def runSCI(id):
if request.method == 'POST':
auth = HydroShareAuthBasic(username=request.form['username'],
password=request.form['password'])
hs = HydroShare(auth=auth)
hs.getResource('e987ddcf73a94376a4a70e5db0fb7646',
destination='/home/ubuntu/hydroshareLink/',
unzip=True)
subprocess.Popen(
'sciunit open /home/ubuntu/hydroshareLink/e987ddcf73a94376a4a70e5db0fb7646/e987ddcf73a94376a4a70e5db0fb7646/data/contents/modflow.zip',
stdout=subprocess.PIPE,
shell=True)
os.chdir("/home/ubuntu/test/")
hs.getResource(id, destination='/home/ubuntu/test/', unzip=True)
proc = subprocess.Popen('sciunit repeat e2 ' + str(id),
stdout=subprocess.PIPE,
shell=True)
output = proc.stdout.read()
abstract = ''
title = 'MODFLOW_NWT_SCIUNIT_OUTPUT'
keywords = ('my keyword 1', 'my keyword 2')
rtype = 'MODFLOWModelInstanceResource'
output_id = hs.createResource(rtype,
title,
abstract=abstract,
keywords=keywords)
for file in os.listdir("/home/ubuntu/test/MODFLOW/"):
if file != "mfnwt":
hs.addResourceFile(output_id,
"/home/ubuntu/test/MODFLOW/" + file)
title = 'ModflowNwtCollection'
keywords = ('MODFLOW-NWT Input data', 'MODFLOW-NWT Output data',
'MODFLOW-NWT')
rtype = 'CollectionResource'
resource_id = hs.createResource(rtype,
title,
abstract=abstract,
keywords=keywords)
metaData = {'relations': []}
newObject = {}
newObject['type'] = 'hasPart'
newObject['value'] = 'http://www.hydroshare.org/resource/' + str(
id) + '/'
metaData['relations'].append(newObject)
newObject = {}
newObject['type'] = 'hasPart'
newObject['value'] = 'http://www.hydroshare.org/resource/' + str(
output_id) + '/'
metaData['relations'].append(newObject)
hs.updateScienceMetadata(resource_id, metadata=metaData)
return output
return render_template('login.html', id=str(id))
def download_executable_lubuntu_hs(save_filepath):
resource_id = 'a5dbd5b198c9468387f59f3fefc11e22'
hs = HydroShare()
hs.getResource(resource_id, destination=save_filepath, unzip=True)
resource_name = 'summa-master.zip'
executable_filepath = save_filepath + '/' + resource_id + '/' + resource_id + '/data/contents/' + resource_name
shutil.unpack_archive(executable_filepath,
extract_dir=os.path.dirname(executable_filepath))
executable = save_filepath + '/' + resource_id + '/' + resource_id + '/data/contents/summa-master/bin'
return os.path.dirname(executable)
def install_test_cases_hs(save_filepath):
resource_id = 'a0105d479c334764ba84633c5b9c1c01'
hs = HydroShare()
hs.getResource(resource_id, destination=save_filepath, unzip=True)
resource_name = 'summatestcases-2.x.tar.gz'
testcase_filepath = save_filepath + '/' + resource_id + '/' + resource_id + '/data/contents/' + resource_name
shutil.unpack_archive(testcase_filepath,
extract_dir=os.path.dirname(testcase_filepath))
cmd = "cd {}/summaTestCases_2.x/; ./installTestCases_local.sh".format(
os.path.dirname(testcase_filepath))
subprocess.run(cmd, shell=True)
return os.path.dirname(testcase_filepath)
def get_hs_resource(resource_id, file_path):
hs = HydroShare()
hs.getResource(resource_id, destination=file_path, unzip=True)
# unpack the simulation archive and remove unncessary files
hs_resource_dir = os.path.join(file_path, resource_id, resource_id,
'data/contents/')
hs_resource = os.listdir(hs_resource_dir)
shutil.unpack_archive(hs_resource_dir + hs_resource[0],
extract_dir=file_path)
cmd = "rm -rf " + os.path.join(file_path, resource_id)
subprocess.run(cmd, shell=True)
def get_hs_resource(resource_id, file_path):
hs = HydroShare()
hs.getResource(resource_id, destination=file_path, unzip=True)
# unpack the simulation archive and remove unncessary files
hs_resource_dir = os.path.join(file_path, resource_id, resource_id,
'data/contents/')
hs_resource = os.listdir(hs_resource_dir)
shutil.unpack_archive(hs_resource_dir + hs_resource[0],
extract_dir=file_path)
shutil.rmtree(os.path.join(file_path, resource_id))
return hs_resource[0].split(".")[0]
def download_model_instance(resource_id):
path = (os.getcwd() + '/' + resource_id + '/' + resource_id +
'/data/contents/')
hs = HydroShare()
hs.getResource(resource_id, destination=os.getcwd(), unzip=True)
# unpack the simulation archive and remove unncessary files
Model_Instance_Name = os.listdir(path)[0]
shutil.unpack_archive(path + Model_Instance_Name, extract_dir=os.getcwd())
cmd = "rm -rf " + resource_id
subprocess.run(cmd, shell=True)
return Model_Instance_Name.split('.')[0]
def test_create_get_delete_resource(self):
hs = HydroShare()
abstract = 'Abstract for hello world resource'
title = 'Minimal hello world resource'
keywords = ('hello', 'world')
rtype = 'GenericResource'
fname = 'mocks/data/minimal_resource_file.txt'
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Create
newres = hs.createResource(rtype,
title,
resource_file=fname,
keywords=keywords,
abstract=abstract)
self.assertIsNotNone(newres)
sysmeta = hs.getSystemMetadata(newres)
self.assertEqual(sysmeta['resource_id'], newres)
self.assertEqual(sysmeta['resource_type'], rtype)
self.assertFalse(sysmeta['public'])
with HTTMock(mocks.hydroshare.accessRules_put):
# Make resource public
hs.setAccessRules(newres, public=True)
sysmeta = hs.getSystemMetadata(newres)
self.assertTrue(sysmeta['public'])
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Get
tmpdir = tempfile.mkdtemp()
hs.getResource(newres, destination=tmpdir)
with ZipFile(
os.path.join(tmpdir,
'511debf8858a4ea081f78d66870da76c.zip'),
'r') as zfile:
self.assertTrue(
'511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt'
in zfile.namelist())
downloaded = zfile.open(
'511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt',
'r')
original = open('mocks/data/minimal_resource_file.txt', 'r')
self.assertEqual(downloaded.read(), original.read())
downloaded.close()
original.close()
shutil.rmtree(tmpdir)
# Delete
delres = hs.deleteResource(newres)
self.assertEqual(delres, newres)
def test_create_get_delete_resource(self):
hs = HydroShare(prompt_auth=False)
abstract = 'Abstract for hello world resource'
title = 'Minimal hello world resource'
keywords = ('hello', 'world')
rtype = 'GenericResource'
fname = 'mocks/data/minimal_resource_file.txt'
metadata = json.dumps([{'coverage': {'type': 'period', 'value': {'start': '01/01/2000',
'end': '12/12/2010'}}},
{'creator': {'name': 'John Smith'}},
{'contributor': {'name': 'Lisa Miller'}}])
extra_metadata = json.dumps({'latitude': '40', 'longitude': '-111'})
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Create
newres = hs.createResource(rtype, title, resource_file=fname, keywords=keywords,
abstract=abstract, metadata=metadata, extra_metadata=extra_metadata)
self.assertIsNotNone(newres)
sysmeta = hs.getSystemMetadata(newres)
self.assertEqual(sysmeta['resource_id'], newres)
self.assertEqual(sysmeta['resource_type'], rtype)
self.assertFalse(sysmeta['public'])
with HTTMock(mocks.hydroshare.accessRules_put):
# Make resource public
hs.setAccessRules(newres, public=True)
sysmeta = hs.getSystemMetadata(newres)
self.assertTrue(sysmeta['public'])
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Get
tmpdir = tempfile.mkdtemp()
hs.getResource(newres, destination=tmpdir)
with ZipFile(os.path.join(tmpdir, '511debf8858a4ea081f78d66870da76c.zip'), 'r') as zfile:
self.assertTrue('511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt' in zfile.namelist())
downloaded = zfile.open('511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt', 'r')
original = open('mocks/data/minimal_resource_file.txt', 'rb')
self.assertEqual(downloaded.read(), original.read())
downloaded.close()
original.close()
shutil.rmtree(tmpdir)
# Delete
delres = hs.deleteResource(newres)
self.assertEqual(delres, newres)
def download_hs_res(resquest):
# get the value of para my_res_id from the url
res_id = resquest.GET['my_res_id']
# download the hydroshare res from hydroshare server to tethys server
hs = HydroShare()
hs.getResource(res_id, destination='/tmp')
# return the res stored on tethys server to frontend/client
response = HttpResponse(open("/tmp/{0}.zip".format(res_id), 'rb').read(), content_type='application/zip')
#{0} is the place from the .format.
#rb is readable binary
response['Content-Disposition'] = "attachment; filename={0}.zip".format(res_id)
#This tells you what type of files it is
response['Content-Length'] = os.path.getsize('/tmp/{0}.zip'.format(res_id))
# So this line helps the browser know how large the file is and calculate time.
return response
def download_model_instance_pangeo(resource_id):
path = (os.getcwd() + '/' + resource_id + '/' + resource_id +
'/data/contents/')
hs = HydroShare()
hs.getResource(resource_id, destination=os.getcwd(), unzip=True)
# unpack the simulation archive and remove unncessary files
Model_Instance_Name = os.listdir(path)[1]
shutil.unpack_archive(path + Model_Instance_Name, extract_dir=os.getcwd())
cmd = "rm -rf " + resource_id
subprocess.run(cmd, shell=True)
cmd = ('cd ' + Model_Instance_Name.split('.')[0] +
'/; chmod +x ./installTestCases_local.sh')
subprocess.run(cmd, shell=True, stderr=subprocess.STDOUT)
cmd = ('cd ' + Model_Instance_Name.split('.')[0] +
'/; ./installTestCases_local.sh')
subprocess.run(cmd, shell=True, stderr=subprocess.STDOUT)
return Model_Instance_Name.split('.')[0]
def run_service(user_input):
auth = HydroShareAuthBasic(hs_username, hs_password)
hs = HydroShare(auth=auth)
client = HydroDS(username=ci_username, password=ci_password)
# step1: get raster resource files from HydroShare # TODO remember to check if the resource is downloadable
resource_id = user_input['input_raster_url_path']
destination = tempfile.mkdtemp()
hs.getResource(resource_id, destination, unzip=True)
raster_file_folder = '{0}/{1}/{2}/data/contents'.format(destination, resource_id, resource_id)
raster_file_path_list = [os.path.join(raster_file_folder, f) for f in os.listdir(raster_file_folder) if
'.vrt' not in f]
upload_file_url = client.upload_file(file_to_upload=raster_file_path_list[0])
# step2: processing files in HydroDS
output_raster_name = 'process_{}'.format(upload_file_url.split('/')[-1])
output_file = client.project_resample_raster(input_raster_url_path=upload_file_url,
cell_size_dx=int(user_input['cell_size_dx']),
cell_size_dy=int(user_input['cell_size_dy']),
output_raster=output_raster_name,
resample=user_input['resample'],
epsg_code=int(user_input['proj_code']) if user_input['proj_code_type']=='epsg_code' else None,
utm_zone=int(user_input['proj_code']) if user_input['proj_code_type']=='utm_zone' else None,
)
# step3: download file and create HydroShare resource
save_as = '{}/{}'.format(destination, output_file['output_raster'].split('/')[-1])
client.download_file(file_url_path=output_file['output_raster'], save_as=save_as)
title = user_input['output_raster']
rtype = 'RasterResource'
resource_id = hs.createResource(rtype, title, resource_file=save_as)
# step4: clean up the temp in Tethys and HydroDS
shutil.rmtree(destination)
client.delete_my_file(output_file['output_raster'].split('/')[-1])
client.delete_my_file(upload_file_url.split('/')[-1])
return {'is_success': True, 'message': 'http://www.hydroshare.org/resource/{}/'.format(resource_id)}
def test_create_get_delete_resource(self):
hs = HydroShare()
abstract = 'Abstract for hello world resource'
title = 'Minimal hello world resource'
keywords = ('hello', 'world')
rtype = 'GenericResource'
fname = 'mocks/data/minimal_resource_file.txt'
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Create
newres = hs.createResource(rtype, title, resource_file=fname, keywords=keywords, abstract=abstract)
self.assertIsNotNone(newres)
sysmeta = hs.getSystemMetadata(newres)
self.assertEqual(sysmeta['resource_id'], newres)
self.assertEqual(sysmeta['resource_type'], rtype)
self.assertFalse(sysmeta['public'])
with HTTMock(mocks.hydroshare.accessRules_put):
# Make resource public
hs.setAccessRules(newres, public=True)
sysmeta = hs.getSystemMetadata(newres)
self.assertTrue(sysmeta['public'])
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Get
tmpdir = tempfile.mkdtemp()
hs.getResource(newres, destination=tmpdir)
with ZipFile(os.path.join(tmpdir, '511debf8858a4ea081f78d66870da76c.zip'), 'r') as zfile:
self.assertTrue('511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt' in zfile.namelist())
downloaded = zfile.open('511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt', 'r')
original = open('mocks/data/minimal_resource_file.txt', 'r')
self.assertEqual(downloaded.read(), original.read())
downloaded.close()
original.close()
shutil.rmtree(tmpdir)
# Delete
delres = hs.deleteResource(newres)
self.assertEqual(delres, newres)
def runScript(id):
auth = HydroShareAuthBasic(username='', password='')
hs = HydroShare(auth=auth)
hs.getResource(id, destination='/home/ubuntu/hydroshare_app/', unzip=True)
subprocess.call("sudo cp " + str(id) + '/' + str(id) +
'/data/contents/* /home/ubuntu/hydroshare_app/Data',
shell=True)
subprocess.call("sudo rm -r " + str(id), shell=True)
process()
#Locate the file with the .nam extension
os.chdir('MODFLOW')
for file in glob.glob("*.nam"):
filename = file
# Run the model
subprocess.call("sudo ./mfnwt " + filename, shell=True)
try:
hs.deleteResourceFile(id, filename.split(".")[0] + '.list')
except:
pass
#Upload to hydroshare
hs.addResourceFile(id, filename.split(".")[0] + '.list')
subprocess.call("sudo rm /home/ubuntu/hydroshare_app/MODFLOW/*.*",
shell=True)
subprocess.call("sudo rm -r /home/ubuntu/hydroshare_app/Scratch",
shell=True)
subprocess.call("sudo rm -r /home/ubuntu/hydroshare_app/Framework",
shell=True)
subprocess.call("sudo rm /home/ubuntu/hydroshare_app/Data/*", shell=True)
return json.dumps(hs.getScienceMetadata(id))
def test_get_resource(self):
hs = HydroShare(hostname=self.url)
# ideally, look a system metadata, and if file is small, then load it into memory.
sysmeta = hs.getSystemMetadata(self.a_resource_id)
self.assertEqual(sysmeta['resource_id'], self.a_resource_id)
self.assertEqual(sysmeta['resource_type'], self.a_resource_type)
self.assertTrue(sysmeta['public'])
# if (sysmeta['size']) < 1000000:
stream = hs.getResource(self.a_resource_id)
in_memory = StringIO.StringIO()
for chunk in stream:
in_memory.write(chunk)
self.assertTrue(zipfile.is_zipfile(in_memory))
with zipfile.ZipFile(in_memory, 'r') as myzip:
filelist = myzip.infolist()
success = False
for f in filelist:
if self.a_resource_filename in f.filename:
success = True
break
self.assertTrue(success, "did not find file")
class hydroshare():
def __init__(self, username=None):
self.hs = None
self.content = {}
# load the HS environment variables
# self.load_environment()
uname = username
if uname is None:
uname = os.environ['HS_USR_NAME']
# get a secure connection to hydroshare
auth = self.getSecureConnection(uname)
try:
self.hs = HydroShare(auth=auth)
self.hs.getUserInfo()
display(HTML('<b style="color:green;">Successfully established a connection with HydroShare</b>'))
except HydroShareHTTPException as e:
display(HTML(
'<p style="color:red;"><b>Failed to establish a connection with HydroShare. Please check that you provided the correct credentials</b><br>%s </p>' % e))
# remove the cached authentication
auth_path = os.path.join(os.path.dirname(__file__), '../../../.auth')
os.remove(auth_path)
return None
def _getResourceFromHydroShare(self, resourceid, destination='.', unzip=True):
# download the resource
pid = self.hs.getResource(resourceid, destination=destination, unzip=unzip)
threadResults.put(pid)
def _createHydroShareResource(self, res_type, title, abstract, content_file,
keywords=[]):
resid = self.hs.createResource(res_type, title, resource_file=content_file,
keywords=keywords, abstract=abstract)
threadResults.put(resid)
def _addContentToExistingResource(self, resid, content_files):
for f in content_files:
self.hs.addResourceFile(resid, f)
def load_environment(self):
env_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'env')
with open(env_path, 'r') as f:
lines = f.readlines()
print('Adding the following system variables:')
for line in lines:
k, v = line.strip().split('=')
os.environ[k] = v
print(' %s = %s' % (k, v))
print('\nThese can be accessed using the following command: ')
print(' os.environ[key]')
print('\n (e.g.)\n os.environ["HS_USR_NAME"] => %s' % os.environ['HS_USR_NAME'])
def getSecureConnection(self, username):
"""
Establishes a secure connection with HydroShare.
Args:
email: email address associated with HydroShare
Returns:
HydroShare connection
"""
auth_path = os.path.join(os.path.dirname(__file__), '../../../.auth')
if not os.path.exists(auth_path):
print('\nThe hs_utils library requires a secure connection to your HydroShare account.')
# p = getpass.getpass('Enter the HydroShare password for user \'%s\': ' % username)
p = '7jmftUpata'
auth = HydroShareAuthBasic(username=username, password=p)
with open(auth_path, 'wb') as f:
pickle.dump(auth, f, protocol=2)
else:
with open(auth_path, 'rb') as f:
auth = pickle.load(f)
return auth
def getResourceMetadata(self, resid):
science_meta = self.hs.getScienceMetadata(resid)
system_meta = self.hs.getSystemMetadata(resid)
return ResourceMetadata(system_meta, science_meta)
def createHydroShareResource(self, abstract, title, derivedFromId, keywords=[], resource_type='GenericResource',
content_files=[], public=False):
# query the hydroshare resource types and make sure that resource_type is valid
restypes = {r.lower(): r for r in self.hs.getResourceTypes()}
try:
res_type = restypes[resource_type]
except KeyError:
display(HTML('<b style="color:red;">[%s] is not a valid HydroShare resource type.</p>' % resource_type))
return None
# get the 'derived resource' metadata
if derivedFromId is not None:
try:
# update the abstract and keyword metadata
meta = self.getResourceMetadata(derivedFromId)
abstract = meta.abstract + '\n\n[Modified in JupyterHub on %s]\n%s' % (dt.now(), abstract)
keywords = set(keywords + meta.keywords)
except:
display(HTML(
'<b style="color:red;">[%s] is not a valid HydroShare resource id for setting the "derivedFrom" attribute.</p>' % derivedFromId))
return None
else:
response = input(
'You have indicated that this resource is NOT derived from any existing HydroShare resource. Are you sure that this is what you intended? [Y/n]')
if response == 'n':
display(HTML('<b style="color:red;">Resource creation aborted.</p>'))
return
f = None if len(content_files) == 0 else content_files[0]
# create the hs resource (1 content file allowed)
t = threading.Thread(target=self._createHydroShareResource, args=(res_type, title, abstract, f),
kwargs={'keywords': keywords})
resid = runThreadedFunction(t, msg='Creating HydroShare Resource', success='Resource Creation Successful')
# add the remaining content files to the hs resource
self.addContentToExistingResource(resid, content_files[1:])
display(HTML('Resource id: %s' % resid))
display(HTML('<a href=%s target="_blank">%s<a>' % (
'https://www.hydroshare.org/resource/%s' % resid, 'Open Resource in HydroShare')))
def getResourceFromHydroShare(self, resourceid, destination='.'):
"""
Downloads the content of HydroShare resource to the JupyterHub userspace
Args:
resourceid: id of the HydroShare resource to query
destination: path relative to /user/[username]/notebooks/data
"""
default_dl_path = 'C:\\Users\\12672\\Box\\data\\NEON\\lczodata\\' # os.environ['DATA']
dst = os.path.abspath(os.path.join(default_dl_path, destination))
download = True
# check if the data should be overwritten
dst_res_folder = os.path.join(dst, resourceid)
if os.path.exists(dst_res_folder):
res = input(
'This resource already exists in your userspace.\nWould you like to overwrite this data [Y/n]? ')
if res != 'n':
shutil.rmtree(dst_res_folder)
else:
download = False
# re-download the content if desired
if download:
try:
# get some metadata about the resource that will be downloaded
res_meta = self.hs.getSystemMetadata(resourceid)
header = requests.head(res_meta['bag_url'])
# download the resource (threaded)
t = threading.Thread(target=self._getResourceFromHydroShare,
args=(resourceid,), kwargs={'destination': dst, 'unzip': True})
runThreadedFunction(t, msg='Downloading', success='Download Completed Successfully')
except Exception as e:
display(HTML('<b style="color:red">Failed to retrieve resource content from HydroShare: %s</b>' % e))
return None
# load the resource content
outdir = os.path.join(dst, '%s/%s' % (resourceid, resourceid))
content_files = glob.glob(os.path.join(outdir, 'data/contents/*'))
# display(HTML('Your Content is located at: %s' % outdir))
content = {}
for f in content_files:
fname = os.path.basename(f)
content[fname] = f
display_resource_content_files(content)
# check_for_ipynb(content_files)
# update the content dictionary
self.content.update(content)
def addContentToExistingResource(self, resid, content):
t = threading.Thread(target=self._addContentToExistingResource, args=(resid, content))
runThreadedFunction(t, msg='Adding Content to Resource', success='Successfully Added Content Files')
def loadResource(self, resourceid):
resdir = find_resource_directory(resourceid)
if resdir is None:
display(HTML(
'<b style="color:red">Could not find any resource matching the id [%s].</b> <br> It is likely that this resource has not yet been downloaded from HydroShare.org, or it was removed from the JupyterHub server. Please use the following command to aquire the resource content: <br><br> <code> hs.getResourceFromHydroShare(%s)</code>.' % (
resourceid, resourceid)))
return
content_files = glob.glob(os.path.join(resdir, '%s/data/contents/*' % resourceid))
display(HTML('<p>Downloaded content is located at: %s</p>' % resdir))
display(HTML('<p>Found %d content file(s). \n</p>' % len(content_files)))
content = {}
for f in content_files:
fname = os.path.basename(f)
content[fname] = f
display_resource_content_files(content)
self.content = content
def test_create_get_delete_resource(self):
hs = HydroShare(prompt_auth=False)
abstract = 'Abstract for hello world resource'
title = 'Minimal hello world resource'
keywords = ('hello', 'world')
rtype = 'GenericResource'
fname = 'mocks/data/minimal_resource_file.txt'
metadata = json.dumps([{
'coverage': {
'type': 'period',
'value': {
'start': '01/01/2000',
'end': '12/12/2010'
}
}
}, {
'creator': {
'name': 'John Smith'
}
}, {
'contributor': {
'name': 'Lisa Miller'
}
}])
extra_metadata = json.dumps({'latitude': '40', 'longitude': '-111'})
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Create
newres = hs.createResource(rtype,
title,
resource_file=fname,
keywords=keywords,
abstract=abstract,
metadata=metadata,
extra_metadata=extra_metadata)
self.assertIsNotNone(newres)
sysmeta = hs.getSystemMetadata(newres)
self.assertEqual(sysmeta['resource_id'], newres)
self.assertEqual(sysmeta['resource_type'], rtype)
self.assertFalse(sysmeta['public'])
with HTTMock(mocks.hydroshare.accessRules_put):
# Make resource public
hs.setAccessRules(newres, public=True)
sysmeta = hs.getSystemMetadata(newres)
self.assertTrue(sysmeta['public'])
with HTTMock(mocks.hydroshare.createResourceCRUD):
# Get
tmpdir = tempfile.mkdtemp()
hs.getResource(newres, destination=tmpdir)
with ZipFile(
os.path.join(tmpdir,
'511debf8858a4ea081f78d66870da76c.zip'),
'r') as zfile:
self.assertTrue(
'511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt'
in zfile.namelist())
downloaded = zfile.open(
'511debf8858a4ea081f78d66870da76c/data/contents/minimal_resource_file.txt',
'r')
original = open('mocks/data/minimal_resource_file.txt', 'rb')
self.assertEqual(downloaded.read(), original.read())
downloaded.close()
original.close()
shutil.rmtree(tmpdir)
# Delete
hs.deleteResource(newres)
class ResourceManager:
""" Class that defines a handler for working with all of a user's resources.
This is where they will be able to delete a resource, create a new one, or
just get the list of a user's resources in hydroshare or jupyterhub.
"""
def __init__(self):
"""Makes an output folder for storing HS files locally, if none exists,
and sets up authentication on hydroshare API.
"""
config = get_config_values(['dataPath', 'hydroShareHostname'])
self.hs_hostname = 'www.hydroshare.org'
# TODO: Rename to hydroshare_resource_data
self.output_folder = Path('local_hs_resources')
if config:
if 'hydroShareHostname' in config:
self.hs_hostname = config['hydroShareHostname']
if 'dataPath' in config:
self.output_folder = Path(config['dataPath'])
if not self.output_folder.is_dir():
# Let any exceptions that occur bubble up
self.output_folder.mkdir(parents=True)
self.hs_api_conn = None # Use 'authenticate' to initialize
self.username = None
def authenticate(self, username=None, password=None, save=False):
""" Attempts to authenticate with HydroShare.
:param username: the user's HydroShare username
:type username: str
:param password: the user's HydroShare password
:type password: str
:param save: whether or not to save the credentials to the config file if the authentication succeeds
:type save: bool
:return: the user's information (name, email, etc) from HydroShare if successful, None otherwise
"""
if not username or not password:
# Check the config file for a username and password
config = get_config_values(['u', 'p'])
if not config or 'u' not in config or 'p' not in config:
return None # No passed credentials and no saved credentials -- can't authenticate
username = config['u']
password = base64.b64decode(config['p']).decode('utf-8')
# Try to authenticate
auth = HydroShareAuthBasic(username=username, password=password)
self.hs_api_conn = HydroShare(auth=auth, hostname=self.hs_hostname)
try:
user_info = self.hs_api_conn.getUserInfo()
self.username = user_info.get('username')
except HydroShareHTTPException as e:
if e.status_code == 401: # Unauthorized
return None # Authentication failed
raise e # Some other error -- bubble it up
# Authentication succeeded
if save:
# Save the username and password
saved_successfully = set_config_values({
'u':
username,
'p':
str(
base64.b64encode(
password.encode('utf-8')).decode('utf-8')),
})
if saved_successfully:
logging.info(
'Successfully saved HydroShare credentials to config file.'
)
return user_info # Authenticated successfully
def is_authenticated(self):
if self.hs_api_conn is None:
self.authenticate()
return self.hs_api_conn is not None
def save_resource_locally(self, res_id):
""" Downloads a resource to the local filesystem if a copy does not already exist locally
:param res_id: the resource ID
:type res_id: str
"""
# Get resource from HS if it doesn't already exist locally
if not (self.output_folder / res_id).exists():
logging.info(f"Downloading resource {res_id} from HydroShare...")
self.hs_api_conn.getResource(res_id,
destination=self.output_folder,
unzip=True)
def get_user_info(self):
"""Gets information about the user currently logged into HydroShare
"""
user_info = None
error = None
try:
user_info = self.hs_api_conn.getUserInfo()
except HydroShareHTTPException as e:
if e.status_code == 401: # Unauthorized
error = HYDROSHARE_AUTHENTICATION_ERROR
else:
error = {
'type': 'GenericHydroShareHTTPException',
'message': e.status_msg,
}
return user_info, error
def delete_resource_locally(self, res_id):
""" Attempts to delete the local copy of the resource files from the disk
:param res_id: the ID of the resource to delete
:type res_id: str
"""
resource_path = self.output_folder / res_id
if not resource_path.exists():
return {
'type':
'FileNotFoundError',
'message':
f'Could not find a local copy of resource {res_id} to delete.',
}
try:
shutil.rmtree(str(resource_path))
except IOError as e:
return {
'type':
'IOError',
'message':
f'Something went wrong. Could not delete resource {res_id}.',
}
return None # No error
def delete_resource_from_hs(self, res_id):
try:
self.hs_api_conn.deleteResource(res_id)
except HydroShareHTTPException as e:
return {
'type': 'GenericHydroShareHTTPException',
'message': e.status_msg,
}
return None # No error
def get_local_resource_ids(self):
""" Gets a list of IDs of all the resources saved locally
:return a set of strings containing all of the resource IDs
:rtype set<str>
"""
return set(map(lambda p: p.name, self.output_folder.glob('*')))
def get_list_of_user_resources(self):
# TODO: speed this up
"""Gets list of all the resources for the logged in user, including
those stored on hydroshare and those stored locally on jupyterhub
and information about each one including whether HS ones are stored
locally.
Assumes there are no local resources that don't exist in HS
"""
error = None
resources = {}
# Get local res_ids
self.local_res_ids = self.get_local_resource_ids()
# Get the user's resources from HydroShare
user_hs_resources = self.hs_api_conn.resources(owner=self.username)
try:
hs_resources = list(
user_hs_resources) # Resources can't be listed if auth fails
except AttributeError:
return None, HYDROSHARE_AUTHENTICATION_ERROR
for res in hs_resources:
res_id = res['resource_id']
resources[res_id] = {
'abstract': res.get('abstract'),
'authors': res.get('authors'),
'creator': res.get('creator'),
'created': res.get('date_created'),
'lastUpdated': res.get('date_last_updated'),
'localCopyExists': res_id in self.local_res_ids,
'localFiles': res.get('localFiles'),
'id': res_id,
'isPublic': res.get('public'),
'published': res.get('published'),
'status': res.get('status'),
'title': res.get('resource_title'),
'url': res.get('resource_url'),
}
return list(resources.values()), error
def create_HS_resource(self,
resource_title,
creators,
abstract="",
privacy="Private"):
"""
Creates a hydroshare resource from the metadata specified in a dict
using the given resource_title and specified creators
"""
error = None
resource_id = None
# Type errors for resource_title and creators
if not isinstance(resource_title, str):
error = {
'type': 'IncorrectType',
'message': 'Resource title should be a string.'
}
return resource_id, error
if not isinstance(creators, list) or not all(
isinstance(creator, str) for creator in creators):
error = {
'type': 'IncorrectType',
'message': '"Creators" object should be a list of strings.'
}
return resource_id, error
if abstract is None:
abstract = ""
if privacy == "Public":
public = True
else:
public = False
meta_metadata = []
for creator in creators:
meta_metadata.append({"creator": {"name": creator}})
meta_metadata = json.dumps(meta_metadata)
metadata = {
'abstract': abstract,
'title': resource_title,
'keywords': (),
'rtype': 'GenericResource',
'fpath': '',
'metadata': meta_metadata,
'extra_metadata': ''
}
resource_id = ''
try:
resource_id = self.hs_api_conn.createResource(
metadata['rtype'],
metadata['title'],
resource_file=metadata['fpath'],
keywords=metadata['keywords'],
abstract=metadata['abstract'],
metadata=metadata['metadata'],
extra_metadata=metadata['extra_metadata'])
self.hs_api_conn.setAccessRules(resource_id, public=public)
except:
error = {
'type': 'UnknownError',
'message': 'Unable to create resource.'
}
return resource_id, error
def create_copy_of_resource_in_hs(self, src_res_id):
""" Makes a copy of a resource in HydroShare and updates the local copy of the
old resource to point to then ew copy.
:param src_res_id: the ID of the resource in HydroShare to duplicate
:type src_res_id: str
:returns the new resource ID
"""
response = self.hs_api_conn.resource(src_res_id).copy()
new_id = response.content.decode("utf-8") # b'id'
is_local = src_res_id in self.local_res_ids
# if a local version exists under the old resource ID, rename it to point to the new one
if is_local:
og_path = self.output_folder / src_res_id / src_res_id
new_path = self.output_folder / new_id / new_id
shutil.move(str(og_path), str(new_path))
# Change name to 'Copy of []'
title = self.hs_api_conn.getScienceMetadata(new_id)['title']
new_title = "Copy of " + title
self.hs_api_conn.updateScienceMetadata(new_id, {"title": new_title})
return new_id
def get_archive_message(self):
""" Gets the message to display on the resource page prompting the user to archive
their resources to HydroShare
"""
loaded_archive_message = get_config_values(['archiveMessage'])
if loaded_archive_message and loaded_archive_message['archiveMessage']:
archive_message = loaded_archive_message['archiveMessage']
else:
archive_message = input("Please enter the archive message: ")
#Save the archive message
saved_successfully = set_config_values({
'archiveMessage':
archive_message,
})
if saved_successfully:
logging.info(
'Successfully saved archive message to config file.')
return archive_message
from hs_restclient import HydroShare, HydroShareAuthBasic
# Download LCZO sesnor database from Hydroshare
# link to the Hydroshare resource https://www.hydroshare.org/resource/b38bc00887ec45ac9499f9dea45eb8d5/
auth = HydroShareAuthBasic(username="******", password="******")
hs = HydroShare(auth=auth)
hs.getResource('b38bc00887ec45ac9499f9dea45eb8d5',
destination='./lczodata',
unzip=True)
