def get_uuid(session: Session, uuid: str, not_found='raise'):
"""
.. versionadded:: 0.1.13
Return the Metacatalog object of given
version 4 UUID. The supported objects are:
- Entry
- EntryGroup
- Keyword
.. versionadded:: 0.2.7
- Person
"""
# check if an Entry exists
entry = api.find_entry(session, uuid=uuid)
if entry is not None:
return entry
# check if Entrygroup exists
group = api.find_group(session, uuid=uuid)
if group is not None:
return group
# check if a Person exists
person = api.find_person(session, uuid=uuid)
if person is not None:
return person
# handle keyword
keyword = api.find_keyword(session, uuid=uuid)
if keyword is not None:
return keyword
if not_found == 'raise':
raise NoResultFound("The UUID='%s' was not found." % uuid)
else:
return None
def find(args):
# get the session
session = connect(args)
# get the entity
entity = args.entity
# set by to an empty list if not given
if args.by is None:
args.by = []
# parse out the BY arguments
kwargs = dict()
for by in args.by:
# if len(by) != 2:
kwargs[by[0]] = by[1]
# switch entity
if entity.lower() == 'units' or entity.lower() == 'unit':
results = api.find_unit(session, **kwargs)
elif entity.lower() == 'variables' or entity.lower() == 'variable':
results = api.find_variable(session, **kwargs)
elif entity.lower() == 'licenses' or entity.lower() == 'license':
results = api.find_license(session, **kwargs)
elif entity.lower() == 'keywords' or entity.lower() == 'keyword':
results = api.find_keyword(session, **kwargs)
elif entity.lower() == 'roles' or entity.lower() == 'role':
results = api.find_role(session, **kwargs)
elif entity.lower() == 'persons' or entity.lower() == 'person':
results = api.find_person(session, **kwargs)
elif entity.lower() == 'group_types' or entity.lower() == 'group_type':
results = api.find_group_type(session, **kwargs)
elif entity.lower() == 'groups' or entity.lower() == 'group':
results = api.find_group(session, **kwargs)
elif entity.lower() == 'entries' or entity.lower() == 'entry':
results = api.find_entry(session, **kwargs)
elif entity.lower() == 'thesaurus':
results = api.find_thesaurus(session, **kwargs)
else:
cprint(args, 'Oops. Finding %s is not supported.' % entity)
exit(0)
# switch the output
if args.json:
obj = [serialize(r) for r in results]
cprint(args, json.dumps(obj, indent=4))
elif args.csv:
obj = [flatten(serialize(r)) for r in results]
f = io.StringIO(newline='')
colnames = set([n for o in obj for n in o.keys()])
writer = csv.DictWriter(f,
fieldnames=colnames,
quotechar='"',
quoting=csv.QUOTE_NONNUMERIC,
lineterminator='\r')
writer.writeheader()
for o in obj:
writer.writerow(o)
f.seek(0)
cprint(args, f.getvalue())
else: # stdOut
for result in results:
cprint(args, result)
def add_keywords_to_entries(session, entries, keywords, alias=None):
r"""Associate keyword(s) to entrie(s)
Adds associations between entries and keywords. The Entry and Keyword
instances have to already exist in the database. Keywords are usually
prepopulated. You might want to alias an keyword or associate a value to
it. Use the alias and value lists for this.
Parameters
----------
session : sqlalchemy.Session
SQLAlchemy session connected to the database.
entries : list
List of identifier or single identifier to load entries.
If int, the Entry.id is assumed. If str, title is assumed.
Can also pass a metacatalog.Entry object.
keywords : list
List of identifier or single identifier to load keywords.
If int, Keyword.id is assumed, If str, Keyword.value is assumed.
Can also pass a metacatalog.Keyword object.
alias : list
List of, or single alias names. The shape has to match the
keywords parameter. These alias will rename the keywords on
association. In case one instance should not recive an alias,
pass None instead.
.. deprecated:: 0.4.5
'alias' will be removed with a future release
Returns
-------
void
See Also
--------
metacatalog.Entry
metacatalog.Keyword
"""
# check the input shapes
if not isinstance(entries, list):
entries = [entries]
if not isinstance(keywords, list):
keywords = [keywords]
# if not isinstance(alias, list):
# alias = [alias] * len(keywords)
# add for each entry
for entry_id in entries:
# load the entry
if isinstance(entry_id, models.Entry):
entry = entry_id
elif isinstance(entry_id, int):
# TODO sort by version descending to get the lastest
entry = api.find_entry(session=session,
id=entry_id,
return_iterator=True).first()
elif isinstance(entry_id, str):
# TODO sort by version descending to get the lastest
entry = api.find_entry(session=session,
title=entry_id,
return_iterator=True).first()
else:
raise AttributeError("Value '%s' not allowed for entries" %
str(type(entry_id)))
# add each keyword
assocs = []
for keyword_id in keywords:
# load the keyword
if isinstance(keyword_id, models.Keyword):
keyword = keyword_id
elif isinstance(keyword_id, int):
keyword = api.find_keyword(session=session,
id=keyword_id,
return_iterator=True).first()
elif isinstance(keyword_id, str):
keyword = api.find_keyword(session=session,
value=keyword_id,
return_iterator=True).first()
else:
raise AttributeError("Value '%s' not allowed for keywords" %
str(type(keyword_id)))
# create a new keyword association
assocs.append(
models.KeywordAssociation(entry=entry, keyword=keyword))
# add keyword to current entry
try:
entry.keywords.extend(assocs)
session.add(entry)
session.commit()
except Exception as e:
session.rollback()
raise e
def find(args):
# get the session
session = connect(args)
# get the entity
entity = args.entity
# set by to an empty list if not given
if args.by is None:
args.by = []
# parse out the BY arguments
kwargs=dict()
for by in args.by:
# if len(by) != 2:
kwargs[by[0]] = by[1]
# switch entity
if entity.lower() == 'units' or entity.lower() == 'unit':
results = api.find_unit(session, **kwargs)
elif entity.lower() == 'variables' or entity.lower() == 'variable':
results = api.find_variable(session, **kwargs)
elif entity.lower() == 'licenses' or entity.lower() == 'license':
results = api.find_license(session, **kwargs)
elif entity.lower() == 'keywords' or entity.lower() == 'keyword':
results = api.find_keyword(session, **kwargs)
elif entity.lower() == 'roles' or entity.lower() == 'role':
results = api.find_role(session, **kwargs)
elif entity.lower() == 'persons' or entity.lower() == 'person':
results = api.find_person(session, **kwargs)
elif entity.lower() == 'group_types' or entity.lower() == 'group_type':
results = api.find_group_type(session, **kwargs)
elif entity.lower() == 'groups' or entity.lower() == 'group':
results = api.find_group(session, **kwargs)
elif entity.lower() == 'entries' or entity.lower() == 'entry':
if args.include_partial:
kwargs['include_partial'] = True
results = api.find_entry(session, **kwargs)
elif entity.lower() == 'thesaurus':
results = api.find_thesaurus(session, **kwargs)
else:
cprint(args, 'Oops. Finding %s is not supported.' % entity)
exit(0)
if args.export is not None and args.export != '':
# only entry and group can be exported
if entity.lower() not in ('entry', 'group'):
cprint(args, 'Can only export entity=Entry and entity=Group')
return
# get the fmt and path
path = args.export
fmt = args.export.split('.')[-1]
fmt = 'netCDF' if fmt == 'nc' else fmt
# check amount of results
if len(results) == 1:
results[0].export(path=path, fmt=fmt)
cprint(args, f'Wrote {path}.')
else:
for i, result in enumerate(results):
path = '.'.join([*args.export.split('.')[:-1], f'_{i}', args.export.split('.')[-1]])
result.export(path=path, fmt=fmt)
cprint(args, f'Wrote {len(results)} files.')
return
# switch the output
if args.json:
obj = [serialize(r) for r in results]
cprint(args, json.dumps(obj, indent=4))
elif args.csv:
obj = [flatten(serialize(r)) for r in results]
f = io.StringIO(newline='')
colnames = set([n for o in obj for n in o.keys()])
writer = csv.DictWriter(f, fieldnames=colnames, quotechar='"', quoting=csv.QUOTE_NONNUMERIC, lineterminator='\r')
writer.writeheader()
for o in obj:
writer.writerow(o)
f.seek(0)
cprint(args, f.getvalue())
else: # stdOut
for result in results:
cprint(args, result)