self, start_container): # noqa: F811 Prevent start_container unused warning.18 """Install the data_managers on galaxy"""19 container = start_container20 data_managers = [21 dict(name="data_manager_fetch_genome_dbkeys_all_fasta",22 owner="devteam"),23 dict(name="data_manager_sam_fasta_index_builder",24 owner="devteam"),25 dict(name="data_manager_bwa_mem_index_builder",26 owner="devteam")27 ]28 irm = InstallRepositoryManager(container.gi)29 irm.install_repositories(data_managers)30 # Galaxy is restarted because otherwise data tables are not watched.31 container.container.exec_run("supervisorctl restart galaxy:")32 time.sleep(10) # give time for the services to go down33 galaxy_wait(container.url)34 def test_run_data_managers(self, start_container): # noqa: F811 Prevent start_container unused warning.35 """Tests an installation using the command line"""36 container = start_container37 argv = ["run-data-managers"]38 if AUTH_BY == "user":39 argv.extend([40 "--user", GALAXY_ADMIN_USER,41 "-p", GALAXY_ADMIN_PASSWORD,42 ])43 else:44 argv.extend(["-a", GALAXY_ADMIN_KEY])45 argv.extend([46 "-g", container.url,47 "--config", "tests/run_data_managers.yaml.test"48 ])49 sys.argv = argv50 run_data_managers.main()51 def test_run_data_managers_installation_skipped(self, start_container): # noqa: F811 Prevent start_container unused warning.52 container = start_container53 with open("tests/run_data_managers.yaml.test") as config_file:54 configuration = yaml.safe_load(config_file)55 dm = DataManagers(container.gi, configuration)56 install_results = dm.run()57 assert (len(install_results.successful_jobs) == 0)58 assert (len(install_results.skipped_jobs) == 9)59 assert (len(install_results.failed_jobs) == 0)60 def test_run_data_managers_installation_fail(self, start_container, caplog): # noqa: F811 Prevent start_container unused warning.61 container = start_container62 configuration = dict(63 data_managers=[64 dict(65 id="data_manager_fetch_genome_all_fasta_dbkey",66 params=[67 {'dbkey_source|dbkey_source_selector': 'new'},68 {'dbkey_source|dbkey': 'INVALID'},69 {'dbkey_source|dbkey_name': 'INVALID_KEY'},70 {'sequence_name': 'INVALID'},71 {'sequence_id': 'INVALID'},72 {'reference_source|reference_source_selector': 'ncbi'},73 {'reference_source|requested_identifier': 'INVALID0123'}74 ],75 data_table_reload=[76 "all_fasta",77 "__dbkeys__"78 ]79 )80 ]81 )82 dm = DataManagers(container.gi, configuration)83 with pytest.raises(RuntimeError):84 dm.run()85 assert ("HTTP Error 404" in caplog.text)86 assert ("Not all jobs successful! aborting..." in caplog.text)...
sort.py
Source:sort.py
1#! /usr/bin/python2'''Sorts bed/gff file with a respect to strandness'''3import argparse4import sys;5import os;6from collections import defaultdict;7from pybedtools import BedTool;8parser = argparse.ArgumentParser(description='Sorts bed/gff file with a respect to strandness');9parser.add_argument('path', metavar = 'N', nargs = '?', type = str, help = "Path to the bed/gff file to be sorted");10args = parser.parse_args();11def clear_dict(d):12 for v in d.values():13 v[:]=[];14 15 16def flush(chrom_container, start_container):17 for strand, intervals in start_container.items():18 chrom_container[strand].extend(list(sorted(intervals, key = lambda x: x.end)));19 20sortedbed = BedTool(args.path).sort();21if(len(sortedbed) == 0):22 sys.stderr.write("input file is empty\n");23 sys.exit();24chrom_container = defaultdict(list)25start_container = defaultdict(list)26start_container[sortedbed[0].strand].append(sortedbed[0])27chrom = sortedbed[0].chrom;28start = sortedbed[0].start29for interval in sortedbed[1:]:30 if(chrom == interval.chrom):31 if(start == interval.start):32 start_container[interval.strand].append(interval);33 else:34 flush(chrom_container, start_container);35 clear_dict(start_container)36 start = interval.start;37 start_container[interval.strand].append(interval);38 39 else:40 flush(chrom_container, start_container);41 for strand, intervals in chrom_container.items():42 for si in intervals:43 sys.stdout.write(str(si))44 45 chrom = interval.chrom;46 start = interval.start;47 clear_dict(start_container);48 clear_dict(chrom_container);49 start_container[interval.strand].append(interval);50 51else: 52 flush(chrom_container, start_container);53 for strand, intervals in chrom_container.items():54 for si in intervals:...
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