def replace_resource_file_on_irods(new_file, original_resource_file, user):
"""
Replaces the specified resource file with file (new_file) by copying to iRODS
(local or federated zone)
:param new_file: file path for the file to be copied to iRODS
:param original_resource_file: an instance of ResourceFile that is to be replaced
:param user: user who is replacing the resource file.
:return:
"""
ori_res = original_resource_file.resource
if original_resource_file.resource_file:
istorage = IrodsStorage()
destination_file = original_resource_file.resource_file.name
else:
istorage = IrodsStorage('federated')
if original_resource_file.fed_resource_file:
destination_file = original_resource_file.fed_resource_file.name
else:
destination_file = os.path.join(
ori_res.resource_federation_path, ori_res.short_id,
original_resource_file.fed_resource_file_name_or_path)
istorage.saveFile(new_file, destination_file, True)
# need to do this so that the bag will be regenerated prior to download of the bag
resource_modified(ori_res, by_user=user, overwrite_bag=False)
class TestCaseCommonUtilities(object):
"""Enable common utilities for iRODS testing."""
def is_federated_irods_available(self):
"""Check if federated iRODS is available."""
if not settings.REMOTE_USE_IRODS or settings.HS_USER_ZONE_HOST != 'users.local.org' \
or settings.IRODS_HOST != 'data.local.org':
return False
else:
return True
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 using the same IrodsStorage() object.
: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:
"""
self.irods_storage = IrodsStorage('federated')
for file_name, target_name in file_name_to_target_name_dict.iteritems(
):
self.irods_storage.saveFile(file_name, target_name)
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")
with self.assertRaises(SessionException):
unzip_file(user, res.short_id, 'data/contents/sub_test_dir.zip',
False)
# Resource should still contain three files: file3_new.txt, sub_test_dir.zip, and file1.txt
file_cnt = res.files.all().count()
self.assertEqual(file_cnt,
3,
msg="resource file count didn't match - " +
str(file_cnt) + " != 3")
# test unzipping the file succeeds now after deleting the existing folder
# TODO: this causes a multiple delete because the paths are valid now.
istorage = res.get_irods_storage()
remove_folder(user, res.short_id, 'data/contents/sub_test_dir')
# Now resource should contain two files: file3_new.txt and 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/' + file_name_list[0],
updated_res_file_names,
msg='resource does not contain unzipped file ' +
file_name_list[0])
self.assertIn('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',
'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/' + 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/' + 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(box_coverage.value['northlimit'], 42.11270614966863)
self.assertEqual(box_coverage.value['eastlimit'], -111.45699925047542)
self.assertEqual(box_coverage.value['southlimit'], 41.66222054591102)
self.assertEqual(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(ori_coverage.value['northlimit'], 4662392.446916306)
self.assertEqual(ori_coverage.value['eastlimit'], 461954.01909127034)
self.assertEqual(ori_coverage.value['southlimit'], 4612592.446916306)
self.assertEqual(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(box_coverage.value['northlimit'], 41.867126409)
self.assertEqual(box_coverage.value['eastlimit'], -111.505940368)
self.assertEqual(box_coverage.value['southlimit'], 41.8639080745)
self.assertEqual(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(ori_coverage.value['northlimit'], '4.63515e+06')
self.assertEqual(ori_coverage.value['eastlimit'], '458010.0')
self.assertEqual(ori_coverage.value['southlimit'], '4.63479e+06')
self.assertEqual(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(box_coverage.value['northlimit'], 41.718473)
self.assertEqual(box_coverage.value['eastlimit'], -111.799324)
self.assertEqual(box_coverage.value['southlimit'], 41.495409)
self.assertEqual(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('01/31/2008').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 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 create_bag_files(resource):
"""
create and update all files needed by bagit operation that is conducted on iRODS server; no bagit operation
is performed, only files that will be included in the bag are created or updated.
Parameters:
:param resource: A resource whose files will be created or updated to be included in the resource bag.
:return: istorage, an IrodsStorage object,that will be used by subsequent operation to create a bag on demand as needed.
"""
from . import utils as hs_core_utils
DATE_FORMAT = "YYYY-MM-DDThh:mm:ssTZD"
istorage = IrodsStorage()
dest_prefix = getattr(settings, 'BAGIT_TEMP_LOCATION', '/tmp/hydroshare/')
bagit_path = os.path.join(
dest_prefix, resource.short_id,
arrow.get(resource.updated).format("YYYY.MM.DD.HH.mm.ss"))
for d in (dest_prefix, bagit_path):
try:
os.makedirs(d)
except OSError as ex:
if ex.errno == errno.EEXIST:
shutil.rmtree(d)
os.makedirs(d)
else:
raise Exception(ex.message)
# an empty visualization directory will not be put into the zipped bag file by ibun command, so creating an empty
# visualization directory to be put into the zip file as done by the two statements below does not work. However,
# if visualization directory has content to be uploaded, it will work. This is to be implemented as part of the
# resource model in the future. The following two statements are placeholders serving as reminder
# to_file_name = '{res_id}/data/visualization/'.format(res_id=resource.short_id)
# istorage.saveFile('', to_file_name, create_directory=True)
# create resourcemetadata.xml and upload it to iRODS
from_file_name = '{path}/resourcemetadata.xml'.format(path=bagit_path)
with open(from_file_name, 'w') as out:
out.write(resource.metadata.get_xml())
to_file_name = '{res_id}/data/resourcemetadata.xml'.format(
res_id=resource.short_id)
istorage.saveFile(from_file_name, to_file_name, True)
# make the resource map
current_site_url = hs_core_utils.current_site_url()
hs_res_url = '{hs_url}/resource/{res_id}/data'.format(
hs_url=current_site_url, res_id=resource.short_id)
metadata_url = os.path.join(hs_res_url, 'resourcemetadata.xml')
res_map_url = os.path.join(hs_res_url, 'resourcemap.xml')
##make the resource map:
# utils.namespaces['hsterms'] = Namespace('{hs_url}/hsterms/'.format(hs_url=current_site_url))
# utils.namespaceSearchOrder.append('hsterms')
utils.namespaces['citoterms'] = Namespace('http://purl.org/spar/cito/')
utils.namespaceSearchOrder.append('citoterms')
ag_url = os.path.join(hs_res_url, 'resourcemap.xml#aggregation')
a = Aggregation(ag_url)
#Set properties of the aggregation
a._dc.title = resource.title
a._dcterms.type = resource._meta.object_name
a._citoterms.isDocumentedBy = metadata_url
a._ore.isDescribedBy = res_map_url
#Create a description of the metadata document that describes the whole resource and add it to the aggregation
resMetaFile = AggregatedResource(metadata_url)
resMetaFile._dc.title = "Dublin Core science metadata document describing the HydroShare resource"
resMetaFile._citoterms.documents = ag_url
resMetaFile._ore.isAggregatedBy = ag_url
resMetaFile._dc.format = "application/rdf+xml"
#Create a description of the content file and add it to the aggregation
files = ResourceFile.objects.filter(object_id=resource.id)
resFiles = []
for n, f in enumerate(files):
filename = os.path.basename(f.resource_file.name)
resFiles.append(
AggregatedResource(
os.path.join(
'{hs_url}/resource/{res_id}/data/contents/{file_name}'.
format(hs_url=current_site_url,
res_id=resource.short_id,
file_name=filename))))
resFiles[n]._ore.isAggregatedBy = ag_url
resFiles[n]._dc.format = hs_core_utils.get_file_mime_type(filename)
#Add the resource files to the aggregation
a.add_resource(resMetaFile)
for f in resFiles:
a.add_resource(f)
#Register a serializer with the aggregation. The registration creates a new ResourceMap, which needs a URI
serializer = RdfLibSerializer('xml')
resMap = a.register_serialization(serializer, res_map_url)
resMap._dc.identifier = resource.short_id #"resource_identifier"
#Fetch the serialization
remdoc = a.get_serialization()
# change the namespace for the 'creator' element from 'dcterms' to 'dc'
xml_string = remdoc.data.replace('dcterms:creator', 'dc:creator')
# create resourcemap.xml and upload it to iRODS
from_file_name = os.path.join(bagit_path, 'resourcemap.xml')
with open(from_file_name, 'w') as out:
out.write(xml_string)
to_file_name = os.path.join(resource.short_id, 'data', 'resourcemap.xml')
istorage.saveFile(from_file_name, to_file_name, False)
shutil.rmtree(bagit_path)
return istorage
def create_bag_files(resource):
"""
create and update all files needed by bagit operation that is conducted on iRODS server; no bagit operation
is performed, only files that will be included in the bag are created or updated.
Parameters:
:param resource: A resource whose files will be created or updated to be included in the resource bag.
:return: istorage, an IrodsStorage object,that will be used by subsequent operation to create a bag on demand as needed.
"""
from . import utils as hs_core_utils
DATE_FORMAT = "YYYY-MM-DDThh:mm:ssTZD"
istorage=IrodsStorage()
dest_prefix = getattr(settings, 'BAGIT_TEMP_LOCATION', '/tmp/hydroshare/')
bagit_path = os.path.join(dest_prefix, resource.short_id, arrow.get(resource.updated).format("YYYY.MM.DD.HH.mm.ss"))
for d in (dest_prefix, bagit_path):
try:
os.makedirs(d)
except OSError as ex:
if ex.errno == errno.EEXIST:
shutil.rmtree(d)
os.makedirs(d)
else:
raise Exception(ex.message)
# an empty visualization directory will not be put into the zipped bag file by ibun command, so creating an empty
# visualization directory to be put into the zip file as done by the two statements below does not work. However,
# if visualization directory has content to be uploaded, it will work. This is to be implemented as part of the
# resource model in the future. The following two statements are placeholders serving as reminder
# to_file_name = '{res_id}/data/visualization/'.format(res_id=resource.short_id)
# istorage.saveFile('', to_file_name, create_directory=True)
# create resourcemetadata.xml and upload it to iRODS
from_file_name = '{path}/resourcemetadata.xml'.format(path=bagit_path)
with open(from_file_name, 'w') as out:
out.write(resource.metadata.get_xml())
to_file_name = '{res_id}/data/resourcemetadata.xml'.format(res_id=resource.short_id)
istorage.saveFile(from_file_name, to_file_name, True)
# make the resource map
current_site_url = hs_core_utils.current_site_url()
hs_res_url = '{hs_url}/resource/{res_id}/data'.format(hs_url=current_site_url, res_id=resource.short_id)
metadata_url = os.path.join(hs_res_url, 'resourcemetadata.xml')
res_map_url = os.path.join(hs_res_url, 'resourcemap.xml')
##make the resource map:
# utils.namespaces['hsterms'] = Namespace('{hs_url}/hsterms/'.format(hs_url=current_site_url))
# utils.namespaceSearchOrder.append('hsterms')
utils.namespaces['citoterms'] = Namespace('http://purl.org/spar/cito/')
utils.namespaceSearchOrder.append('citoterms')
ag_url = os.path.join(hs_res_url, 'resourcemap.xml#aggregation')
a = Aggregation(ag_url)
#Set properties of the aggregation
a._dc.title = resource.title
a._dcterms.type = resource._meta.object_name
a._citoterms.isDocumentedBy = metadata_url
a._ore.isDescribedBy = res_map_url
#Create a description of the metadata document that describes the whole resource and add it to the aggregation
resMetaFile = AggregatedResource(metadata_url)
resMetaFile._dc.title = "Dublin Core science metadata document describing the HydroShare resource"
resMetaFile._citoterms.documents = ag_url
resMetaFile._ore.isAggregatedBy = ag_url
resMetaFile._dc.format = "application/rdf+xml"
#Create a description of the content file and add it to the aggregation
files = ResourceFile.objects.filter(object_id=resource.id)
resFiles = []
for n, f in enumerate(files):
filename = os.path.basename(f.resource_file.name)
resFiles.append(AggregatedResource(os.path.join('{hs_url}/resource/{res_id}/data/contents/{file_name}'.format(
hs_url=current_site_url, res_id=resource.short_id, file_name=filename))))
resFiles[n]._ore.isAggregatedBy = ag_url
resFiles[n]._dc.format = hs_core_utils.get_file_mime_type(filename)
#Add the resource files to the aggregation
a.add_resource(resMetaFile)
for f in resFiles:
a.add_resource(f)
#Register a serializer with the aggregation. The registration creates a new ResourceMap, which needs a URI
serializer = RdfLibSerializer('xml')
resMap = a.register_serialization(serializer, res_map_url)
resMap._dc.identifier = resource.short_id #"resource_identifier"
#Fetch the serialization
remdoc = a.get_serialization()
# change the namespace for the 'creator' element from 'dcterms' to 'dc'
xml_string = remdoc.data.replace('dcterms:creator', 'dc:creator')
# create resourcemap.xml and upload it to iRODS
from_file_name = os.path.join(bagit_path, 'resourcemap.xml')
with open(from_file_name, 'w') as out:
out.write(xml_string)
to_file_name = os.path.join(resource.short_id, 'data', 'resourcemap.xml')
istorage.saveFile(from_file_name, to_file_name, False)
shutil.rmtree(bagit_path)
return istorage
