def nightly_zips_cleanup():
# delete 2 days ago
date_folder = (date.today() - timedelta(2)).strftime('%Y-%m-%d')
zips_daily_date = "zips/{daily_date}".format(daily_date=date_folder)
istorage = IrodsStorage()
if istorage.exists(zips_daily_date):
istorage.delete(zips_daily_date)
def migrate_tif_file(apps, schema_editor):
# create a vrt file from tif file for each of the Raster Resources
log = logging.getLogger()
istorage = IrodsStorage()
for res in RasterResource.objects.all():
try:
if len(res.files.all()) == 1:
res_file = res.files.all().first()
vrt_file_path = create_vrt_file(res_file.resource_file)
if os.path.isfile(vrt_file_path):
files = (UploadedFile(file=open(vrt_file_path, 'r'),
name=os.path.basename(vrt_file_path)))
hydroshare.add_resource_files(res.short_id, files)
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
print("Deleted bag for resource ID:" + str(res.short_id))
resource_modified(res, res.creator)
log.info('Tif file conversion to VRT successful for resource:ID:{} '
'Title:{}'.format(res.short_id, res.metadata.title.value))
else:
log.error('Tif file conversion to VRT unsuccessful for resource:ID:{} '
'Title:{}'.format(res.short_id, res.metadata.title.value))
if os.path.exists(vrt_file_path):
shutil.rmtree(os.path.dirname(vrt_file_path))
except:
pass
def tearDown(self):
super(TestFolderDownloadZip, self).tearDown()
if self.res:
self.res.delete()
GenericResource.objects.all().delete()
istorage = IrodsStorage()
if istorage.exists(self.output_path):
istorage.delete(self.output_path)
def delete_fed_zone_file(file_name_with_full_path):
'''
Args:
file_name_with_full_path: the absolute full logical path in a federated iRODS zone
Returns:
None, but exceptions will be raised if there is an issue with iRODS delete operation
'''
istorage = IrodsStorage('federated')
istorage.delete(file_name_with_full_path)
def tearDown(self):
super(TestFolderDownloadZip, self).tearDown()
if self.res:
self.res.delete()
if self.test_file:
os.remove(self.test_file.name)
if self.refts_file:
os.remove(self.refts_file.name)
GenericResource.objects.all().delete()
istorage = IrodsStorage()
if istorage.exists("zips"):
istorage.delete("zips")
def tearDown(self):
super(TestFolderDownloadZip, self).tearDown()
if self.res:
self.res.delete()
if self.test_file:
self.test_file.close()
os.remove(self.test_file.name)
if self.refts_file:
self.refts_file.close()
os.remove(self.refts_file.name)
GenericResource.objects.all().delete()
istorage = IrodsStorage()
if istorage.exists("zips"):
istorage.delete("zips")
def migrate_tif_file(apps, schema_editor):
# create a vrt file from tif file for each of the Raster Resources
log = logging.getLogger()
istorage = IrodsStorage()
for res in RasterResource.objects.all():
try:
if len(res.files.all()) == 1:
res_file = res.files.all().first()
vrt_file_path = create_vrt_file(res_file.resource_file)
if os.path.isfile(vrt_file_path):
files = (UploadedFile(
file=open(vrt_file_path, 'r'),
name=os.path.basename(vrt_file_path)))
hydroshare.add_resource_files(res.short_id, files)
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
print("Deleted bag for resource ID:" +
str(res.short_id))
resource_modified(res, res.creator)
log.info(
'Tif file conversion to VRT successful for resource:ID:{} '
'Title:{}'.format(res.short_id,
res.metadata.title.value))
else:
log.error(
'Tif file conversion to VRT unsuccessful for resource:ID:{} '
'Title:{}'.format(res.short_id,
res.metadata.title.value))
if os.path.exists(vrt_file_path):
shutil.rmtree(os.path.dirname(vrt_file_path))
except:
pass
def nightly_zips_cleanup():
# delete 2 days ago
date_folder = (date.today() - timedelta(2)).strftime('%Y-%m-%d')
zips_daily_date = "zips/{daily_date}".format(daily_date=date_folder)
if __debug__:
logger.debug("cleaning up {}".format(zips_daily_date))
istorage = IrodsStorage()
if istorage.exists(zips_daily_date):
istorage.delete(zips_daily_date)
federated_prefixes = BaseResource.objects.all().values_list('resource_federation_path')\
.distinct()
for p in federated_prefixes:
prefix = p[0] # strip tuple
if prefix != "":
zips_daily_date = "{prefix}/zips/{daily_date}"\
.format(prefix=prefix, daily_date=date_folder)
if __debug__:
logger.debug("cleaning up {}".format(zips_daily_date))
istorage = IrodsStorage("federated")
if istorage.exists(zips_daily_date):
istorage.delete(zips_daily_date)
def nightly_zips_cleanup():
# delete 2 days ago
date_folder = (date.today() - timedelta(2)).strftime('%Y-%m-%d')
zips_daily_date = "zips/{daily_date}".format(daily_date=date_folder)
if __debug__:
logger.debug("cleaning up {}".format(zips_daily_date))
istorage = IrodsStorage()
if istorage.exists(zips_daily_date):
istorage.delete(zips_daily_date)
federated_prefixes = BaseResource.objects.all().values_list('resource_federation_path')\
.distinct()
for p in federated_prefixes:
prefix = p[0] # strip tuple
if prefix != "":
zips_daily_date = "{prefix}/zips/{daily_date}"\
.format(prefix=prefix, daily_date=date_folder)
if __debug__:
logger.debug("cleaning up {}".format(zips_daily_date))
istorage = IrodsStorage("federated")
if istorage.exists(zips_daily_date):
istorage.delete(zips_daily_date)
def delete_bag(resource):
"""
delete the resource bag
Parameters:
:param resource: the resource to delete the bag for.
:return: none
"""
res_id = resource.short_id
istorage = IrodsStorage()
# delete resource directory first to remove all generated bag-related files for the resource
istorage.delete(res_id)
# the resource bag may not exist due to on-demand bagging
bagname = 'bags/{res_id}.zip'.format(res_id=res_id)
if istorage.exists(bagname):
# delete the resource bag
istorage.delete(bagname)
# delete the bags table
for bag in resource.bags.all():
bag.delete()
def delete_bag(resource):
"""
delete the resource bag
Parameters:
:param resource: the resource to delete the bag for.
:return: none
"""
res_id = resource.short_id
istorage = IrodsStorage()
# delete resource directory first to remove all generated bag-related files for the resource
istorage.delete(res_id)
# the resource bag may not exist due to on-demand bagging
bagname = 'bags/{res_id}.zip'.format(res_id=res_id)
if istorage.exists(bagname):
# delete the resource bag
istorage.delete(bagname)
# delete the bags table
for bag in resource.bags.all():
bag.delete()
def migrate_tif_file(apps, schema_editor):
log = logging.getLogger()
istorage = IrodsStorage()
copy_res_fail = []
vrt_update_fail = []
vrt_update_success = []
meta_update_fail = []
meta_update_success = []
# start migration for each raster resource that has raster files
for res in RasterResource.objects.all():
if res.files.all():
# copy all the resource files to temp dir
try:
temp_dir = tempfile.mkdtemp()
for res_file in res.files.all():
shutil.copy(res_file.resource_file.file.name,
os.path.join(temp_dir, os.path.basename(res_file.resource_file.name)))
vrt_file_path = [os.path.join(temp_dir, f) for f in os.listdir(temp_dir) if '.vrt' == f[-4:]].pop()
except Exception as e:
log.exception(e.message)
copy_res_fail.append('{}:{}'.format(res.short_id, res.metadata.title.value))
continue
# update vrt file if the raster resource that has a single tif file
try:
if len(os.listdir(temp_dir)) == 2:
# create new vrt file
tif_file_path = [os.path.join(temp_dir, f) for f in os.listdir(temp_dir) if '.tif' == f[-4:]].pop()
with open(os.devnull, 'w') as fp:
subprocess.Popen(['gdal_translate', '-of', 'VRT', tif_file_path, vrt_file_path], stdout=fp, stderr=fp).wait() # remember to add .wait()
# modify the vrt file contents
tree = ET.parse(vrt_file_path)
root = tree.getroot()
for element in root.iter('SourceFilename'):
element.attrib['relativeToVRT'] = '1'
tree.write(vrt_file_path)
# delete vrt res file
for f in res.files.all():
if 'vrt' == f.resource_file.name[-3:]:
f.resource_file.delete()
f.delete()
# add new vrt file to resource
new_file = UploadedFile(file=open(vrt_file_path, 'r'), name=os.path.basename(vrt_file_path))
hydroshare.add_resource_files(res.short_id, new_file)
# update the bag
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
resource_modified(res, res.creator)
vrt_update_success.append('{}:{}'.format(res.short_id,res.metadata.title.value))
except Exception as e:
log.exception(e.message)
vrt_update_fail.append('{}:{}'.format(res.short_id,res.metadata.title.value))
# update the metadata for the band information of all the raster resources
try:
meta_updated = False
# extract meta
ori_dir = os.getcwd()
os.chdir(temp_dir)
res_md_dict = raster_meta_extract.get_raster_meta_dict(vrt_file_path)
os.chdir(ori_dir)
shutil.rmtree(temp_dir)
# update band information metadata in django
if res_md_dict['band_info']:
for i, band_meta in res_md_dict['band_info'].items():
band_obj = res.metadata.bandInformation.filter(name='Band_{}'.format(i)).first()
if band_obj:
res.metadata.update_element('bandInformation',
band_obj.id,
maximumValue=band_meta['maximumValue'],
minimumValue=band_meta['minimumValue'],
noDataValue=band_meta['noDataValue'],
)
meta_updated = True
# update the bag if meta is updated
if meta_updated:
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
resource_modified(res, res.creator)
meta_update_success.append('{}:{}'.format(res.short_id, res.metadata.title.value))
except Exception as e:
log.exception(e.message)
meta_update_fail.append('{}:{}'.format(res.short_id, res.metadata.title.value))
# Print migration results
print 'Copy resource to temp folder failure: Number: {} List: {}'.format(len(copy_res_fail), copy_res_fail)
print 'VRT file update success: Number: {} List{}'.format(len(vrt_update_success), vrt_update_success)
print 'VRT file update fail: Number: {} List{}'.format(len(vrt_update_fail), vrt_update_fail)
print 'Meta update success: Number: {} List {}'.format(len(meta_update_success), meta_update_success)
print 'Meta update fail: Number: {} List {}'.format(len(meta_update_fail), meta_update_fail)
def delete_zip(zip_path):
istorage = IrodsStorage()
if istorage.exists(zip_path):
istorage.delete(zip_path)
def migrate_tif_file(apps, schema_editor):
log = logging.getLogger()
istorage = IrodsStorage()
copy_res_fail = []
vrt_update_fail = []
vrt_update_success = []
meta_update_fail = []
meta_update_success = []
# start migration for each raster resource that has raster files
for res in RasterResource.objects.all():
if res.files.all():
# copy all the resource files to temp dir
try:
temp_dir = tempfile.mkdtemp()
for res_file in res.files.all():
shutil.copy(
res_file.resource_file.file.name,
os.path.join(
temp_dir,
os.path.basename(res_file.resource_file.name)))
vrt_file_path = [
os.path.join(temp_dir, f) for f in os.listdir(temp_dir)
if '.vrt' == f[-4:]
].pop()
except Exception as e:
log.exception(e.message)
copy_res_fail.append('{}:{}'.format(res.short_id,
res.metadata.title.value))
continue
# update vrt file if the raster resource that has a single tif file
try:
if len(os.listdir(temp_dir)) == 2:
# create new vrt file
tif_file_path = [
os.path.join(temp_dir, f) for f in os.listdir(temp_dir)
if '.tif' == f[-4:]
].pop()
with open(os.devnull, 'w') as fp:
subprocess.Popen(
[
'gdal_translate', '-of', 'VRT', tif_file_path,
vrt_file_path
],
stdout=fp,
stderr=fp).wait() # remember to add .wait()
# modify the vrt file contents
tree = ET.parse(vrt_file_path)
root = tree.getroot()
for element in root.iter('SourceFilename'):
element.attrib['relativeToVRT'] = '1'
tree.write(vrt_file_path)
# delete vrt res file
for f in res.files.all():
if 'vrt' == f.resource_file.name[-3:]:
f.resource_file.delete()
f.delete()
# add new vrt file to resource
new_file = UploadedFile(
file=open(vrt_file_path, 'r'),
name=os.path.basename(vrt_file_path))
hydroshare.add_resource_files(res.short_id, new_file)
# update the bag
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
resource_modified(res, res.creator)
vrt_update_success.append('{}:{}'.format(
res.short_id, res.metadata.title.value))
except Exception as e:
log.exception(e.message)
vrt_update_fail.append('{}:{}'.format(
res.short_id, res.metadata.title.value))
# update the metadata for the band information of all the raster resources
try:
meta_updated = False
# extract meta
ori_dir = os.getcwd()
os.chdir(temp_dir)
res_md_dict = raster_meta_extract.get_raster_meta_dict(
vrt_file_path)
os.chdir(ori_dir)
shutil.rmtree(temp_dir)
# update band information metadata in django
if res_md_dict['band_info']:
for i, band_meta in res_md_dict['band_info'].items():
band_obj = res.metadata.bandInformation.filter(
name='Band_{}'.format(i)).first()
if band_obj:
res.metadata.update_element(
'bandInformation',
band_obj.id,
maximumValue=band_meta['maximumValue'],
minimumValue=band_meta['minimumValue'],
noDataValue=band_meta['noDataValue'],
)
meta_updated = True
# update the bag if meta is updated
if meta_updated:
bag_name = 'bags/{res_id}.zip'.format(res_id=res.short_id)
if istorage.exists(bag_name):
# delete the resource bag as the old bag is not valid
istorage.delete(bag_name)
resource_modified(res, res.creator)
meta_update_success.append('{}:{}'.format(
res.short_id, res.metadata.title.value))
except Exception as e:
log.exception(e.message)
meta_update_fail.append('{}:{}'.format(
res.short_id, res.metadata.title.value))
# Print migration results
print 'Copy resource to temp folder failure: Number: {} List: {}'.format(
len(copy_res_fail), copy_res_fail)
print 'VRT file update success: Number: {} List{}'.format(
len(vrt_update_success), vrt_update_success)
print 'VRT file update fail: Number: {} List{}'.format(
len(vrt_update_fail), vrt_update_fail)
print 'Meta update success: Number: {} List {}'.format(
len(meta_update_success), meta_update_success)
print 'Meta update fail: Number: {} List {}'.format(
len(meta_update_fail), meta_update_fail)
class TestCaseCommonUtilities(object):
"""Enable common utilities for iRODS testing."""
def assert_federated_irods_available(self):
"""assert federated iRODS is available before proceeding with federation-related tests."""
self.assertTrue(
settings.REMOTE_USE_IRODS
and settings.HS_USER_ZONE_HOST == 'users.local.org'
and settings.IRODS_HOST == 'data.local.org',
"irods docker containers are not set up properly for federation testing"
)
self.irods_fed_storage = IrodsStorage('federated')
self.irods_storage = IrodsStorage()
def create_irods_user_in_user_zone(self):
"""Create corresponding irods account in user zone."""
try:
exec_cmd = "{0} {1} {2}".format(
settings.LINUX_ADMIN_USER_CREATE_USER_IN_USER_ZONE_CMD,
self.user.username, self.user.username)
output = run_ssh_command(
host=settings.HS_USER_ZONE_HOST,
uname=settings.LINUX_ADMIN_USER_FOR_HS_USER_ZONE,
pwd=settings.LINUX_ADMIN_USER_PWD_FOR_HS_USER_ZONE,
exec_cmd=exec_cmd)
for out_str in output:
if 'ERROR:' in out_str.upper():
# irods account failed to create
self.assertRaises(SessionException(-1, out_str, out_str))
user_profile = UserProfile.objects.filter(user=self.user).first()
user_profile.create_irods_user_account = True
user_profile.save()
except Exception as ex:
self.assertRaises(SessionException(-1, str(ex), str(ex)))
def delete_irods_user_in_user_zone(self):
"""Delete irods test user in user zone."""
try:
exec_cmd = "{0} {1}".format(
settings.LINUX_ADMIN_USER_DELETE_USER_IN_USER_ZONE_CMD,
self.user.username)
output = run_ssh_command(
host=settings.HS_USER_ZONE_HOST,
uname=settings.LINUX_ADMIN_USER_FOR_HS_USER_ZONE,
pwd=settings.LINUX_ADMIN_USER_PWD_FOR_HS_USER_ZONE,
exec_cmd=exec_cmd)
if output:
for out_str in output:
if 'ERROR:' in out_str.upper():
# there is an error from icommand run, report the error
self.assertRaises(
SessionException(-1, out_str, out_str))
user_profile = UserProfile.objects.filter(user=self.user).first()
user_profile.create_irods_user_account = False
user_profile.save()
except Exception as ex:
# there is an error from icommand run, report the error
self.assertRaises(SessionException(-1, str(ex), str(ex)))
def save_files_to_user_zone(self, file_name_to_target_name_dict):
"""Save a list of files to iRODS user zone.
:param file_name_to_target_name_dict: a dictionary in the form of {ori_file, target_file}
where ori_file is the file to be save to, and the target_file is the full path file name
in iRODS user zone to save ori_file to
:return:
"""
for file_name, target_name in list(
file_name_to_target_name_dict.items()):
self.irods_fed_storage.saveFile(file_name, target_name)
def check_file_exist(self, irods_path):
"""Check whether the input irods_path exist in iRODS.
:param irods_path: the iRODS path to check whether it exists or not
:return: True if exist, False otherwise.
"""
return self.irods_storage.exists(irods_path)
def delete_directory(self, irods_path):
"""delete the input irods_path.
:param irods_path: the iRODS path to be deleted
:return:
"""
self.irods_fed_storage.delete(irods_path)
def verify_user_quota_usage_avu_in_user_zone(self, attname, qsize):
'''
Have to use LINUX_ADMIN_USER_FOR_HS_USER_ZONE with rodsadmin role to get user type AVU
in user zone and verify its quota usage is set correctly
:param attname: quota usage attribute name set on iRODS proxy user in user zone
:param qsize: quota size (type string) to be verified to equal to the value set for attname.
'''
istorage = IrodsStorage()
istorage.set_user_session(
username=settings.LINUX_ADMIN_USER_FOR_HS_USER_ZONE,
password=settings.LINUX_ADMIN_USER_PWD_FOR_HS_USER_ZONE,
host=settings.HS_USER_ZONE_HOST,
port=settings.IRODS_PORT,
zone=settings.HS_USER_IRODS_ZONE,
sess_id='user_proxy_session')
uz_bagit_path = os.path.join('/', settings.HS_USER_IRODS_ZONE, 'home',
settings.HS_IRODS_PROXY_USER_IN_USER_ZONE,
settings.IRODS_BAGIT_PATH)
get_qsize = istorage.getAVU(uz_bagit_path, attname)
self.assertEqual(qsize, get_qsize)
def resource_file_oprs(self):
"""Test common iRODS file operations.
This is a common test utility function to be called by both regular folder operation
testing and federated zone folder operation testing.
Make sure the calling TestCase object has the following attributes defined before calling
this method:
self.res: resource that has been created that contains files listed in file_name_list
self.user: owner of the resource
self.file_name_list: a list of three file names that have been added to the res object
self.test_file_1 needs to be present for the calling object for doing regular folder
operations without involving federated zone so that the same opened file can be re-added
to the resource for testing the case where zipping cannot overwrite existing file
"""
user = self.user
res = self.res
file_name_list = self.file_name_list
# create a folder, if folder is created successfully, no exception is raised, otherwise,
# an iRODS exception will be raised which will be caught by the test runner and mark as
# a test failure
create_folder(res.short_id, 'data/contents/sub_test_dir')
istorage = res.get_irods_storage()
res_path = res.file_path
store = istorage.listdir(res_path)
self.assertIn('sub_test_dir',
store[0],
msg='resource does not contain created sub-folder')
# create a temporary zips folder to make sure no duplicate folders are returned from listdir()
zip_res_coll_path = os.path.join('zips', '2020-02-03', res.short_id,
'data', 'contents', 'sub_test_dir')
istorage.session.run("imkdir", None, '-p', zip_res_coll_path)
store = istorage.listdir(res_path)
self.assertEqual(store[0].count('sub_test_dir'),
1,
msg='duplicate folder: sub_test_dir occurred more '
'than once')
# rename the third file in file_name_list
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/' + file_name_list[2],
'data/contents/new_' + file_name_list[2])
# move the first two files in file_name_list to the new folder
move_or_rename_file_or_folder(
user, res.short_id, 'data/contents/' + file_name_list[0],
'data/contents/sub_test_dir/' + file_name_list[0])
move_or_rename_file_or_folder(
user, res.short_id, 'data/contents/' + file_name_list[1],
'data/contents/sub_test_dir/' + file_name_list[1])
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertIn('new_' + file_name_list[2],
updated_res_file_names,
msg="resource does not contain the updated file new_" +
file_name_list[2])
self.assertNotIn(file_name_list[2],
updated_res_file_names,
msg='resource still contains the old file ' +
file_name_list[2] + ' after renaming')
self.assertIn('sub_test_dir/' + file_name_list[0],
updated_res_file_names,
msg='resource does not contain ' + file_name_list[0] +
' moved to a folder')
self.assertNotIn(file_name_list[0],
updated_res_file_names,
msg='resource still contains the old ' +
file_name_list[0] + 'after moving to a folder')
self.assertIn('sub_test_dir/' + file_name_list[1],
updated_res_file_names,
msg='resource does not contain ' + file_name_list[1] +
'moved to a new folder')
self.assertNotIn(file_name_list[1],
updated_res_file_names,
msg='resource still contains the old ' +
file_name_list[1] + ' after moving to a folder')
# zip the folder
output_zip_fname, size = \
zip_folder(user, res.short_id, 'data/contents/sub_test_dir',
'sub_test_dir.zip', True)
self.assertGreater(size, 0, msg='zipped file has a size of 0')
# Now resource should contain only two files: new_file3.txt and sub_test_dir.zip
# since the folder is zipped into sub_test_dir.zip with the folder deleted
self.assertEqual(res.files.all().count(),
2,
msg="resource file count didn't match-")
# test unzip does not allow override of existing files
# add an existing file in the zip to the resource
if res.resource_federation_path:
fed_test_file1_full_path = '/{zone}/home/{uname}/{fname}'.format(
zone=settings.HS_USER_IRODS_ZONE,
uname=user.username,
fname=file_name_list[0])
# TODO: why isn't this a method of resource?
# TODO: Why do we repeat the resource_federation_path?
add_resource_files(res.short_id,
source_names=[fed_test_file1_full_path],
move=False)
else:
# TODO: Why isn't this a method of resource?
add_resource_files(res.short_id, self.test_file_1)
# TODO: use ResourceFile.create_folder, which doesn't require data/contents prefix
create_folder(res.short_id, 'data/contents/sub_test_dir')
# TODO: use ResourceFile.rename, which doesn't require data/contents prefix
move_or_rename_file_or_folder(
user, res.short_id, 'data/contents/' + file_name_list[0],
'data/contents/sub_test_dir/' + file_name_list[0])
# Now resource should contain three files: file3_new.txt, sub_test_dir.zip, and file1.txt
self.assertEqual(res.files.all().count(),
3,
msg="resource file count didn't match")
unzip_file(user, res.short_id, 'data/contents/sub_test_dir.zip', False)
# Resource should still contain 5 files: file3_new.txt (2), sub_test_dir.zip,
# and file1.txt (2)
file_cnt = res.files.all().count()
self.assertEqual(file_cnt,
5,
msg="resource file count didn't match - " +
str(file_cnt) + " != 5")
# remove all files except the zippped file
remove_folder(user, res.short_id, 'data/contents/sub_test_dir')
remove_folder(user, res.short_id, 'data/contents/sub_test_dir-1')
# Now resource should contain two files: file3_new.txt sub_test_dir.zip
file_cnt = res.files.all().count()
self.assertEqual(file_cnt,
2,
msg="resource file count didn't match - " +
str(file_cnt) + " != 2")
unzip_file(user, res.short_id, 'data/contents/sub_test_dir.zip', True)
# Now resource should contain three files: file1.txt, file2.txt, and file3_new.txt
self.assertEqual(res.files.all().count(),
3,
msg="resource file count didn't match")
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertNotIn(
'sub_test_dir.zip',
updated_res_file_names,
msg="resource still contains the zip file after unzipping")
self.assertIn('sub_test_dir/sub_test_dir/' + file_name_list[0],
updated_res_file_names,
msg='resource does not contain unzipped file ' +
file_name_list[0])
self.assertIn('sub_test_dir/sub_test_dir/' + file_name_list[1],
updated_res_file_names,
msg='resource does not contain unzipped file ' +
file_name_list[1])
self.assertIn('new_' + file_name_list[2],
updated_res_file_names,
msg='resource does not contain unzipped file new_' +
file_name_list[2])
# rename a folder
move_or_rename_file_or_folder(
user, res.short_id, 'data/contents/sub_test_dir/sub_test_dir',
'data/contents/sub_dir')
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertNotIn('sub_test_dir/sub_test_dir/' + file_name_list[0],
updated_res_file_names,
msg='resource still contains ' + file_name_list[0] +
' in the old folder after renaming')
self.assertIn('sub_dir/' + file_name_list[0],
updated_res_file_names,
msg='resource does not contain ' + file_name_list[0] +
' in the new folder after renaming')
self.assertNotIn('sub_test_dir/sub_test_dir/' + file_name_list[1],
updated_res_file_names,
msg='resource still contains ' + file_name_list[1] +
' in the old folder after renaming')
self.assertIn('sub_dir/' + file_name_list[1],
updated_res_file_names,
msg='resource does not contain ' + file_name_list[1] +
' in the new folder after renaming')
# remove a folder
# TODO: utilize ResourceFile.remove_folder instead. Takes a short path.
remove_folder(user, res.short_id, 'data/contents/sub_dir')
# Now resource only contains one file
self.assertEqual(res.files.all().count(),
1,
msg="resource file count didn't match")
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertEqual(len(updated_res_file_names), 1)
self.assertEqual(updated_res_file_names[0], 'new_' + file_name_list[2])
def raster_metadata_extraction(self):
"""Test raster metadata extraction.
This is a common test utility function to be called by both regular raster metadata
extraction testing and federated zone raster metadata extraction testing.
Make sure the calling TestCase object has self.resRaster attribute defined before calling
this method which is the raster resource that has been created containing valid raster
files.
"""
# there should be 2 content files
self.assertEqual(self.resRaster.files.all().count(), 2)
# test core metadata after metadata extraction
extracted_title = "My Test Raster Resource"
self.assertEqual(self.resRaster.metadata.title.value, extracted_title)
# there should be 1 creator
self.assertEqual(self.resRaster.metadata.creators.all().count(), 1)
# there should be 1 coverage element - box type
self.assertEqual(self.resRaster.metadata.coverages.all().count(), 1)
self.assertEqual(
self.resRaster.metadata.coverages.all().filter(type='box').count(),
1)
box_coverage = self.resRaster.metadata.coverages.all().filter(
type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']),
42.11270614966863)
self.assertEqual(float(box_coverage.value['eastlimit']),
-111.45699925047542)
self.assertEqual(float(box_coverage.value['southlimit']),
41.66222054591102)
self.assertEqual(float(box_coverage.value['westlimit']),
-111.81761887121905)
# there should be 2 format elements
self.assertEqual(self.resRaster.metadata.formats.all().count(), 2)
self.assertEqual(
self.resRaster.metadata.formats.all().filter(
value='application/vrt').count(), 1)
self.assertEqual(
self.resRaster.metadata.formats.all().filter(
value='image/tiff').count(), 1)
# testing extended metadata element: original coverage
ori_coverage = self.resRaster.metadata.originalCoverage
self.assertNotEqual(ori_coverage, None)
self.assertEqual(float(ori_coverage.value['northlimit']),
4662392.446916306)
self.assertEqual(float(ori_coverage.value['eastlimit']),
461954.01909127034)
self.assertEqual(float(ori_coverage.value['southlimit']),
4612592.446916306)
self.assertEqual(float(ori_coverage.value['westlimit']),
432404.01909127034)
self.assertEqual(ori_coverage.value['units'], 'meter')
self.assertEqual(ori_coverage.value['projection'],
"NAD83 / UTM zone 12N")
self.assertEqual(ori_coverage.value['datum'],
"North_American_Datum_1983")
projection_string = 'PROJCS["NAD83 / UTM zone 12N",GEOGCS["NAD83",' \
'DATUM["North_American_Datum_1983",' \
'SPHEROID["GRS 1980",6378137,298.257222101,' \
'AUTHORITY["EPSG","7019"]],' \
'TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6269"]],' \
'PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],' \
'UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],' \
'AUTHORITY["EPSG","4269"]],PROJECTION["Transverse_Mercator"],' \
'PARAMETER["latitude_of_origin",0],' \
'PARAMETER["central_meridian",-111],' \
'PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],' \
'PARAMETER["false_northing",0],' \
'UNIT["metre",1,AUTHORITY["EPSG","9001"]],' \
'AXIS["Easting",EAST],AXIS["Northing",' \
'NORTH],AUTHORITY["EPSG","26912"]]'
self.assertEqual(ori_coverage.value['projection_string'],
projection_string)
# testing extended metadata element: cell information
cell_info = self.resRaster.metadata.cellInformation
self.assertEqual(cell_info.rows, 1660)
self.assertEqual(cell_info.columns, 985)
self.assertEqual(cell_info.cellSizeXValue, 30.0)
self.assertEqual(cell_info.cellSizeYValue, 30.0)
self.assertEqual(cell_info.cellDataType, 'Float32')
# testing extended metadata element: band information
self.assertEqual(self.resRaster.metadata.bandInformations.count(), 1)
band_info = self.resRaster.metadata.bandInformations.first()
self.assertEqual(band_info.noDataValue, '-3.4028234663852886e+38')
self.assertEqual(band_info.maximumValue, '3031.443115234375')
self.assertEqual(band_info.minimumValue, '1358.3345947265625')
def netcdf_metadata_extraction(self, expected_creators_count=1):
"""Test NetCDF metadata extraction.
This is a common test utility function to be called by both regular netcdf metadata
extraction testing and federated zone netCDF metadata extraction testing.
Make sure the calling TestCase object has self.resNetcdf attribute defined before calling
this method which is the netCDF resource that has been created containing valid netCDF
files.
"""
# there should 2 content file
self.assertEqual(self.resNetcdf.files.all().count(), 2)
# test core metadata after metadata extraction
extracted_title = "Snow water equivalent estimation at TWDEF site from " \
"Oct 2009 to June 2010"
self.assertEqual(self.resNetcdf.metadata.title.value, extracted_title)
# there should be an abstract element
self.assertNotEqual(self.resNetcdf.metadata.description, None)
extracted_abstract = "This netCDF data is the simulation output from Utah Energy " \
"Balance (UEB) model.It includes the simulation result " \
"of snow water equivalent during the period " \
"Oct. 2009 to June 2010 for TWDEF site in Utah."
self.assertEqual(self.resNetcdf.metadata.description.abstract,
extracted_abstract)
# there should be one source element
self.assertEqual(self.resNetcdf.metadata.sources.all().count(), 1)
# there should be one license element:
self.assertNotEqual(self.resNetcdf.metadata.rights.statement, 1)
# there should be one relation element
self.assertEqual(
self.resNetcdf.metadata.relations.all().filter(
type='cites').count(), 1)
# there should be creators equal to expected_creators_count
self.assertEqual(self.resNetcdf.metadata.creators.all().count(),
expected_creators_count)
# there should be one contributor
self.assertEqual(self.resNetcdf.metadata.contributors.all().count(), 1)
# there should be 2 coverage element - box type and period type
self.assertEqual(self.resNetcdf.metadata.coverages.all().count(), 2)
self.assertEqual(
self.resNetcdf.metadata.coverages.all().filter(type='box').count(),
1)
self.assertEqual(
self.resNetcdf.metadata.coverages.all().filter(
type='period').count(), 1)
box_coverage = self.resNetcdf.metadata.coverages.all().filter(
type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']),
41.86712640899591)
self.assertEqual(float(box_coverage.value['eastlimit']),
-111.50594036845686)
self.assertEqual(float(box_coverage.value['southlimit']),
41.8639080745171)
self.assertEqual(float(box_coverage.value['westlimit']),
-111.51138807956221)
temporal_coverage = self.resNetcdf.metadata.coverages.all().filter(
type='period').first()
self.assertEqual(
parser.parse(temporal_coverage.value['start']).date(),
parser.parse('10/01/2009').date())
self.assertEqual(
parser.parse(temporal_coverage.value['end']).date(),
parser.parse('05/30/2010').date())
# there should be 2 format elements
self.assertEqual(self.resNetcdf.metadata.formats.all().count(), 2)
self.assertEqual(
self.resNetcdf.metadata.formats.all().filter(
value='text/plain').count(), 1)
self.assertEqual(
self.resNetcdf.metadata.formats.all().filter(
value='application/x-netcdf').count(), 1)
# there should be one subject element
self.assertEqual(self.resNetcdf.metadata.subjects.all().count(), 1)
subj_element = self.resNetcdf.metadata.subjects.all().first()
self.assertEqual(subj_element.value, 'Snow water equivalent')
# testing extended metadata element: original coverage
ori_coverage = self.resNetcdf.metadata.ori_coverage.all().first()
self.assertNotEqual(ori_coverage, None)
self.assertEqual(ori_coverage.projection_string_type, 'Proj4 String')
proj_text = '+proj=tmerc +y_0=0.0 +x_0=500000.0 +k_0=0.9996 +lat_0=0.0 +lon_0=-111.0'
self.assertEqual(ori_coverage.projection_string_text, proj_text)
self.assertEqual(float(ori_coverage.value['northlimit']), 4.63515e+06)
self.assertEqual(float(ori_coverage.value['eastlimit']), 458010.0)
self.assertEqual(float(ori_coverage.value['southlimit']), 4.63479e+06)
self.assertEqual(float(ori_coverage.value['westlimit']), 457560.0)
self.assertEqual(ori_coverage.value['units'], 'Meter')
self.assertEqual(ori_coverage.value['projection'],
'transverse_mercator')
# testing extended metadata element: variables
self.assertEqual(self.resNetcdf.metadata.variables.all().count(), 5)
# test time variable
var_time = self.resNetcdf.metadata.variables.all().filter(
name='time').first()
self.assertNotEqual(var_time, None)
self.assertEqual(var_time.unit, 'hours since 2009-10-1 0:0:00 UTC')
self.assertEqual(var_time.type, 'Float')
self.assertEqual(var_time.shape, 'time')
self.assertEqual(var_time.descriptive_name, 'time')
# test x variable
var_x = self.resNetcdf.metadata.variables.all().filter(
name='x').first()
self.assertNotEqual(var_x, None)
self.assertEqual(var_x.unit, 'Meter')
self.assertEqual(var_x.type, 'Float')
self.assertEqual(var_x.shape, 'x')
self.assertEqual(var_x.descriptive_name, 'x coordinate of projection')
# test y variable
var_y = self.resNetcdf.metadata.variables.all().filter(
name='y').first()
self.assertNotEqual(var_y, None)
self.assertEqual(var_y.unit, 'Meter')
self.assertEqual(var_y.type, 'Float')
self.assertEqual(var_y.shape, 'y')
self.assertEqual(var_y.descriptive_name, 'y coordinate of projection')
# test SWE variable
var_swe = self.resNetcdf.metadata.variables.all().filter(
name='SWE').first()
self.assertNotEqual(var_swe, None)
self.assertEqual(var_swe.unit, 'm')
self.assertEqual(var_swe.type, 'Float')
self.assertEqual(var_swe.shape, 'y,x,time')
self.assertEqual(var_swe.descriptive_name, 'Snow water equivalent')
self.assertEqual(var_swe.method, 'model simulation of UEB model')
self.assertEqual(var_swe.missing_value, '-9999')
# test grid mapping variable
var_grid = self.resNetcdf.metadata.variables.all().\
filter(name='transverse_mercator').first()
self.assertNotEqual(var_grid, None)
self.assertEqual(var_grid.unit, 'Unknown')
self.assertEqual(var_grid.type, 'Unknown')
self.assertEqual(var_grid.shape, 'Not defined')
def timeseries_metadata_extraction(self):
"""Test timeseries metadata extraction.
This is a common test utility function to be called by both regular timeseries metadata
extraction testing and federated zone timeseries metadata extraction testing.
Make sure the calling TestCase object has self.resTimeSeries attribute defined before
calling this method which is the timeseries resource that has been created containing
valid timeseries file.
"""
# there should one content file
self.assertEqual(self.resTimeSeries.files.all().count(), 1)
# there should be one contributor element
self.assertEqual(
self.resTimeSeries.metadata.contributors.all().count(), 1)
# test core metadata after metadata extraction
extracted_title = "Water temperature data from the Little Bear River, UT"
self.assertEqual(self.resTimeSeries.metadata.title.value,
extracted_title)
# there should be an abstract element
self.assertNotEqual(self.resTimeSeries.metadata.description, None)
extracted_abstract = "This dataset contains time series of observations of water " \
"temperature in the Little Bear River, UT. Data were recorded every " \
"30 minutes. The values were recorded using a HydroLab MS5 " \
"multi-parameter water quality sonde connected to a Campbell " \
"Scientific datalogger."
self.assertEqual(
self.resTimeSeries.metadata.description.abstract.strip(),
extracted_abstract)
# there should be 2 coverage element - box type and period type
self.assertEqual(self.resTimeSeries.metadata.coverages.all().count(),
2)
self.assertEqual(
self.resTimeSeries.metadata.coverages.all().filter(
type='box').count(), 1)
self.assertEqual(
self.resTimeSeries.metadata.coverages.all().filter(
type='period').count(), 1)
box_coverage = self.resTimeSeries.metadata.coverages.all().filter(
type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']), 41.718473)
self.assertEqual(float(box_coverage.value['eastlimit']), -111.799324)
self.assertEqual(float(box_coverage.value['southlimit']), 41.495409)
self.assertEqual(float(box_coverage.value['westlimit']), -111.946402)
temporal_coverage = self.resTimeSeries.metadata.coverages.all().filter(
type='period').first()
self.assertEqual(
parser.parse(temporal_coverage.value['start']).date(),
parser.parse('01/01/2008').date())
self.assertEqual(
parser.parse(temporal_coverage.value['end']).date(),
parser.parse('01/30/2008').date())
# there should be one format element
self.assertEqual(self.resTimeSeries.metadata.formats.all().count(), 1)
format_element = self.resTimeSeries.metadata.formats.all().first()
self.assertEqual(format_element.value, 'application/sqlite')
# there should be one subject element
self.assertEqual(self.resTimeSeries.metadata.subjects.all().count(), 1)
subj_element = self.resTimeSeries.metadata.subjects.all().first()
self.assertEqual(subj_element.value, 'Temperature')
# there should be a total of 7 timeseries
self.assertEqual(
self.resTimeSeries.metadata.time_series_results.all().count(), 7)
# testing extended metadata elements
# test 'site' - there should be 7 sites
self.assertEqual(self.resTimeSeries.metadata.sites.all().count(), 7)
# each site be associated with one series id
for site in self.resTimeSeries.metadata.sites.all():
self.assertEqual(len(site.series_ids), 1)
# test the data for a specific site
site = self.resTimeSeries.metadata.sites.filter(
site_code='USU-LBR-Paradise').first()
self.assertNotEqual(site, None)
site_name = 'Little Bear River at McMurdy Hollow near Paradise, Utah'
self.assertEqual(site.site_name, site_name)
self.assertEqual(site.elevation_m, 1445)
self.assertEqual(site.elevation_datum, 'NGVD29')
self.assertEqual(site.site_type, 'Stream')
# test 'variable' - there should be 1 variable element
self.assertEqual(self.resTimeSeries.metadata.variables.all().count(),
1)
variable = self.resTimeSeries.metadata.variables.all().first()
# there should be 7 series ids associated with this one variable
self.assertEqual(len(variable.series_ids), 7)
# test the data for a variable
self.assertEqual(variable.variable_code, 'USU36')
self.assertEqual(variable.variable_name, 'Temperature')
self.assertEqual(variable.variable_type, 'Water Quality')
self.assertEqual(variable.no_data_value, -9999)
self.assertEqual(variable.variable_definition, None)
self.assertEqual(variable.speciation, 'Not Applicable')
# test 'method' - there should be 1 method element
self.assertEqual(self.resTimeSeries.metadata.methods.all().count(), 1)
method = self.resTimeSeries.metadata.methods.all().first()
# there should be 7 series ids associated with this one method element
self.assertEqual(len(method.series_ids), 7)
self.assertEqual(method.method_code, '28')
method_name = 'Quality Control Level 1 Data Series created from raw QC Level 0 data ' \
'using ODM Tools.'
self.assertEqual(method.method_name, method_name)
self.assertEqual(method.method_type, 'Instrument deployment')
method_des = 'Quality Control Level 1 Data Series created from raw QC Level 0 data ' \
'using ODM Tools.'
self.assertEqual(method.method_description, method_des)
self.assertEqual(method.method_link, None)
# test 'processing_level' - there should be 1 processing_level element
self.assertEqual(
self.resTimeSeries.metadata.processing_levels.all().count(), 1)
proc_level = self.resTimeSeries.metadata.processing_levels.all().first(
)
# there should be 7 series ids associated with this one element
self.assertEqual(len(proc_level.series_ids), 7)
self.assertEqual(proc_level.processing_level_code, '1')
self.assertEqual(proc_level.definition, 'Quality controlled data')
explanation = 'Quality controlled data that have passed quality assurance procedures ' \
'such as routine estimation of timing and sensor calibration or visual ' \
'inspection and removal of obvious errors. An example is USGS published ' \
'streamflow records following parsing through USGS quality control ' \
'procedures.'
self.assertEqual(proc_level.explanation, explanation)
# test 'timeseries_result' - there should be 7 timeseries_result element
self.assertEqual(
self.resTimeSeries.metadata.time_series_results.all().count(), 7)
ts_result = self.resTimeSeries.metadata.time_series_results.filter(
series_ids__contains=['182d8fa3-1ebc-11e6-ad49-f45c8999816f'
]).first()
self.assertNotEqual(ts_result, None)
# there should be only 1 series id associated with this element
self.assertEqual(len(ts_result.series_ids), 1)
self.assertEqual(ts_result.units_type, 'Temperature')
self.assertEqual(ts_result.units_name, 'degree celsius')
self.assertEqual(ts_result.units_abbreviation, 'degC')
self.assertEqual(ts_result.status, 'Unknown')
self.assertEqual(ts_result.sample_medium, 'Surface Water')
self.assertEqual(ts_result.value_count, 1441)
self.assertEqual(ts_result.aggregation_statistics, 'Average')
# test for CV lookup tables
# there should be 23 CV_VariableType records
self.assertEqual(
self.resTimeSeries.metadata.cv_variable_types.all().count(), 23)
# there should be 805 CV_VariableName records
self.assertEqual(
self.resTimeSeries.metadata.cv_variable_names.all().count(), 805)
# there should be 145 CV_Speciation records
self.assertEqual(
self.resTimeSeries.metadata.cv_speciations.all().count(), 145)
# there should be 51 CV_SiteType records
self.assertEqual(
self.resTimeSeries.metadata.cv_site_types.all().count(), 51)
# there should be 5 CV_ElevationDatum records
self.assertEqual(
self.resTimeSeries.metadata.cv_elevation_datums.all().count(), 5)
# there should be 25 CV_MethodType records
self.assertEqual(
self.resTimeSeries.metadata.cv_method_types.all().count(), 25)
# there should be 179 CV_UnitsType records
self.assertEqual(
self.resTimeSeries.metadata.cv_units_types.all().count(), 179)
# there should be 4 CV_Status records
self.assertEqual(self.resTimeSeries.metadata.cv_statuses.all().count(),
4)
# there should be 17 CV_Medium records
self.assertEqual(self.resTimeSeries.metadata.cv_mediums.all().count(),
18)
# there should be 17 CV_aggregationStatistics records
self.assertEqual(
self.resTimeSeries.metadata.cv_aggregation_statistics.all().count(
), 17)
# there should not be any UTCOffset element
self.assertEqual(self.resTimeSeries.metadata.utc_offset, None)
class TestFolderDownloadZip(TestCase):
def setUp(self):
super(TestFolderDownloadZip, self).setUp()
self.group, _ = Group.objects.get_or_create(name='Hydroshare Author')
self.user = create_account('*****@*****.**',
username='******',
first_name='Shaun',
last_name='Livingston',
superuser=False,
groups=[])
self.res = create_resource(resource_type='CompositeResource',
owner=self.user,
title='Test Resource',
metadata=[])
ResourceFile.create_folder(self.res, 'foo')
# create files
self.n1 = "test1.txt"
test_file = open(self.n1, 'w')
test_file.write("Test text file in test1.txt")
test_file.close()
self.test_file = open(self.n1, "rb")
add_resource_files(self.res.short_id, self.test_file, folder='foo')
# copy refts file into new file to be added to the resource as an aggregation
reft_data_file = open(
'hs_core/tests/data/multi_sites_formatted_version1.0.refts.json',
'rb')
refts_file = open('multi_sites_formatted_version1.0.refts.json', 'wb')
refts_file.writelines(reft_data_file.readlines())
refts_file.close()
self.refts_file = open('multi_sites_formatted_version1.0.refts.json',
'rb')
add_resource_files(self.res.short_id, self.refts_file)
self.res.create_aggregation_xml_documents()
self.istorage = IrodsStorage()
def tearDown(self):
super(TestFolderDownloadZip, self).tearDown()
if self.res:
self.res.delete()
if self.test_file:
self.test_file.close()
os.remove(self.test_file.name)
if self.refts_file:
self.refts_file.close()
os.remove(self.refts_file.name)
GenericResource.objects.all().delete()
if self.istorage.exists("zips"):
self.istorage.delete("zips")
def test_create_temp_zip(self):
input_path = "{}/data/contents/foo".format(self.res.short_id)
output_path = "zips/rand/foo.zip"
self.assertTrue(
create_temp_zip(self.res.short_id, input_path, output_path, None,
False))
self.assertTrue(self.istorage.exists(output_path))
# test aggregation
input_path = "{}/data/contents/multi_sites_formatted_version1.0.refts.json"\
.format(self.res.short_id)
output_path = "zips/rand/multi_sites_formatted_version1.0.refts.json.zip"
self.assertTrue(
create_temp_zip(self.res.short_id,
input_path,
output_path,
None,
sf_zip=True))
self.assertTrue(self.istorage.exists(output_path))
def test_create_temp_zip_aggregation(self):
input_path = "{}/data/contents/" \
"multi_sites_formatted_version1.0.refts.json".format(self.res.short_id)
output_path = "zips/rand/aggregation.zip"
self.assertTrue(
create_temp_zip(self.res.short_id, input_path, output_path,
"multi_sites_formatted_version1.0.refts.json",
False))
self.assertTrue(self.istorage.exists(output_path))
def handle(self, *args, **options):
resource_counter = 0
storage = IrodsStorage()
avu_list = ['bag_modified', 'metadata_dirty', 'isPublic', 'resourceType']
for resource in BaseResource.objects.all():
if resource.storage_type == 'user':
# resource is in user zone, so migrate it to data zone
# copy files from iRODS user zone to data zone
try:
src_coll = resource.root_path
tgt_coll = resource.short_id
if storage.exists(tgt_coll):
storage.delete(tgt_coll)
storage.copyFiles(src_coll, tgt_coll)
# copy AVU over for the resource collection from iRODS user zone to data zone
for avu_name in avu_list:
value = storage.getAVU(src_coll, avu_name)
# bag_modified AVU needs to be set to true for the new resource so the bag
# can be regenerated in the data zone
if avu_name == 'bag_modified':
storage.setAVU(tgt_coll, avu_name, 'true')
# everything else gets copied literally
else:
storage.setAVU(tgt_coll, avu_name, value)
# Just to be on the safe side, it is better not to delete resources from user
# zone after it is migrated over to data zone in case there are issues with
# migration. A simple irm iRODS command can be issued to delete all resource
# collections afterwards if all works well after some time. Commenting the
# deletion statement below rather than deleting it to serve as a reminder
# that additional cleanup to delete all resource collections in user zone
# is needed after we can confirm migration is successfully.
# delete the original resource from user zone
# storage.delete(src_coll)
path_migrated = False
for res_file in resource.files.all():
if res_file.resource_file.name:
print('The resource_file field should be empty for resource {} but '
'have the value of {}'.format(resource.short_id,
res_file.resource_file.name))
break
file_path = res_file.fed_resource_file.name
if not file_path:
print('The fed_resource_file field should not be empty for '
'resource {}'.format(resource.short_id))
break
elif file_path.startswith(resource.resource_federation_path):
file_path = file_path[len(resource.resource_federation_path)+1:]
res_file.resource_file.name = file_path
res_file.fed_resource_file.name = ''
res_file.save()
path_migrated = True
else:
res_file.resource_file.name = file_path
res_file.fed_resource_file.name = ''
res_file.save()
path_migrated = True
print('fed_resource_file field does not contain absolute federation '
'path which is an exception but can work after migration. '
'file_path is {}'.format(file_path))
if path_migrated or resource.files.count() == 0:
# update resource federation path to point resource to data zone
resource.resource_federation_path = ''
resource.save()
print("Resource {} has been moved from user zone to data zone "
"successfully".format(resource.short_id))
resource_counter += 1
else:
continue
except SessionException as ex:
print("Resource {} failed to move: {}".format(resource.short_id, ex.stderr))
print("{} resources have been moved from user zone to data zone successfully".format(
resource_counter))
class TestCaseCommonUtilities(object):
"""Enable common utilities for iRODS testing."""
def assert_federated_irods_available(self):
"""assert federated iRODS is available before proceeding with federation-related tests."""
self.assertTrue(settings.REMOTE_USE_IRODS and
settings.HS_USER_ZONE_HOST == 'users.local.org' and
settings.IRODS_HOST == 'data.local.org',
"irods docker containers are not set up properly for federation testing")
self.irods_fed_storage = IrodsStorage('federated')
self.irods_storage = IrodsStorage()
def create_irods_user_in_user_zone(self):
"""Create corresponding irods account in user zone."""
try:
exec_cmd = "{0} {1} {2}".format(settings.HS_USER_ZONE_PROXY_USER_CREATE_USER_CMD,
self.user.username, self.user.username)
output = run_ssh_command(host=settings.HS_USER_ZONE_HOST,
uname=settings.HS_USER_ZONE_PROXY_USER,
pwd=settings.HS_USER_ZONE_PROXY_USER_PWD,
exec_cmd=exec_cmd)
if output:
if 'ERROR:' in output.upper():
# irods account failed to create
self.assertRaises(SessionException(-1, output, output))
user_profile = UserProfile.objects.filter(user=self.user).first()
user_profile.create_irods_user_account = True
user_profile.save()
except Exception as ex:
self.assertRaises(SessionException(-1, ex.message, ex.message))
def delete_irods_user_in_user_zone(self):
"""Delete irods test user in user zone."""
try:
exec_cmd = "{0} {1}".format(settings.HS_USER_ZONE_PROXY_USER_DELETE_USER_CMD,
self.user.username)
output = run_ssh_command(host=settings.HS_USER_ZONE_HOST,
uname=settings.HS_USER_ZONE_PROXY_USER,
pwd=settings.HS_USER_ZONE_PROXY_USER_PWD,
exec_cmd=exec_cmd)
if output:
if 'ERROR:' in output.upper():
# there is an error from icommand run, report the error
self.assertRaises(SessionException(-1, output, output))
user_profile = UserProfile.objects.filter(user=self.user).first()
user_profile.create_irods_user_account = False
user_profile.save()
except Exception as ex:
# there is an error from icommand run, report the error
self.assertRaises(SessionException(-1, ex.message, ex.message))
def save_files_to_user_zone(self, file_name_to_target_name_dict):
"""Save a list of files to iRODS user zone.
:param file_name_to_target_name_dict: a dictionary in the form of {ori_file, target_file}
where ori_file is the file to be save to, and the target_file is the full path file name
in iRODS user zone to save ori_file to
:return:
"""
for file_name, target_name in file_name_to_target_name_dict.iteritems():
self.irods_fed_storage.saveFile(file_name, target_name)
def check_file_exist(self, irods_path):
"""Check whether the input irods_path exist in iRODS.
:param irods_path: the iRODS path to check whether it exists or not
:return: True if exist, False otherwise.
"""
return self.irods_storage.exists(irods_path)
def delete_directory(self, irods_path):
"""delete the input irods_path.
:param irods_path: the iRODS path to be deleted
:return:
"""
self.irods_fed_storage.delete(irods_path)
def verify_user_quota_usage_avu_in_user_zone(self, attname, qsize):
'''
Have to use HS_USER_ZONE_PROXY_USER with rodsadmin role to get user type AVU in user zone
and verify its quota usage is set correctly
:param attname: quota usage attribute name set on iRODS proxy user in user zone
:param qsize: quota size (type string) to be verified to equal to the value set for attname.
'''
istorage = IrodsStorage()
istorage.set_user_session(username=settings.HS_USER_ZONE_PROXY_USER,
password=settings.HS_USER_ZONE_PROXY_USER_PWD,
host=settings.HS_USER_ZONE_HOST,
port=settings.IRODS_PORT,
zone=settings.HS_USER_IRODS_ZONE,
sess_id='user_proxy_session')
uz_bagit_path = os.path.join('/', settings.HS_USER_IRODS_ZONE, 'home',
settings.HS_LOCAL_PROXY_USER_IN_FED_ZONE,
settings.IRODS_BAGIT_PATH)
get_qsize = istorage.getAVU(uz_bagit_path, attname)
self.assertEqual(qsize, get_qsize)
def resource_file_oprs(self):
"""Test common iRODS file operations.
This is a common test utility function to be called by both regular folder operation
testing and federated zone folder operation testing.
Make sure the calling TestCase object has the following attributes defined before calling
this method:
self.res: resource that has been created that contains files listed in file_name_list
self.user: owner of the resource
self.file_name_list: a list of three file names that have been added to the res object
self.test_file_1 needs to be present for the calling object for doing regular folder
operations without involving federated zone so that the same opened file can be re-added
to the resource for testing the case where zipping cannot overwrite existing file
"""
user = self.user
res = self.res
file_name_list = self.file_name_list
# create a folder, if folder is created successfully, no exception is raised, otherwise,
# an iRODS exception will be raised which will be caught by the test runner and mark as
# a test failure
create_folder(res.short_id, 'data/contents/sub_test_dir')
istorage = res.get_irods_storage()
res_path = res.file_path
store = istorage.listdir(res_path)
self.assertIn('sub_test_dir', store[0], msg='resource does not contain created sub-folder')
# rename the third file in file_name_list
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/' + file_name_list[2],
'data/contents/new_' + file_name_list[2])
# move the first two files in file_name_list to the new folder
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/' + file_name_list[0],
'data/contents/sub_test_dir/' + file_name_list[0])
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/' + file_name_list[1],
'data/contents/sub_test_dir/' + file_name_list[1])
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertIn('new_' + file_name_list[2], updated_res_file_names,
msg="resource does not contain the updated file new_" + file_name_list[2])
self.assertNotIn(file_name_list[2], updated_res_file_names,
msg='resource still contains the old file ' + file_name_list[2] +
' after renaming')
self.assertIn('sub_test_dir/' + file_name_list[0], updated_res_file_names,
msg='resource does not contain ' + file_name_list[0] + ' moved to a folder')
self.assertNotIn(file_name_list[0], updated_res_file_names,
msg='resource still contains the old ' + file_name_list[0] +
'after moving to a folder')
self.assertIn('sub_test_dir/' + file_name_list[1], updated_res_file_names,
msg='resource does not contain ' + file_name_list[1] +
'moved to a new folder')
self.assertNotIn(file_name_list[1], updated_res_file_names,
msg='resource still contains the old ' + file_name_list[1] +
' after moving to a folder')
# zip the folder
output_zip_fname, size = \
zip_folder(user, res.short_id, 'data/contents/sub_test_dir',
'sub_test_dir.zip', True)
self.assertGreater(size, 0, msg='zipped file has a size of 0')
# Now resource should contain only two files: new_file3.txt and sub_test_dir.zip
# since the folder is zipped into sub_test_dir.zip with the folder deleted
self.assertEqual(res.files.all().count(), 2,
msg="resource file count didn't match-")
# test unzip does not allow override of existing files
# add an existing file in the zip to the resource
if res.resource_federation_path:
fed_test_file1_full_path = '/{zone}/home/{uname}/{fname}'.format(
zone=settings.HS_USER_IRODS_ZONE, uname=user.username, fname=file_name_list[0])
# TODO: why isn't this a method of resource?
# TODO: Why do we repeat the resource_federation_path?
add_resource_files(res.short_id, source_names=[fed_test_file1_full_path],
move=False)
else:
# TODO: Why isn't this a method of resource?
add_resource_files(res.short_id, self.test_file_1)
# TODO: use ResourceFile.create_folder, which doesn't require data/contents prefix
create_folder(res.short_id, 'data/contents/sub_test_dir')
# TODO: use ResourceFile.rename, which doesn't require data/contents prefix
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/' + file_name_list[0],
'data/contents/sub_test_dir/' + file_name_list[0])
# Now resource should contain three files: file3_new.txt, sub_test_dir.zip, and file1.txt
self.assertEqual(res.files.all().count(), 3, msg="resource file count didn't match")
unzip_file(user, res.short_id, 'data/contents/sub_test_dir.zip', False)
# Resource should still contain 5 files: file3_new.txt (2), sub_test_dir.zip,
# and file1.txt (2)
file_cnt = res.files.all().count()
self.assertEqual(file_cnt, 5, msg="resource file count didn't match - " +
str(file_cnt) + " != 5")
# remove all files except the zippped file
remove_folder(user, res.short_id, 'data/contents/sub_test_dir')
remove_folder(user, res.short_id, 'data/contents/sub_test_dir-1')
# Now resource should contain two files: file3_new.txt sub_test_dir.zip
file_cnt = res.files.all().count()
self.assertEqual(file_cnt, 2, msg="resource file count didn't match - " +
str(file_cnt) + " != 2")
unzip_file(user, res.short_id, 'data/contents/sub_test_dir.zip', True)
# Now resource should contain three files: file1.txt, file2.txt, and file3_new.txt
self.assertEqual(res.files.all().count(), 3, msg="resource file count didn't match")
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertNotIn('sub_test_dir.zip', updated_res_file_names,
msg="resource still contains the zip file after unzipping")
self.assertIn('sub_test_dir/sub_test_dir/' + file_name_list[0], updated_res_file_names,
msg='resource does not contain unzipped file ' + file_name_list[0])
self.assertIn('sub_test_dir/sub_test_dir/' + file_name_list[1], updated_res_file_names,
msg='resource does not contain unzipped file ' + file_name_list[1])
self.assertIn('new_' + file_name_list[2], updated_res_file_names,
msg='resource does not contain unzipped file new_' + file_name_list[2])
# rename a folder
move_or_rename_file_or_folder(user, res.short_id,
'data/contents/sub_test_dir/sub_test_dir',
'data/contents/sub_dir')
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertNotIn('sub_test_dir/sub_test_dir/' + file_name_list[0], updated_res_file_names,
msg='resource still contains ' + file_name_list[0] +
' in the old folder after renaming')
self.assertIn('sub_dir/' + file_name_list[0], updated_res_file_names,
msg='resource does not contain ' + file_name_list[0] +
' in the new folder after renaming')
self.assertNotIn('sub_test_dir/sub_test_dir/' + file_name_list[1], updated_res_file_names,
msg='resource still contains ' + file_name_list[1] +
' in the old folder after renaming')
self.assertIn('sub_dir/' + file_name_list[1], updated_res_file_names,
msg='resource does not contain ' + file_name_list[1] +
' in the new folder after renaming')
# remove a folder
# TODO: utilize ResourceFile.remove_folder instead. Takes a short path.
remove_folder(user, res.short_id, 'data/contents/sub_dir')
# Now resource only contains one file
self.assertEqual(res.files.all().count(), 1, msg="resource file count didn't match")
updated_res_file_names = []
for rf in ResourceFile.objects.filter(object_id=res.id):
updated_res_file_names.append(rf.short_path)
self.assertEqual(len(updated_res_file_names), 1)
self.assertEqual(updated_res_file_names[0], 'new_' + file_name_list[2])
def raster_metadata_extraction(self):
"""Test raster metadata extraction.
This is a common test utility function to be called by both regular raster metadata
extraction testing and federated zone raster metadata extraction testing.
Make sure the calling TestCase object has self.resRaster attribute defined before calling
this method which is the raster resource that has been created containing valid raster
files.
"""
# there should be 2 content files
self.assertEqual(self.resRaster.files.all().count(), 2)
# test core metadata after metadata extraction
extracted_title = "My Test Raster Resource"
self.assertEqual(self.resRaster.metadata.title.value, extracted_title)
# there should be 1 creator
self.assertEqual(self.resRaster.metadata.creators.all().count(), 1)
# there should be 1 coverage element - box type
self.assertEqual(self.resRaster.metadata.coverages.all().count(), 1)
self.assertEqual(self.resRaster.metadata.coverages.all().filter(type='box').count(), 1)
box_coverage = self.resRaster.metadata.coverages.all().filter(type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']), 42.11270614966863)
self.assertEqual(float(box_coverage.value['eastlimit']), -111.45699925047542)
self.assertEqual(float(box_coverage.value['southlimit']), 41.66222054591102)
self.assertEqual(float(box_coverage.value['westlimit']), -111.81761887121905)
# there should be 2 format elements
self.assertEqual(self.resRaster.metadata.formats.all().count(), 2)
self.assertEqual(self.resRaster.metadata.formats.all().filter(
value='application/vrt').count(), 1)
self.assertEqual(self.resRaster.metadata.formats.all().filter(
value='image/tiff').count(), 1)
# testing extended metadata element: original coverage
ori_coverage = self.resRaster.metadata.originalCoverage
self.assertNotEquals(ori_coverage, None)
self.assertEqual(float(ori_coverage.value['northlimit']), 4662392.446916306)
self.assertEqual(float(ori_coverage.value['eastlimit']), 461954.01909127034)
self.assertEqual(float(ori_coverage.value['southlimit']), 4612592.446916306)
self.assertEqual(float(ori_coverage.value['westlimit']), 432404.01909127034)
self.assertEqual(ori_coverage.value['units'], 'meter')
self.assertEqual(ori_coverage.value['projection'], "NAD83 / UTM zone 12N")
self.assertEqual(ori_coverage.value['datum'], "North_American_Datum_1983")
projection_string = u'PROJCS["NAD83 / UTM zone 12N",GEOGCS["NAD83",' \
u'DATUM["North_American_Datum_1983",' \
u'SPHEROID["GRS 1980",6378137,298.257222101,' \
u'AUTHORITY["EPSG","7019"]],' \
u'TOWGS84[0,0,0,0,0,0,0],AUTHORITY["EPSG","6269"]],' \
u'PRIMEM["Greenwich",0,AUTHORITY["EPSG","8901"]],' \
u'UNIT["degree",0.0174532925199433,AUTHORITY["EPSG","9122"]],' \
u'AUTHORITY["EPSG","4269"]],PROJECTION["Transverse_Mercator"],' \
u'PARAMETER["latitude_of_origin",0],' \
u'PARAMETER["central_meridian",-111],' \
u'PARAMETER["scale_factor",0.9996],PARAMETER["false_easting",500000],' \
u'PARAMETER["false_northing",0],' \
u'UNIT["metre",1,AUTHORITY["EPSG","9001"]],' \
u'AXIS["Easting",EAST],AXIS["Northing",' \
u'NORTH],AUTHORITY["EPSG","26912"]]'
self.assertEqual(ori_coverage.value['projection_string'], projection_string)
# testing extended metadata element: cell information
cell_info = self.resRaster.metadata.cellInformation
self.assertEqual(cell_info.rows, 1660)
self.assertEqual(cell_info.columns, 985)
self.assertEqual(cell_info.cellSizeXValue, 30.0)
self.assertEqual(cell_info.cellSizeYValue, 30.0)
self.assertEqual(cell_info.cellDataType, 'Float32')
# testing extended metadata element: band information
self.assertEqual(self.resRaster.metadata.bandInformations.count(), 1)
band_info = self.resRaster.metadata.bandInformations.first()
self.assertEqual(band_info.noDataValue, '-3.40282346639e+38')
self.assertEqual(band_info.maximumValue, '3031.44311523')
self.assertEqual(band_info.minimumValue, '1358.33459473')
def netcdf_metadata_extraction(self, expected_creators_count=1):
"""Test NetCDF metadata extraction.
This is a common test utility function to be called by both regular netcdf metadata
extraction testing and federated zone netCDF metadata extraction testing.
Make sure the calling TestCase object has self.resNetcdf attribute defined before calling
this method which is the netCDF resource that has been created containing valid netCDF
files.
"""
# there should 2 content file
self.assertEqual(self.resNetcdf.files.all().count(), 2)
# test core metadata after metadata extraction
extracted_title = "Snow water equivalent estimation at TWDEF site from " \
"Oct 2009 to June 2010"
self.assertEqual(self.resNetcdf.metadata.title.value, extracted_title)
# there should be an abstract element
self.assertNotEqual(self.resNetcdf.metadata.description, None)
extracted_abstract = "This netCDF data is the simulation output from Utah Energy " \
"Balance (UEB) model.It includes the simulation result " \
"of snow water equivalent during the period " \
"Oct. 2009 to June 2010 for TWDEF site in Utah."
self.assertEqual(self.resNetcdf.metadata.description.abstract, extracted_abstract)
# there should be one source element
self.assertEqual(self.resNetcdf.metadata.sources.all().count(), 1)
# there should be one license element:
self.assertNotEquals(self.resNetcdf.metadata.rights.statement, 1)
# there should be one relation element
self.assertEqual(self.resNetcdf.metadata.relations.all().filter(type='cites').count(), 1)
# there should be creators equal to expected_creators_count
self.assertEqual(self.resNetcdf.metadata.creators.all().count(), expected_creators_count)
# there should be one contributor
self.assertEqual(self.resNetcdf.metadata.contributors.all().count(), 1)
# there should be 2 coverage element - box type and period type
self.assertEqual(self.resNetcdf.metadata.coverages.all().count(), 2)
self.assertEqual(self.resNetcdf.metadata.coverages.all().filter(type='box').count(), 1)
self.assertEqual(self.resNetcdf.metadata.coverages.all().filter(type='period').count(), 1)
box_coverage = self.resNetcdf.metadata.coverages.all().filter(type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']), 41.867126409)
self.assertEqual(float(box_coverage.value['eastlimit']), -111.505940368)
self.assertEqual(float(box_coverage.value['southlimit']), 41.8639080745)
self.assertEqual(float(box_coverage.value['westlimit']), -111.51138808)
temporal_coverage = self.resNetcdf.metadata.coverages.all().filter(type='period').first()
self.assertEqual(parser.parse(temporal_coverage.value['start']).date(),
parser.parse('10/01/2009').date())
self.assertEqual(parser.parse(temporal_coverage.value['end']).date(),
parser.parse('05/30/2010').date())
# there should be 2 format elements
self.assertEqual(self.resNetcdf.metadata.formats.all().count(), 2)
self.assertEqual(self.resNetcdf.metadata.formats.all().
filter(value='text/plain').count(), 1)
self.assertEqual(self.resNetcdf.metadata.formats.all().
filter(value='application/x-netcdf').count(), 1)
# there should be one subject element
self.assertEqual(self.resNetcdf.metadata.subjects.all().count(), 1)
subj_element = self.resNetcdf.metadata.subjects.all().first()
self.assertEqual(subj_element.value, 'Snow water equivalent')
# testing extended metadata element: original coverage
ori_coverage = self.resNetcdf.metadata.ori_coverage.all().first()
self.assertNotEquals(ori_coverage, None)
self.assertEqual(ori_coverage.projection_string_type, 'Proj4 String')
proj_text = u'+proj=tmerc +y_0=0.0 +k_0=0.9996 +x_0=500000.0 +lat_0=0.0 +lon_0=-111.0'
self.assertEqual(ori_coverage.projection_string_text, proj_text)
self.assertEqual(float(ori_coverage.value['northlimit']), 4.63515e+06)
self.assertEqual(float(ori_coverage.value['eastlimit']), 458010.0)
self.assertEqual(float(ori_coverage.value['southlimit']), 4.63479e+06)
self.assertEqual(float(ori_coverage.value['westlimit']), 457560.0)
self.assertEqual(ori_coverage.value['units'], 'Meter')
self.assertEqual(ori_coverage.value['projection'], 'transverse_mercator')
# testing extended metadata element: variables
self.assertEqual(self.resNetcdf.metadata.variables.all().count(), 5)
# test time variable
var_time = self.resNetcdf.metadata.variables.all().filter(name='time').first()
self.assertNotEquals(var_time, None)
self.assertEqual(var_time.unit, 'hours since 2009-10-1 0:0:00 UTC')
self.assertEqual(var_time.type, 'Float')
self.assertEqual(var_time.shape, 'time')
self.assertEqual(var_time.descriptive_name, 'time')
# test x variable
var_x = self.resNetcdf.metadata.variables.all().filter(name='x').first()
self.assertNotEquals(var_x, None)
self.assertEqual(var_x.unit, 'Meter')
self.assertEqual(var_x.type, 'Float')
self.assertEqual(var_x.shape, 'x')
self.assertEqual(var_x.descriptive_name, 'x coordinate of projection')
# test y variable
var_y = self.resNetcdf.metadata.variables.all().filter(name='y').first()
self.assertNotEquals(var_y, None)
self.assertEqual(var_y.unit, 'Meter')
self.assertEqual(var_y.type, 'Float')
self.assertEqual(var_y.shape, 'y')
self.assertEqual(var_y.descriptive_name, 'y coordinate of projection')
# test SWE variable
var_swe = self.resNetcdf.metadata.variables.all().filter(name='SWE').first()
self.assertNotEquals(var_swe, None)
self.assertEqual(var_swe.unit, 'm')
self.assertEqual(var_swe.type, 'Float')
self.assertEqual(var_swe.shape, 'y,x,time')
self.assertEqual(var_swe.descriptive_name, 'Snow water equivalent')
self.assertEqual(var_swe.method, 'model simulation of UEB model')
self.assertEqual(var_swe.missing_value, '-9999')
# test grid mapping variable
var_grid = self.resNetcdf.metadata.variables.all().\
filter(name='transverse_mercator').first()
self.assertNotEquals(var_grid, None)
self.assertEqual(var_grid.unit, 'Unknown')
self.assertEqual(var_grid.type, 'Unknown')
self.assertEqual(var_grid.shape, 'Not defined')
def timeseries_metadata_extraction(self):
"""Test timeseries metadata extraction.
This is a common test utility function to be called by both regular timeseries metadata
extraction testing and federated zone timeseries metadata extraction testing.
Make sure the calling TestCase object has self.resTimeSeries attribute defined before
calling this method which is the timeseries resource that has been created containing
valid timeseries file.
"""
# there should one content file
self.assertEqual(self.resTimeSeries.files.all().count(), 1)
# there should be one contributor element
self.assertEqual(self.resTimeSeries.metadata.contributors.all().count(), 1)
# test core metadata after metadata extraction
extracted_title = "Water temperature data from the Little Bear River, UT"
self.assertEqual(self.resTimeSeries.metadata.title.value, extracted_title)
# there should be an abstract element
self.assertNotEqual(self.resTimeSeries.metadata.description, None)
extracted_abstract = "This dataset contains time series of observations of water " \
"temperature in the Little Bear River, UT. Data were recorded every " \
"30 minutes. The values were recorded using a HydroLab MS5 " \
"multi-parameter water quality sonde connected to a Campbell " \
"Scientific datalogger."
self.assertEqual(self.resTimeSeries.metadata.description.abstract.strip(),
extracted_abstract)
# there should be 2 coverage element - box type and period type
self.assertEqual(self.resTimeSeries.metadata.coverages.all().count(), 2)
self.assertEqual(self.resTimeSeries.metadata.coverages.all().filter(type='box').count(), 1)
self.assertEqual(self.resTimeSeries.metadata.coverages.all().filter(
type='period').count(), 1)
box_coverage = self.resTimeSeries.metadata.coverages.all().filter(type='box').first()
self.assertEqual(box_coverage.value['projection'], 'WGS 84 EPSG:4326')
self.assertEqual(box_coverage.value['units'], 'Decimal degrees')
self.assertEqual(float(box_coverage.value['northlimit']), 41.718473)
self.assertEqual(float(box_coverage.value['eastlimit']), -111.799324)
self.assertEqual(float(box_coverage.value['southlimit']), 41.495409)
self.assertEqual(float(box_coverage.value['westlimit']), -111.946402)
temporal_coverage = self.resTimeSeries.metadata.coverages.all().filter(
type='period').first()
self.assertEqual(parser.parse(temporal_coverage.value['start']).date(),
parser.parse('01/01/2008').date())
self.assertEqual(parser.parse(temporal_coverage.value['end']).date(),
parser.parse('01/30/2008').date())
# there should be one format element
self.assertEqual(self.resTimeSeries.metadata.formats.all().count(), 1)
format_element = self.resTimeSeries.metadata.formats.all().first()
self.assertEqual(format_element.value, 'application/sqlite')
# there should be one subject element
self.assertEqual(self.resTimeSeries.metadata.subjects.all().count(), 1)
subj_element = self.resTimeSeries.metadata.subjects.all().first()
self.assertEqual(subj_element.value, 'Temperature')
# there should be a total of 7 timeseries
self.assertEqual(self.resTimeSeries.metadata.time_series_results.all().count(), 7)
# testing extended metadata elements
# test 'site' - there should be 7 sites
self.assertEqual(self.resTimeSeries.metadata.sites.all().count(), 7)
# each site be associated with one series id
for site in self.resTimeSeries.metadata.sites.all():
self.assertEqual(len(site.series_ids), 1)
# test the data for a specific site
site = self.resTimeSeries.metadata.sites.filter(site_code='USU-LBR-Paradise').first()
self.assertNotEqual(site, None)
site_name = 'Little Bear River at McMurdy Hollow near Paradise, Utah'
self.assertEqual(site.site_name, site_name)
self.assertEqual(site.elevation_m, 1445)
self.assertEqual(site.elevation_datum, 'NGVD29')
self.assertEqual(site.site_type, 'Stream')
# test 'variable' - there should be 1 variable element
self.assertEqual(self.resTimeSeries.metadata.variables.all().count(), 1)
variable = self.resTimeSeries.metadata.variables.all().first()
# there should be 7 series ids associated with this one variable
self.assertEqual(len(variable.series_ids), 7)
# test the data for a variable
self.assertEqual(variable.variable_code, 'USU36')
self.assertEqual(variable.variable_name, 'Temperature')
self.assertEqual(variable.variable_type, 'Water Quality')
self.assertEqual(variable.no_data_value, -9999)
self.assertEqual(variable.variable_definition, None)
self.assertEqual(variable.speciation, 'Not Applicable')
# test 'method' - there should be 1 method element
self.assertEqual(self.resTimeSeries.metadata.methods.all().count(), 1)
method = self.resTimeSeries.metadata.methods.all().first()
# there should be 7 series ids associated with this one method element
self.assertEqual(len(method.series_ids), 7)
self.assertEqual(method.method_code, '28')
method_name = 'Quality Control Level 1 Data Series created from raw QC Level 0 data ' \
'using ODM Tools.'
self.assertEqual(method.method_name, method_name)
self.assertEqual(method.method_type, 'Instrument deployment')
method_des = 'Quality Control Level 1 Data Series created from raw QC Level 0 data ' \
'using ODM Tools.'
self.assertEqual(method.method_description, method_des)
self.assertEqual(method.method_link, None)
# test 'processing_level' - there should be 1 processing_level element
self.assertEqual(self.resTimeSeries.metadata.processing_levels.all().count(), 1)
proc_level = self.resTimeSeries.metadata.processing_levels.all().first()
# there should be 7 series ids associated with this one element
self.assertEqual(len(proc_level.series_ids), 7)
self.assertEqual(proc_level.processing_level_code, '1')
self.assertEqual(proc_level.definition, 'Quality controlled data')
explanation = 'Quality controlled data that have passed quality assurance procedures ' \
'such as routine estimation of timing and sensor calibration or visual ' \
'inspection and removal of obvious errors. An example is USGS published ' \
'streamflow records following parsing through USGS quality control ' \
'procedures.'
self.assertEqual(proc_level.explanation, explanation)
# test 'timeseries_result' - there should be 7 timeseries_result element
self.assertEqual(self.resTimeSeries.metadata.time_series_results.all().count(), 7)
ts_result = self.resTimeSeries.metadata.time_series_results.filter(
series_ids__contains=['182d8fa3-1ebc-11e6-ad49-f45c8999816f']).first()
self.assertNotEqual(ts_result, None)
# there should be only 1 series id associated with this element
self.assertEqual(len(ts_result.series_ids), 1)
self.assertEqual(ts_result.units_type, 'Temperature')
self.assertEqual(ts_result.units_name, 'degree celsius')
self.assertEqual(ts_result.units_abbreviation, 'degC')
self.assertEqual(ts_result.status, 'Unknown')
self.assertEqual(ts_result.sample_medium, 'Surface Water')
self.assertEqual(ts_result.value_count, 1441)
self.assertEqual(ts_result.aggregation_statistics, 'Average')
# test for CV lookup tables
# there should be 23 CV_VariableType records
self.assertEqual(self.resTimeSeries.metadata.cv_variable_types.all().count(), 23)
# there should be 805 CV_VariableName records
self.assertEqual(self.resTimeSeries.metadata.cv_variable_names.all().count(), 805)
# there should be 145 CV_Speciation records
self.assertEqual(self.resTimeSeries.metadata.cv_speciations.all().count(), 145)
# there should be 51 CV_SiteType records
self.assertEqual(self.resTimeSeries.metadata.cv_site_types.all().count(), 51)
# there should be 5 CV_ElevationDatum records
self.assertEqual(self.resTimeSeries.metadata.cv_elevation_datums.all().count(), 5)
# there should be 25 CV_MethodType records
self.assertEqual(self.resTimeSeries.metadata.cv_method_types.all().count(), 25)
# there should be 179 CV_UnitsType records
self.assertEqual(self.resTimeSeries.metadata.cv_units_types.all().count(), 179)
# there should be 4 CV_Status records
self.assertEqual(self.resTimeSeries.metadata.cv_statuses.all().count(), 4)
# there should be 17 CV_Medium records
self.assertEqual(self.resTimeSeries.metadata.cv_mediums.all().count(), 18)
# there should be 17 CV_aggregationStatistics records
self.assertEqual(self.resTimeSeries.metadata.cv_aggregation_statistics.all().count(), 17)
# there should not be any UTCOffset element
self.assertEqual(self.resTimeSeries.metadata.utc_offset, None)
def delete_zip(zip_path):
istorage = IrodsStorage()
if istorage.exists(zip_path):
istorage.delete(zip_path)
