def init(loc='.'):
fp = os.path.abspath(os.path.join(loc, '.hs_auth'))
if os.path.exists(fp):
print(f'Auth already exists: {fp}')
remove = input('Do you want to replace it [Y/n]')
if remove.lower() == 'n':
sys.exit(0)
os.remove(fp)
usr = input('Enter HydroShare Username: '******'Enter HydroShare Password: '******'usr': usr,
'pwd': pwd}
cred_json_string = str.encode(json.dumps(dat))
cred_encoded = base64.b64encode(cred_json_string)
with open(fp, 'w') as f:
f.write(cred_encoded.decode('utf-8'))
try:
hydroshare.hydroshare(authfile=fp)
except Exception:
print('Authentication Failed')
os.remove(fp)
sys.exit(1)
print(f'Auth saved to: {fp}')
def main(args):
if args.v:
log.set_verbose()
if args.q:
log.set_quiet()
title = ' '.join(args.title)
abstract = ' '.join(args.abstract)
# make sure input files exist
for f in args.files:
if not os.path.exists(f):
raise Exception(f'Could not find file: {f}')
sys.exit(1)
# connect to hydroshare
hs = hydroshare.hydroshare()
if hs is None:
raise Exception(f'Connection to HydroShare failed')
sys.exit(1)
# get the hydroshare data
resource_id = create_resource(hs,
abstract,
title,
keywords=args.keywords,
content_files=args.files)
# return the path to the data
logger.info(f'\nhttps://hydroshare.org/resource/{resource_id}')
def test_file_doesnt_exist(self):
title = 'unit testing'
abstract = 'this is a resource created by a unittest'
keywords = ['test']
# test that an exception is raised if an input file doesn't exist
hs = hydroshare.hydroshare(authfile=self.authfile)
with self.assertRaises(Exception):
resid = hs.createResource(abstract,
title,
keywords,
content_files=['wrong_name.txt'])
hs.close()
def test_add_file_to_resource(self):
# test that resource is created successfully without files
hs = hydroshare.hydroshare(authfile=self.authfile)
resid = hs.createResource(self.abstract,
self.title,
self.keywords,
content_files=[])
self.assertTrue(resid is not None)
resid = hs.addContentToExistingResource(resid, self.testfile)
self.assertTrue(resid is not None)
hs.hs.deleteResource(resid)
hs.close()
def test_set_directory(self):
"""
tests that the download directory is set properly
"""
# test no download directory set
hs = hydroshare.hydroshare(authfile=self.authfile)
self.assertTrue(hs.download_dir == '.')
hs.close()
# test that an exception is raised if the save directory doesn't exist
with self.assertRaises(Exception) as context:
hs = hydroshare.hydroshare(authfile=self.authfile,
save_dir='/dir_doesnt_exist')
self.assertTrue('does not exist' in str(context.exception))
hs.close()
# test with directory as input
d = 'test_directory_please_remove'
os.makedirs(d)
hs = hydroshare.hydroshare(authfile=self.authfile, save_dir=d)
self.assertTrue(hs.download_dir == d)
hs.close()
os.rmdir(d)
def test_file_already_exists(self):
hs = hydroshare.hydroshare(authfile=self.authfile)
resid = hs.createResource(self.abstract,
self.title,
self.keywords,
content_files=[self.testfile])
self.assertTrue(resid is not None)
# test adding file that already exists in the resource
with self.assertRaises(Exception):
files = [self.testfile]
resid = hs.addContentToExistingResource(resid, files)
hs.hs.deleteResource(resid)
hs.close()
def test_add_wrong_path(self):
hs = hydroshare.hydroshare(authfile=self.authfile)
resid = hs.createResource(self.abstract,
self.title,
self.keywords,
content_files=[])
self.assertTrue(resid is not None)
# test that an exception is raised if an input file doesn't exist
with self.assertRaises(Exception):
f = 'file_that_doesnt_exist.txt'
resid = hs.addContentToExistingResource(resid, f)
hs.hs.deleteResource(resid)
hs.close()
def test_one_file(self):
title = 'unit testing'
abstract = 'this is a resource created by a unittest'
keywords = ['test']
# test that resource is created successfully
hs = hydroshare.hydroshare(authfile=self.authfile)
resid = hs.createResource(abstract,
title,
keywords,
content_files=[self.testfile])
self.assertTrue(resid is not None)
scimeta = hs.getResourceMetadata(resid)
self.assertTrue(type(scimeta) == ResourceMetadata)
hs.hs.deleteResource(resid)
hs.close()
def main(args):
if args.v:
log.set_verbose()
if args.q:
log.set_quiet()
# connect to hydroshare
hs = hydroshare.hydroshare()
if hs is None:
raise Exception(f'Connection to HydroShare failed')
sys.exit(1)
for resid in args.resource_id:
try:
delete_resource(hs, resid)
except Exception as e:
print(f' {str(e)}')
def test_get_file(self):
# create a temp dir
d = os.path.join(os.path.dirname(__file__),
'test_directory_please_remove')
os.makedirs(d)
# instantiate HS
hs = hydroshare.hydroshare(authfile=self.authfile, save_dir=d)
self.assertTrue(hs.download_dir == d)
# download a published resource
resid = '1be4d7902c87481d85b93daad99cf471'
hs.getResource(resid)
self.assertTrue(os.path.exists(os.path.join(d, f'{resid}')))
# clean up
hs.close()
shutil.rmtree(d)
def test_no_files(self):
title = 'unit testing'
abstract = 'this is a resource created by a unittest'
keywords = ['test']
# test that resource is created successfully without files
hs = hydroshare.hydroshare(authfile=self.authfile)
try:
resid = hs.createResource(abstract,
title,
keywords,
content_files=[])
self.assertTrue(resid is not None)
except Exception as e:
print(e.status_msg)
scimeta = hs.getResourceMetadata(resid)
self.assertTrue(type(scimeta) == ResourceMetadata)
hs.hs.deleteResource(resid)
hs.close()
def test_add_multiple(self):
hs = hydroshare.hydroshare(authfile=self.authfile)
resid = hs.createResource(self.abstract,
self.title,
self.keywords,
content_files=[])
self.assertTrue(resid is not None)
# test that resource is created successfully with list input
files = [self.testfile, self.testfile2]
for f in files:
resid = hs.addContentToExistingResource(resid, f)
self.assertTrue(resid is not None)
# get file from resource, make sure it exists in the resource
filenames = [r['file_name'] for r in hs.getResourceFiles(resid)]
self.assertTrue(self.testfile in filenames)
hs.hs.deleteResource(resid)
hs.close()
def main(args):
# check filter
filters = {}
if args.filter:
for f in args.filter:
pf = parse_filter(f)
if pf is not None:
filters.update(pf)
else:
sys.exit(1)
# connect to hydroshare
hs = hydroshare.hydroshare()
userinfo = hs.userInfo()
print_resource_list(hs,
userinfo['username'],
filter_dict=filters,
count=args.n,
long_format=args.l,
size=args.s)
def main(args):
if args.v:
log.set_verbose()
if args.q:
log.set_quiet()
# create output directory if it doesn't already exist
try:
if not os.path.exists(args.save_dir):
os.makedirs(args.save_dir)
except Exception as e:
raise Exception(f'Could not create output directory: {e}')
sys.exit(1)
# connect to hydroshare
hs = hydroshare.hydroshare(save_dir=args.save_dir)
if hs is None:
sys.exit(1)
# get the hydroshare data
get_resource(hs, args.resource_id, args.f)
def main(args):
if args.v:
log.set_verbose()
if args.q:
log.set_quiet()
# connect to hydroshare
hs = hydroshare.hydroshare()
if hs is None:
raise Exception(f'Connection to HydroShare failed')
sys.exit(1)
# separate the file source and target paths
sources = []
targets = []
for f in args.files:
if ':' in f:
src, tar = f.split(':')
# make sure the target doesn't contain a beginning
# or trailing slash
tar = tar.strip('/')
else:
src = f
tar = os.path.basename(src)
sources.append(src)
targets.append(tar)
# make sure input files exist
for f in sources:
if not os.path.exists(f):
raise Exception(f'Could not find file: {f}')
sys.exit(1)
# get the resource files
try:
response = hs.getResourceFiles(args.resource_id)
res_files = []
if len(response) > 0:
for r in response:
# get the filepath from the content url field
file_path = r['url'].split('contents')[-1]
# remove slash at beginning
file_path = file_path[1:] if file_path[0] == '/' else file_path
res_files.append(file_path)
except Exception:
raise Exception('Error connecting to HydroShare resource')
# make sure files don't already exist in the resource
file_conflicts = []
if len(res_files) > 0:
for rf in res_files:
if rf in targets:
file_conflicts.append(rf)
if len(file_conflicts) > 0:
if not args.overwrite:
for fc in file_conflicts:
print(f' - {fc} already exists, use --overwrite to replace')
res_files.pop(res_files.index(fc))
tidx = targets.index(fc)
sources.pop(tidx)
targets.pop(tidx)
else:
for fc in file_conflicts:
logger.info(f'- removing: {fc}')
hs.hs.deleteResourceFile(args.resource_id, fc)
# create folders if necessary
res_dirs = [os.path.dirname(p) for p in res_files]
for i in range(0, len(targets)):
target_path = os.path.dirname(targets[i])
if target_path not in res_dirs:
print(f'+ creating resource directory: {target_path}')
# need a try/except loop here because hs.getResourceFiles will
# not return empty directories. There is a chance that the
# target directory already exists on HS but is empty
try:
hs.hs.createResourceFolder(args.resource_id,
pathname=target_path)
except Exception:
pass
# loop through the files and add each individually
for i in range(0, len(sources)):
try:
add_file(hs, args.resource_id, sources[i], targets[i])
except Exception:
print(f'- failed to add file {sources[i]:targets[i]}')
def main(args):
if args.v:
log.set_verbose()
# connect to hydroshare
hs = hydroshare.hydroshare()
if hs is None:
raise Exception(f'Connection to HydroShare failed')
sys.exit(1)
if args.resource_id:
print('-' * 50)
# loop through input resources
for r in args.resource_id:
try:
meta = hs.getResourceMetadata(r)
meta_dict = {k: v for k, v in vars(meta).items()
if not k.startswith('_')}
if args.terms:
# filter based on specified data types
meta_filtered = {}
for term in args.terms:
if term in meta_dict.keys():
meta_filtered[term] = meta_dict[term]
else:
logger.error(f' - Unknown metadata term {term}')
meta_dict = meta_filtered
# if not verbose, remove some of the metadata
elif not args.long:
short_keys = ['abstract',
'authors',
'creators',
'date_created',
'title']
meta_dict = {k: meta_dict[k] for k in short_keys}
# clean strings
for k, v in meta_dict.items():
if type(v) == type(str):
meta_dict[k] = v.replace('\n', '')
# shorten author and creator data
meta_dict['authors'] = ';'.join(meta_dict['authors'])
creator_values = []
for creator in meta_dict['creators']:
creator_values.append(creator['name'])
meta_dict['creators'] = ';'.join(creator_values)
if args.yaml:
class literal(str):
pass
def literal_presenter(dumper, data):
return dumper.represent_scalar('tag:yaml.org,2002:str',
data, style='|')
yaml.add_representer(literal, literal_presenter)
v = meta_dict['abstract']
meta_dict['abstract'] = literal(v)
print(yaml.dump(meta_dict))
if args.json:
# query scientific metadata
print(json.dumps(meta_dict,
indent=4,
sort_keys=True))
# organize files for tree printing
urls = []
for file_info in hs.getResourceFiles(r):
rpth = file_info['url'].split('contents/')[-1]
urls.append(rpth)
ftree = dict([get_tree('tree', urls, '')])['tree']
tree_print(ftree)
print('-' * 50)
except Exception as e:
print(e)
