queries.py

"""
:Author: Franziska Koehn
:Created: 2015/01/13

This module includes functions around sending and defining queries.

to query the xnat server define:

one string including one Root-Type like:

.. sourcecode:: python

   'xnat:mrScanData'

one list including the search-constraints like:

.. code-block:: python

    [
        ('xnat:mrScanData/TYPE', 'LIKE', '%t2%'),
        ('xnat:mrScanData/PARAMETERS_FLIP', '>=', '10'),
        'AND',
        [('xnat:mrScanData/PARAMETERS_TE', '>', '2.0'),
         ('xnat:mrScanData/PARAMETERS_TE', '<', '2.0'),
         'OR'
         ]
    ]

a list of search-fields like:

.. code-block:: python

    [ 'xnat:mrScanData/TYPE','xnat:mrScanData/ID']

"""

from threading import Lock
requests_lock = Lock()

def get_query_methods():
    """Returns all applicable methods for creating a query."""
    return ["AND", "OR"]

def get_operators():
    """Returns all applicable Operators for creating a query."""
    return ["LIKE", ">", "<", "<=", ">=", "="]


def download_async(result, host, creds, rest, dest_folder='', cb=(lambda *_: None), cb_args=()):
    """
    Downloads file by using threads (So the GUI will not be blocked while downloading).

    **Parameters**
        :result: dict, resultset from which will be downloaded
        :host: str, address of host
        :creds: tuple (username, userpassword), credentials (including user-name and -password)
        :rest: str, REST-API definition
        :dest_folder: str, folder where the downloaded files will be saved
        :cb: function, that will be called, when download is finished with the arguments from cb_args
        :cb_args: args for function cb
    """
    from threading import Thread
    download_thread = Thread(target=download, args=(result, host, creds, rest, dest_folder, cb, cb_args))
    download_thread.start()
    return download_thread

def download(result, host, creds, rest, dest_folder='', cb=(lambda *_: None), cb_args=()):
    """
    Downloads a Result.

    **Parameters**
        :result: dict, resultset from which will be downloaded
        :host: str, address of host
        :creds: tuple (username, userpassword), credentials (including user-name and -password)
        :rest: str, REST-API definition
        :dest_folder: str, folder where the downloaded files will be saved
        :cb: function, that will be called, when download is finished with the arguments from cb_args
        :cb_args: args for function cb
    """

    requests_lock.acquire()

    import re
    import os

    names=[]
    def subfunc(f):
        key = f.group(0).strip("{}")
        r = result[key]
        names.append(r)
        return r
    ret = re.sub('\{\w+\}', subfunc, rest)

    path = os.path.join(dest_folder, '-'.join(names))
    url = "%s%s" % (host, ret)

    download_file(url, creds, path)
    requests_lock.release()
    cb(*cb_args)

def download_file(url, creds, path):
    """
    Downloads a file from given 'url' and saves it to 'path'.

    Returns True if download was finished without problems
    Returns False if download raised an exception.

    **Parameters**
        :url: str, host/REST-API with filled values
        :creds: tuple(user-name, user-password), credentials
        :path: str, folder where the downloaded files will be saved
    """

    import requests
    from base64 import b64encode
    from requests.auth import HTTPBasicAuth

    if not path.endswith(".zip"):
        path += ".zip"

    user, passw = creds

    try:
        with open(path, 'wb') as handle:
            response = requests.get(url, stream=True, auth=HTTPBasicAuth(user, passw))
            if not response.ok:
                raise ValueError(response.status_code)
            for block in response.iter_content(1024):
                if not block:
                    break
                handle.write(block)
        return True
    except IOError as e:
        print "Error writing file %s, %s" % (path, e)
    except ValueError as e:
        print "Error downloading file %s, Status Code %s" % (url, e)
    return False


def get_xnat_server_connection(force=False, host="", user="", passw=""):
    from pyxnat import Interface
    from tempfile import mkdtemp
    import xsa.errors

    if get_xnat_server_connection.cache and not force:
        return get_xnat_server_connection.cache
    elif force and host=="":
        raise xsa.errors.ServerNotFoundError("The host was not defined.")
    elif force and (user=="" or passw==""):
        raise xsa.errors.UnauthorizedError("The user-name and/or the user-password were not defined.")

    disconnect_xnat_server()
    try:
        get_xnat_server_connection.cache = Interface(server=host, user=user, password=passw, cachedir=mkdtemp())
    except IndexError as e:
        raise xsa.errors.ServerNotFoundError("Server not found, check your host-address.")
    return get_xnat_server_connection()
get_xnat_server_connection.cache = None

def disconnect_xnat_server():
    import xsa.errors
    try:
        get_xnat_server_connection.cache.disconnect()
        get_xnat_server_connection.cache = None
    except:
       return

def query_for_additional_data(rest, result, host, user, passw):

    import re
    def subfunc(f):
        key = f.group(0).strip("{}")
        return result[key]
    ret = re.sub('\{\w+\}', subfunc, rest)

    central = get_xnat_server_connection(host=host, user=user, passw=passw)
    exp = central.select(ret)

    new_fields = exp.xpath("//xnat:field")
    new_result = result.copy()
    for f in new_fields:
        fieldname = f.get("name")
        value = exp.xpath("//xnat:field[@name='"+fieldname+"']/child::text()")
        new_result[fieldname] = ''.join(value).replace("\n","")
    return new_result


def search_for(host, root_element, constraints, search_fields, user, passw):
    """
    Does a search for given values. raises xsa -Exceptions

    **Parameters**
        :host: str, host-address
        :root_element: str, Root-Type of search
        :constraints: list, constraints of query
        :search_fields: list of str, fields which will be returned from server
        :user: str, user-name
        :passw: str, user-password

    **Raises**
        :xsa.errors.ServerNotFoundError:
        :xsa.errors.UnauthorizedError:
        :xsa.errors.ResponseNotReady:
        :xsa.errors.QueryError:


    """
    import xsa.errors

    from pyxnat.core import errors
    from httplib2 import ServerNotFoundError
    from httplib import ResponseNotReady

    from tempfile import mkdtemp
    tmp_dir=mkdtemp()

    central = get_xnat_server_connection(host=host, user=user, passw=passw)

    result = []

    try:
        result =  central.select(root_element,search_fields).where(constraints)
    except errors.DatabaseError as e:
        if '401' in str(e):
            raise xsa.errors.UnauthorizedError("Unauthorizied attempt. Check your User and Password")
        else:
            raise e
    except ServerNotFoundError:
        raise xsa.errors.ServerNotFoundError("Server not found, check your host-address.")
    except ResponseNotReady:
        raise xsa.errors.ResponseNotReady("Please check your Host-Address")

    if result == []:
        raise xsa.errors.QueryError("Please check your query.")

    try:
        from shutil import rmtree
        rmtree(tmp_dir)
    except:
        pass

    return result