def siloview(self, silo):
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
c.ident = ident
c.silo_name = silo
c.editor = False
if ag.metadata_embargoed:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
c.editor = True
elif ident:
silos = ag.authz(ident)
if silo in silos:
c.editor = True
rdfsilo = ag.granary.get_rdf_silo(silo)
state_info = ag.granary.describe_silo(silo)
if 'title' in state_info and state_info['title']:
c.title = state_info['title']
c.embargos = {}
c.items = []
for item in rdfsilo.list_items():
c.embargos[item] = None
try:
c.embargos[item] = is_embargoed(rdfsilo, item)
except:
pass
c.items.append(item)
#c.embargos[item] = ()
# conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render('/siloview.html')
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.embargos)
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/html
return render('/siloview.html')
def datasetview(self, silo, id):
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission='administrator')
silos_manager = ag.authz(ident, permission='manager')
rdfsilo = ag.granary.get_rdf_silo(silo)
if not rdfsilo.exists(id):
abort(404)
item = rdfsilo.get_item(id)
creator = None
if item.manifest and item.manifest.state and 'metadata' in item.manifest.state and item.manifest.state['metadata'] and \
'createdby' in item.manifest.state['metadata'] and item.manifest.state['metadata']['createdby']:
creator = item.manifest.state['metadata']['createdby']
#if not (ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]):
if not (ident['repoze.who.userid'] == creator or silo in silos_admin or silo in silos_manager):
abort(403, "Forbidden. You should be the creator or manager or administrator to view this information")
options = request.GET
if 'version' in options and options['version']:
if not options['version'] in item.manifest['versions']:
abort(404)
currentversion = str(item.currentversion)
vnum = str(options['version'])
if vnum and not vnum == currentversion:
item.set_version_cursor(vnum)
parts = item.list_parts(detailed=True)
dataset = {}
dataset['parts'] = {}
for part in parts:
dataset['parts'][part] = serialisable_stat(parts[part])
if item.manifest:
dataset['state'] = item.manifest.state
# Always return application/json
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(dataset)
def siloview(self, silo):
if not request.environ.get('repoze.who.identity'):
abort(401, "Not Authorised")
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
c.ident = ident
silos = ag.authz(ident, permission=['administrator', 'manager'])
if not silo in silos:
abort(403, "Do not have administrator or manager credentials for silo %s"%silo)
user_groups = list_user_groups(ident['user'].user_name)
if ('*', 'administrator') in user_groups:
c.roles = ["admin", "manager", "user"]
elif (silo, 'administrator') in user_groups:
c.roles = ["admin", "manager", "user"]
elif (silo, 'manager') in user_groups:
c.roles = ["manager", "user"]
else:
abort(403, "Do not have administrator or manager credentials for silo %s"%silo)
c.silo = silo
http_method = request.environ['REQUEST_METHOD']
if http_method == "GET":
c.users = list_group_users(silo)
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/silo_users.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.users)
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/plain
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.users)
def service_document(self, path=None):
"""
Construct the Service Document. This takes the set of collections that are in the store, and places them in
an Atom Service document as the individual entries
"""
service = ServiceDocument(version=self.config.sword_version,
max_upload_size=self.config.max_upload_size)
# get the authorised list of silos
silos = ag.authz(self.auth_credentials.identity)
# now for each collection create an sdcollection
collections = []
for col_name in silos:
href = self.um.silo_url(col_name)
title = col_name
mediation = self.config.mediation
# content types accepted
accept = []
multipart_accept = []
if not self.config.accept_nothing:
if self.config.app_accept is not None:
for acc in self.config.app_accept:
accept.append(acc)
if self.config.multipart_accept is not None:
for acc in self.config.multipart_accept:
multipart_accept.append(acc)
# SWORD packaging formats accepted
accept_package = []
for format in self.config.sword_accept_package:
accept_package.append(format)
col = SDCollection(href=href,
title=title,
accept=accept,
multipart_accept=multipart_accept,
accept_package=accept_package,
mediation=mediation)
collections.append(col)
service.add_workspace("Silos", collections)
# serialise and return
return service.serialise()
def subitemview(self, silo, id, path, subpath):
# Function to retreive a file from the zipfile
# TODO
# I check to see the path is avlid and it is a zip file.
# I do not deal with subpath. if it is a file - serve it. If it is a dir, show the contents of it.
# tmpl_context variables needed: c.silo_name, c.zipfile_contents c.ident, c.id, c.path
if not ag.granary.issilo(silo):
abort(404)
if not (path or subpath):
abort(400, "You must supply a filename to unpack")
rdfsilo = ag.granary.get_rdf_silo(silo)
if not rdfsilo.exists(id):
abort(404)
c.silo_name = silo
c.id = id
c.path = path
c.subpath = subpath
ident = request.environ.get("repoze.who.identity")
c.ident = ident
dataset = rdfsilo.get_item(id)
if dataset.metadata.get("embargoed") not in ["false", 0, False]:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
item_real_filepath = dataset.to_dirpath()
target_filepath = "%s/%s" % (item_real_filepath, path)
# c.parts = dataset.list_parts(detailed=False)
if not dataset.isfile(path):
abort(404, "File not found")
if not os.path.isfile(target_filepath):
abort(404, "File not found")
if not check_file_mimetype(target_filepath, "application/zip"):
abort(415, "File is not of type application/zip")
# TODO : if subpath is a file - serve it. If subpath is a dir, show the contents of the dir
return render("/zipfilesubitemview.html")
def index(self):
ident = request.environ.get('repoze.who.identity')
c.ident = ident
#granary_list = ag.granary.silos
#c.silos = granary_list
c.silos = list_silos()
if ag.metadata_embargoed:
if not ident:
abort(401, "Not Authorised")
c.silos = ag.authz(ident)
c.silo_infos = {}
for silo in c.silos:
c.silo_infos[silo] = []
state_info = ag.granary.describe_silo(silo)
if 'title' in state_info and state_info['title']:
c.silo_infos[silo].append(state_info['title'])
else:
c.silo_infos[silo].append(silo)
c.silo_infos[silo].append(get_datasets_count(silo))
c.silo_infos[silo].append(getSiloModifiedDate(silo))
# conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render('/list_of_silos.html')
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.silos)
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/html
return render('/list_of_silos.html')
def service_document(self, path=None):
"""
Construct the Service Document. This takes the set of collections that are in the store, and places them in
an Atom Service document as the individual entries
"""
service = ServiceDocument(version=self.config.sword_version,
max_upload_size=self.config.max_upload_size)
# get the authorised list of silos
silos = ag.authz(self.auth_credentials.identity)
# now for each collection create an sdcollection
collections = []
for col_name in silos:
href = self.um.silo_url(col_name)
title = col_name
mediation = self.config.mediation
# content types accepted
accept = []
multipart_accept = []
if not self.config.accept_nothing:
if self.config.app_accept is not None:
for acc in self.config.app_accept:
accept.append(acc)
if self.config.multipart_accept is not None:
for acc in self.config.multipart_accept:
multipart_accept.append(acc)
# SWORD packaging formats accepted
accept_package = []
for format in self.config.sword_accept_package:
accept_package.append(format)
col = SDCollection(href=href, title=title, accept=accept, multipart_accept=multipart_accept,
accept_package=accept_package, mediation=mediation)
collections.append(col)
service.add_workspace("Silos", collections)
# serialise and return
return service.serialise()
def container_exists(self, path):
# extract information from the path
silo, dataset_id, accept_parameters = self.um.interpret_path(path)
# is this a silo?
if not ag.granary.issilo(silo):
return False
# is this an authorised silo?
silos = ag.authz(self.auth_credentials.identity)
if silo not in silos:
return False
# get a full silo object
rdf_silo = ag.granary.get_rdf_silo(silo)
# is the dataset in the authorised silo?
if not rdf_silo.exists(dataset_id):
return False
# if we get here without failing, then the container exists (from the
# perspective of the user)
return True
def container_exists(self, path):
# extract information from the path
silo, dataset_id, accept_parameters = self.um.interpret_path(path)
# is this a silo?
if not ag.granary.issilo(silo):
return False
# is this an authorised silo?
silos = ag.authz(self.auth_credentials.identity)
if silo not in silos:
return False
# get a full silo object
rdf_silo = ag.granary.get_rdf_silo(silo)
# is the dataset in the authorised silo?
if not rdf_silo.exists(dataset_id):
return False
# if we get here without failing, then the container exists (from the
# perspective of the user)
return True
def _get_authorised_rdf_silo(self, silo):
if not ag.granary.issilo(silo):
return SwordError(status=404, empty=True)
# get the authorised list of silos
#granary_list = ag.granary.silos
granary_list = list_silos()
silos = ag.authz(self.auth_credentials.identity)
# does the collection/silo exist? If not, we can't do a deposit
if silo not in silos:
# if it's not in the silos it is either non-existant or it is
# forbidden...
if silo in granary_list:
# forbidden
raise SwordError(status=403, empty=True)
else:
# not found
raise SwordError(status=404, empty=True)
# get a full silo object
rdf_silo = ag.granary.get_rdf_silo(silo)
return rdf_silo
def _get_authorised_rdf_silo(self, silo):
if not ag.granary.issilo(silo):
return SwordError(status=404, empty=True)
# get the authorised list of silos
#granary_list = ag.granary.silos
granary_list = list_silos()
silos = ag.authz(self.auth_credentials.identity)
# does the collection/silo exist? If not, we can't do a deposit
if silo not in silos:
# if it's not in the silos it is either non-existant or it is
# forbidden...
if silo in granary_list:
# forbidden
raise SwordError(status=403, empty=True)
else:
# not found
raise SwordError(status=404, empty=True)
# get a full silo object
rdf_silo = ag.granary.get_rdf_silo(silo)
return rdf_silo
def datasetview(self, silo, id):
"""Get a list of zipfiles in dataset 'id' within the silo 'silo' and unpack a dataset."""
if not ag.granary.issilo(silo):
abort(404)
rdfsilo = ag.granary.get_rdf_silo(silo)
if not rdfsilo.exists(id):
abort(404)
# tmpl_context variables needed: c.silo_name, c.zipfiles, c.ident, c.id, c.path
c.silo_name = silo
c.id = id
ident = request.environ.get("repoze.who.identity")
c.ident = ident
dataset = rdfsilo.get_item(id)
creator = None
if (
dataset.manifest
and dataset.manifest.state
and "metadata" in dataset.manifest.state
and dataset.manifest.state["metadata"]
and "createdby" in dataset.manifest.state["metadata"]
and dataset.manifest.state["metadata"]["createdby"]
):
creator = dataset.manifest.state["metadata"]["createdby"]
http_method = request.environ["REQUEST_METHOD"]
if http_method == "GET":
c.editor = False
if ag.metadata_embargoed:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission="administrator")
silos_manager = ag.authz(ident, permission="manager")
# if ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]:
if ident["repoze.who.userid"] == creator or silo in silos_admin or silo in silos_manager:
c.editor = True
elif ident:
silos = ag.authz(ident)
if silo in silos:
silos_admin = ag.authz(ident, permission="administrator")
silos_manager = ag.authz(ident, permission="manager")
# if ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]:
if ident["repoze.who.userid"] == creator or silo in silos_admin or silo in silos_manager:
c.editor = True
else:
# identity management of item
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission="administrator")
silos_manager = ag.authz(ident, permission="manager")
# if not (ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]):
if not (ident["repoze.who.userid"] == creator or silo in silos_admin or silo in silos_manager):
abort(403, "Forbidden")
if http_method == "GET":
c.zipfiles = get_zipfiles_in_dataset(dataset)
# conneg return
accept_list = None
if "HTTP_ACCEPT" in request.environ:
try:
accept_list = conneg_parse(request.environ["HTTP_ACCEPT"])
except:
accept_list = [MT("text", "html")]
if not accept_list:
accept_list = [MT("text", "html")]
mimetype = accept_list.pop(0)
while mimetype:
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/list_of_zipfiles.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
# return simplejson.dumps(dict(c.zipfiles))
return simplejson.dumps(list(c.zipfiles.keys()))
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops nothing satisfies - return text/html
return render("/list_of_zipfiles.html")
elif http_method == "POST":
params = request.POST
if not (params.has_key("filename") and params["filename"]):
abort(400, "You must supply a filename to unpack")
item_real_filepath = dataset.to_dirpath()
target_filepath = "%s/%s" % (item_real_filepath, params["filename"])
if not os.path.isfile(target_filepath):
abort(404, "File to unpack not found")
if not check_file_mimetype(target_filepath, "application/zip"):
abort(415, "File is not of type application/zip")
if params.has_key("id") and params["id"]:
target_dataset_name = params["id"]
else:
# (head, fn) = os.path.split(params['filename'])
# (fn, ext) = os.path.splitext(fn)
# target_dataset_name = "%s-%s"%(id,fn)
target_dataset_name = id
# step 1: Create / initialize target dataset
if not rdfsilo.exists(target_dataset_name):
if not allowable_id2(target_dataset_name):
response.content_type = "text/plain"
response.status_int = 400
response.status = "400 Bad request. Data package name not valid"
return (
"Data package name can contain only the following characters - %s and has to be more than 1 character"
% ag.naming_rule_humanized
)
target_dataset = create_new(rdfsilo, target_dataset_name, ident["repoze.who.userid"])
response.status_int = 201
response.status = "201 Created"
response.headers["Content-Location"] = url(
controller="datasets", action="datasetview", silo=silo, id=target_dataset_name
)
response_message = "201 Created"
else:
target_dataset = rdfsilo.get_item(target_dataset_name)
response.status = "204 Updated"
response.status_int = 204
response_message = None
# step 2: Unpack zip item
try:
unpack_zip_item(target_dataset, dataset, params["filename"], rdfsilo, ident["repoze.who.userid"])
except BadZipfile:
abort(400, "BadZipfile: Couldn't unpack zipfile")
target_dataset.sync()
target_dataset.sync()
target_dataset.sync()
if response.status_int == 201:
try:
ag.b.creation(silo, id, ident=ident["repoze.who.userid"])
except:
pass
else:
try:
ag.b.change(silo, id, ident=ident["repoze.who.userid"])
except:
pass
# conneg return
accept_list = None
if "HTTP_ACCEPT" in request.environ:
try:
accept_list = conneg_parse(request.environ["HTTP_ACCEPT"])
except:
accept_list = [MT("text", "html")]
if not accept_list:
accept_list = [MT("text", "html")]
mimetype = accept_list.pop(0)
while mimetype:
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
redirect(url(controller="datasets", action="datasetview", silo=silo, id=target_dataset_name))
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = "text/plain"
return response_message
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/plain
response.content_type = "text/plain"
return response_message
def itemview(self, silo, id, path):
"""API call to
GET - read the contents of a zip-file (without having to unpack) and
POST- unpack a zip file into a new / existing dataset
PUT - Add the zipfile and unpack it onto the existing dataset"""
# tmpl_context variables needed: c.silo_name, c.zipfile_contents c.ident, c.id, c.path
if not path:
abort(400, "You must supply a filename to unpack")
if not ag.granary.issilo(silo):
abort(404)
rdfsilo = ag.granary.get_rdf_silo(silo)
if not rdfsilo.exists(id):
abort(404)
c.silo_name = silo
c.id = id
c.path = path
ident = request.environ.get("repoze.who.identity")
c.ident = ident
dataset = rdfsilo.get_item(id)
creator = None
if (
dataset.manifest
and dataset.manifest.state
and "metadata" in dataset.manifest.state
and dataset.manifest.state["metadata"]
and "createdby" in dataset.manifest.state["metadata"]
and dataset.manifest.state["metadata"]["createdby"]
):
creator = dataset.manifest.state["metadata"]["createdby"]
http_method = request.environ["REQUEST_METHOD"]
if http_method == "GET":
if dataset.metadata.get("embargoed") not in ["false", 0, False]:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
else:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission="administrator")
silos_manager = ag.authz(ident, permission="manager")
# if not (ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]):
if not (ident["repoze.who.userid"] == creator or silo in silos_admin or silo in silos_manager):
abort(403, "Forbidden")
item_real_filepath = dataset.to_dirpath()
target_filepath = "%s/%s" % (item_real_filepath, path)
# c.parts = dataset.list_parts(detailed=False)
if http_method in ["GET", "POST"]:
if not dataset.isfile(path):
abort(404, "File not found")
if not os.path.isfile(target_filepath):
abort(404, "File not found")
if not check_file_mimetype(target_filepath, "application/zip"):
abort(415, "File is not of type application/zip")
if http_method == "GET":
try:
c.zipfile_contents = read_zipfile(target_filepath)
except BadZipfile:
abort(400, "Could not read zipfile")
# conneg return
accept_list = None
if "HTTP_ACCEPT" in request.environ:
try:
accept_list = conneg_parse(request.environ["HTTP_ACCEPT"])
except:
accept_list = [MT("text", "html")]
if not accept_list:
accept_list = [MT("text", "html")]
mimetype = accept_list.pop(0)
while mimetype:
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/zipfileview.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.zipfile_contents)
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/html
return render("/zipfileview.html")
elif http_method == "POST":
params = request.POST
# if not (params.has_key("filename") and params['filename']):
# abort(400, "You must supply a filename to unpack")
if params.has_key("id") and params["id"]:
target_dataset_name = params["id"]
else:
# (head, fn) = os.path.split(path)
# (fn, ext) = os.path.splitext(fn)
# target_dataset_name = "%s-%s"%(id,fn)
target_dataset_name = id
# step 1: Create / initialize target dataset
if not rdfsilo.exists(target_dataset_name):
if not allowable_id2(target_dataset_name):
response.content_type = "text/plain"
response.status_int = 400
response.status = "400 Bad request. Data package name not valid"
return (
"Data package name can contain only the following characters - %s and has to be more than 1 character"
% ag.naming_rule_humanized
)
target_dataset = create_new(rdfsilo, target_dataset_name, ident["repoze.who.userid"])
response.status_int = 201
response.status = "201 Created"
response.headers["Content-Location"] = url(
controller="datasets", action="datasetview", silo=silo, id=target_dataset_name
)
response_message = "201 Created"
else:
target_dataset = rdfsilo.get_item(target_dataset_name)
response.status = "204 Updated"
response.status_int = 204
response_message = None
# step 2: Unpack zip item
try:
unpack_zip_item(target_dataset_name, dataset, path, rdfsilo, ident["repoze.who.userid"])
except BadZipfile:
abort(400, "Couldn't unpack zipfile")
target_dataset.sync()
target_dataset.sync()
target_dataset.sync()
if response.status_int == 201:
try:
ag.b.creation(silo, id, ident=ident["repoze.who.userid"])
except:
pass
else:
try:
ag.b.change(silo, id, ident=ident["repoze.who.userid"])
except:
pass
# conneg return
accept_list = None
if "HTTP_ACCEPT" in request.environ:
try:
accept_list = conneg_parse(request.environ["HTTP_ACCEPT"])
except:
accept_list = [MT("text", "html")]
if not accept_list:
accept_list = [MT("text", "html")]
mimetype = accept_list.pop(0)
while mimetype:
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
redirect(url(controller="datasets", action="datasetview", silo=silo, id=target_dataset_name))
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = "text/plain"
return response_message
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/plain
response.content_type = "text/plain"
return response_message
elif http_method == "PUT":
# Pylons loads the request body into request.body...
# This is not going to work for large files... ah well
# POST will handle large files as they are pushed to disc,
# but this won't
content = request.body
if JAILBREAK.search(path) != None:
abort(400, "'..' cannot be used in the path")
# Step 1: Put zipfile in dataset
if dataset.isdir(path):
response.content_type = "text/plain"
response.status_int = 403
response.status = "403 Forbidden"
return "Cannot PUT a file on to an existing directory"
if dataset.isfile(path):
code = 204
else:
code = 201
if code == 204:
dataset.increment_version_delta(clone_previous_version=True, copy_filenames=["manifest.rdf", path])
else:
dataset.increment_version_delta(clone_previous_version=True, copy_filenames=["manifest.rdf"])
dataset.put_stream(path, content)
dataset.del_triple(dataset.uri, u"dcterms:modified")
dataset.add_triple(dataset.uri, u"dcterms:modified", datetime.now())
dataset.del_triple(dataset.uri, u"oxds:currentVersion")
dataset.add_triple(dataset.uri, u"oxds:currentVersion", dataset.currentversion)
dataset.sync()
target_dataset = rdfsilo.get_item(id)
# step 2: Unpack zip item
if not check_file_mimetype(target_filepath, "application/zip"):
abort(415, "File is not of type application/zip")
try:
unpack_zip_item(target_dataset, dataset, path, rdfsilo, ident["repoze.who.userid"])
except BadZipfile:
abort(400, "Couldn't unpack zipfile")
target_dataset.sync()
target_dataset.sync()
target_dataset.sync()
response.status = "204 Updated"
response.status_int = 204
response_message = None
try:
ag.b.change(silo, id, path, ident=ident["repoze.who.userid"])
except:
pass
# conneg return
accept_list = None
if "HTTP_ACCEPT" in request.environ:
try:
accept_list = conneg_parse(request.environ["HTTP_ACCEPT"])
except:
accept_list = [MT("text", "html")]
if not accept_list:
accept_list = [MT("text", "html")]
mimetype = accept_list.pop(0)
while mimetype:
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
redirect(url(controller="datasets", action="datasetview", silo=silo, id=id))
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = "text/plain"
return response_message
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/plain
response.content_type = "text/plain"
return response_message
def raw(self):
ident = request.environ.get('repoze.who.identity')
c.ident = ident
silos = None
if ag.metadata_embargoed:
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silos and not isinstance(silos, basestring) and type(silos).__name__ == 'list':
silos = ' '.join(silos)
http_method = request.environ['REQUEST_METHOD']
if http_method == "GET":
params = request.GET
elif http_method == "POST":
params = request.POST
if not "q" in params:
abort(400, "Parameter 'q' is not available")
#If ag.metadata_embargoed, search only within your silos
if params['q'] == '*':
if silos:
params['q'] = """silo:(%s)"""%silos
else:
params['q'] = "*:*"
elif silos and not 'silo:' in params['q']:
params['q'] = """%s AND silo:(%s)"""%(params['q'], silos)
accept_list = None
if 'wt' in params and params['wt'] == "json":
accept_list = [MT("application", "json")]
elif 'wt' in params and params['wt'] == "xml":
accept_list = [MT("text", "xml")]
else:
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
params['wt'] = 'json'
accept_list= [MT("text", "html")]
break
elif str(mimetype).lower() in ["text/plain", "application/json"]:
params['wt'] = 'json'
accept_list= [MT("application", "json")]
break
elif str(mimetype).lower() in ["application/rdf+xml", "text/xml"]:
params['wt'] = 'xml'
accept_list = [MT("text", "xml")]
break
# Whoops - nothing satisfies
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
if not 'wt' in params or not params['wt'] in ['json', 'xml']:
params['wt'] = 'json'
accept_list= [MT("text", "html")]
if not 'fl' in params or not params['fl']:
#Also include the following fields - date modified, publication year / publication date, embargo status, embargo date, version
params['fl'] = "id,silo,mediator,creator,title,score"
if not 'start' in params or not params['start']:
params['start'] = '0'
if not 'rows' in params or not params['rows']:
params['rows'] = '100'
try:
result = ag.solr.raw_query(**params)
except:
result = {}
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
c.result = result
return render('/raw_search.html')
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return result
elif str(mimetype).lower() in ["application/rdf+xml", "text/xml"]:
response.content_type = 'text/xml; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return result
# Whoops - nothing satisfies
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops - nothing staisfies - default to text/html
c.result = result
return render('/raw_search.html')
def index(self):
if not request.environ.get('repoze.who.identity'):
abort(401, "Not Authorised")
ident = request.environ.get('repoze.who.identity')
c.ident = ident
c.granary_list = ag.authz(ident, permission=['administrator', 'manager'])
http_method = request.environ['REQUEST_METHOD']
if http_method == 'GET':
if not 'administrator' in ident['permissions'] and not 'manager' in ident['permissions']:
abort(403, "Do not have administrator or manager credentials")
else:
if not 'administrator' in ident['permissions']:
abort(403, "Do not have administrator credentials")
if http_method == "GET":
#c.granary = ag.granary
# conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/admin_silos.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(list(c.granary_list))
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/html
return render("admin_silos.html")
elif http_method == "POST":
params = request.POST
if 'silo' in params:
if ag.granary.issilo(params['silo']):
abort(403, "The silo %s exists"%params['silo'])
if not allowable_id2(params['silo']):
response.content_type = "text/plain"
response.status_int = 400
response.status = "400 Bad request. Silo name not valid"
return "Silo name can contain only the following characters - %s and has to be more than 1 character"%ag.naming_rule_humanized
#NOTE:
#If any userid in params['administrators']/params['managers']/params['submitters'] does not exist, return 403
#if administartor list is empty, append current user to administartor list
#Owner is the superset of adminstrators, managers and submitters
existing_users = list_usernames()
owners = []
admins = []
managers = []
submitters = []
#if 'owners' in params and params['owners']:
# owners = [x.strip() for x in kw['owners'].split(",") if x]
if 'administrators' in params and params['administrators']:
admins = [x.strip() for x in params['administrators'].split(",") if x]
owners.extend(admins)
if 'managers' in params and params['managers']:
managers = [x.strip() for x in params['managers'].split(",") if x]
owners.extend(managers)
if 'submitters' in params and params['submitters']:
submitters = [x.strip() for x in params['submitters'].split(",") if x]
owners.extend(submitters)
if not admins:
owners.append(ident['user'].user_name)
admins.append(ident['user'].user_name)
owners = list(set(owners))
for o in owners:
if not o in existing_users:
abort (403, "User %s does not exist"%o)
admins = list(set(admins))
managers = list(set(managers))
submitters = list(set(submitters))
# Create new silo
silo = params['silo']
g_root = config.get("granary.uri_root", "info:")
c.silo = ag.granary.get_rdf_silo(silo, uri_base="%s%s/datasets/" % (g_root, silo))
ag.granary._register_silos()
kw = {}
for term in accepted_params:
if term in params:
kw[term] = params[term]
kw['owners'] = ','.join(owners)
kw['administrators'] = ','.join(admins)
kw['managers'] = ','.join(managers)
kw['submitters'] = ','.join(submitters)
du = ag.granary.disk_usage_silo(silo)
kw['disk_usage'] = du
ag.granary.describe_silo(silo, **kw)
ag.granary.sync()
# Add silo to database
add_silo(silo)
try:
ag.b.silo_creation(silo, ident=ident['repoze.who.userid'])
except:
pass
#Add users belonging to the silo, to the database
all_silo_users = []
for a in admins:
all_silo_users.append((a, 'administrator'))
for a in managers:
all_silo_users.append((a, 'manager'))
for a in submitters:
all_silo_users.append((a, 'submitter'))
add_group_users(params['silo'], all_silo_users)
ag.granary.state.revert()
ag.granary._register_silos()
# conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
redirect(url(controller="datasets", action="siloview", silo=silo))
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = "text/plain"
response.status_int = 201
response.status = "201 Created"
response.headers['Content-Location'] = url(controller="datasets", action="siloview", silo=silo)
return "201 Created Silo %s" % silo
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/plain
response.content_type = "text/plain"
response.status_int = 201
response.status = "201 Created"
response.headers['Content-Location'] = url(controller="datasets", action="siloview", silo=silo)
return "201 Created Silo %s" % silo
else:
response.content_type = "text/plain"
response.status_int = 400
response.status = "400 Bad Request"
return "400 Bad request. No valid parameters found."
def siloview(self, silo):
if not request.environ.get('repoze.who.identity'):
abort(401, "Not Authorised")
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
c.ident = ident
c.silo = silo
silos = ag.authz(ident, permission=['administrator', 'manager'])
if not silo in silos:
abort(403, "Do not have administrator or manager credentials for silo %s"%silo)
user_groups = list_user_groups(ident['user'].user_name)
if ('*', 'administrator') in user_groups:
#User is super user
c.roles = ["admin", "manager", "user"]
elif (silo, 'administrator') in user_groups:
c.roles = ["admin", "manager", "user"]
elif (silo, 'manager') in user_groups:
c.roles = ["manager", "user"]
else:
abort(403, "Do not have administrator or manager credentials for silo %s"%silo)
http_method = request.environ['REQUEST_METHOD']
c.kw = ag.granary.describe_silo(silo)
if http_method == "GET":
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/admin_siloview.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(dict(c.kw))
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/html
return render("/admin_siloview.html")
elif http_method == "POST":
params = request.POST
#Get existing owners, admins, managers and submitters
owners = []
admins = []
managers = []
submitters = []
if 'owners' in c.kw and c.kw['owners']:
owners = [x.strip() for x in c.kw['owners'].split(",") if x]
if 'administrators' in c.kw and c.kw['administrators']:
admins = [x.strip() for x in c.kw['administrators'].split(",") if x]
if 'managers' in c.kw and c.kw['managers']:
managers = [x.strip() for x in c.kw['managers'].split(",") if x]
if 'submitters' in c.kw and c.kw['submitters']:
submitters = [x.strip() for x in c.kw['submitters'].split(",") if x]
#Get new members
new_owners = []
#Get new admins
new_admins = []
if 'administrators' in params and params['administrators']:
returned_admins = [x.strip() for x in params['administrators'].split(",") if x]
new_admins = [x for x in returned_admins if not x in admins]
new_owners.extend(new_admins)
#Get new managers
new_managers = []
if 'managers' in params and params['managers']:
returned_managers = [x.strip() for x in params['managers'].split(",") if x]
new_managers = [x for x in returned_managers if not x in managers]
new_owners.extend(new_managers)
#Get new submitters
new_submitters = []
if 'submitters' in params and params['submitters']:
returned_submitters = [x.strip() for x in params['submitters'].split(",") if x]
new_submitters = [x for x in returned_submitters if not x in submitters]
new_owners.extend(new_submitters)
#Check if the new members exist. If not return 403
existing_users = list_usernames()
new_owners = list(set(new_owners))
for o in new_owners:
if not o in existing_users:
abort (403, "User %s does not exist"%o)
if new_admins and not 'admin' in c.roles:
abort (403, "Only administrators can assing users to role 'administrator'")
owners.extend(new_owners)
new_admins = list(set(new_admins))
admins.extend(new_admins)
new_managers = list(set(new_managers))
managers.extend(new_managers)
new_submitters = list(set(new_submitters))
submitters.extend(new_submitters)
# Update silo info
updateMetadata = False
for term in accepted_params:
if term in params and not term in ['owners', 'administrators', 'managers', 'submitters'] and params[term]:
c.kw[term] = params[term]
updateMetadata = True
if new_owners or new_admins or new_managers or new_submitters or updateMetadata:
new_silo_users = []
if new_owners:
c.kw['owners'] = ','.join(owners)
if new_admins:
c.kw['administrators'] = ','.join(admins)
for a in new_admins:
new_silo_users.append((a, 'administrator'))
if new_managers:
c.kw['managers'] = ','.join(managers)
for a in new_managers:
new_silo_users.append((a, 'manager'))
if new_submitters:
c.kw['submitters'] = ','.join(submitters)
for a in new_submitters:
new_silo_users.append((a, 'submitter'))
#Add metadat changes to the silo
ag.granary.describe_silo(silo, **c.kw)
ag.granary.sync()
#Add new silo users into database
if new_silo_users:
add_group_users(silo, new_silo_users)
if updateMetadata:
try:
ag.b.silo_change(silo, ident=ident['repoze.who.userid'])
except:
pass
# conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
c.message = "Metadata updated"
c.kw = ag.granary.describe_silo(silo)
return render("/admin_siloview.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = "text/plain"
response.status_int = 204
response.status = "204 Updated"
#return "Updated Silo %s" % silo
return
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
# Whoops - nothing satisfies - return text/plain
response.content_type = "text/plain"
response.status_int = 204
response.status = "204 Updated"
return
elif http_method == "DELETE":
# Deletion of an entire Silo...
# Serious consequences follow this action
# Walk through all the items, emit a delete msg for each
# and then remove the silo
todelete_silo = ag.granary.get_rdf_silo(silo)
#for item in todelete_silo.list_items():
# try:
# ag.b.deletion(silo, item, ident=ident['repoze.who.userid'])
# except:
# pass
ag.granary.delete_silo(silo)
try:
ag.b.silo_deletion(silo, ident=ident['repoze.who.userid'])
except:
pass
try:
del ag.granary.state[silo]
except:
pass
ag.granary.sync()
ag.granary._register_silos()
#Delete silo from database
delete_silo(silo)
# conneg return
accept_list = None
response.content_type = "text/plain"
response.status_int = 200
response.status = "200 OK"
return "{'ok':'true'}"
def datasetview(self, silo, id):
c.silo_name = silo
c.id = id
http_method = request.environ['REQUEST_METHOD']
granary_list = list_silos()
if not silo in granary_list:
abort(404)
c_silo = ag.granary.get_rdf_silo(silo)
if not c_silo.exists(id):
abort(404)
if ag.metadata_embargoed:
abort(403, "DOIs cannot be issued to data packages whose metadata ia also under embargo")
ident = request.environ.get('repoze.who.identity')
c.ident = ident
item = c_silo.get_item(id)
creator = None
if item.manifest and item.manifest.state and 'metadata' in item.manifest.state and item.manifest.state['metadata'] and \
'createdby' in item.manifest.state['metadata'] and item.manifest.state['metadata']['createdby']:
creator = item.manifest.state['metadata']['createdby']
c.version = item.currentversion
c.version_doi = None
c.editor = False
#Get version number
vnum = request.params.get('version', '') or ""
if vnum:
vnum = str(vnum)
if not vnum in item.manifest['versions']:
abort(404, "Version %s of data package %s not found"%(vnum, c.silo_name))
c.version = vnum
if not (http_method == "GET"):
#identity management of item
if not request.environ.get('repoze.who.identity'):
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission='administrator')
silos_manager = ag.authz(ident, permission='manager')
#if not (ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]):
if not (ident['repoze.who.userid'] == creator or silo in silos_admin or silo in silos_manager):
abort(403, "Forbidden")
elif http_method == "GET":
silos_admin = ag.authz(ident, permission='administrator')
silos_manager = ag.authz(ident, permission='manager')
#if ident['repoze.who.userid'] == creator or ident.get('role') in ["admin", "manager"]:
if ident and ident['repoze.who.userid'] == creator or silo in silos_admin or silo in silos_manager:
c.editor = True
version_uri = "%s?version=%s"%(item.uri.rstrip('/'), c.version)
c.version_doi = item.list_rdf_objects(URIRef(version_uri), u"http://purl.org/ontology/bibo/doi")
if not c.version_doi or not c.version_doi[0]:
c.version_doi = None
else:
c.version_doi = c.version_doi[0]
doi_conf = OxDataciteDoi()
doi_api = HTTPRequest(endpointhost=doi_conf.endpoint_host, secure=True)
doi_api.setRequestUserPass(endpointuser=doi_conf.account, endpointpass=doi_conf.password)
# conneg:
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
c.message = None
c.resp_status = None
c.resp_reason = None
c.metadata = None
if http_method == "GET":
#Get a list of all dois registered for this data package
c.dois = {}
for v in item.manifest['versions']:
doi_ans = None
doi_ans = item.list_rdf_objects(URIRef("%s/version%s"%(item.uri.rstrip('/'), v)), u"http://purl.org/ontology/bibo/doi")
if doi_ans and doi_ans[0]:
c.dois[v] = doi_ans[0]
c.heading = "Doi metadata information from Datacite"
if not c.version_doi:
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
#Doint this to avoid displaying the erro page!!!
response.status_int = 200
response.status = "200 OK"
c.metadata = None
return render('/doiview.html')
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
c.message = 'DOI not registered for version %s of data package %s'%(c.version, c.silo_name)
return render('/doiview.html')
resource = "%s?doi=%s"%(doi_conf.endpoint_path_metadata, c.version_doi)
(resp, respdata) = doi_api.doHTTP_GET(resource=resource, expect_type='application/xml')
c.resp_reason = resp.reason
c.resp_status = resp.status
if resp.status < 200 or resp.status >= 300:
response.status_int = 400
response.status = "400 Bad Request"
response_msg = ''
c.metadata = ''
if resp.status == 403:
#TODO: Confirm 403 is not due to authorization
msg = "403 Forbidden - login error with Datacite or data package belongs to another party at Datacite."
elif resp.status == 404:
msg = "404 Not Found - DOI does not exist in DatCite's database"
elif resp.status == 410:
msg = "410 Gone - the requested data package was marked inactive (using DELETE method) at Datacite"
elif resp.status == 500:
msg = "500 Internal Server Error - Error retreiving the metadata from Datacite."
else:
msg = "Error retreiving the metadata from Datacite. %s"%str(resp.status)
c.message = msg
else:
response.status_int = 200
response.status = "200 OK"
c.metadata = respdata
response_msg = respdata
# conneg:
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
#Setting headers to 200 to avoid displaying the error page!!!
response.status_int = 200
response.status = "200 OK"
return render('/doiview.html')
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'text/plain; charset="UTF-8"'
return str(respdata.decode('utf-8'))
elif str(mimetype).lower() in ["application/rdf+xml", "text/xml"]:
response.status_int = 200
response.status = "200 OK"
response.content_type = 'text/xml; charset="UTF-8"'
return response_msg
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops - nothing staisfies - default to text/html
#Setting headers to 200 to avoid displaying the error page!!!
response.status_int = 200
response.status = "200 OK"
return render('/doiview.html')
if http_method == "POST":
item.set_version_cursor(c.version)
#1a. If doi doen not exist for this version, generate doi
register_doi = False
if not c.version_doi:
cnt = doi_count()
if not cnt:
abort(400, "Error generating DOI")
register_doi = True
tiny_pid = short_pid.encode_url(cnt)
c.version_doi = "%s/bodleian%s.%s"%(doi_conf.prefix, tiny_pid, c.version)
#1b. Construct XML metadata
if c.version_doi:
xml_metadata = get_doi_metadata(c.version_doi, item)
c.metadata = xml_metadata
#FOR TEST PURPOSES ONLY
#xml_metadata = False
# Have commented out the sections below as we will only register a DOI if there is metadata
"""
if not xml_metadata and not register_doi:
#2a. If the doi already exists and there is no xml metadata to update, return bad request
c.message = "Coud not update metadata"
response.status_int = 400
response.status = "Bad request"
respdata = c.message
c.metadata = ''
elif not xml_metadata and register_doi:
#2b. If the doi is not registered, but there is no xml metadata to update, register just the doi with datacite
c.heading = "Registering new DOI with Datacite"
resource = "%s"%doi_conf.endpoint_path_doi
body = "%s\n%s"%(c.version_doi, version_uri)
#body_unicode = unicode(body, "utf-8")
body_unicode = unicode(body)
(resp, respdata) = doi_api.doHTTP_POST(body_unicode, resource=resource, data_type='text/plain;charset=UTF-8')
c.resp_reason = resp.reason
c.resp_status = resp.status
if resp.status < 200 or resp.status >= 300:
response.status_int = 400
response.status = "400 Bad Request"
response_msg = "DOI not registered"
c.metadata = ''
if resp.status == 400:
msg = "400 Bad Request - Request body must be exactly two lines: DOI and URL"
elif resp.status == 403:
#TODO: Confirm 403 is not due to authorization
msg = "403 Forbidden - From Datacite: login problem, quota excceded, wrong domain, wrong prefix"
elif resp.status == 500:
msg = "500 Internal Server Error - Error registering the DOI."
else:
msg = "Error retreiving the metadata from Datacite. %s"%str(resp.status)
c.message = msg
else:
#3. Add the DOI to the rdf metadata
item.add_namespace('bibo', "http://purl.org/ontology/bibo/")
item.add_triple(URIRef(version_uri), u"bibo:doi", Literal(c.version_doi))
item.del_triple(item.uri, u"dcterms:modified")
item.add_triple(item.uri, u"dcterms:modified", datetime.now())
item.sync()
response.status_int = 200
response.status = "200 OK"
response_msg = "DOI Registered. %s"%respdata
c.metadata = ''
c.message = "201 Created - DOI registered. %s"%respdata
"""
if not xml_metadata:
#2a. If the doi already exists and there is no xml metadata to update, return bad request
c.message = "Could not generate metadata"
c.metadata = ''
abort(400, "Error generating metadata")
elif not register_doi:
c.message = "Could not generate DOI"
abort(400, "Error generating DOI")
else:
#register the DOI with Datacite
resource = "%s"%doi_conf.endpoint_path_doi
body = "doi=%s\nurl=%s"%(c.version_doi, version_uri)
body_unicode = unicode(body)
(resp, respdata) = doi_api.doHTTP_POST(body_unicode, resource=resource, data_type='text/plain;charset=UTF-8')
c.resp_reason1 = resp.reason
c.resp_status1 = resp.status
#Add the metadata within Datacite
c.heading = "Registering new DOI along with its metadata with Datacite"
#body_unicode = unicode(xml_metadata, "utf-8")
#body_unicode = unicode(xml_metadata)
body_unicode = xml_metadata
resource = "%s?doi=%s&url=%s"%(doi_conf.endpoint_path_metadata, c.version_doi, version_uri)
(resp, respdata) = doi_api.doHTTP_POST(body_unicode, resource=resource, data_type='application/xml;charset=UTF-8')
c.resp_reason = resp.reason
c.resp_status = resp.status
if (c.resp_status1>= 200 and c.resp_status1 < 300) or (resp.status >= 200 and resp.status < 300):
#3. Add the DOI to the rdf metadata
item.add_namespace('bibo', "http://purl.org/ontology/bibo/")
item.add_triple(URIRef(version_uri), u"bibo:doi", Literal(c.version_doi))
item.del_triple(item.uri, u"dcterms:modified")
item.add_triple(item.uri, u"dcterms:modified", datetime.now())
item.sync()
#4. Broadcast changes to redis
try:
ag.b.change(silo, id, ident=ident['repoze.who.userid'])
except:
pass
if resp.status < 200 or resp.status >= 300:
response.status_int = 400
response.status = "400 Bad Request"
response_msg = "DOI and metadata not registered"
c.metadata = body_unicode
if resp.status == 400:
msg = "400 Bad Request - Invalid XML metadata"
elif resp.status == 403:
#TODO: Confirm 403 is not due to authorization
msg = "403 Forbidden - From Datacite: login problem, quota excceded, wrong domain, wrong prefix"
elif resp.status == 500:
msg = "500 Internal Server Error - Error registering the DOI."
else:
msg = "Error retreiving the metadata from Datacite. %s"%str(resp.status)
c.message = msg
else:
response.status_int = 200
response.status = "200 OK"
response_msg = body_unicode
c.metadata = body_unicode
c.message = "201 Created - DOI registered. %s"%respdata
# conneg:
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
#Setting headers to 200 to avoid displaying the error page!!!
response.status_int = 200
response.status = "200 OK"
return render('/doiview.html')
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'text/plain'
return str(respdata.decode('utf-8'))
elif str(mimetype).lower() in ["application/rdf+xml", "text/xml"]:
response.status_int = 200
response.status = "200 OK"
response.content_type = 'text/xml; charset="UTF-8"'
return response_msg
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops - nothing staisfies - default to text/html
#Setting headers to 200 to avoid displaying the error page!!!
response.status_int = 200
response.status = "200 OK"
return render('/doiview.html')
def silouserview(self, silo, username):
if not request.environ.get('repoze.who.identity'):
abort(401, "Not Authorised")
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
http_method = request.environ['REQUEST_METHOD']
if http_method == 'GET':
silos = ag.authz(ident)
if not silo in silos:
abort(403, "User is not a member of the silo %s"%silo)
if not ('administrator' in ident['permissions'] or \
'manager' in ident['permissions'] or ident['user'].user_name == username):
abort(403, "Do not have administrator or manager credentials to view profiles of other users")
else:
silos = ag.authz(ident, permission=['administrator', 'manager'])
if not silo in silos:
abort(403, "Do not have administrator or manager credentials for silo %s"%silo)
if not ('administrator' in ident['permissions'] or 'manager' in ident['permissions']):
abort(403, "Do not have administrator or manager credentials")
existing_users = list_usernames()
if not username in existing_users:
abort(404, "User not found")
c.ident = ident
c.silo = silo
c.username = username
if http_method == "GET":
a, m, s = list_group_usernames(silo)
if not (username in a or username in m or username in s):
abort(404, "User not found in silo")
c.user = list_user(username)
#if 'groups' in c.user and c.user['groups']:
# for i in c.user['groups']:
# if i[0] != silo:
# c.user['groups'].remove(i)
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
return render("/silo_user.html")
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.user)
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/plain
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(c.user)
elif http_method == "POST":
params = request.POST
if not ('role' in params and params['role'] and params['role'] in ['administrator', 'manager', 'submitter']):
abort(400, "Parameters 'role' not found or is invalid")
kw = ag.granary.describe_silo(silo)
#Get existing owners, admins, managers and users
owners = []
admins = []
managers = []
submitters = []
if 'owners' in kw and kw['owners']:
owners = [x.strip() for x in kw['owners'].split(",") if x]
if 'administrators' in kw and kw['administrators']:
admins = [x.strip() for x in kw['administrators'].split(",") if x]
if 'managers' in kw and kw['managers']:
managers = [x.strip() for x in kw['managers'].split(",") if x]
if 'submitters' in kw and kw['submitters']:
submitters = [x.strip() for x in kw['submitters'].split(",") if x]
to_remove = []
to_add = []
if params['role'] == 'administrator':
if not 'administrator' in ident['permissions']:
abort(403, "Need to be administrator to add user to role admin")
if not username in admins:
to_add.append((username, 'administrator'))
admins.append(username)
if not username in owners:
owners.append(username)
if username in managers:
managers.remove(username)
to_remove.append((username, 'manager'))
if username in submitters:
submitters.remove(username)
to_remove.append((username, 'submitter'))
elif params['role'] == 'manager':
if not username in managers:
to_add.append((username, 'manager'))
managers.append(username)
if not username in owners:
owners.append(username)
if username in admins:
if not 'administrator' in ident['permissions']:
abort(403, "Need to be admin to modify user of role admin")
if len(admins) == 1:
abort(403, "Add another administrator to silo before updating user role")
admins.remove(username)
to_remove.append((username, 'administrator'))
if username in submitters:
submitters.remove(username)
to_remove.append((username, 'submitter'))
elif params['role'] == 'submitter':
if not username in submitters:
to_add.append((username, 'submitter'))
submitters.append(username)
if not username in owners:
owners.append(username)
if username in admins:
if not 'administrator' in ident['permissions']:
abort(403, "Need to be admin to modify user of role admin")
if len(admins) == 1:
abort(403, "Add another administrator to silo before updating user role")
admins.remove(username)
to_remove.append((username, 'administrator'))
if username in managers:
if len(managers) == 1 and len(admins) == 0:
abort(403, "Add another administrator or manager to silo before updating user role")
managers.remove(username)
to_remove.append((username, 'manager'))
owners = list(set(owners))
admins = list(set(admins))
managers = list(set(managers))
submitters = list(set(submitters))
# Update silo info
if to_remove or to_add:
kw['owners'] = ','.join(owners)
kw['administrators'] = ','.join(admins)
kw['managers'] = ','.join(managers)
kw['submitters'] = ','.join(submitters)
ag.granary.describe_silo(silo, **kw)
ag.granary.sync()
#Add new silo users into database
if to_add:
add_group_users(silo, to_add)
response.status_int = 201
response.status = "201 Created"
response.headers['Content-Location'] = url(controller="users", action="silouserview", silo=silo, username=username)
response_message = "201 Created"
if to_remove:
delete_group_users(silo, to_remove)
response.status_int = 204
response.status = "204 Updated"
response_message = None
else:
response.status_int = 400
response.status = "400 Bad Request"
response_message = "No updates to user role"
#Conneg return
accept_list = None
if 'HTTP_ACCEPT' in request.environ:
try:
accept_list = conneg_parse(request.environ['HTTP_ACCEPT'])
except:
accept_list= [MT("text", "html")]
if not accept_list:
accept_list= [MT("text", "html")]
mimetype = accept_list.pop(0)
while(mimetype):
if str(mimetype).lower() in ["text/html", "text/xhtml"]:
redirect(url(controller="users", action="silouserview", silo=silo, username=username))
elif str(mimetype).lower() in ["text/plain", "application/json"]:
response.content_type = 'application/json; charset="UTF-8"'
return response_message
try:
mimetype = accept_list.pop(0)
except IndexError:
mimetype = None
#Whoops nothing satisfies - return text/plain
response.content_type = 'application/json; charset="UTF-8"'
return response_message
elif http_method == "DELETE":
kw = ag.granary.describe_silo(silo)
#Get existing owners, admins, managers and users
owners = []
admins = []
managers = []
submitters = []
if 'owners' in kw and kw['owners']:
owners = [x.strip() for x in kw['owners'].split(",") if x]
if 'administrators' in kw and kw['administrators']:
admins = [x.strip() for x in kw['administrators'].split(",") if x]
if 'managers' in kw and kw['managers']:
managers = [x.strip() for x in kw['managers'].split(",") if x]
if 'submitters' in kw and kw['submitters']:
submitters = [x.strip() for x in kw['submitters'].split(",") if x]
#Gather user roles to delete
to_remove = []
if username in admins:
if not 'administrator' in ident['permissions']:
abort(403, "Need to be admin to modify user of role admin")
if len(admins) == 1:
abort(403, "Add another administrator to silo before deleting user")
to_remove.append((username, 'administrator'))
admins.remove(username)
if username in managers:
if len(managers) == 1 and len(admins) == 0:
abort(403, "Add another administrator or manager to silo before deleting user")
managers.remove(username)
to_remove.append((username, 'manager'))
if username in submitters:
submitters.remove(username)
to_remove.append((username, 'submitter'))
if username in owners:
owners.remove(username)
owners = list(set(owners))
admins = list(set(admins))
managers = list(set(managers))
submitters = list(set(submitters))
if to_remove:
# Update silo info
kw['owners'] = ','.join(owners)
kw['administrators'] = ','.join(admins)
kw['managers'] = ','.join(managers)
kw['submitters'] = ','.join(submitters)
ag.granary.describe_silo(silo, **kw)
ag.granary.sync()
delete_group_users(silo, to_remove)
else:
abort(400, "No user to delete")
accept_list = None
response.content_type = "text/plain"
response.status_int = 200
response.status = "200 OK"
return "{'ok':'true'}"
def siloview(self, silo):
"""
Returns the state information of a silo.
Only authorized users with role 'admin' or 'manager' can view this information
The state information for a silo contains the following:
Name of the silo (machine name, used in uris) - ans["silo"]
Base URI for the silo - ans["uri_base"]
Users who can access the silo (silo owners) - ans["owners"]
Silo description - ans["description"]
Title of the silo (human readable) - ans["title"]
Disk allocation for the silo (in kB) - ans["disk_allocation"]
List of datasets in the silo (ans["datasets"])
with embargo information for each of the datasets
(ans["datasets"]["dataset_name"]["embargo_info"])
"""
# Only authorized users can view state information.
# Should this be restricted to admins and managers only, or shoud users too be able to see this information?
# Going with restricting this information to admins and managers
if not ag.granary.issilo(silo):
abort(404)
ident = request.environ.get('repoze.who.identity')
if not ident:
abort(401, "Not Authorised")
silos = ag.authz(ident)
if silo not in silos:
abort(403, "Forbidden")
silos_admin = ag.authz(ident, permission='administrator')
silos_manager = ag.authz(ident, permission='manager')
#if not ident.get('role') in ["admin", "manager"]:
if not (silo in silos_admin or silo in silos_manager):
abort(403, "Forbidden. You should be an administrator or manager to view this information")
options = request.GET
start = 0
if 'start' in options and options['start']:
try:
start = int(options['start'])
except:
start = 0
rows = 1000
if 'rows' in options and options['rows']:
try:
rows = int(options['rows'])
except:
rows = 1000
rdfsilo = ag.granary.get_rdf_silo(silo)
state_info = ag.granary.describe_silo(silo)
state_info['silo'] = silo
state_info['uri_base'] = ''
if rdfsilo.state and rdfsilo.state['uri_base']:
state_info['uri_base'] = rdfsilo.state['uri_base']
state_info['number of data packages'] = get_datasets_count(silo)
state_info['params'] = {'start':start, 'rows':rows}
items = {}
#for item in rdfsilo.list_items():
for item in get_datasets(silo, start=start, rows=rows):
items[item] = {}
try:
items[item]['embargo_info'] = is_embargoed(rdfsilo, item)
except:
pass
state_info['datasets'] = items
# conneg return
# Always return application/json
response.content_type = 'application/json; charset="UTF-8"'
response.status_int = 200
response.status = "200 OK"
return simplejson.dumps(state_info)
