def __init__(self, description, epilog, version):
BaseCLI.__init__(self, description, epilog, version)
self.remove_options(['--config-file'])
self.parser.add_argument('--config-file',
metavar='<file>',
help="Path to a configuration file.",
required=True)
self.parser.add_argument('-s',
'--schema',
help="schema name",
default=None,
action='append')
self.parser.add_argument('-t',
'--table',
help="table name",
default=None,
action='append')
self.parser.add_argument('-n',
'--dryrun',
help="dryrun",
action="store_true")
self.parser.add_argument('-v',
'--verbose',
help="verbose",
action="store_true")
self.parser.add_argument('catalog', help="catalog number", type=int)
self.parser.set_defaults(host=platform.uname()[1])
def main():
sys.excepthook = excepthook
QApplication.setDesktopSettingsAware(False)
QApplication.setStyle(QStyleFactory.create("Fusion"))
app = QApplication(sys.argv)
app.setAttribute(QtCore.Qt.AA_UseHighDpiPixmaps)
sys.stderr.write("\n")
cli = BaseCLI(
"DERIVA Authentication Agent",
"For more information see: https://github.com/informatics-isi-edu/deriva-qt",
VERSION)
cli.parser.add_argument(
"--cookie-persistence",
action="store_true",
help="Enable cookie and local storage persistence for QtWebEngine.")
args = cli.parse_cli()
config = read_config(args.config_file,
create_default=False) if args.config_file else None
authWindow = AuthWindow(config,
args.credential_file,
cookie_persistence=args.cookie_persistence)
authWindow.show()
ret = app.exec_()
return ret
def __init__(self, description, epilog):
BaseCLI.__init__(self, description, epilog, __version__)
self.remove_options(['--host', '--config-file'])
self.parser.add_argument("--catalog",
default=1,
metavar="<1>",
help="Catalog number. Default: 1")
self.parser.add_argument('host',
default='localhost',
metavar='<host>',
help="Fully qualified host name.")
self.parser.add_argument('config',
metavar='<config file>',
help="Path to a configuration file.")
self.parser.add_argument("path",
metavar="<output dir>",
help="Path to an output directory.")
self.parser.add_argument(
"kwargs",
metavar="[key=value key=value ...]",
nargs=argparse.REMAINDER,
action=KeyValuePairArgs,
help=
"Variable length of whitespace-delimited key=value pair arguments used for "
"string interpolation in specific parts of the configuration file. "
"For example: key1=value1 key2=value2")
def main():
cli = BaseCLI("annotation rollback tool", None, version=__version__, hostname_required=True)
cli.parser.add_argument("--catalog", default=1, metavar="<1>", help="Catalog number. Default: 1")
cli.parser.add_argument("--snapshot", metavar="<snapshot ID", help="Catalog snapshot ID. Example: 2QG-VWP6-0YG0")
args = cli.parse_cli()
credential = get_credential(args.host, args.credential_file)
rollback_annotation(args.host, args.catalog, snaptime=args.snapshot, credential=credential)
def __init__(self, uploader, description, epilog, cookie_persistence=True, window_icon=":/images/upload.png"):
if not issubclass(uploader, DerivaUpload):
raise TypeError("DerivaUpload subclass required")
BaseCLI.__init__(self, description, epilog, uploader.getVersion())
self.uploader = uploader
self.cookie_persistence = cookie_persistence
self.window_icon = window_icon
def create_parser(description):
cli = BaseCLI(description, None, 1, hostname_required=True)
cli.remove_options(['--config-file'])
cli.parser.add_argument('config_file',
help='project-specific config file')
cli.parser.add_argument('--catalog-id', type=int, default=1)
cli.parser.add_argument(
'--scratch-directory',
help='directory for temporary storage of downloaded files')
return (cli)
def __init__(self, uploader, description, epilog):
if not issubclass(uploader, DerivaUpload):
raise TypeError("DerivaUpload subclass required")
BaseCLI.__init__(self, description, epilog, uploader.getVersion())
self.remove_options(['--host'])
self.parser.add_argument('--no-cfg-update', action="store_true", help="Do not update local config from server.")
self.parser.add_argument("--catalog", default=1, metavar="<1>", help="Catalog number. Default: 1")
self.parser.add_argument('host', metavar='<host>', help="Fully qualified host name.")
self.parser.add_argument("path", metavar="<dir>", help="Path to an input directory.")
self.uploader = uploader
def __init__(self, uploader, description, epilog):
if not issubclass(uploader, DerivaUpload):
raise TypeError("DerivaUpload subclass required")
BaseCLI.__init__(self, description, epilog, uploader.getVersion(), hostname_required=True)
self.parser.add_argument('--no-config-update', action="store_true",
help="Do not check for (and download) an updated configuration from the server.")
self.parser.add_argument('--purge-state', action="store_true",
help="Purge (delete) any existing transfer state files found in the directory "
"hierarchy of the input path.")
self.parser.add_argument("--catalog", default=1, metavar="<1>", help="Catalog number. Default: 1")
self.parser.add_argument("path", metavar="<input dir>", help="Path to an input directory.")
self.uploader = uploader
def main():
logger = logging.getLogger(__name__)
logger.setLevel("WARNING")
cli = BaseCLI(__name__,
"Create a sitemap from a table specified on the command line or a set of tables from a config file",
__version__, hostname_required=True)
cli.remove_options(["--credential-file", "--token", "--oauth2-token"])
cli.parser.add_argument("--catalog", default=1, metavar="<1>", help="Catalog number")
cli.parser.add_argument("-p", "--priority", type=float,
help="A floating-point number between 0.0 and 1.0 indicating the table's priority")
cli.parser.add_argument("-s", "--schema", help="the name of the schema of the (single) table to include")
cli.parser.add_argument("-t", "--table", help="the name of the (single) table to include")
args = cli.parse_cli()
if args.priority is not None:
if args.priority < 0 or args.priority > 1:
logger.error("priority should be a floating-point number between 0 and 1")
sys.exit(1)
if not ((args.schema and args.table) or args.config_file):
logger.error("must specify either a schema and table or a config file")
sys.exit(1)
sb = SitemapBuilder("https", args.host, args.catalog)
if args.schema and args.table:
sb.add_table_spec(args.schema, args.table, priority=args.priority)
if args.config_file:
rows = json.load(open(args.config_file))
for row in rows:
if row.get("schema") is None or row.get("table") is None:
logger.warning("malformed entry in {f}: schema or table is missing. Skipping".format(f=args.config_file))
next
if row.get("priority") is None:
priority = args.priority
else:
try:
priority = float(row.get("priority"))
if priority < 0 or priority > 1:
logger.warning("bad priority '{p}' - should be a floating-point number between 0 and 1. Ignoring".format(p=priority))
priority = args.priority
except ValueError:
logger.warning("malformed priority '{p}' - should be a floating-point number between 0 and 1. Ignoring".format(p=row.get("priority")))
priority = args.priority
sb.add_table_spec(row["schema"], row["table"], priority=priority)
sb.write_sitemap(sys.stdout)
return 0
def __init__(self, description, epilog, **kwargs):
BaseCLI.__init__(self, description, epilog, **kwargs)
self.parser.add_argument("--catalog",
default=1,
metavar="<1>",
help="Catalog number. Default: 1")
self.parser.add_argument("output_dir",
metavar="<output dir>",
help="Path to an output directory.")
self.parser.add_argument(
"envars",
metavar="[key=value key=value ...]",
nargs=argparse.REMAINDER,
action=KeyValuePairArgs,
default={},
help=
"Variable length of whitespace-delimited key=value pair arguments used for "
"string interpolation in specific parts of the configuration file. "
"For example: key1=value1 key2=value2")
utils.set_foreign_key_acls(catalog, 'PDB', 'ihm_hdx_restraint',
'ihm_hdx_restraint_structure_id_fkey',
foreign_key_acls)
utils.set_foreign_key_acls(
catalog, 'PDB', 'ihm_derived_angle_restraint',
'ihm_derived_angle_restraint_structure_id_fkey', foreign_key_acls)
utils.set_foreign_key_acls(
catalog, 'PDB', 'ihm_derived_dihedral_restraint',
'ihm_derived_dihedral_restraint_structure_id_fkey', foreign_key_acls)
utils.set_foreign_key_acls(catalog, 'PDB', 'struct_ref',
'struct_ref_structure_id_fkey',
foreign_key_acls)
utils.set_foreign_key_acls(catalog, 'PDB', 'struct_ref',
'struct_ref_db_name_fkey', foreign_key_acls)
utils.set_foreign_key_acls(catalog, 'PDB', 'struct_ref_seq',
'struct_ref_seq_structure_id_fkey',
foreign_key_acls)
utils.set_foreign_key_acls(catalog, 'PDB', 'struct_ref_seq_dif',
'struct_ref_seq_dif_structure_id_fkey',
foreign_key_acls)
utils.set_foreign_key_acls(catalog, 'PDB', 'struct_ref_seq_dif',
'struct_ref_seq_dif_details_fkey',
foreign_key_acls)
if __name__ == '__main__':
args = BaseCLI("ad-hoc table creation tool", None, 1).parse_cli()
credentials = get_credential(args.host, args.credential_file)
main(args.host, 99, credentials)
transform(entry["dest"], data)
if entry.get("extra_defaults") is None:
entry['dest'].insert(data, nondefaults=set(["RID"]))
else:
entry['dest'].insert(data,
defaults=entry.get("extra_defaults"),
nondefaults=set(["RID"]))
def vocab_to_vocabulary(self, table, data):
for row in data:
if row.get("Description") is None:
row["Description"] = row["Name"]
if __name__ == '__main__':
cli = BaseCLI("load tables into demo server", None, hostname_required=True)
cli.parser.add_argument("--directory",
"-d",
type=str,
help="Parent directory of data files",
default="./data")
cli.parser.add_argument("--all",
"-a",
action="store_const",
const=True,
help="load all tables")
cli.parser.add_argument("catalog", type=int)
cli.parser.add_argument("--table",
type=str,
action="append",
help="table(s) to load")
'Sequence_Trimming': True,
'Duplicate_Removal': True
}]
table.insert(rows)
# -- =================================================================================
def main(server_name, catalog_id, credentials):
server = DerivaServer('https', server_name, credentials)
catalog = server.connect_ermrest(catalog_id)
catalog.dcctx['cid'] = "oneoff/data"
model = catalog.getCatalogModel()
#load_table_RNASeq_Reference_Genome(catalog)
load_table_RNASeq_Workflow(catalog)
# -- --------------------------------------------------------------
# arguments:
# --credential-file (optional if authenticated through deriva-auth)
# -- host
# e.g. python3 row_mutation.py --credential-file ~/.deriva/credential.json --host staging.gudmap.org
if __name__ == '__main__':
args = BaseCLI("mutate rows", None, 1).parse_cli()
credentials = get_credential(args.host, args.credential_file)
main(args.host, 2, credentials)
def dump_study_collection(self):
table = self.pb.RNASeq.Experiment
data = table.filter(table.Species=='Mus musculus')\
.filter(table.Sequencing_Type=="mRNA-Seq")\
.link(self.pb.RNASeq.Study)\
.link(self.pb.RNASeq.Sequencing_Study_Collection)\
.entities()
self.finalize_and_write("Sequencing_Study_Collection", self.DATA,
list(data))
def dump_collection(self):
table = self.pb.RNASeq.Experiment
data = table.filter(table.Species=='Mus musculus')\
.filter(table.Sequencing_Type=="mRNA-Seq")\
.link(self.pb.RNASeq.Study)\
.link(self.pb.RNASeq.Sequencing_Study_Collection)\
.link(self.pb.Common.Collection)\
.entities()
self.finalize_and_write("Collection", self.DATA, list(data))
if __name__ == '__main__':
cli = BaseCLI("dump tables to import into demo",
None,
hostname_required=True)
cli.parser.add_argument("catalog", type=int, default=None)
args = cli.parse_cli()
dmp = RBKDump(args.host, args.catalog)
dmp.dump_all()
"Input_Bag": args.inputBagRID,
"Notes": args.notes,
"Execution_Status": args.status,
"Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
}
entities = run_table.insert([run_data])
rid = entities[0]["RID"]
else:
run_data = {
"RID": args.update,
"Replicate": args.repRID,
"Workflow": args.workflowRID,
"Reference_Genome": args.referenceRID,
"Input_Bag": args.inputBagRID,
"Notes": args.notes,
"Execution_Status": args.status,
"Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
}
entities = run_table.update([run_data])
rid = args.update
print(rid)
if __name__ == '__main__':
args = get_args()
cli = BaseCLI("Custom RNASeq query", None, 1)
cli.remove_options(["--config-file"])
host = args.host
credentials = {"cookie": args.cookie}
main(host, 2, credentials)
changed_catlog_acl = setCatalogACL(model_root)
changed_tables_acl = setTablesACL(model_root)
changed_tables_acl_bindings = setTablesACLBindings(model_root)
changed_columns_acl = setColumnsACL(model_root)
changed_columns_acl_bindings = setColumnsACLBindings(model_root)
changed_foreign_key_acl = setForeignKeyACL(model_root)
changed_foreign_key_acl_bindings = setForeignKeyACLBindings(model_root)
changed = changed_catlog_acl or changed_tables_acl or changed_tables_acl_bindings or changed_columns_acl or changed_columns_acl_bindings or changed_foreign_key_acl or changed_foreign_key_acl_bindings
if changed == True:
print('Applying ACLs changes...')
model_root.apply()
else:
print('No ACLs changes detected.')
def main(server_name, catalog_id, credentials):
server = DerivaServer('https', server_name, credentials)
catalog = server.connect_ermrest(catalog_id)
catalog.dcctx['cid'] = 'ACL/model'
model = catalog.getCatalogModel()
setACLs(model)
if __name__ == '__main__':
args = BaseCLI('ACL Configuration Tool', None, 1).parse_cli()
credentials = get_credential(args.host, args.credential_file)
main(args.host, 99, credentials)
Column.define("Collection", builtin_types.text, nullok=False)
],
key_defs=[Key.define(["Study", "Collection"])],
fkey_defs=[
ForeignKey.define(["Study"],
self.DATA,
"Study", ["RID"],
constraint_names=[[
self.DATA, "Study_Collection_Study_fkey"
]]),
ForeignKey.define(["Collection"],
self.DATA,
"Collection", ["RID"],
constraint_names=[[
self.DATA,
"Study_Collection_Collection_fkey"
]])
],
comment="Many-to-many associations between studies and collection")
self.try_create_table(schema, table_def)
if __name__ == '__main__':
cli = BaseCLI("demo database creation tool", None, hostname_required=True)
cli.parser.add_argument("--use-catalog", type=int, default=None)
args = cli.parse_cli()
credentials = get_credential(args.host)
dc = DemoCatalog(args.host, credentials, catalog_number=args.use_catalog)
dc.create_tables()
print(dc.catalog.catalog_id)
