def test_get_torque(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'torque')
conf_setter('TORQUE_JOB_OWNER', '')
obs._get_torque(self.conf)
self.assertIsNone(obs.trq_owner)
def test_get_torque(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'torque')
conf_setter('TORQUE_JOB_OWNER', '')
obs._get_torque(self.conf)
self.assertIsNone(obs.trq_owner)
def test_get_postgres(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'postgres')
conf_setter('PASSWORD', '')
conf_setter('ADMIN_PASSWORD', '')
obs._get_postgres(self.conf)
self.assertIsNone(obs.password)
self.assertIsNone(obs.admin_password)
def test_get_postgres(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'postgres')
conf_setter('PASSWORD', '')
conf_setter('ADMIN_PASSWORD', '')
obs._get_postgres(self.conf)
self.assertIsNone(obs.password)
self.assertIsNone(obs.admin_password)
def _test_wrapper_remote(func):
"""Execute a function on a remote ipengine"""
from IPython.parallel import Client
from qiita_core.configuration_manager import ConfigurationManager
config = ConfigurationManager()
c = Client(profile=config.ipython_default)
bv = c.load_balanced_view()
return _ipy_wait(bv.apply_async(func))
def test_get_portal(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'portal')
# Default portal_dir
conf_setter('PORTAL_DIR', '')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "")
# Portal dir does not start with /
conf_setter('PORTAL_DIR', 'gold_portal')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "/gold_portal")
# Portal dir endswith /
conf_setter('PORTAL_DIR', '/gold_portal/')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "/gold_portal")
def redis_test(**kwargs):
"""Put and get a key from redis"""
from uuid import uuid4
from redis import Redis
from qiita_core.configuration_manager import ConfigurationManager
config = ConfigurationManager()
r_client = Redis(host=config.redis_host,
port=config.redis_port,
password=config.redis_password,
db=config.redis_db)
key = str(uuid4())
r_client.set(key, 42, ex=1)
return int(r_client.get(key))
def test_get_portal(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'portal')
# Default portal_dir
conf_setter('PORTAL_DIR', '')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "")
# Portal dir does not start with /
conf_setter('PORTAL_DIR', 'gold_portal')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "/gold_portal")
# Portal dir endswith /
conf_setter('PORTAL_DIR', '/gold_portal/')
obs._get_portal(self.conf)
self.assertEqual(obs.portal_dir, "/gold_portal")
def generate_plugin_releases():
"""Generate releases for plugins
"""
ARCHIVE = qdb.archive.Archive
qiita_config = ConfigurationManager()
working_dir = qiita_config.working_dir
commands = [
c for s in qdb.software.Software.iter(active=True) for c in s.commands
if c.post_processing_cmd is not None
]
tnow = datetime.now()
ts = tnow.strftime('%m%d%y-%H%M%S')
tgz_dir = join(working_dir, 'releases', 'archive')
create_nested_path(tgz_dir)
tgz_dir_release = join(tgz_dir, ts)
create_nested_path(tgz_dir_release)
for cmd in commands:
cmd_name = cmd.name
mschemes = [
v for _, v in ARCHIVE.merging_schemes().items() if cmd_name in v
]
for ms in mschemes:
ms_name = sub('[^0-9a-zA-Z]+', '', ms)
ms_fp = join(tgz_dir_release, ms_name)
create_nested_path(ms_fp)
pfp = join(ms_fp, 'archive.json')
archives = {
k: loads(v)
for k, v in ARCHIVE.retrieve_feature_values(
archive_merging_scheme=ms).items() if v != ''
}
with open(pfp, 'w') as f:
dump(archives, f)
# now let's run the post_processing_cmd
ppc = cmd.post_processing_cmd
# concatenate any other parameters into a string
params = ' '.join(
["%s=%s" % (k, v) for k, v in ppc['script_params'].items()])
# append archives file and output dir parameters
params = ("%s --fp_archive=%s --output_dir=%s" %
(params, pfp, ms_fp))
ppc_cmd = "%s %s %s" % (ppc['script_env'], ppc['script_path'],
params)
p_out, p_err, rv = qdb.processing_job._system_call(ppc_cmd)
p_out = p_out.rstrip()
if rv != 0:
raise ValueError('Error %d: %s' % (rv, p_out))
p_out = loads(p_out)
# tgz-ing all files
tgz_name = join(tgz_dir, 'archive-%s-building.tgz' % ts)
tgz_name_final = join(tgz_dir, 'archive.tgz')
with topen(tgz_name, "w|gz") as tgz:
tgz.add(tgz_dir_release, arcname=basename(tgz_dir_release))
# getting the release md5
with open(tgz_name, "rb") as f:
md5sum = md5()
for c in iter(lambda: f.read(4096), b""):
md5sum.update(c)
rename(tgz_name, tgz_name_final)
vals = [('filepath', tgz_name_final[len(working_dir):], r_client.set),
('md5sum', md5sum.hexdigest(), r_client.set),
('time', tnow.strftime('%m-%d-%y %H:%M:%S'), r_client.set)]
for k, v, f in vals:
redis_key = 'release-archive:%s' % k
# important to "flush" variables to avoid errors
r_client.delete(redis_key)
f(redis_key, v)
def generate_biom_and_metadata_release(study_status='public'):
"""Generate a list of biom/meatadata filepaths and a tgz of those files
Parameters
----------
study_status : str, optional
The study status to search for. Note that this should always be set
to 'public' but having this exposed helps with testing. The other
options are 'private' and 'sandbox'
"""
studies = qdb.study.Study.get_by_status(study_status)
qiita_config = ConfigurationManager()
working_dir = qiita_config.working_dir
portal = qiita_config.portal
bdir = qdb.util.get_db_files_base_dir()
time = datetime.now().strftime('%m-%d-%y %H:%M:%S')
data = []
for s in studies:
# [0] latest is first, [1] only getting the filepath
sample_fp = relpath(s.sample_template.get_filepaths()[0][1], bdir)
for a in s.artifacts(artifact_type='BIOM'):
if a.processing_parameters is None or a.visibility != study_status:
continue
merging_schemes, parent_softwares = a.merging_scheme
software = a.processing_parameters.command.software
software = '%s v%s' % (software.name, software.version)
for x in a.filepaths:
if x['fp_type'] != 'biom' or 'only-16s' in x['fp']:
continue
fp = relpath(x['fp'], bdir)
for pt in a.prep_templates:
categories = pt.categories()
platform = ''
target_gene = ''
if 'platform' in categories:
platform = ', '.join(
set(pt.get_category('platform').values()))
if 'target_gene' in categories:
target_gene = ', '.join(
set(pt.get_category('target_gene').values()))
for _, prep_fp in pt.get_filepaths():
if 'qiime' not in prep_fp:
break
prep_fp = relpath(prep_fp, bdir)
# format: (biom_fp, sample_fp, prep_fp, qiita_artifact_id,
# platform, target gene, merging schemes,
# artifact software/version,
# parent sofware/version)
data.append(
(fp, sample_fp, prep_fp, a.id, platform, target_gene,
merging_schemes, software, parent_softwares))
# writing text and tgz file
ts = datetime.now().strftime('%m%d%y-%H%M%S')
tgz_dir = join(working_dir, 'releases')
create_nested_path(tgz_dir)
tgz_name = join(tgz_dir, '%s-%s-building.tgz' % (portal, study_status))
tgz_name_final = join(tgz_dir, '%s-%s.tgz' % (portal, study_status))
txt_lines = [
"biom fp\tsample fp\tprep fp\tqiita artifact id\tplatform\t"
"target gene\tmerging scheme\tartifact software\tparent software"
]
with topen(tgz_name, "w|gz") as tgz:
for biom_fp, sample_fp, prep_fp, aid, pform, tg, ms, asv, psv in data:
txt_lines.append(
"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s" %
(biom_fp, sample_fp, prep_fp, aid, pform, tg, ms, asv, psv))
tgz.add(join(bdir, biom_fp), arcname=biom_fp, recursive=False)
tgz.add(join(bdir, sample_fp), arcname=sample_fp, recursive=False)
tgz.add(join(bdir, prep_fp), arcname=prep_fp, recursive=False)
info = TarInfo(name='%s-%s-%s.txt' % (portal, study_status, ts))
txt_hd = BytesIO()
txt_hd.write(bytes('\n'.join(txt_lines), 'ascii'))
txt_hd.seek(0)
info.size = len(txt_hd.read())
txt_hd.seek(0)
tgz.addfile(tarinfo=info, fileobj=txt_hd)
with open(tgz_name, "rb") as f:
md5sum = md5()
for c in iter(lambda: f.read(4096), b""):
md5sum.update(c)
rename(tgz_name, tgz_name_final)
vals = [('filepath', tgz_name_final[len(working_dir):], r_client.set),
('md5sum', md5sum.hexdigest(), r_client.set),
('time', time, r_client.set)]
for k, v, f in vals:
redis_key = '%s:release:%s:%s' % (portal, study_status, k)
# important to "flush" variables to avoid errors
r_client.delete(redis_key)
f(redis_key, v)
def test_init(self):
obs = ConfigurationManager()
# Main section
self.assertEqual(obs.conf_fp, self.conf_fp)
self.assertTrue(obs.test_environment)
self.assertEqual(obs.base_data_dir, "/tmp/")
self.assertEqual(obs.log_dir, "/tmp/")
self.assertEqual(obs.base_url, "https://localhost")
self.assertEqual(obs.max_upload_size, 100)
self.assertTrue(obs.require_approval)
self.assertEqual(obs.qiita_env, "source activate qiita")
self.assertEqual(obs.private_launcher, 'qiita-private-launcher')
self.assertEqual(obs.plugin_launcher, "qiita-plugin-launcher")
self.assertEqual(obs.plugin_dir, "/tmp/")
self.assertEqual(
obs.valid_upload_extension,
["fastq", "fastq.gz", "txt", "tsv", "sff", "fna", "qual"])
self.assertEqual(obs.certificate_file, "/tmp/server.cert")
self.assertEqual(obs.cookie_secret, "SECRET")
self.assertEqual(obs.key_file, "/tmp/server.key")
# Torque section
self.assertEqual(obs.trq_owner, "*****@*****.**")
self.assertEqual(obs.trq_poll_val, 15)
self.assertEqual(obs.trq_dependency_q_cnt, 2)
# Postgres section
self.assertEqual(obs.user, "postgres")
self.assertEqual(obs.admin_user, "postgres")
self.assertEqual(obs.password, "andanotherpwd")
self.assertEqual(obs.admin_password, "thishastobesecure")
self.assertEqual(obs.database, "qiita_test")
self.assertEqual(obs.host, "localhost")
self.assertEqual(obs.port, 5432)
# Redis section
self.assertEqual(obs.redis_host, "localhost")
self.assertEqual(obs.redis_password, "anotherpassword")
self.assertEqual(obs.redis_db, 13)
self.assertEqual(obs.redis_port, 6379)
# SMTP section
self.assertEqual(obs.smtp_host, "localhost")
self.assertEqual(obs.smtp_port, 25)
self.assertEqual(obs.smtp_user, "qiita")
self.assertEqual(obs.smtp_password, "supersecurepassword")
self.assertFalse(obs.smtp_ssl)
self.assertEqual(obs.smtp_email, "*****@*****.**")
# EBI section
self.assertEqual(obs.ebi_seq_xfer_user, "Webin-41528")
self.assertEqual(obs.ebi_seq_xfer_pass, "passwordforebi")
self.assertEqual(obs.ebi_seq_xfer_url, "webin.ebi.ac.uk")
self.assertEqual(
obs.ebi_dropbox_url,
"https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/")
self.assertEqual(obs.ebi_center_name, "qiita-test")
self.assertEqual(obs.ebi_organization_prefix, "example_organization")
# VAMPS section
self.assertEqual(obs.vamps_user, "user")
self.assertEqual(obs.vamps_pass, "password")
self.assertEqual(obs.vamps_url,
"https://vamps.mbl.edu/mobe_workshop/getfile.php")
# Portal section
self.assertEqual(obs.portal_fp, "/tmp/portal.cfg")
self.assertEqual(obs.portal, "QIITA")
self.assertEqual(obs.portal_dir, "/portal")
# iframe section
self.assertEqual(obs.iframe_qiimp, "https://localhost:8898/")
def test_get_main(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'main')
conf_setter('COOKIE_SECRET', '')
conf_setter('JWT_SECRET', '')
conf_setter('BASE_DATA_DIR', '')
conf_setter('PLUGIN_DIR', '')
conf_setter('CERTIFICATE_FILE', '')
conf_setter('KEY_FILE', '')
conf_setter('QIITA_ENV', '')
# Warning raised if No files will be allowed to be uploaded
# Warning raised if no cookie_secret
with warnings.catch_warnings(record=True) as warns:
obs._get_main(self.conf)
obs_warns = [str(w.message) for w in warns]
exp_warns = [
'Random cookie secret generated.',
'Random JWT secret generated. Non Public Artifact '
'Download Links will expire upon system restart.'
]
self.assertCountEqual(obs_warns, exp_warns)
self.assertNotEqual(obs.cookie_secret, "SECRET")
# Test default base_data_dir
self.assertTrue(
obs.base_data_dir.endswith("/qiita_db/support_files/test_data"))
# Test default plugin dir
self.assertTrue(obs.plugin_dir.endswith("/.qiita_plugins"))
# Default certificate_file
self.assertTrue(
obs.certificate_file.endswith(
"/qiita_core/support_files/server.crt"))
# Default key_file
self.assertTrue(
obs.key_file.endswith("/qiita_core/support_files/server.key"))
# BASE_DATA_DIR does not exist
conf_setter('BASE_DATA_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# WORKING_DIR does not exist
conf_setter('BASE_DATA_DIR', '/tmp')
conf_setter('WORKING_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# PLUGIN_DIR does not exist
conf_setter('WORKING_DIR', '/tmp')
conf_setter('PLUGIN_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# No files can be uploaded
conf_setter('PLUGIN_DIR', '/tmp')
conf_setter('VALID_UPLOAD_EXTENSION', '')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
self.assertEqual(obs.qiita_env, "")
def test_init_error(self):
with open(self.conf_fp, 'w') as f:
f.write("\n")
with self.assertRaises(MissingConfigSection):
ConfigurationManager()
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -----------------------------------------------------------------------------
from __future__ import division
from redis import Redis
from qiita_core.configuration_manager import ConfigurationManager
qiita_config = ConfigurationManager()
r_client = Redis(host=qiita_config.redis_host,
port=qiita_config.redis_port,
password=qiita_config.redis_password,
db=qiita_config.redis_db)
def test_get_main(self):
obs = ConfigurationManager()
conf_setter = partial(self.conf.set, 'main')
conf_setter('COOKIE_SECRET', '')
conf_setter('BASE_DATA_DIR', '')
conf_setter('PLUGIN_DIR', '')
conf_setter('CERTIFICATE_FILE', '')
conf_setter('KEY_FILE', '')
conf_setter('QIITA_ENV', '')
# Warning raised if No files will be allowed to be uploaded
# Warning raised if no cookie_secret
with warnings.catch_warnings(record=True) as warns:
obs._get_main(self.conf)
obs_warns = [str(w.message) for w in warns]
exp_warns = ['Random cookie secret generated.']
self.assertItemsEqual(obs_warns, exp_warns)
self.assertNotEqual(obs.cookie_secret, "SECRET")
# Test default base_data_dir
self.assertTrue(
obs.base_data_dir.endswith("/qiita_db/support_files/test_data"))
# Test default plugin dir
self.assertTrue(obs.plugin_dir.endswith("/.qiita_plugins"))
# Default certificate_file
self.assertTrue(
obs.certificate_file.endswith(
"/qiita_core/support_files/server.crt"))
# Default key_file
self.assertTrue(
obs.key_file.endswith("/qiita_core/support_files/server.key"))
# BASE_DATA_DIR does not exist
conf_setter('BASE_DATA_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# WORKING_DIR does not exist
conf_setter('BASE_DATA_DIR', '/tmp')
conf_setter('WORKING_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# PLUGIN_DIR does not exist
conf_setter('WORKING_DIR', '/tmp')
conf_setter('PLUGIN_DIR', '/surprised/if/this/dir/exists')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
# No files can be uploaded
conf_setter('PLUGIN_DIR', '/tmp')
conf_setter('VALID_UPLOAD_EXTENSION', '')
with self.assertRaises(ValueError):
obs._get_main(self.conf)
self.assertEqual(obs.qiita_env, "")
def generate_biom_and_metadata_release(study_status='public'):
"""Generate a list of biom/meatadata filepaths and a tgz of those files
Parameters
----------
study_status : str, optional
The study status to search for. Note that this should always be set
to 'public' but having this exposed helps with testing. The other
options are 'private' and 'sandbox'
"""
studies = qdb.study.Study.get_by_status(study_status)
qiita_config = ConfigurationManager()
working_dir = qiita_config.working_dir
portal = qiita_config.portal
bdir = qdb.util.get_db_files_base_dir()
time = datetime.now().strftime('%m-%d-%y %H:%M:%S')
data = []
for s in studies:
# [0] latest is first, [1] only getting the filepath
sample_fp = relpath(s.sample_template.get_filepaths()[0][1], bdir)
for a in s.artifacts(artifact_type='BIOM'):
if a.processing_parameters is None:
continue
cmd_name = a.processing_parameters.command.name
# this loop is necessary as in theory an artifact can be
# generated from multiple prep info files
human_cmd = []
for p in a.parents:
pp = p.processing_parameters
pp_cmd_name = pp.command.name
if pp_cmd_name == 'Trimming':
human_cmd.append('%s @ %s' % (
cmd_name, str(pp.values['length'])))
else:
human_cmd.append('%s, %s' % (cmd_name, pp_cmd_name))
human_cmd = ', '.join(human_cmd)
for _, fp, fp_type in a.filepaths:
if fp_type != 'biom' or 'only-16s' in fp:
continue
fp = relpath(fp, bdir)
# format: (biom_fp, sample_fp, prep_fp, qiita_artifact_id,
# human readable name)
for pt in a.prep_templates:
for _, prep_fp in pt.get_filepaths():
if 'qiime' not in prep_fp:
break
prep_fp = relpath(prep_fp, bdir)
data.append((fp, sample_fp, prep_fp, a.id, human_cmd))
# writing text and tgz file
ts = datetime.now().strftime('%m%d%y-%H%M%S')
tgz_dir = join(working_dir, 'releases')
if not exists(tgz_dir):
makedirs(tgz_dir)
tgz_name = join(tgz_dir, '%s-%s-building.tgz' % (portal, study_status))
tgz_name_final = join(tgz_dir, '%s-%s.tgz' % (portal, study_status))
txt_hd = StringIO()
with topen(tgz_name, "w|gz") as tgz:
# writing header for txt
txt_hd.write(
"biom_fp\tsample_fp\tprep_fp\tqiita_artifact_id\tcommand\n")
for biom_fp, sample_fp, prep_fp, artifact_id, human_cmd in data:
txt_hd.write("%s\t%s\t%s\t%s\t%s\n" % (
biom_fp, sample_fp, prep_fp, artifact_id, human_cmd))
tgz.add(join(bdir, biom_fp), arcname=biom_fp, recursive=False)
tgz.add(join(bdir, sample_fp), arcname=sample_fp, recursive=False)
tgz.add(join(bdir, prep_fp), arcname=prep_fp, recursive=False)
txt_hd.seek(0)
info = TarInfo(name='%s-%s-%s.txt' % (portal, study_status, ts))
info.size = len(txt_hd.buf)
tgz.addfile(tarinfo=info, fileobj=txt_hd)
with open(tgz_name, "rb") as f:
md5sum = md5()
for c in iter(lambda: f.read(4096), b""):
md5sum.update(c)
rename(tgz_name, tgz_name_final)
vals = [
('filepath', tgz_name_final[len(working_dir):], r_client.set),
('md5sum', md5sum.hexdigest(), r_client.set),
('time', time, r_client.set)]
for k, v, f in vals:
redis_key = '%s:release:%s:%s' % (portal, study_status, k)
# important to "flush" variables to avoid errors
r_client.delete(redis_key)
f(redis_key, v)