def biomaj_remove(options, config):
'''
Remove a bank
'''
if not options.bank:
return (False, "Bank name is missing")
if options.remove and not options.release:
return (False, "Bank release is missing")
no_log = True
if not options.proxy:
no_log = False
# If removeall, do not set logs as log dir will be deleted
if options.removeall:
no_log = True
bmaj = Bank(options.bank, options=options, no_log=no_log)
if bmaj.is_locked():
return (False, 'Bank is locked due to an other action')
res = True
if options.removeall:
if not options.proxy:
res = bmaj.removeAll(options.force)
return (res, '')
res = biomaj_remove_request(options, config)
else:
if not options.proxy:
res = bmaj.remove(options.release)
Notify.notifyBankAction(bmaj)
return (res, '')
res = biomaj_remove_request(options, config)
if not res:
return (False, 'Failed to send removal request')
return (True, 'Bank removal request sent')
def test_directhttp_release(self):
b = Bank('directhttp')
res = b.update()
self.assertTrue(b.session.get('update'))
self.assertTrue(
os.path.exists(b.session.get_full_release_directory() +
'/flat/debian/README.html'))
def test_update_hardlinks(self):
"""
Update a bank twice with hard links^. Files copied from previous release
must be links.
"""
b = Bank('local')
b.config.set('keep.old.version', '3')
b.config.set('use_hardlinks', '1')
# First update
b.update()
self.assertTrue(b.session.get('update'))
old_release = b.session.get_full_release_directory()
# Update test.fasta to force update (not that this file is modified in the
# source tree)
remote_file = b.session.config.get('remote.dir') + 'test.fasta.gz'
stat = os.stat(remote_file)
one_day = 3600 * 24
os.utime(remote_file, (stat.st_atime + one_day, stat.st_atime + one_day))
# Second update
b.update()
self.assertTrue(b.session.get('update'))
new_release = b.session.get_full_release_directory()
# Test that test2.fasta in both release are the same file (we can't use
# test.fasta because it is uncompressed and then not the same file)
file_old_release = os.path.join(old_release, 'flat', 'test2.fasta')
file_new_release = os.path.join(new_release, 'flat', 'test2.fasta')
try:
self.assertTrue(os.path.samefile(file_old_release, file_new_release))
except AssertionError:
msg = "In %s: copy worked but hardlinks were not used." % self.id()
logging.info(msg)
# Restore date (otherwise repeated tests fail)
os.utime(remote_file, (stat.st_atime, stat.st_atime))
def test_computed_ref_release(self):
b = Bank('computed2')
res = b.update(True)
self.assertTrue(b.session.get('update'))
b2 = Bank('computed2')
res = b2.update(True)
self.assertFalse(b2.session.get('update'))
def biomaj_bank_update(options):
'''
Update a bank
'''
if not options.bank:
return (False, "Bank name is missing")
banks = options.bank.split(',')
gres = True
msg = ''
for bank in banks:
options.bank = bank
bmaj = Bank(bank, options=options, no_log=True)
if bmaj.is_locked():
return (False, 'Bank is locked due to an other action')
check_status = bmaj.check()
if not check_status:
msg += 'Skip bank ' + options.bank + ': wrong config\n'
gres = False
continue
else:
msg += 'Bank update request sent for ' + options.bank + '\n'
if not options.proxy:
res = bmaj.update(depends=True)
return (res, '')
res = biomaj_bank_update_request(options)
if not res:
msg += 'Failed to send update request for ' + options.bank + '\n'
if not gres:
return (False, msg)
return (True, msg)
def biomaj_bank_repair(options, config):
'''
Repair a bank
'''
if not options.bank:
return (False, "Bank name is missing")
banks = options.bank.split(',')
gres = True
msg = ''
for bank in banks:
options.bank = bank
no_log = True
if not options.proxy:
no_log = False
# logging.debug('Options: '+str(options.__dict__))
bmaj = Bank(bank, options=options, no_log=no_log)
check_status = bmaj.check()
if not check_status:
msg += 'Skip bank ' + options.bank + ': wrong config\n'
gres = False
continue
else:
msg += 'Bank repair request sent for ' + options.bank + '\n'
if not options.proxy:
res = bmaj.repair()
Notify.notifyBankAction(bmaj)
else:
res = biomaj_bank_repair_request(options, config)
if not res:
msg += 'Failed to send repair request for ' + options.bank + '\n'
gres = False
if not gres:
return (False, msg)
return (True, msg)
def biomaj_remove(options):
'''
Remove a bank
'''
if not options.bank:
return (False, "Bank name is missing")
if options.remove and not options.release:
return (False, "Bank release is missing")
bmaj = Bank(options.bank, options=options, no_log=True)
if bmaj.is_locked():
return (False, 'Bank is locked due to an other action')
res = True
if options.removeall:
if not options.proxy:
res = bmaj.removeAll(options.force)
return (res, '')
res = biomaj_remove_request(options)
else:
if not options.proxy:
res = bmaj.remove(options.release)
return (res, '')
res = biomaj_remove_request(options)
if not res:
return (False, 'Failed to send removal request')
return (True, 'Bank removal request sent')
def test_extract_release_from_file_content(self):
b = Bank("local")
b.load_session(UpdateWorkflow.FLOW)
b.session.config.set("release.file", "test_100\.txt")
b.session.config.set("release.regexp", "Release\s*(\d+)")
w = UpdateWorkflow(b)
w.wf_release()
self.assertTrue(b.session.get("release") == "103")
def test_new_session(self):
"""
Checks an empty session is created
"""
b = Bank("alu")
b.load_session(UpdateWorkflow.FLOW)
for key in b.session._session["status"].keys():
self.assertFalse(b.session.get_status(key))
def test_extract_release_from_file_content(self):
b = Bank('local')
b.load_session(UpdateWorkflow.FLOW)
b.session.config.set('release.file', 'test_100\.txt')
b.session.config.set('release.regexp', 'Release\s*(\d+)')
w = UpdateWorkflow(b)
w.wf_release()
self.assertTrue(b.session.get('release') == '103')
def bank_status(request):
bank = Bank(request.matchdict['id'], no_log=True)
if not can_read_bank(request, bank.bank):
return HTTPForbidden('Not authorized to access this resource')
if 'status' not in bank.bank:
return HTTPNotFound('no current status')
return bank.get_status()
def test_new_session(self):
'''
Checks an empty session is created
'''
b = Bank('alu')
b.load_session(UpdateWorkflow.FLOW)
for key in b.session._session['status'].keys():
self.assertFalse(b.session.get_status(key))
def test_new_session(self):
'''
Checks an empty session is created
'''
b = Bank('alu')
b.load_session(UpdateWorkflow.FLOW)
for key in b.session._session['status'].keys():
self.assertFalse(b.session.get_status(key))
def test_computed_nofile(self):
b = Bank('computed2')
b.load_session(UpdateWorkflow.FLOW)
b.session.config.set('protocol', 'none')
b.session.config.set('sub1.files.move', 'flat/test_.*')
res = b.update(True)
self.assertTrue(res)
self.assertTrue(os.path.exists(b.session.get_full_release_directory()+'/sub1/flat/test_100.txt'))
def test_computed_ref_release(self):
b = Bank('computed2')
res = b.update(True)
b2 = Bank('sub1')
b2release = b2.bank['production'][len(b2.bank['production'])-1]['release']
brelease = b.bank['production'][len(b.bank['production'])-1]['release']
self.assertTrue(res)
self.assertTrue(brelease == b2release)
def test_computed_ref_release(self):
b = Bank("computed2")
res = b.update(True)
b2 = Bank("sub1")
b2release = b2.bank["production"][len(b2.bank["production"]) - 1]["release"]
brelease = b.bank["production"][len(b.bank["production"]) - 1]["release"]
self.assertTrue(res)
self.assertTrue(brelease == b2release)
def test_extract_release_from_file_content(self):
b = Bank('local')
b.load_session(UpdateWorkflow.FLOW)
b.session.config.set('release.file', 'test_100\.txt')
b.session.config.set('release.regexp', 'Release\s*(\d+)')
w = UpdateWorkflow(b)
w.wf_release()
self.assertTrue(b.session.get('release') == '103')
def test_remoterelease_check(self):
b = Bank('local')
b.load_session(ReleaseCheckWorkflow.FLOW)
b.session.config.set('release.file', 'test_(\d+)\.txt')
b.session.config.set('release.regexp', '')
workflow = ReleaseCheckWorkflow(b)
res = workflow.start()
remoterelease = b.session.get('remoterelease')
self.assertTrue(remoterelease == '100')
def test_stats(self):
b = Bank("local")
b.update()
rel = b.session.get("release")
stats = Bank.get_banks_disk_usage()
self.assertTrue(stats[0]["size"] > 0)
for release in stats[0]["releases"]:
if release["name"] == rel:
self.assertTrue(release["size"] > 0)
def test_stats(self):
b = Bank('local')
b.update()
rel = b.session.get('release')
stats = Bank.get_banks_disk_usage()
self.assertTrue(stats[0]['size'] > 0)
for release in stats[0]['releases']:
if release['name'] == rel:
self.assertTrue(release['size'] > 0)
def test_remoterelease_check(self):
b = Bank('local')
b.load_session(ReleaseCheckWorkflow.FLOW)
b.session.config.set('release.file', 'test_(\d+)\.txt')
b.session.config.set('release.regexp', '')
workflow = ReleaseCheckWorkflow(b)
res = workflow.start()
remoterelease = b.session.get('remoterelease')
self.assertTrue(remoterelease == '100')
def biomaj_owner(options):
'''
Bank ownership management
'''
if not options.bank:
return (False, "Bank option is missing")
bank = Bank(options.bank, options=options, no_log=True)
bank.set_owner(options.owner)
return (True, None)
def test_stats(self):
b = Bank('local')
b.update()
rel = b.session.get('release')
stats = Bank.get_banks_disk_usage()
self.assertTrue(stats[0]['size']>0)
for release in stats[0]['releases']:
if release['name'] == rel:
self.assertTrue(release['size']>0)
def bank_locked(request):
bank = Bank(request.matchdict['id'], no_log=True)
if not can_read_bank(request, bank.bank):
return HTTPForbidden('Not authorized to access this resource')
if bank.is_locked():
return {'status': 1}
else:
return {'status': 0}
def biomaj_check(options):
'''
Check bank properties
'''
if not options.bank:
return (False, "Bank name is missing")
bank = Bank(options.bank, options=options, no_log=True)
msg = options.bank + " check: " + str(bank.check()) + "\n"
return (True, msg)
def test_computed(self):
b = Bank('computed')
res = b.update(True)
self.assertTrue(res)
self.assertTrue(os.path.exists(b.session.get_full_release_directory()+'/sub1/flat/test_100.txt'))
self.assertTrue(b.session.get('update'))
# Check that, with depends non updated, bank is not updated itself
nextb = Bank('computed')
res = nextb.update(True)
self.assertFalse(nextb.session.get('update'))
def test_reupdate_from_task_wrong_release(self):
b = Bank('local')
b.options.stop_after = 'download'
b.update()
self.assertFalse(b.session.get_status('postprocess'))
b2 = Bank('local')
b2.options.from_task = 'postprocess'
b2.options.release = 'wrongrelease'
res = b2.update()
self.assertFalse(res)
def test_reupdate_from_task_error(self):
b = Bank('local')
b.options.stop_after = 'check'
b.update()
self.assertFalse(b.session.get_status('postprocess'))
b2 = Bank('local')
b2.options.from_task = 'postprocess'
b2.options.release = b.session.get('release')
res = b2.update()
self.assertFalse(res)
def test_get_release(self):
'''
Get release
'''
b = Bank('alu')
b.load_session(UpdateWorkflow.FLOW)
res = b.update()
self.assertTrue(b.session.get('update'))
self.assertTrue(res)
self.assertTrue(b.session._session['release'] is not None)
def test_no_update(self):
'''
Try updating twice, at second time, bank should not be updated
'''
b = Bank('local')
b.update()
self.assertTrue(b.session.get('update'))
b.update()
self.assertFalse(b.session.get('update'))
self.assertFalse(b.session.get_status(Workflow.FLOW_POSTPROCESS))
def test_reupdate_from_task_wrong_release(self):
b = Bank("local")
b.options.stop_after = "download"
b.update()
self.assertFalse(b.session.get_status("postprocess"))
b2 = Bank("local")
b2.options.from_task = "postprocess"
b2.options.release = "wrongrelease"
res = b2.update()
self.assertFalse(res)
def test_get_release(self):
'''
Get release
'''
b = Bank('alu')
b.load_session(UpdateWorkflow.FLOW)
res = b.update()
self.assertTrue(b.session.get('update'))
self.assertTrue(res)
self.assertTrue(b.session._session['release'] is not None)
def test_no_update(self):
"""
Try updating twice, at second time, bank should not be updated
"""
b = Bank("local")
b.update()
self.assertTrue(b.session.get("update"))
b.update()
self.assertFalse(b.session.get("update"))
self.assertFalse(b.session.get_status(Workflow.FLOW_POSTPROCESS))
def test_computed_ref_release(self):
b = Bank('computed2')
res = b.update(True)
b2 = Bank('sub1')
b2release = b2.bank['production'][len(b2.bank['production']) -
1]['release']
brelease = b.bank['production'][len(b.bank['production']) -
1]['release']
self.assertTrue(res)
self.assertTrue(brelease == b2release)
def test_computed_nofile(self):
b = Bank('computed2')
b.load_session(UpdateWorkflow.FLOW)
b.session.config.set('protocol', 'none')
b.session.config.set('sub1.files.move', 'flat/test_.*')
res = b.update(True)
self.assertTrue(res)
self.assertTrue(
os.path.exists(b.session.get_full_release_directory() +
'/sub1/flat/test_100.txt'))
def test_get_release(self):
"""
Get release
"""
b = Bank("alu")
b.load_session(UpdateWorkflow.FLOW)
res = b.update()
self.assertTrue(b.session.get("update"))
self.assertTrue(res)
self.assertTrue(b.session._session["release"] is not None)
def test_reupdate_from_task_error(self):
b = Bank("local")
b.options.stop_after = "check"
b.update()
self.assertFalse(b.session.get_status("postprocess"))
b2 = Bank("local")
b2.options.from_task = "postprocess"
b2.options.release = b.session.get("release")
res = b2.update()
self.assertFalse(res)
def test_postprocesses_restart_from_proc(self):
b = Bank('localprocess')
b.update()
proc1file = os.path.join(b.session.get_full_release_directory(),'proc1.txt')
proc2file = os.path.join(b.session.get_full_release_directory(),'proc2.txt')
self.assertTrue(os.path.exists(proc1file))
self.assertTrue(os.path.exists(proc2file))
os.remove(proc1file)
os.remove(proc2file)
# Restart from postprocess, reexecute all processes
b2 = Bank('localprocess')
b2.options.from_task = 'postprocess'
b2.options.release = b.session.get('release')
b2.update()
self.assertTrue(os.path.exists(proc1file))
self.assertTrue(os.path.exists(proc2file))
os.remove(proc1file)
os.remove(proc2file)
# Restart from postprocess, but at process PROC2 and following
b3 = Bank('localprocess')
b3.options.from_task = 'postprocess'
b3.options.process = 'PROC2'
b3.options.release = b.session.get('release')
b3.update()
#self.assertFalse(os.path.exists(proc1file))
self.assertTrue(os.path.exists(proc2file))
def execute(self, options):
'''
List remote content
'''
start_time = datetime.datetime.now()
start_time = time.mktime(start_time.timetuple())
error = None
try:
options.no_log = False
if options.update:
bmaj = Bank(options.bank, options)
self.logger.debug('Log file: ' + bmaj.config.log_file)
error = bmaj.update(depends=True)
Notify.notifyBankAction(bmaj)
elif options.remove or options.removeall:
if options.removeall:
bmaj = Bank(options.bank, options, no_log=True)
print('Log file: ' + bmaj.config.log_file)
error = bmaj.removeAll(options.force)
else:
bmaj = Bank(options.bank, options)
self.logger.debug('Log file: ' + bmaj.config.log_file)
error = bmaj.remove(options.release)
Notify.notifyBankAction(bmaj)
except Exception as e:
self.logger.exception('Exception: ' + str(e))
error = True
end_time = datetime.datetime.now()
end_time = time.mktime(end_time.timetuple())
execution_time = end_time - start_time
return {'error': error, 'execution_time': execution_time}
def biomaj_status(options):
'''
Get bank status information
'''
msg = ''
if options.bank:
bank = Bank(options.bank, options=options, no_log=True)
if bank.bank['properties']['visibility'] != 'public' and not bank.is_owner():
return (False, 'Access forbidden')
info = bank.get_bank_release_info(full=True)
msg += tabulate(info['info'], headers='firstrow', tablefmt='psql') + '\n'
msg += tabulate(info['prod'], headers='firstrow', tablefmt='psql') + '\n'
# do we have some pending release(s)
if 'pend' in info and len(info['pend']) > 1:
msg += tabulate(info['pend'], headers='firstrow', tablefmt='psql') + '\n'
else:
banks = Bank.list()
# Headers of output table
banks_list = [["Name", "Type(s)", "Release", "Visibility", "Last update"]]
for bank in sorted(banks, key=lambda k: k['name']):
bank = Bank(bank['name'], options=options, no_log=True)
if bank.bank['properties']['visibility'] == 'public' or bank.is_owner():
banks_list.append(bank.get_bank_release_info()['info'])
msg += tabulate(banks_list, headers="firstrow", tablefmt="psql") + '\n'
return (True, msg)
def test_multi(self):
b = Bank('multi')
res = b.update()
with open(os.path.join(b.session.get_full_release_directory(),'flat/test1.json'), 'r') as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json['args']['key1'] == 'value1')
with open(os.path.join(b.session.get_full_release_directory(),'flat/test2.json'), 'r') as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json['form']['key1'] == 'value1')
def test_multi(self):
b = Bank("multi")
res = b.update()
with open(os.path.join(b.session.get_full_release_directory(), "flat/test1.json"), "r") as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json["args"]["key1"] == "value1")
with open(os.path.join(b.session.get_full_release_directory(), "flat/test2.json"), "r") as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json["form"]["key1"] == "value1")
def test_publish(self):
"""
Update a bank, then publish it
"""
b = Bank("local")
b.update()
current_link = os.path.join(b.config.get("data.dir"), b.config.get("dir.version"), "current")
self.assertFalse(os.path.exists(current_link))
self.assertTrue(b.bank["current"] is None)
b.publish()
self.assertTrue(os.path.exists(current_link))
self.assertTrue(b.bank["current"] == b.session._session["id"])
def test_fromscratch_update(self):
"""
Try updating twice, at second time, bank should be updated (force with fromscratc)
"""
b = Bank("local")
b.update()
self.assertTrue(b.session.get("update"))
sess = b.session.get("release")
b.options.fromscratch = True
b.update()
self.assertTrue(b.session.get("update"))
self.assertEqual(b.session.get("release"), sess + "__1")
def biomaj_daemon_bank_isowner(bank):
'''
Checks that logged user is admin or owner of the bank
'''
(http_code, options, error) = daemon_api_auth(request)
if error:
abort(http_code, error)
bank_log = Bank(bank, options=options, no_log=True)
if bank_log.is_owner():
return jsonify({'is_admin_or_owner': True})
else:
return jsonify({'is_admin_or_owner': False})
def biomaj_visibility(options):
'''
Bank visibility management
'''
if not options.bank:
return (False, "Bank option is missing")
if options.visibility not in ['public', 'private']:
return (False, "Valid values are public|private")
bank = Bank(options.bank, options=options, no_log=True)
bank.set_visibility(options.visibility)
return (True, "Do not forget to update accordingly the visibility.default parameter in the configuration file")
def test_fromscratch_update(self):
'''
Try updating twice, at second time, bank should be updated (force with fromscratc)
'''
b = Bank('local')
b.update()
self.assertTrue(b.session.get('update'))
sess = b.session.get('release')
b.options.fromscratch = True
b.update()
self.assertTrue(b.session.get('update'))
self.assertEqual(b.session.get('release'), sess+'__1')
def biomaj_show(options, config):
'''
show bank details
'''
if not options.bank:
return (False, "Bank option is required")
bank = Bank(options.bank, options=options, no_log=True)
results = []
headers = ["Name", "Release", "Format(s)", "Type(s)", "Tag(s)", "File(s)"]
if not options.json:
results.append(headers)
current = None
fformat = None
if 'current' in bank.bank and bank.bank['current']:
current = bank.bank['current']
for prod in bank.bank['production']:
include = True
release = prod['release']
if current == prod['session']:
release += ' (current)'
if options.release and (prod['release'] != options.release
and prod['prod_dir'] != options.release):
include = False
if include:
session = bank.get_session_from_release(prod['release'])
formats = session['formats']
afiles = []
atags = []
atypes = []
for fformat in list(formats.keys()):
for elt in formats[fformat]:
if options.json:
atypes.append(elt['types'])
else:
atypes.append(','.join(elt['types']))
for tag in list(elt['tags'].keys()):
atags.append(elt['tags'][tag])
for eltfile in elt['files']:
afiles.append(eltfile)
if options.json:
results.append([
bank.bank['name'], release, fformat, atypes, atags, afiles
])
msg = {'details': results, 'headers': headers}
else:
results.append([
bank.bank['name'], release, fformat, ','.join(atypes),
','.join(atags), ','.join(afiles)
])
msg = tabulate(results, headers="firstrow", tablefmt="grid")
return (True, msg)
def test_postprocess_wrong_process_name(self):
"""If a wrong process name is given, update returns False and prints an error message"""
b = Bank('local')
b.options.stop_after = 'download'
b.update()
self.assertFalse(b.session.get_status('postprocess'))
b2 = Bank('local')
b2.options.from_task = 'postprocess'
b2.options.release = b.session.get('release')
b2.options.process = 'fake'
self.assertFalse(b2.update())
self.assertFalse(b2.session.get_status('postprocess'))
self.assertEqual(b.session.get_full_release_directory(), b2.session.get_full_release_directory())
def biomaj_freeze(options):
'''
freeze a bank
'''
if not options.bank:
return (False, "Bank name is missing")
if not options.release:
return (False, "Bank release is missing")
bmaj = Bank(options.bank, options=options)
res = bmaj.freeze(options.release)
if not res:
return (False, 'Failed to freeze the bank release')
return (True, None)
def test_mix_stop_from_task4(self):
'''
Get a first release, then fromscratch --stop-after, then restart from-task
'''
b = Bank('local')
b.update()
rel = b.session.get('release')
b2 = Bank('local')
b2.options.stop_before = 'download'
b2.options.fromscratch = True
res = b2.update()
b3 = Bank('local')
b3.options.from_task = 'postprocess'
res = b3.update()
self.assertFalse(res)
def test_multi(self):
b = Bank('multi')
res = b.update()
with open(
os.path.join(b.session.get_full_release_directory(),
'flat/test1.json'), 'r') as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json['args']['key1'] == 'value1')
with open(
os.path.join(b.session.get_full_release_directory(),
'flat/test2.json'), 'r') as content_file:
content = content_file.read()
my_json = json.loads(content)
self.assertTrue(my_json['form']['key1'] == 'value1')
def test_mix_stop_from_task(self):
'''
Get a first release, then fromscratch --stop-after, then restart from-task
'''
b = Bank('local')
b.update()
rel = b.session.get('release')
b2 = Bank('local')
b2.options.stop_after = 'download'
b2.options.fromscratch = True
res = b2.update()
self.assertTrue(b2.session.get('release') == rel + '__1')
b3 = Bank('local')
res = b3.update()
self.assertTrue(b3.session.get('release') == rel + '__1')
self.assertTrue(res)
def test_download_from_list(self):
"""
Use remote.list to define a list of files to download
"""
b = Bank('local')
fd, file_path = tempfile.mkstemp()
try:
b.config.set('remote.list', file_path)
with os.fdopen(fd, 'w') as tmp:
tmp.write('[{"name": "test_100.txt", "root": "' +
b.config.get('remote.dir') + '"}]')
b.update()
self.assertTrue(b.session.get('update'))
finally:
#os.remove(file_path)
print(file_path)
def biomaj_remove_pending(options):
'''
Remove pending releases
'''
if not options.bank:
return (False, "Bank name is missing")
bmaj = Bank(options.bank, options=options, no_log=True)
if bmaj.is_locked():
return (False, 'Bank is locked due to an other action')
if not options.proxy:
res = bmaj.remove_pending(options.release)
return (res, '')
res = biomaj_remove_pending_request(options)
if not res:
return (False, 'Failed to send removal request')
return (True, 'Request sent')
def biomaj_bank_log_tail(bank, tail=100):
apikey = request.headers.get('Authorization')
token = None
if apikey:
bearer = apikey.split()
if bearer[0] == 'APIKEY':
token = bearer[1]
log_file = None
try:
user = None
options_object = Options(OPTIONS_PARAMS)
if token:
proxy = Utils.get_service_endpoint(config, 'user')
r = requests.get(proxy + '/api/user/info/apikey/' + token)
if not r.status_code == 200:
abort(404, {'message': 'Invalid API Key or connection issue'})
user = r.json()['user']
options_object = Options({'user': user['id']})
bank_log = Bank(bank, options=options_object, no_log=True)
if bank_log.bank['properties'][
'visibility'] != 'public' and not bank_log.is_owner():
abort(403, {'message': 'not authorized to access this bank'})
if 'status' not in bank_log.bank or 'log_file' not in bank_log.bank[
'status'] or not bank_log.bank['status']['log_file']['status']:
return "No log file available"
log_file = bank_log.bank['status']['log_file']['status']
except Exception as e:
logging.exception(e)
return "Failed to access log file: " + str(e)
if not log_file or not os.path.exists(log_file):
return "Cannot access log file %s" % (str(log_file))
def generate():
with open(log_file) as fp:
tail_l = int(tail)
if tail_l == 0:
for line in fp:
yield line
else:
dq = deque(fp, maxlen=tail_l)
for line in dq:
yield line
yield "##END_OF_LOG"
return Response(generate(), mimetype='text/plain')
def test_removeAll(self):
b = Bank('local')
b.update()
b.removeAll()
self.assertFalse(os.path.exists(b.get_data_dir()))
bdb = b.banks.find_one({'name': b.name})
self.assertTrue(bdb is None)
def test_session_reload_notover(self):
'''
Checks a session is used if present
'''
b = Bank('alu')
for i in range(1, 5):
s = Session('alu', self.config, UpdateWorkflow.FLOW)
s._session['status'][Workflow.FLOW_INIT] = True
b.session = s
b.save_session()
b = Bank('alu')
b.load_session(UpdateWorkflow.FLOW)
self.assertTrue(b.session.get_status(Workflow.FLOW_INIT))
def biomaj_move_production_directories(options):
'''
Change bank production directories
'''
if not options.bank:
return (False, "Bank option is missing")
if not os.path.exists(options.newdir):
return (False, "Destination directory does not exists")
bank = Bank(options.bank, options=options, no_log=True)
if not bank.bank['production']:
return (False, "Nothing to move, no production directory")
bank.load_session(Workflow.FLOW, None)
w = Workflow(bank)
res = w.wf_init()
if not res:
return (False, 'Bank initialization failure')
for prod in bank.bank['production']:
session = bank.get_session_from_release(prod['release'])
bank.load_session(Workflow.FLOW, session)
prod_path = bank.session.get_full_release_directory()
if os.path.exists(prod_path):
shutil.move(prod_path, options.newdir)
prod['data_dir'] = options.newdir
bank.banks.update({'name': options.bank}, {'$set': {'production': bank.bank['production']}})
w.wf_over()
return (True, "Bank production directories moved to " + options.newdir + "\nWARNING: do not forget to update accordingly the data.dir and dir.version properties")
def test_search(self):
b = Bank('localprocess')
b.update()
search_res = Bank.search(['blast'], [])
self.assertTrue(len(search_res) == 1)
search_res = Bank.search([], ['nucleic'])
self.assertTrue(len(search_res) == 1)
search_res = Bank.search(['blast'], ['nucleic'])
self.assertTrue(len(search_res) == 1)
search_res = Bank.search(['blast'], ['proteic'])
self.assertTrue(len(search_res) == 0)
