def check_ezeml_manifest(zipfile_name):
zip_object = ZipFile(zipfile_name, 'r')
# Get list of files in the archive
files = zip_object.namelist()
# flash(files)
# Unzip into the work path
user_path = user_data.get_user_folder_name(
) # os.path.join(current_path, USER_DATA_DIR)
work_path = os.path.join(user_path, 'zip_temp')
zip_object.extractall(path=work_path)
MANIFEST = 'ezEML_manifest.txt'
if MANIFEST not in files:
raise FileNotFoundError(MANIFEST)
manifest_data = zip_object.read(MANIFEST)
manifest = manifest_data.decode('utf-8').split('\n')
user_path = user_data.get_user_folder_name()
i = 3
while True:
# Each group of three lines will have the form:
# file type (e.g., JSON)
# filename
# checksum
filename = manifest[i + 1]
checksum = manifest[i + 2]
found = get_md5_hash(f'{work_path}/{filename}')
if checksum != found:
# flash(f'Checksum error: {filename} Expected:{checksum} Found:{found}')
raise ValueError(filename)
i += 3
if i + 2 >= len(manifest):
break
def determine_package_name(package_name=None):
user_path = user_data.get_user_folder_name()
work_path = os.path.join(user_path, 'zip_temp')
# Determine the output package name to use
# package_name may already be of the form foobar_COPYn
files = list_files_in_dir(user_path)
base_package_name = package_name
name_with_copy = base_package_name + '_COPY'
name_with_copy_len = len(name_with_copy)
max_copy = 0
for file in files:
if file.startswith(name_with_copy) and file.lower().endswith('.json'):
max_copy = max(max_copy, 1)
i = file[name_with_copy_len:-5] # 5 is len('.json')
try:
i = int(i)
if i > max_copy:
max_copy = i
except:
pass
suffix = ''
if max_copy >= 1:
suffix = str(max_copy + 1)
output_package_name = name_with_copy + suffix
# src_file = os.path.join(work_path, package_name) + '.zip'
# dest_file = os.path.join(work_path, output_package_name) + '.zip'
# shutil.move(src_file, dest_file)
return output_package_name
def cull_uploads(package_name=None):
# Remove uploads not represented in the metadata.
# Formerly, Import Package removed all uploads on the assumption that it was a new package.
# But, we may want to replace the metadata without losing the uploads. This is especially
# true when the "without data" form of the package is being used to replace the existing
# package in order to update the metadata without losing the uploads.
eml_node = load_eml(filename=package_name)
# Get all of the uploads represented in the metadata
object_names = []
object_name_nodes = []
eml_node.find_all_descendants(names.OBJECTNAME, object_name_nodes)
for object_name_node in object_name_nodes:
if object_name_node.content:
object_names.append(object_name_node.content)
# Remove any uploads that aren't in the list
user_path = user_data.get_user_folder_name(
) # os.path.join(current_path, USER_DATA_DIR)
upload_folder = os.path.join(user_path, 'uploads', package_name)
to_delete = [
file for file in os.listdir(upload_folder) if file not in object_names
]
for file in to_delete:
os.remove(os.path.join(user_path, 'uploads', package_name, file))
def move_metadata_files(metadata_file_name, upload_dir):
src_dir = upload_dir
dest_dir = user_data.get_user_folder_name()
src_file = os.path.join(src_dir, metadata_file_name)
dest_file = os.path.join(dest_dir, metadata_file_name)
shutil.move(src_file, dest_file)
json_file_name = metadata_file_name[:-4] + ".json"
src_file = os.path.join(src_dir, json_file_name)
dest_file = os.path.join(dest_dir, json_file_name)
shutil.move(src_file, dest_file)
def upload_ezeml_package(file, package_name=None):
# Determines the name of the data package by looking at the JSON file in the zip archive.
# The filename for the archive may have had a version number appended by the file system,
# and we need to know what the actual package name is, so the caller can determine if
# the package already exists in the user's account. Besides returning that unversioned
# package name, this function renames the zip file to the unversioned name.
# Also checks the ezEML manifest. If the manifest is missing or indicates that files have
# been changed outside of ezEML, this function raises ValueError.
user_path = user_data.get_user_folder_name()
work_path = os.path.join(user_path, 'zip_temp')
try:
shutil.rmtree(work_path)
except FileNotFoundError:
pass
try:
os.mkdir(work_path)
except FileExistsError:
pass
dest = os.path.join(work_path, package_name) + '.zip'
file.save(dest)
# Get the package name
try:
zip_object = ZipFile(dest, 'r')
except FileNotFoundError:
# flash(f'FileNotFoundError: {dest}')
raise FileNotFoundError(dest)
# Get list of files in the archive
files = zip_object.namelist()
unversioned_package_name = None
renamed_zip = None
for filename in files:
if filename.lower().endswith('.json'):
unversioned_package_name = filename.replace('.json', '')
renamed_zip = os.path.join(work_path,
unversioned_package_name) + '.zip'
shutil.move(dest, renamed_zip)
break
if not renamed_zip:
# flash(f'FileNotFoundError: {unversioned_package_name}.zip')
raise FileNotFoundError
check_ezeml_manifest(renamed_zip)
return unversioned_package_name
def save_xml_file(file):
user_path = user_data.get_user_folder_name()
work_path = os.path.join(user_path, 'zip_temp')
try:
shutil.rmtree(work_path)
except FileNotFoundError:
pass
try:
os.mkdir(work_path)
except FileExistsError:
pass
filename = file.filename
filepath = os.path.join(work_path, filename)
file.save(filepath)
return filepath
def perform_evaluation(eml_node, doc_name):
global evaluation
evaluation = []
# print('\nEntering perform_evaluation')
start = time.perf_counter()
user_folder = user_data.get_user_folder_name()
json_filename = f'{user_folder}/{doc_name}.json'
md5, validation_errs, evaluation_warnings = check_evaluation_memo(
json_filename, eml_node)
need_to_memoize = False
if validation_errs == None or evaluation_warnings == None:
# print('memoize')
need_to_memoize = True
validation_errs = validate_via_metapype(eml_node)
evaluation_warnings = evaluate_via_metapype(eml_node)
check_dataset_title(eml_node, doc_name, validation_errs)
check_data_tables(eml_node, doc_name, evaluation_warnings)
check_creators(eml_node, doc_name, validation_errs)
check_contacts(eml_node, doc_name, validation_errs)
check_associated_parties(eml_node, doc_name)
check_metadata_providers(eml_node, doc_name)
check_dataset_abstract(eml_node, doc_name, evaluation_warnings)
check_keywords(eml_node, doc_name, evaluation_warnings)
check_intellectual_rights(eml_node, doc_name, evaluation_warnings)
check_coverage(eml_node, doc_name, evaluation_warnings)
check_geographic_coverage(eml_node, doc_name)
check_maintenance(eml_node, doc_name, evaluation_warnings)
check_method_steps(eml_node, doc_name, evaluation_warnings)
check_project(eml_node, doc_name)
check_other_entities(eml_node, doc_name)
check_data_package_id(eml_node, doc_name, validation_errs)
if need_to_memoize:
memoize_evaluation(json_filename, eml_node, md5, validation_errs,
evaluation_warnings)
end = time.perf_counter()
# print(f"Leaving perform_evaluation: {end - start}")
return evaluation
def import_ezeml_package(output_package_name=None):
user_path = user_data.get_user_folder_name(
) # os.path.join(current_path, USER_DATA_DIR)
work_path = os.path.join(user_path, 'zip_temp')
dest = os.path.join(work_path, output_package_name) + '.zip'
try:
zip_object = ZipFile(dest, 'r')
except FileNotFoundError:
raise FileNotFoundError
zip_object.extractall(path=work_path)
# Remove the data package zip file
os.remove(dest)
# Create the uploads folder
upload_folder = os.path.join(user_path, 'uploads', output_package_name)
try:
os.mkdir(upload_folder)
except FileExistsError:
pass
# Get list of files
files = zip_object.namelist()
# Copy the files to their proper destinations
for filename in files:
src_file = os.path.join(work_path, filename)
if filename.startswith('data/'):
filename = filename[5:]
dest_file = os.path.join(upload_folder, filename)
user_data.add_data_table_upload_filename(
filename, document_name=output_package_name)
else:
if filename.endswith('.json'):
# Use the output package name
dest_file = os.path.join(user_path,
output_package_name) + '.json'
else:
dest_file = os.path.join(user_path, filename)
shutil.copyfile(src_file, dest_file)
