def delete_manifest(org=None):
"""Deletes a manifest"""
if org is None:
raise InvalidInputError('org should be provided to execute this task')
cmd = ('provider delete_manifest --name "{0}" '
'--org {1}'.format(PROVIDER_NAME, org))
run_command(cmd)
def get_activation_key(name, org):
"""Gets an activation key"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'activation_key info --name {0} --org {1}'.format(name, org)
run_command(cmd)
def main():
parser = argparse.ArgumentParser(description="This script takes in a nucleotide file and filters it by both length and if it is annotated as a resistance gene or not.")
parser.add_argument('-fasta', dest="nucl_fp", help="Path to nucleotide or protein fasta file")
parser.add_argument('-min_len', dest="min_len", help="Minimum length gene to retain")
parser.add_argument('-annotations', dest="annotation_fp", help="Path to annotations file (only necessary if filtering by resfams) - this is the *.final.txt annotation file")
parser.add_argument('--res_filter', dest="res_filter", help="Flag to determine if keeping only resistance genes or all genes.", action='store_true', default=False)
parser.add_argument('-ids', dest="ids", help="gene ids to keep")
parser.add_argument('-o', dest="output_fp", help="Path to filtered fasta output directory")
args = parser.parse_args()
if args.min_len:
min_len = args.min_len
else:
min_len = 0
if not os.path.exists(args.output_fp):
h.run_command("mkdir " + args.output_fp)
filtered_file = args.output_fp.rstrip('/') + "/filtered.fasta"
other_file = args.output_fp.rstrip('/') + "/other.fasta"
# Determine genes that have resfams annotation
if args.res_filter:
resfam_genes = find_res_genes(args.annotation_fp)
# Filter fasta file and output
SeqIO.write(filter_records(args.nucl_fp, min_len, resfams=resfam_genes)[0], filtered_file, "fasta")
SeqIO.write(filter_records(args.nucl_fp, min_len, resfams=resfam_genes)[1], other_file, "fasta")
elif args.ids:
SeqIO.write(filter_records(args.nucl_fp, min_len, ids=[line.rstrip() for line in open(args.ids)])[0], filtered_file, "fasta")
SeqIO.write(filter_records(args.nucl_fp, min_len, ids=[line.rstrip() for line in open(args.ids)])[1], other_file, "fasta")
else:
SeqIO.write(filter_records(args.nucl_fp, min_len)[0], filtered_file, "fasta")
SeqIO.write(filter_records(args.nucl_fp, min_len)[1], other_file, "fasta")
def get_user(username):
"""Gets an user"""
if username is None:
raise InvalidInputError('username should be provided to '
'execute this task')
cmd = 'user info --username {0}'.format(username)
run_command(cmd)
def get_permission(user_role):
"""Gets a permission"""
if user_role is None:
raise InvalidInputError('user_rold should be provided to '
'execute this task')
cmd = 'permission list --user_role {0}'.format(user_role)
run_command(cmd)
def get_role(name):
"""Gets a role"""
if name is None:
raise InvalidInputError('role name should be provided to '
'execute this task')
cmd = 'user_role info --name {0}'.format(name)
run_command(cmd)
def get_distributor(name, org):
"""Gets a distributor"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'distributor info --name {0} --org {1}'.format(name, org)
run_command(cmd)
def quantitize_image(filename, extension, colors):
try:
run_command(
f'magick {filename}.{extension} -kmeans {colors} {filename}_temp.png'
)
except:
print('Something went wrong while quantitizing your image')
def _run(facts):
log.pDebug("Running Apache plugin")
if 'httpd' in facts.processes:
run_command(['httpd', '-S'])
else:
log.pDebug("Apache not in running processes list")
def delete_manifest(org=None):
"""Deletes a manifest"""
if org is None:
raise InvalidInputError('org should be provided to execute this task')
cmd = ('provider delete_manifest --name "{0}" '
'--org {1}'.format(PROVIDER_NAME, org))
run_command(cmd)
def get_system_group(name, org):
"""Gets a system group"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system_group info --name {0} --org {1}'.format(name, org)
run_command(cmd)
def calculate_global_identity_blastp_fasta(args):
# import proteins as fasta
protein_dict = SeqIO.to_dict(SeqIO.parse(args.protein_fp, "fasta"))
proteindb_dict = SeqIO.to_dict(SeqIO.parse(args.protdb_fp, "fasta"))
final = open(args.output_fp + "/final_protein_identity.txt", 'w')
for result in open(args.output_fp + "/blastp_results.txt", 'r'):
id_number1 = result.split()[0]
print(id_number1)
id_number2 = result.split()[1]
print(id_number2)
SeqIO.write(protein_dict[id_number1], args.output_fp + "/temp_fasta1.fa", "fasta")
SeqIO.write(proteindb_dict[id_number2], args.output_fp + "/temp_fasta2.fa", "fasta")
needle = "needle -outfile=" + args.output_fp + "/temp_identity.txt -asequence " + args.output_fp + "/temp_fasta1.fa -bsequence " + args.output_fp + "/temp_fasta2.fa -gapope\
n=10 -gapextend=0.5"
h.run_command(needle)
identity = "NA"
for line in open(args.output_fp + "/temp_identity.txt", 'r'):
if line.startswith("# Identity:"):
identity = line.split("(")[1].rstrip("\n").rstrip(")").rstrip("%")
final.write(id_number1 + "\t" + retrieve_annotations(id_number1, args.anno_tab) + "\t"+ id_number2 + "\t" + identity + "\n")
h.run_command("rm " + args.output_fp + "/temp_*")
def update_org(name, new_description=None):
"""Updates an org."""
if name is None:
raise InvalidInputError('org name should be provided'
'to execute this task')
run_command('org update --name={0} --description={1}'.format(
name, new_description))
return name
def create_system(name=None, org=None):
"""Creates a system"""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
run_command('system register --name {0} --org {1}'.format(name, org))
return name
def create_distributor(name=None, org=None):
"""Creates a distributor"""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
run_command('distributor create --name {0} --org {1}'.format(name, org))
return name
def copy_sample_graphs(head_node, goffish_relative_path): graph_folder_path = head_node.path.source + goffish_relative_path + '/sample/gofs-graphs' sample_path = head_node.path.sample h_add = head_node.address h_user = head_node.username helper.run_command(h_add, h_user,'cp -r ' + graph_folder_path + ' ' + sample_path) return
def get_system(name, org):
"""Gets a system"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system info --name {0} --org {1}'.format(name, org)
# Open bug
run_command(cmd, warn_only=True)
def delete_permission(name, user_role):
"""Creates a permission"""
if name is None or user_role is None:
raise InvalidInputError('name and user_role should be provided to '
'execute this task')
cmd = ('permission delete --name {0} '
'--user_role {1}').format(name, user_role)
run_command(cmd)
def update_org(name, new_description=None):
"""Updates an org."""
if name is None:
raise InvalidInputError('org name should be provided'
'to execute this task')
run_command('org update --name={0} --description={1}'.format(
name, new_description))
return name
def create_system(name=None, org=None):
"""Creates a system"""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
run_command('system register --name {0} --org {1}'.format(name, org))
return name
def create_distributor(name=None, org=None):
"""Creates a distributor"""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
run_command('distributor create --name {0} --org {1}'.format(name, org))
return name
def create_role(name=None, description=None):
"""Creates an user role"""
if name is None:
name = gen_string("alphanumeric", 10)
if description is None:
description = gen_string("alphanumeric", 10)
run_command('user_role create --name {0} --description {1}'.format(
name, description))
return name
def create_role(name=None, description=None):
"""Creates an user role"""
if name is None:
name = gen_string("alphanumeric", 10)
if description is None:
description = gen_string("alphanumeric", 10)
run_command('user_role create --name {0} --description {1}'.format(
name, description))
return name
def copy_compiled_source(head_node, temp_path):
#copies from temp to head node source
os.system("tar -czvf ./source.tar.gz -C " + temp_path + " .")
h_add = head_node.address
h_user = head_node.username
helper.copy_file_to_remote(h_add, h_user,"source.tar.gz", head_node.path.source)
tar_command = "tar -C " + head_node.path.source + " -xzvf " + head_node.path.source + "/source.tar.gz"
helper.run_command(h_add, h_user, tar_command)
helper.run_command(h_add, h_user, "rm " + head_node.path.source + "/source.tar.gz")
os.system("rm ./source.tar.gz")
print "Source Copied To HeadNode"
return
def update_role(name, new_name=None, new_description=None):
"""Updates an user role"""
if name is None:
raise InvalidInputError('role name should be provided to '
'execute this task')
cmd = 'user_role update --name {0} '.format(name)
if new_name is not None:
cmd = cmd + ' --new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + ' --description {0} '.format(new_description)
run_command(cmd)
if new_name is not None:
return new_name
def update_role(name, new_name=None, new_description=None):
"""Updates an user role"""
if name is None:
raise InvalidInputError('role name should be provided to '
'execute this task')
cmd = 'user_role update --name {0} '.format(name)
if new_name is not None:
cmd = cmd + ' --new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + ' --description {0} '.format(new_description)
run_command(cmd)
if new_name is not None:
return new_name
def update_distributor(name, org, new_name=None, new_description=None):
"""Updates a distributor"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'distributor update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0}'.format(new_description)
run_command(cmd)
if new_name is not None:
return new_name
def update_distributor(name, org, new_name=None, new_description=None):
"""Updates a distributor"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'distributor update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0}'.format(new_description)
run_command(cmd)
if new_name is not None:
return new_name
def update_system(name=None, org=None, new_name=None, new_description=None):
"""Updates a system"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0}'.format(new_description)
run_command(cmd, warn_only=True)
if new_name is not None:
return new_name
def update_system(name=None, org=None, new_name=None, new_description=None):
"""Updates a system"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0}'.format(new_description)
run_command(cmd, warn_only=True)
if new_name is not None:
return new_name
def create_activation_key(name=None, org=None, description=None, limit=None):
"""Creates an activation key."""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
if description is None:
description = gen_string("alphanumeric", 10)
if limit is None:
limit = gen_integer(min_value=1, max_value=3)
run_command('activation_key create --name {0} --org {1} --description {2}'
' --limit {3}'.format(name, org, description, limit))
return name
def create_activation_key(name=None, org=None, description=None,
limit=None):
"""Creates an activation key."""
if name is None:
name = gen_string("alphanumeric", 10)
if org is None:
org = create_org()
if description is None:
description = gen_string("alphanumeric", 10)
if limit is None:
limit = gen_integer(min_value=1, max_value=3)
run_command('activation_key create --name {0} --org {1} --description {2}'
' --limit {3}'.format(name, org, description, limit))
return name
def cluster_fasta(output_fp, args):
for fasta in os.listdir(output_fp):
basename = os.path.splitext(os.path.basename(fasta))[0]
if args.protein_fp:
cluster_fp = output_fp + '/' + basename + '_unique.faa'
command = 'cd-hit -i ' + output_fp + '/' + fasta + ' -o ' + cluster_fp + ' -c ' + args.percent_id + ' -aS 1.0 -g 1 -d 0'
elif args.nucleotide_fp:
cluster_fp = output_fp + '/' + basename + '_unique.fna'
command = 'cd-hit-est -i ' + output_fp + '/' + fasta + ' -o ' + cluster_fp + ' -c ' + args.percent_id + ' -aS 1.0 -g 1 -d 0 -r 1'
h.run_command(command)
if args.within_lib and args.within_abx:
if args.nucleotide_fp:
command = 'cat ' + output_fp + '/*_unique.fna > ' + output_fp + '/unique_within_lib-abx_' + args.percent_id + '.fna'
else:
command = 'cat ' + output_fp + '/*_unique.faa > ' + output_fp + '/unique_within_lib-abx_'+ args.percent_id + '.faa'
h.run_command(command)
elif args.within_lib:
if args.nucleotide_fp:
command = 'cat ' + output_fp + '/*_unique.fna > ' + output_fp + '/unique_within_lib_' + args.percent_id + '.fna'
else:
command = 'cat ' + output_fp + '/*_unique.faa > ' + output_fp + '/unique_within_lib_'+ args.percent_id + '.faa'
h.run_command(command)
elif args.within_abx:
if args.nucleotide_fp:
command = 'cat ' + output_fp + '/*_unique.fna > ' + output_fp + '/unique_within_abx_'+ args.percent_id + '.fna'
else:
command = 'cat ' + output_fp + '/*_unique.faa > ' + output_fp + '/unique_within_abx_'+ args.percent_id + '.faa'
h.run_command(command)
def calculate_global_identity_blastp_ncbi(args):
# set NCBI information
Entrez.email = "*****@*****.**"
# import proteins as fasta
protein_dict = SeqIO.to_dict(SeqIO.parse(args.protein_fp, "fasta"))
final = open(args.output_fp + "/final_protein_identity.txt", 'w')
for result in open(args.output_fp + "/blastp_results.txt", 'r'):
id_number1 = result.split()[0]
id_number2 = result.split()[1].split('|')[3]
try:
SeqIO.write(protein_dict[id_number1], args.output_fp + "/temp_fasta1.fa", "fasta")
except:
print("(1) Didn't work for + " + id_number1, file=sys.stderr)
try:
handle = Entrez.efetch(db='protein', id=id_number2, rettype="text", retmode="fasta")
output = open(args.output_fp + "/temp_fasta2.fa", 'w')
output.write(handle.read())
output.close()
except:
print("(1) Didn't work for " + id_number2, file=sys.stderr)
needle = "needle -outfile=" + args.output_fp + "/temp_identity.txt -asequence " + args.output_fp + "/temp_fasta1.fa -bsequence " + args.output_fp + "/temp_fasta2.fa -gapopen=10 -gapextend=0.5"
h.run_command(needle)
identity = "NA"
for line in open(args.output_fp + "/temp_identity.txt", 'r'):
if line.startswith("# Identity:"):
identity = line.split("(")[1].rstrip("\n").rstrip(")").rstrip("%")
try:
handle = Entrez.efetch(db='protein', id=result.split()[1].split('|')[3], rettype="text", retmode="gb")
record = SeqIO.read(handle, "genbank")
if "source" in record.annotations and "taxonomy" in record.annotations:
final.write(id_number1 + "\t" + retrieve_annotations(id_number1, args.anno_tab) + "\t" + id_number2 + "\t" + identity + "\t" + record.description + "\t" + record.annotations["source"] + "\t" + ";".join(record.annotations["taxonomy"]) + "\n")
elif "source" in record.annotations:
final.write(id_number1 + "\t" + retrieve_annotations(id_number1, args.anno_tab) + "\t"+ id_number2 + "\t" + identity + "\t" + record.description + "\t" + record.annotations["source"] + "\n")
else:
final.write(id_number1 + "\t" + retrieve_annotations(id_number1, args.anno_tab) + "\t"+ id_number2 + "\t" + identity + "\t" + record.description + "\t" + "\n")
except:
final.write(id_number1 + "\t" + retrieve_annotations(id_number1, args.anno_tab) + "\t"+ id_number2 + "\t" + identity + "\n")
print("(2) Didn't work for " + id_number1 + " " + id_number2, file=sys.stderr)
h.run_command("rm " + args.output_fp + "/temp_*")
def generate_histogram(filename):
try:
return run_command(
f'magick convert {filename} -format %c -depth 8 histogram:info:-',
get_output=True)
except:
print('Something went wrong while generating the histogram')
def fill_gofs_bin(head_node, machine_list, goffish_relative_path): headnode_source_path = head_node.path.source gofs_zip_path = headnode_source_path + goffish_relative_path +'gofs/code/modules/gofs-distribution/target/gofs-bin.zip' helper.copy_file_from_remote(head_node.address, head_node.username, gofs_zip_path, 'gofs-bin.zip') for m in machine_list: remote_path = m.path.bin + '/gofs-bin' helper.copy_file_to_remote(m.address, m.username, 'gofs-bin.zip', remote_path) helper.run_command(m.address, m.username, "unzip " + remote_path + '/gofs-bin.zip' + " -d " + remote_path) helper.run_command(m.address, m.username, "rm "+ remote_path + '/gofs-bin.zip') helper.run_command(m.address, m.username, "cp -r " + remote_path +'/gofs/* '+remote_path +'/') helper.run_command(m.address, m.username, "chmod 777 "+ remote_path + '/*') helper.run_command(m.address, m.username, "rm -r "+ remote_path + '/gofs') return
def update_activation_key(name, org, new_name=None, new_description=None,
new_limit=None):
"""Updates an activation key."""
if name is None or org is None:
raise InvalidInputError('Activation key name and org name should be '
'provided to execute this task')
cmd = 'activation_key update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name={0} '.format(new_name)
if new_name is not None:
cmd = cmd + '--description={0} '.format(new_description)
if new_name is not None:
cmd = cmd + '--limit={0}'.format(new_limit)
run_command(cmd)
if new_name is not None:
return new_name
def update_system_group(name=None, org=None,
new_name=None, new_description=None,
new_max_systems=None):
"""Updates a system group"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system_group update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0} '.format(new_description)
if new_max_systems is not None:
cmd = cmd + '--max_systems {0}'.format(new_max_systems)
run_command(cmd)
if new_name is not None:
return new_name
def create_user(username=None, password=None, email=None,
default_organization=None, default_locale=None):
"""Creates an user"""
if username is None:
username = gen_string("alphanumeric", 10)
if password is None:
password = gen_string("alphanumeric", 10)
if email is None:
email = gen_email("alphanumeric", 10)
cmd = 'user create --username {0} --password {1} --email {2}'.format(
username, password, email)
if default_organization is not None:
cmd = cmd + ' --default_organization {0}'.format(default_organization)
if default_locale is not None:
cmd = cmd + ' --default_locale {0}'.format(default_locale)
run_command(cmd)
return username
def copy_samples_apps(head_node, goffish_relative_path, temp_path): sample_path = temp_path + goffish_relative_path[:-1] + '/gopher/samples' print sample_path jar_list = get_all_jars_in_folder(os.path.expanduser(sample_path)) print jar_list source_jar_list = map(lambda x: x.replace(os.path.expanduser(temp_path), head_node.path.source), jar_list) print source_jar_list h_add = head_node.address h_sam_path = head_node.path.sample h_user = head_node.username for s in source_jar_list: helper.run_command(h_add, h_user, "cp " + s + " " + h_sam_path + '/gopher-apps') return
def kill(head_node, machine_list):
#kill $(ps aux | grep -v [N]ameNode | grep '[l]ocalhost' | awk '{print $2}')
#we will execute the kill command last on headnode
is_headnode_in_machinelist = False
for m in machine_list:
kill_command = m.path.bin +"/gopher-bin/gopher-server/bin/kill-gopher.sh"
helper.run_command(m.address, m.username, kill_command)
if m.address == head_node.address:
is_headnode_in_machinelist = True
if not is_headnode_in_machinelist:
kill_command = head_node.path.bin +"/gopher-bin/gopher-server/bin/kill-gopher.sh"
helper.run_command(head_node.address, head_node.username, kill_command)
def import_manifest(org=None, filepath=None, deleted=True):
"""Imports a manifest
If delete is set to False, the manifest will not be deleted and the user
has to handle the deletion manually or by calling delete_manifest
"""
if org is None:
org = create_org()
if filepath is None:
filepath = MANIFEST_URL
cmd = ('provider import_manifest create --name "{0}" --org {1} '
'--file "{2}"').format(PROVIDER_NAME, org, filepath)
run_command(cmd)
if deleted is True:
print ('* After manifest import, manifest will be deleted so as '
'to reuse it *')
delete_manifest(org)
def import_manifest(org=None, filepath=None, deleted=True):
"""Imports a manifest
If delete is set to False, the manifest will not be deleted and the user
has to handle the deletion manually or by calling delete_manifest
"""
if org is None:
org = create_org()
if filepath is None:
filepath = MANIFEST_URL
cmd = ('provider import_manifest create --name "{0}" --org {1} '
'--file "{2}"').format(PROVIDER_NAME, org, filepath)
run_command(cmd)
if deleted is True:
print('* After manifest import, manifest will be deleted so as '
'to reuse it *')
delete_manifest(org)
def update_user(username, new_password=None, new_email=None,
new_default_organization=None, new_default_locale=None):
"""Updates an user"""
if username is None:
raise InvalidInputError('username should be provided to '
'execute this task')
cmd = 'user update --username {0} '.format(username)
if new_password is not None:
cmd = cmd + ' --password {0} '.format(new_password)
if new_email is not None:
cmd = cmd + ' --email {0} '.format(new_email)
if new_default_organization is not None:
cmd = cmd + (' --default_organization'
' {0} '.format(new_default_organization))
if new_default_locale is not None:
cmd = cmd + ' --default_locale {0}'.format(new_default_locale)
run_command(cmd)
return username
def update_system_group(name=None,
org=None,
new_name=None,
new_description=None,
new_max_systems=None):
"""Updates a system group"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
cmd = 'system_group update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name {0} '.format(new_name)
if new_description is not None:
cmd = cmd + '--description {0}'.format(new_description)
if new_max_systems is not None:
cmd = cmd + '--max_systems {0}'.format(new_max_systems)
run_command(cmd)
if new_name is not None:
return new_name
def update_activation_key(name,
org,
new_name=None,
new_description=None,
new_limit=None):
"""Updates an activation key."""
if name is None or org is None:
raise InvalidInputError('Activation key name and org name should be '
'provided to execute this task')
cmd = 'activation_key update --name {0} --org {1} '.format(name, org)
if new_name is not None:
cmd = cmd + '--new_name={0} '.format(new_name)
if new_name is not None:
cmd = cmd + '--description={0} '.format(new_description)
if new_name is not None:
cmd = cmd + '--limit={0}'.format(new_limit)
run_command(cmd)
if new_name is not None:
return new_name
def create_user(username=None,
password=None,
email=None,
default_organization=None,
default_locale=None):
"""Creates an user"""
if username is None:
username = gen_string("alphanumeric", 10)
if password is None:
password = gen_string("alphanumeric", 10)
if email is None:
email = gen_email("alphanumeric", 10)
cmd = 'user create --username {0} --password {1} --email {2}'.format(
username, password, email)
if default_organization is not None:
cmd = cmd + ' --default_organization {0}'.format(default_organization)
if default_locale is not None:
cmd = cmd + ' --default_locale {0}'.format(default_locale)
run_command(cmd)
return username
def create_permission(name=None,
user_role=None,
description=None,
scope=None,
verbs=None):
"""Creates a permission"""
if name is None:
name = gen_string("alphanumeric", 10)
if user_role is None:
user_role = create_role()
if description is None:
description = gen_string("alphanumeric", 10)
if scope is None:
scope = 'activation_keys'
if verbs is None:
verbs = 'read_all'
cmd = ('permission create --name {0} --user_role {1} '
'--description {2} --scope {3} '
'--verbs {4}').format(name, user_role, description, scope, verbs)
run_command(cmd)
return name
def update_user(username,
new_password=None,
new_email=None,
new_default_organization=None,
new_default_locale=None):
"""Updates an user"""
if username is None:
raise InvalidInputError('username should be provided to '
'execute this task')
cmd = 'user update --username {0} '.format(username)
if new_password is not None:
cmd = cmd + ' --password {0} '.format(new_password)
if new_email is not None:
cmd = cmd + ' --email {0} '.format(new_email)
if new_default_organization is not None:
cmd = cmd + (' --default_organization'
' {0} '.format(new_default_organization))
if new_default_locale is not None:
cmd = cmd + ' --default_locale {0}'.format(new_default_locale)
run_command(cmd)
return username
def _run(facts):
log.pInfo(
"Ran the example module. This uses the \"processes\" datasource.")
log.pInfo(
"Example of getting data from sources - number of running processes: %s"
% len(facts.processes))
log.pError("Example of an error message")
log.pWarning("Example of a warning message")
log.pDebug("Example of a debug message")
# Example of running a shell command
o = run_command(["uname", "-r"])
log.pInfo("Example command output - kernel version is: %s" % o[0])
def delete_org(name):
"""Deletes an org."""
if name is None:
raise InvalidInputError('name should be provided to execute this task')
run_command('org delete --name={0}'.format(name))
def delete_system_group(name, org):
"""Deletes a system group"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
run_command('system_group delete --name {0} --org {1}'.format(name, org))
def delete_distributor(name, org):
"""Deletes a distributor"""
if name is None or org is None:
raise InvalidInputError('name and org should be provided to '
'execute this task')
run_command('distributor delete --name {0} --org {1}'.format(name, org))
