def get_context_data(self, **kwargs):
"""Update context data to add publication."""
context = super(DataDepotPublishedView,
self).get_context_data(**kwargs)
logger.info('Get context Data')
pub = Publication(project_id=kwargs['project_id'].strip('/'))
logger.debug('pub: %s', pub.to_dict())
context['citation_title'] = pub.project.value.title
context['citation_date'] = pub.created
context['doi'] = pub.project.doi
context['keywords'] = pub.project.value.keywords.split(',')
context['authors'] = [{
'full_name':
'{last_name}, {first_name}'.format(last_name=user['last_name'],
first_name=user['first_name']),
'institution':
getattr(getattr(user, 'profile'), 'institution', '')
} for user in pub.users]
context['publication'] = pub
if self.request.user.is_authenticated:
context['angular_init'] = json.dumps({
'authenticated': True,
})
else:
context['angular_init'] = json.dumps({
'authenticated': False,
})
return context
def get(self, request, project_id):
pub = Publication(project_id=project_id)
if pub is not None and hasattr(pub, 'project'):
return JsonResponse(pub.to_dict())
else:
return JsonResponse({'status': 404,
'message': 'Not found'},
status=404)
def zip_publication_files(self, project_id):
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
try:
pub = Publication(project_id=project_id)
pub.archive()
except Exception as exc:
logger.error('Zip Proj Id: %s. %s', project_id, exc, exc_info=True)
raise self.retry(exc=exc)
def save_publication(self, project_id):
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
from designsafe.apps.api.projects.managers import publication as PublicationManager
try:
pub = Publication(project_id=project_id)
publication = PublicationManager.reserve_publication(pub.to_dict())
pub.update(**publication)
except Exception as exc:
logger.error('Proj Id: %s. %s', project_id, exc, exc_info=True)
raise self.retry(exc=exc)
def save_to_fedora(self, project_id):
import requests
import magic
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
try:
pub = Publication(project_id=project_id)
pub.update(status='published')
_root = os.path.join('/corral-repl/tacc/NHERI/published', project_id)
fedora_base = 'http://fedoraweb01.tacc.utexas.edu:8080/fcrepo/rest/publications_01'
res = requests.get(fedora_base)
if res.status_code == 404 or res.status_code == 410:
requests.put(fedora_base)
fedora_project_base = ''.join([fedora_base, '/', project_id])
res = requests.get(fedora_project_base)
if res.status_code == 404 or res.status_code == 410:
requests.put(fedora_project_base)
headers = {'Content-Type': 'text/plain'}
#logger.debug('walking: %s', _root)
for root, dirs, files in os.walk(_root):
for name in files:
mime = magic.Magic(mime=True)
headers['Content-Type'] = mime.from_file(
os.path.join(root, name))
#files
full_path = os.path.join(root, name)
_path = full_path.replace(_root, '', 1)
_path = _path.replace('[', '-')
_path = _path.replace(']', '-')
url = ''.join([fedora_project_base, urllib.quote(_path)])
#logger.debug('uploading: %s', url)
with open(os.path.join(root, name), 'rb') as _file:
requests.put(url, data=_file, headers=headers)
for name in dirs:
#dirs
full_path = os.path.join(root, name)
_path = full_path.replace(_root, '', 1)
url = ''.join([fedora_project_base, _path])
#logger.debug('creating: %s', _path)
requests.put(url)
except Exception as exc:
logger.error('Proj Id: %s. %s', project_id, exc)
raise self.retry(exc=exc)
def copy_publication_files_to_corral(self, project_id):
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
import shutil
publication = Publication(project_id=project_id)
filepaths = publication.related_file_paths()
if not len(filepaths):
res = get_service_account_client().files.list(
systemId='project-{project_uuid}'.format(
project_uuid=publication.project.uuid
),
filePath='/'
)
filepaths = [
_file.path.strip('/') for _file in res if (
_file.name != '.' and _file.name != 'Trash'
)
]
filepaths = list(set(filepaths))
filepaths = sorted(filepaths)
base_path = ''.join(['/', publication.projectId])
prefix_dest = '/corral-repl/tacc/NHERI/published/{}'.format(project_id)
if not os.path.isdir(prefix_dest):
os.mkdir(prefix_dest)
prefix_src = '/corral-repl/tacc/NHERI/projects/{}'.format(publication.project['uuid'])
for filepath in filepaths:
local_src_path = '{}/{}'.format(prefix_src, filepath)
local_dst_path = '{}/{}'.format(prefix_dest, filepath)
logger.info('Trying to copy: %s to %s', local_src_path, local_dst_path)
if os.path.isdir(local_src_path):
try:
#os.mkdir(local_dst_path)
shutil.copytree(local_src_path, local_dst_path)
except OSError as exc:
logger.info(exc)
except IOError as exc:
logger.info(exc)
else:
try:
if not os.path.isdir(os.path.dirname(local_dst_path)):
os.mkdir(os.path.dirname(local_dst_path))
shutil.copy(local_src_path, local_dst_path)
except OSError as exc:
logger.info(exc)
except IOError as exc:
logger.info(exc)
#for filepath in filepaths:
# filepath = filepath.strip('/')
# logger.info('Copying: {}'.format(filepath))
# path_comps = filepath.split('/')
# parent_path = os.path.join(*path_comps[:-1])
# try:
# file_obj = BaseFileResource.\
# listing(system=proj_system,
# path=filepath,
# agave_client=service)
# if file_obj.type == 'dir':
# logger.info('path is a directory, ensuring path exists')
# base_obj = BaseFileResource.\
# ensure_path(service,
# settings.PUBLISHED_SYSTEM,
# os.path.join(base_path, parent_path))
# else:
# logger.info('path is a file, ensuring parent path exists')
# base_obj = BaseFileResource.\
# ensure_path(service,
# settings.PUBLISHED_SYSTEM,
# os.path.join(base_path, parent_path))
# base_obj.import_data(file_obj.system, file_obj.path)
# except Exception as err:
# logger.error('Error when copying data to published: %s. %s', filepath, err)
# local_src_path = '{}/{}'.format(prefix_src, file_obj.path)
# local_dst_path = '{}/{}'.format(prefix_dest, file_obj.path)
# logger.info('Trying to copy: %s to %s', local_src_path, local_dst_path)
# if os.path.isdir(local_src_path):
# shutil.copytree(local_src_path, local_dst_path)
# else:
# shutil.copy(local_src_path, local_dst_path)
# #self.retry(exc=err)
#try:
# image = BaseFileResource.\
# listing(system=proj_system,
# path='projectimage.jpg',
# agave_client=service)
# base_dir.import_data(image.system, image.path)
#except HTTPError as err:
# logger.debug('No project image')
save_to_fedora.apply_async(args=[project_id])
def copy_publication_files_to_corral(self, project_id):
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
import shutil
publication = Publication(project_id=project_id)
filepaths = publication.related_file_paths()
if not len(filepaths):
res = get_service_account_client().files.list(
systemId='project-{project_uuid}'.format(
project_uuid=publication.project.uuid),
filePath='/')
filepaths = [
_file.path.strip('/') for _file in res
if (_file.name != '.' and _file.name != 'Trash')
]
filepaths = list(set(filepaths))
filepaths = sorted(filepaths)
base_path = ''.join(['/', publication.projectId])
os.chmod('/corral-repl/tacc/NHERI/published', 0755)
prefix_dest = '/corral-repl/tacc/NHERI/published/{}'.format(project_id)
if not os.path.isdir(prefix_dest):
os.mkdir(prefix_dest)
prefix_src = '/corral-repl/tacc/NHERI/projects/{}'.format(
publication.project['uuid'])
for filepath in filepaths:
local_src_path = '{}/{}'.format(prefix_src, filepath)
local_dst_path = '{}/{}'.format(prefix_dest, filepath)
logger.info('Trying to copy: %s to %s', local_src_path, local_dst_path)
if os.path.isdir(local_src_path):
try:
#os.mkdir(local_dst_path)
if not os.path.isdir(os.path.dirname(local_dst_path)):
os.makedirs(os.path.dirname(local_dst_path))
shutil.copytree(local_src_path, local_dst_path)
for root, dirs, files in os.walk(local_dst_path):
for d in dirs:
os.chmod(os.path.join(root, d), 0555)
for f in files:
os.chmod(os.path.join(root, f), 0444)
os.chmod(local_dst_path, 0555)
except OSError as exc:
logger.info(exc)
except IOError as exc:
logger.info(exc)
else:
try:
if not os.path.isdir(os.path.dirname(local_dst_path)):
os.makedirs(os.path.dirname(local_dst_path))
for root, dirs, files in os.walk(
os.path.dirname(local_dst_path)):
for d in dirs:
os.chmod(os.path.join(root, d), 0555)
for f in files:
os.chmod(os.path.join(root, f), 0444)
shutil.copy(local_src_path, local_dst_path)
os.chmod(local_dst_path, 0444)
except OSError as exc:
logger.info(exc)
except IOError as exc:
logger.info(exc)
os.chmod(prefix_dest, 0555)
os.chmod('/corral-repl/tacc/NHERI/published', 0555)
save_to_fedora.apply_async(args=[project_id])
agave_indexer.apply_async(kwargs={
'username': '******',
'systemId': 'designsafe.storage.published',
'filePath': '/' + project_id,
'recurse': True
},
queue='indexing')
def set_publish_status(self, project_id):
from designsafe.apps.api.agave.filemanager.public_search_index import Publication
pub = Publication(project_id=project_id)
pub.update(status='published')
