def move(fileService, path, destinationFileService, destinationPath, replaceExisting=True, doCopy=True):
"""
Moves or copies a file or folder.
:param fileService: name of fileService (string), or object (dictionary) that defines a file service. A list of these kind of objects available to the user is returned by the function Files.getFileServices().
:param path: String defining the origin path (in the remote fileService) of the file or directory to be copied/moved, starting from the root volume level. Example: rootVolume/userVolumeOwner/userVolume/fileToBeMoved.txt.
:param destinationFileService: name of fileService (string), or object (dictionary) that defines a destination file service (where the file is moved/copied into). A list of these kind of objects available to the user is returned by the function Files.getFileServices().
:param destinationRelativePath: String defining the destination path (in the remote destinationFileService) of the file or directory to be copied/moved, starting from the root volume level. Example: rootVolume/userVolumeOwner/userVolume/recentlyMovedFile.txt.
:param replaceExisting: If set to False, it will throw an error if the file already exists, If set to True, it will not throw and eeror in that case.
:param doCopy: if set to True, then it will copy the file or folder. If set to False, then the file or folder will be moved.
:raises: Throws an exception if the user is not logged into SciServer (use Authentication.login for that purpose). Throws an exception if the HTTP request to the FileService API returns an error.
:example: fileServices = Files.getFileServices(); isDownloaded = Files.upload("/myUploadedFile.txt","persistent","myUserName", fileServices[0], localFilePath="/myDownloadedFile.txt");
.. seealso:: Files.getFileServices(), Files.getFileServiceFromName, Files.createDir, Files.delete, Files.upload, Files.dirList
"""
token = Authentication.getToken()
if token is not None and token != "":
if Config.isSciServerComputeEnvironment():
taskName = "Compute.SciScript-Python.Files.Move"
else:
taskName = "SciScript-Python.Files.Move"
(rootVolume, userVolumeOwner, userVolume, relativePath) = splitPath(path);
(destinationRootVolume, destinationUserVolumeOwner, destinationUserVolume, destinationRelativePath) = splitPath(destinationPath);
if userVolumeOwner is None:
userVolumeOwner = Authentication.getKeystoneUserWithToken(token).userName;
if destinationUserVolumeOwner is None:
destinationUserVolumeOwner = Authentication.getKeystoneUserWithToken(token).userName;
if type(fileService) == str:
fileService = getFileServiceFromName(fileService)
if type(destinationFileService) == str:
destinationFileService = getFileServiceFromName(destinationFileService)
url = __getFileServiceAPIUrl(fileService) + "api/data/" + rootVolume + "/" + userVolumeOwner + "/" + userVolume + "/" + relativePath + "?replaceExisting=" + str(replaceExisting) + "&doCopy=" + str(doCopy) + "&TaskName=" + taskName;
headers = {'X-Auth-Token': token, "Content-Type": "application/json"}
if type(destinationFileService) == dict:
destinationFileService = destinationFileService['name']
jsonDict = {'destinationPath': destinationRelativePath, 'destinationRootVolume': destinationRootVolume, 'destinationUserVolume':destinationUserVolume, 'destinationOwnerName': destinationUserVolumeOwner, 'destinationFileService': destinationFileService};
data = json.dumps(jsonDict).encode()
res = requests.put(url, stream=True, headers=headers, json=jsonDict)
if res.status_code < 200 or res.status_code >= 300:
raise Exception("Error when moving '" + str(path) + "' in file service '" + fileService.get("name") + "' to '" + str(path) + "' in file service '" + destinationFileService.get("name)") + "'. \nHttp Response from FileService API returned status code " + str(res.status_code) + ":\n" + res.content.decode());
else:
raise Exception("User token is not defined. First log into SciServer.")
def login(username, password):
token1 = Authentication.login(username, password)
user = Authentication.getKeystoneUserWithToken(token1)
print("userName="******"id=" + user.id)
iden = Authentication.identArgIdentifier()
print("ident=" + iden)
def getSchemaName():
"""
Returns the WebServiceID that identifies the schema for a user in MyScratch database with CasJobs.
:return: WebServiceID of the user (string).
:raises: Throws an exception if the user is not logged into SciServer (use Authentication.login for that purpose). Throws an exception if the HTTP request to the CasJobs API returns an error.
:example: wsid = CasJobs.getSchemaName()
.. seealso:: CasJobs.getTables.
"""
token = Authentication.getToken()
if token is not None and token != "":
keystoneUserId = Authentication.getKeystoneUserWithToken(token).id
usersUrl = Config.CasJobsRESTUri + "/users/" + keystoneUserId
headers = {'X-Auth-Token': token, 'Content-Type': 'application/json'}
getResponse = requests.get(usersUrl, headers=headers)
if getResponse.status_code != 200:
raise Exception(
"Error when getting schema name. Http Response from CasJobs API returned status code "
+ str(getResponse.status_code) + ":\n" +
getResponse.content.decode())
jsonResponse = json.loads(getResponse.content.decode())
return "wsid_" + str(jsonResponse["WebServicesId"])
else:
raise Exception("User token is not defined. First log into SciServer.")
def test_Authentication_allMethods(self):
newToken1 = "myToken1"
newToken2 = "myToken2"
token1 = Authentication.login(Authentication_loginName,
Authentication_loginPassword)
token2 = Authentication.getToken()
token3 = Authentication.getKeystoneToken()
token4 = Authentication.token.value
user = Authentication.getKeystoneUserWithToken(token1)
iden = Authentication.identArgIdentifier()
self.assertEqual(iden, "--ident=")
self.assertNotEqual(token1, "")
self.assertIsNot(token1, None)
self.assertEqual(token1, token2)
self.assertEqual(token1, token3)
self.assertEqual(token1, token4)
self.assertEqual(user.userName, Authentication_loginName)
self.assertIsNot(user.id, None)
self.assertNotEqual(user.id, "")
Authentication.setToken(newToken1)
self.assertEqual(newToken1, Authentication.getToken())
Authentication.setKeystoneToken(newToken2)
self.assertEqual(newToken2, Authentication.getKeystoneToken())
def getSchemaName(token=""):
if token == "":
userToken = Authentication.getToken()
else:
userToken = token
keystoneUserId = Authentication.getKeystoneUserWithToken(userToken).id
usersUrl = Config.CasJobsRESTUri + "/users/" + keystoneUserId
headers = {"X-Auth-Token": userToken, "Content-Type": "application/json"}
getResponse = requests.get(usersUrl, headers=headers)
jsonResponse = json.loads(getResponse.content.decode())
return "wsid_" + str(jsonResponse["WebServicesId"])
def __setupserver(self):
print("Setting up SkyServer...")
Authentication_loginName = self.username
Authentication_loginPassword = self.password
token1 = Authentication.login(Authentication_loginName,
Authentication_loginPassword)
token2 = Authentication.getToken()
token3 = Authentication.getKeystoneToken()
token4 = Authentication.token.value
user = Authentication.getKeystoneUserWithToken(token1)
iden = Authentication.identArgIdentifier()
def createDir(fileService, path, quiet=True):
"""
Create a directory.
:param fileService: name of fileService (string), or object (dictionary) that defines a file service. A list of these kind of objects available to the user is returned by the function Files.getFileServices().
:param path: path (in the remote file service) to the directory (string), starting from the root volume level. Example: rootVolume/userVolumeOwner/userVolume/directory
:param quiet: If set to False, it will throw an error if the directory already exists. If set to True. it will not throw an error.
:raises: Throws an exception if the user is not logged into SciServer (use Authentication.login for that purpose). Throws an exception if the HTTP request to the FileService API returns an error.
:example: fileServices = Files.getFileServices(); Files.createDir(fileServices[0], "myRootVolume","myUserVolume", "myNewDir");
.. seealso:: Files.getFileServices(), Files.getFileServiceFromName, Files.delete, Files.upload, Files.download, Files.dirList
"""
token = Authentication.getToken()
if token is not None and token != "":
if Config.isSciServerComputeEnvironment():
taskName = "Compute.SciScript-Python.Files.createDir"
else:
taskName = "SciScript-Python.Files.createDir"
(rootVolume, userVolumeOwner, userVolume, relativePath) = splitPath(path);
if not relativePath.startswith("/"):
relativePath = "/" + relativePath;
if userVolumeOwner is None:
userVolumeOwner = Authentication.getKeystoneUserWithToken(token).userName;
if type(fileService) == str:
fileService = getFileServiceFromName(fileService)
url = __getFileServiceAPIUrl(fileService) + "api/folder/" + rootVolume + "/" + userVolumeOwner + "/" + userVolume + "/" + relativePath + "?quiet=" + str(quiet) + "&TaskName=" + taskName;
headers = {'X-Auth-Token': token}
res = requests.put(url, headers=headers)
if res.status_code >= 200 and res.status_code < 300:
pass;
else:
raise Exception("Error when creating directory '" + str(path) + "' in file service '" + fileService.get('name') + "'.\nHttp Response from FileService API returned status code " + str(res.status_code) + ":\n" + res.content.decode());
else:
raise Exception("User token is not defined. First log into SciServer.")
def authenticate_user():
try:
token = Authentication.getToken()
user = Authentication.getKeystoneUserWithToken(token)
USERNAME = user.userName
except requests.exceptions.ConnectionError as e:
print("Connection Error: Authentication Token was not generated.")
print(" Please log back in to SciServer and try again.")
sys.exit(1)
except Exception as e:
if "Error when getting the keystone user with token" in str(e.args[0]):
print(
"Connection Error: Authentication failed. User not signed in."
)
print(
" Please log back in to SciServer, reboot terminal, and try again."
)
else:
print("Unexpected error:", sys.exc_info()[0])
raise
sys.exit(1)
else:
return (token, USERNAME)
token1 = Authentication.login(Authentication_loginName, Authentication_loginPassword);
token2 = Authentication.getToken()
token3 = Authentication.getKeystoneToken()
token4 = Authentication.token.value
print("token1=" + token1)#
print("token2=" + token2)#
print("token3=" + token3)#
print("token4=" + token4)#
# In[ ]:
#getting curent user info
user = Authentication.getKeystoneUserWithToken(token1)
print("userName="******"id=" + user.id)
iden = Authentication.identArgIdentifier()
print("ident="+iden)
# In[ ]:
#reseting the current token to another value:
Authentication.setToken("myToken1")
token5 = Authentication.getToken()
Authentication.setKeystoneToken("myToken2")
token6 = Authentication.getKeystoneToken()
#|emphysema| does the patient have a diagnosis for Emphysema |
#|acute_bronchitist| does the patient have a diagnosis for Acute Bronchitis |
#|cystic_fibrosis| does the patient have a diagnosis for Cystic Fibrosis |
#|duration| duration in days between earliest and latest encounter|
# Import Libraries & connect to DB
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
import seaborn as sns
import getpass
from SciServer import Authentication
myUserName = Authentication.getKeystoneUserWithToken(Authentication.getToken()).userName
passwd = getpass.getpass('Password for ' + myUserName + ': ')
user = "******" + myUserName
import sqlalchemy
import urllib.parse
#SQL Driver
driver="FreeTDS"
tds_ver="8.0"
# Database
host_ip="ESMPMDBPR4.WIN.AD.JHU.EDU" # Update this accordingly
db_port="1433"
db="CAMP_PMCoe_Projection" # Update this accordingly
# Create Connection String
conn_str=("DRIVER={};Server={};PORT={};DATABASE={};UID={};PWD={};TDS_VERSION={}"
.format(driver, host_ip, db_port, db, user, passwd, tds_ver))
