def main():
"""
Main entry point for the FunPDBe client
:return: None
"""
logger = FunPDBeClientLogger(name="main", write_mode="w")
try:
opts, args = getopt.getopt(sys.argv[1:], "u:p:m:i:r:f:a:oh", [
"user="******"pwd=", "mode=", "pdb_id=", "resource=", "path=", "api=",
"overwrite", "help"
])
except getopt.GetoptError as err:
generic_error()
logger.log().error(err)
sys.exit(2)
schema = Schema()
user = User()
client = Client(schema, user)
if opts:
Control(opts, client=client).run()
else:
Control([('--help', '')], client=client).run()
def __init__(self, opts, client):
self.opts = opts
self.client = client
self.path = self.loop_options("-f", "--path")
self.pdb_id = self.loop_options("-i", "--pdb_id")
self.mode = self.loop_options("-m", "--mode")
self.resource = self.loop_options("-r", "--resource")
self.user_name = self.loop_options("-u", "--user")
self.pwd = self.loop_options("-p", "--pwd")
self.help = False
self.overwrite = False
self.api_url = self.loop_options("-a", "--api")
self.logger = FunPDBeClientLogger("control")
def __init__(self, opts, client):
self.opts = opts
self.client = client
self.path = self.loop_options("-f", "--path")
self.pdb_id = self.loop_options("-i", "--pdb_id")
self.mode = self.loop_options("-m", "--mode")
self.resource = self.loop_options("-r", "--resource")
self.user_name = self.loop_options("-u", "--user")
self.pwd = self.loop_options("-p", "--pwd")
self.help = False
for option, value in self.opts:
if option in ["-h", "--help"]:
self.help = True
self.logger = FunPDBeClientLogger("control")
def __init__(self, schema, user):
self.user = user
self.schema = schema
self.api_url = API_URL
self.json_data = None
self.logger = FunPDBeClientLogger("client")
class Client(object):
"""
The FunPDBe deposition client allows users to deposit, delete and view
data in the FunPDBe deposition system
"""
def __init__(self, schema, user):
self.user = user
self.schema = schema
self.api_url = API_URL
self.json_data = None
self.logger = FunPDBeClientLogger("client")
def __str__(self):
return """
The FunPDBe deposition client allows users to deposit, delete and view
data in the FunPDBe deposition system
Usage parameters:
-h, --help: Help (this is what you see now)
-u, --user: FunPDBe user name
-p, --pwd: FunPDBe password
-m, --mode: Running mode (get, post, delete, put)
-i, --pdbid: PDB id of an entry
-r, --resource: Name of a resource
-f, --path: Path to JSON file (.json ending), or files (folder name)
-d, --debug: Enable debug logging
"""
def get_one(self, pdb_id, resource=None):
"""
Get one FunPDBe entry based on PDB id and
optionally resource name
:param pdb_id: String, PDB id
:param resource: String, resource name
:return: None
"""
message = "GET entry for %s" % pdb_id
if resource:
message += " from %s" % resource
self.logger.log().info(message)
if not self.check_pdb_id(pdb_id):
return None
self.user_info()
url = self.construct_get_url(resource, pdb_id)
r = requests.get(url, auth=(self.user.user_name, self.user.user_pwd))
if (r.status_code == 200):
self.logger.log().info("[%i] success" % r.status_code)
else:
self.log_api_error(r.status_code, r.text)
print(r.text)
return r
def construct_get_url(self, resource=None, pdb_id=None):
url = self.api_url
if resource and self.check_resource(resource):
url += "resource/%s/" % resource
else:
url += "pdb/"
url += "%s/" % pdb_id
return url
def get_all(self, resource=None):
"""
Get all FunPDBe entries, optionally filtered
by resource name
:param resource: String, resource name
:return: None
"""
message = "GET all entries"
if resource:
message += " from %s" % resource
self.logger.log().info(message)
self.user_info()
url = self.api_url
if resource and self.check_resource(resource):
url += "resource/%s/" % resource
r = requests.get(url, auth=(self.user.user_name, self.user.user_pwd))
print(r.text)
return r
def post(self, path, resource):
"""
POST JSON to deposition API
:param path: String, path to JSON file
:param resource: String, resource name
:return: None
"""
message = "POST %s to %s" % (path, resource)
self.logger.log().info(message)
self.user_info()
if not self.check_resource(resource):
return None
if not self.parse_json(path):
return None
if not self.validate_json():
return None
url = self.api_url
url += "resource/%s/" % resource
r = requests.post(url,
json=self.json_data,
auth=(self.user.user_name, self.user.user_pwd))
self.check_status(r, 201)
return r
def put(self, path, pdb_id, resource):
"""
POST JSON to deposition API
:param path: String, path to JSON file
:param pdb_id, String, PDB id
:param resource: String, resource name
:return: None
"""
message = "UPDATE %s in %s from %s" % (pdb_id, resource, path)
self.logger.log().info(message)
if not self.check_resource(resource) or not self.check_pdb_id(pdb_id):
return None
self.user_info()
if not self.parse_json(path):
return None
if not self.validate_json():
return None
url = self.api_url
url += "resource/%s/%s/" % (resource, pdb_id)
r = requests.post(url,
json=self.json_data,
auth=(self.user.user_name, self.user.user_pwd))
self.check_status(r, 201)
return r
def delete_one(self, pdb_id, resource):
"""
DELETE entry based on PDB id
:param pdb_id: String, PDB id
:param resource: String, resource name
:return: none
"""
message = "DELETE entry %s from %s" % (pdb_id, resource)
self.logger.log().info(message)
if not self.check_resource(resource):
return None
if not self.check_pdb_id(pdb_id):
return None
self.user_info()
url = self.api_url
url += "resource/%s/%s/" % (resource, pdb_id)
r = requests.delete(url,
auth=(self.user.user_name, self.user.user_pwd))
self.check_status(r, 301)
return r
def check_pdb_id(self, pdb_id):
"""
Check if PDB id exists and if it matches
the regular expression pattern of a valid
PDB identifier
:param pdb_id: String
:return: Boolean
"""
if not self.check_exists(pdb_id, "no_pdb"):
return False
if re.match(PDB_ID_PATTERN, pdb_id):
return True
generic_error()
self.logger.log().error(CLIENT_ERRORS["bad_pdb"])
return False
def check_resource(self, resource):
"""
Check if resource name exists and
if it is a known (registered) resource
:param resource: String
:return: Boolean
"""
if not self.check_exists(resource, "no_resource"):
return False
if resource in RESOURCES:
return True
self.logger.log().error(CLIENT_ERRORS["unknown_resource"])
generic_error()
return False
def parse_json(self, path):
"""
Parse user JSON file
:param path: String, path to JSON
:return: Boolean
"""
if not self.check_exists(path, "no_path"):
return None
try:
with open(path) as json_file:
try:
self.json_data = json.load(json_file)
self.logger.log().info("JSON parsed")
return True
except ValueError as valerr:
self.logger.log().error(valerr)
generic_error()
return False
except IOError as ioerr:
self.logger.log().error(ioerr)
generic_error()
return False
def validate_json(self):
"""
Validate JSON against schema
:return: Boolean, True if validated JSON, False if not
"""
if not self.schema.json_schema:
self.schema.get_schema()
if self.schema.validate_json(self.json_data):
self.logger.log().info("JSON complies with FunPDBe schema")
self.json_data = self.schema.clean_json(self.json_data)
return True
self.logger.log().error(CLIENT_ERRORS["bad_json"])
return False
def check_status(self, response, expected):
if response.status_code == expected:
self.logger.log().info("[%i] SUCCESS" % response.status_code)
else:
self.logger.log().error("[%i] FAIL - %s" %
(response.status_code, response.text))
def log_api_error(self, status_code, text):
self.logger.log().error("[%s] - %s" % (status_code, text))
def check_exists(self, value, error):
if value:
return True
self.logger.log().error(CLIENT_ERRORS[error])
return False
def user_info(self):
"""
Prompting user to provide info if missing
:return: None
"""
self.user.set_user()
self.user.set_pwd()
class Client(object):
"""
The FunPDBe deposition client allows users to deposit, delete and view
data in the FunPDBe deposition system
"""
def __init__(self, schema, user):
self.user = user
self.schema = schema
self.api_url = PROD_API_URL
self.json_data = None
self.logger = FunPDBeClientLogger("client")
def __str__(self):
return """
The FunPDBe deposition client allows users to deposit, delete and view
data in the FunPDBe deposition system
Usage parameters:
-h, --help: Help (this is what you see now)
-u, --user: FunPDBe user name
-p, --pwd: FunPDBe password
-m, --mode: Running mode (get, post, delete, validate)
-o, --overwrite: Overwrite existing entries
-i, --pdbid: PDB id of an entry
-r, --resource: Name of a resource
-f, --path: Path to JSON file (.json ending), or files (folder name)
-d, --debug: Enable debug logging
-a, --api: API to be used (prod (default), dev, local)
"""
def set_api_url(self, new_url):
"""
Setting API to other than default
:param new_url: String, API URL
:return: None
"""
self.api_url = new_url
def get_all(self, resource):
"""
Get all FunPDBe entries based on resource name
:param resource: String, resource name
:return: Response
"""
message = "GET all entries for %s" % resource
if not self.check_resource(resource):
return None
self.logger.log().info(message)
self.user_info()
url = self.construct_get_url(resource)
r = requests.get(url, auth=(self.user.user_name, self.user.user_pwd))
if r.status_code == 200:
self.logger.log().info("[%i] success" % r.status_code)
else:
self.log_api_error(r.status_code, r.text)
print(r.text)
return r
def get_one(self, pdb_id, resource):
"""
Get one FunPDBe entry based on PDB id and
resource name
:param pdb_id: String, PDB id
:param resource: String, resource name
:return: Response
"""
message = "GET entry for %s" % pdb_id
if resource and self.check_pdb_id(pdb_id):
message += " from %s" % resource
self.logger.log().info(message)
else:
return None
self.user_info()
url = self.construct_get_url(resource, pdb_id)
r = requests.get(url, auth=(self.user.user_name, self.user.user_pwd))
if r.status_code == 200:
self.logger.log().info("[%i] success" % r.status_code)
else:
self.log_api_error(r.status_code, r.text)
print(r.text)
return r
def post(self, path, resource, overwrite, plugin=False):
"""
POST JSON to deposition API
:param path: String, path to JSON file
:param resource: String, resource name
:param plugin: Boolean, plugin mode
:return: None
"""
message = "POST %s to %s (overwrite=%s)" % (path, resource, overwrite)
self.logger.log().info(message)
self.user_info()
if not self.pre_post_checks(path, resource, plugin):
return None
if overwrite:
return self.post_with_overwrite(resource)
else:
return self.post_without_overwrite(resource)
def pre_post_checks(self, path, resource, plugin):
if not self.check_resource(resource):
return False
if not self.parse_json(path) and not plugin:
return False
if not self.validate_json():
return False
return True
def post_with_overwrite(self, resource):
pdb_id = self.json_data["pdb_id"]
if not self.check_pdb_id(pdb_id):
return None
url = self.api_url
url += "resource/%s/%s/" % (resource, pdb_id)
r = requests.post(url,
json=self.json_data,
auth=(self.user.user_name, self.user.user_pwd))
check_status(r, 201, self.logger)
return r
def post_without_overwrite(self, resource):
url = self.api_url
url += "resource/%s/" % resource
r = requests.post(url,
json=self.json_data,
auth=(self.user.user_name, self.user.user_pwd))
check_status(r, 201, self.logger)
return r
def delete_one(self, pdb_id, resource):
"""
DELETE entry based on PDB id
:param pdb_id: String, PDB id
:param resource: String, resource name
:return: none
"""
message = "DELETE entry %s from %s" % (pdb_id, resource)
print(message)
self.logger.log().info(message)
if not self.check_resource(resource):
return None
if not self.check_pdb_id(pdb_id):
return None
self.user_info()
url = self.api_url
url += "resource/%s/%s/" % (resource, pdb_id)
r = requests.delete(url,
auth=(self.user.user_name, self.user.user_pwd))
check_status(r, 301, self.logger)
return r
def construct_get_url(self, resource, pdb_id=None):
"""
Create the GET URL based on resource
and pdb_id
:param resource: String
:param pdb_id: String
:return: String
"""
url = self.api_url
if resource and self.check_resource(resource):
url += "resource/%s/" % resource
if pdb_id:
url += "%s/" % pdb_id
return url
return None
def check_pdb_id(self, pdb_id):
"""
Check if PDB id exists and if it matches
the regular expression pattern of a valid
PDB identifier
:param pdb_id: String
:return: Boolean
"""
if not check_exists(pdb_id, "no_pdb", self.logger):
return False
if re.match(PDB_ID_PATTERN, pdb_id):
return True
generic_error()
self.logger.log().error(CLIENT_ERRORS["bad_pdb"])
return False
def check_resource(self, resource):
"""
Check if resource name exists and
if it is a known (registered) resource
:param resource: String
:return: Boolean
"""
if not check_exists(resource, "no_resource", self.logger):
return False
if resource in RESOURCES:
return True
self.logger.log().error(CLIENT_ERRORS["unknown_resource"])
generic_error()
return False
def parse_json(self, path):
"""
Parse user JSON file
:param path: String, path to JSON
:return: Boolean
"""
if not check_exists(path, "no_path", self.logger):
return None
try:
with open(path) as json_file:
try:
self.json_data = json.load(json_file)
self.logger.log().info("JSON parsed")
return True
except ValueError as valerr:
self.logger.log().error(valerr)
generic_error()
return False
except IOError as ioerr:
self.logger.log().error(ioerr)
generic_error()
return False
def validate_json(self):
"""
Validate JSON against schema
:return: Boolean
"""
if not self.schema.json_schema:
self.schema.get_schema()
if self.schema.validate_json(self.json_data):
self.logger.log().info("JSON complies with FunPDBe schema")
self.json_data = self.schema.clean_json(self.json_data)
return True
self.logger.log().error(CLIENT_ERRORS["bad_json"])
generic_error()
return False
def log_api_error(self, status_code, text):
"""
Log error based on status code and
response text
:param status_code: Int
:param text: String
:return: None
"""
self.logger.log().error("[%s] - %s" % (status_code, text))
def user_info(self):
"""
Prompting user to provide info if missing
:return: None
"""
self.user.set_user()
self.user.set_pwd()
class Control(object):
def __init__(self, opts, client):
self.opts = opts
self.client = client
self.path = self.loop_options("-f", "--path")
self.pdb_id = self.loop_options("-i", "--pdb_id")
self.mode = self.loop_options("-m", "--mode")
self.resource = self.loop_options("-r", "--resource")
self.user_name = self.loop_options("-u", "--user")
self.pwd = self.loop_options("-p", "--pwd")
self.help = False
self.overwrite = False
self.api_url = self.loop_options("-a", "--api")
self.logger = FunPDBeClientLogger("control")
def set_help_and_overwrite_flags(self):
for option, value in self.opts:
if option in ["-h", "--help"]:
self.help = True
elif option in ["-o", "--overwrite"]:
self.overwrite = True
def run(self):
"""
Main entry point
:return: Response.text or None
"""
self.configure()
self.set_help_and_overwrite_flags()
if self.help:
print(self.client)
elif not self.mode:
generic_error()
self.logger.log().error(CONTROL_ERRORS["no_mode"])
else:
return self.action()
return None
def action(self):
"""
API calls that can be performed by
the client
:return: Response.text or None
"""
actions = {
"get": self.get,
"post": self.post,
"delete": self.delete,
"validate": self.validate
}
if self.mode in actions.keys():
return actions[self.mode]()
return None
def configure(self):
"""
Set the user name and password
:return: None
"""
self.client.user.user_name = self.user_name
self.client.user.user_pwd = self.pwd
if self.api_url:
url_to_use = map_url(self.api_url)
if url_to_use:
self.client.set_api_url(url_to_use)
def validate(self):
"""
Validate one or more JSON files against
FunPDBe Schema
:return: True or False
"""
if not self.check_path():
return False
if self.path.endswith(".json"):
return self.single_validate(self.path)
else:
return self.multi_validate()
def multi_validate(self):
"""
Validate multiple JSON files against
FunPDBe Schema
:return: True or False
"""
all_valid = True
for json_path in glob.glob("%s/*.json" % self.path):
if not self.single_validate(json_path):
all_valid = False
return all_valid
def single_validate(self, path):
"""
Validate a single JSON
:param path: String
:return: Boolean
"""
print("Parsing and validating %s" % path)
if self.client.parse_json(path):
return self.client.validate_json()
return False
def get(self):
"""
Make GET call
:return: Response.text or None
"""
if self.pdb_id and self.resource:
return self.client.get_one(self.pdb_id, self.resource)
self.logger.log().error(CONTROL_ERRORS["no_pdb_or_resource"])
print("Please provide both --pdb_id and --resource")
return None
def post(self):
"""
Make POST call
:return: Response.text or None
"""
response = None
if not self.check_path():
return response
if self.path.endswith(".json"):
response = self.client.post(self.path, self.resource,
self.overwrite)
else:
response = self.batch_post()
return response
def batch_post(self):
"""
Make batch POST call
:return: Response
"""
response = None
attempted = 0
succeeded = 0
for json_path in glob.glob("%s/*.json" % self.path):
self.log_delimiter("start")
response = self.client.post(json_path, self.resource,
self.overwrite)
self.client.json_data = None
if response and response.status_code == 201:
succeeded += 1
attempted += 1
self.log_delimiter("end")
message = "Batch POSTing: %i out of %i POSTed successfully" % (
succeeded, attempted)
self.logger.log().info(message)
print(message)
return response
def check_entry_exists(self):
response = self.client.get_one(self.pdb_id, self.resource)
if response.status_code == 200:
return True
return False
def delete(self):
"""
Make DELETE call
:return: Response.text or None
"""
self.log_delimiter("start")
response = self.client.delete_one(self.pdb_id, self.resource)
self.log_delimiter("end")
return response
def loop_options(self, opt1, opt2):
"""
Loop through options
:param opt1: String
:param opt2: String
:return: String or None
"""
for option, value in self.opts:
if option == opt1 or option == opt2:
return value
return None
def log_delimiter(self, mode):
if mode == "start":
self.logger.log().info("BEGIN")
elif mode == "end":
self.logger.log().info("END\n")
def check_path(self):
"""
Check if path exists
:return: Boolean
"""
if not self.path:
self.logger.log().error(CONTROL_ERRORS["no_path"])
return False
return True
class Control(object):
def __init__(self, opts, client):
self.opts = opts
self.client = client
self.path = self.loop_options("-f", "--path")
self.pdb_id = self.loop_options("-i", "--pdb_id")
self.mode = self.loop_options("-m", "--mode")
self.resource = self.loop_options("-r", "--resource")
self.user_name = self.loop_options("-u", "--user")
self.pwd = self.loop_options("-p", "--pwd")
self.help = False
for option, value in self.opts:
if option in ["-h", "--help"]:
self.help = True
self.logger = FunPDBeClientLogger("control")
def run(self):
self.configure()
if self.help:
print(self.client)
elif not self.mode:
generic_error()
self.logger.log().error(CONTROL_ERRORS["no_mode"])
else:
return self.action()
return None
def action(self):
actions = {
"get": self.get,
"post": self.post,
"put": self.put,
"delete": self.delete
}
if self.mode in actions.keys():
return actions[self.mode]()
return None
def configure(self):
self.client.user.user_name = self.user_name
self.client.user.user_pwd = self.pwd
def get(self):
if self.pdb_id:
return self.client.get_one(self.pdb_id, self.resource)
else:
return self.client.get_all(self.resource)
def post(self):
if not self.check_path():
return None
if self.path.endswith(".json"):
return self.client.post(self.path, self.resource)
else:
for json_path in glob.glob("%s/*.json" % self.path):
self.client.post(json_path, self.resource)
self.client.json_data = None
return True
def put(self):
if not self.check_path():
return None
return self.client.put(self.path, self.pdb_id, self.resource)
def delete(self):
return self.client.delete_one(self.pdb_id, self.resource)
def loop_options(self, opt1, opt2):
for option, value in self.opts:
if option == opt1 or option == opt2:
return value
return None
def check_path(self):
if not self.path:
self.logger.log().error(CONTROL_ERRORS["no_path"])
return False
return True