firecloud-api-cds 0.2.0__py3-none-any.whl

firecloud_api_cds/api.py

@@ -0,0 +1,1774 @@
+"""
+This module provides python bindings for the Firecloud API.
+For more details see https://software.broadinstitute.org/firecloud/
+
+To see how the python bindings map to the RESTful endpoints view
+the README at https://pypi.python.org/pypi/firecloud.
+"""
+
+from __future__ import print_function
+import json
+import sys
+import os
+import io
+import logging
+import subprocess
+try:
+    from collections.abc import Iterable
+except ImportError:
+    from collections import Iterable
+
+from six.moves.urllib.parse import urlencode, urljoin
+from six import string_types
+
+import inspect
+
+import google.auth
+from google.auth.exceptions import DefaultCredentialsError, RefreshError
+from google.auth.transport.requests import AuthorizedSession, Request
+from google.oauth2 import id_token
+
+from .errors import FireCloudServerError
+from .fccore import __fcconfig as fcconfig
+
+FISS_USER_AGENT = "FISS/0.16.38"
+
+# Set Global Authorized Session
+__SESSION = None
+__USER_ID = None
+
+# Suppress warnings about project ID
+logging.getLogger('google.auth').setLevel(logging.ERROR)
+
+#################################################
+# Utilities
+#################################################
+def _set_session():
+    """ Sets global __SESSION and __USER_ID if they haven't been set """
+    global __SESSION
+    global __USER_ID
+    
+    if __SESSION is None:
+        # determine if clock_skew_in_seconds is a parameter for id_token.verify_oauth2_token()
+        try:  # PY3
+            argspec = inspect.getfullargspec(id_token.verify_oauth2_token)
+        except AttributeError:  # PY2
+            argspec = inspect.getargspec(id_token.verify_oauth2_token)
+            
+        try:
+            __SESSION = AuthorizedSession(google.auth.default(['https://www.googleapis.com/auth/userinfo.profile',
+                                                               'https://www.googleapis.com/auth/userinfo.email'])[0])
+            health()
+            # google.auth 2.1.0 introduced a restrictive clock skew that was unmodifiable until 2.3.2
+            if 'clock_skew_in_seconds' in argspec.args:
+                __USER_ID = id_token.verify_oauth2_token(__SESSION.credentials.id_token,
+                                                         Request(session=__SESSION),
+                                                         clock_skew_in_seconds=10)['email']
+            else:
+                __USER_ID = id_token.verify_oauth2_token(__SESSION.credentials.id_token,
+                                                         Request(session=__SESSION))['email']
+        except AttributeError:
+            __USER_ID = __SESSION.credentials.service_account_email
+        except (DefaultCredentialsError, RefreshError) as gae:
+            if os.getenv('SERVER_SOFTWARE', '').startswith('Google App Engine/'):
+                raise
+            logging.warning("Unable to determine/refresh application credentials")
+            try:
+                subprocess.check_call(['gcloud', 'auth', 'application-default',
+                                       'login', '--no-launch-browser'])
+                __SESSION = AuthorizedSession(google.auth.default(['https://www.googleapis.com/auth/userinfo.profile',
+                                                                   'https://www.googleapis.com/auth/userinfo.email'])[0])
+            except subprocess.CalledProcessError as cpe:
+                if cpe.returncode < 0:
+                    logging.exception("%s was terminated by signal %d",
+                                      cpe.cmd, -cpe.returncode)
+                else:
+                    logging.exception("%s returned %d", cpe.cmd,
+                                      cpe.returncode)
+                raise gae
+
+def _fiss_agent_header(headers=None):
+    """ Return request headers for fiss.
+        Inserts FISS as the User-Agent.
+        Initializes __SESSION if it hasn't been set.
+
+    Args:
+        headers (dict): Include additional headers as key-value pairs
+
+    """
+    _set_session()
+
+    fiss_headers = {"User-Agent" : FISS_USER_AGENT}
+    if headers is not None:
+        fiss_headers.update(headers)
+    return fiss_headers
+
+def __get(methcall, headers=None, root_url=None, **kwargs):
+    if not headers:
+        headers = _fiss_agent_header()
+    if root_url is None:
+        root_url = fcconfig.root_url
+    r = __SESSION.get(urljoin(root_url, methcall), headers=headers, **kwargs)
+    if fcconfig.verbosity > 1:
+        print('FISSFC call: %s' % r.url, file=sys.stderr)
+    return r
+
+def __patch(methcall, headers=None, root_url=None, **kwargs):
+    if not headers:
+        headers = _fiss_agent_header({"Content-type":  "application/json"})
+    if root_url is None:
+        root_url = fcconfig.root_url
+    r = __SESSION.patch(urljoin(root_url, methcall), headers=headers, **kwargs)
+    if fcconfig.verbosity > 1:
+        info = r.url
+        data = kwargs.get("data", None)
+        if data:
+            info += " \n(data=%s) " % data
+        json = kwargs.get("json", None)
+        if json:
+            info += " \n(json=%s) " % json
+        print('FISSFC call: PATCH %s' % info, file=sys.stderr)
+    return r
+
+def __post(methcall, headers=None, root_url=None, **kwargs):
+    if not headers:
+        headers = _fiss_agent_header({"Content-type":  "application/json"})
+    if root_url is None:
+        root_url = fcconfig.root_url
+    r = __SESSION.post(urljoin(root_url, methcall), headers=headers, **kwargs)
+    if fcconfig.verbosity > 1:
+        info = r.url
+        json = kwargs.get("json", None)
+        if json:
+            info += " \n(json=%s) " % json
+        print('FISSFC call: POST %s' % info, file=sys.stderr)
+    return r
+
+def __put(methcall, headers=None, root_url=None, **kwargs):
+    if not headers:
+        headers = _fiss_agent_header()
+    if root_url is None:
+        root_url = fcconfig.root_url
+    r = __SESSION.put(urljoin(root_url, methcall), headers=headers, **kwargs)
+    if fcconfig.verbosity > 1:
+        info = r.url
+        json = kwargs.get("json", None)
+        if json:
+            info += " \n(json=%s) " % json
+        print('FISSFC call: PUT %s' % info, file=sys.stderr)
+    return r
+
+def __delete(methcall, headers=None, root_url=None):
+    if not headers:
+        headers = _fiss_agent_header()
+    if root_url is None:
+        root_url = fcconfig.root_url
+    r = __SESSION.delete(urljoin(root_url, methcall), headers=headers)
+    if fcconfig.verbosity > 1:
+        print('FISSFC call: DELETE %s' % r.url, file=sys.stderr)
+    return r
+
+def _check_response_code(response, codes):
+    """
+    Throws an exception if the http response is not expected. Can check single
+    integer or list of valid responses.
+
+    Example usage:
+        >>> r = api.get_workspace("broad-firecloud-testing", "Fake-Bucket")
+        >>> _check_response_code(r, 200)
+         ... FireCloudServerError ...
+    """
+    if type(codes) == int:
+        codes = [codes]
+    if response.status_code not in codes:
+        try:
+            msg = json.dumps(response.json())
+        except:
+            msg = response.text
+        raise FireCloudServerError(response.status_code, msg)
+
+def whoami():
+    """ Return __USER_ID """
+    _set_session()
+    return __USER_ID
+
+##############################################################
+# 1. Orchestration API calls, see https://api.firecloud.org/
+##############################################################
+
+##################
+### 1.1 Entities
+##################
+
+def get_entities_with_type(namespace, workspace):
+    """List entities in a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/getEntitiesWithType
+    """
+    uri = "workspaces/{0}/{1}/entities_with_type".format(namespace, workspace)
+    return __get(uri)
+
+def list_entity_types(namespace, workspace):
+    """List the entity types present in a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/getEntityTypes
+    """
+    headers = _fiss_agent_header({"Content-type":  "application/json"})
+    uri = "workspaces/{0}/{1}/entities".format(namespace, workspace)
+    return __get(uri, headers=headers)
+
+def upload_entities(namespace, workspace, entity_data, model='firecloud',
+                    delete_empty=False):
+    """Upload entities from tab-delimited string.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        entity_data (str): TSV string describing entites
+        model (str): Data Model type. "firecloud" (default) or "flexible"
+        delete_empty (bool): Values left blank in the TSV will be deleted if set to true
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/importEntities
+        https://api.firecloud.org/#!/Entities/flexibleImportEntities
+    """
+    params = {"deleteEmptyValues": delete_empty}
+    body = urlencode({"entities" : entity_data})
+    headers = _fiss_agent_header({
+        'Content-type':  "application/x-www-form-urlencoded"
+    })
+    endpoint = 'importEntities'
+    if model == 'flexible':
+        endpoint = 'flexibleImportEntities'
+    uri = "workspaces/{0}/{1}/{2}".format(namespace, workspace, endpoint)
+    return __post(uri, headers=headers, data=body, params=params)
+
+def upload_entities_tsv(namespace, workspace, entities_tsv, model='firecloud'):
+    """Upload entities from a tsv loadfile.
+
+    File-based wrapper for api.upload_entities().
+    A loadfile is a tab-separated text file with a header row
+    describing entity type and attribute names, followed by
+    rows of entities and their attribute values.
+
+        Ex:
+            entity:participant_id   age   alive
+            participant_23           25       Y
+            participant_27           35       N
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        entities_tsv (file): FireCloud loadfile, see format above
+        model (str): Data Model type. "firecloud" (default) or "flexible"
+    """
+    if isinstance(entities_tsv, string_types):
+        with open(entities_tsv, "r") as tsv:
+            entity_data = tsv.read()
+    elif isinstance(entities_tsv, io.StringIO):
+        entity_data = entities_tsv.getvalue()
+    else:
+        raise ValueError('Unsupported input type.')
+    return upload_entities(namespace, workspace, entity_data, model)
+
+def copy_entities(from_namespace, from_workspace, to_namespace,
+                  to_workspace, etype, enames, link_existing_entities=False):
+    """Copy entities between workspaces
+
+    Args:
+        from_namespace (str): project (namespace) to which source workspace belongs
+        from_workspace (str): Source workspace name
+        to_namespace (str): project (namespace) to which target workspace belongs
+        to_workspace (str): Target workspace name
+        etype (str): Entity type
+        enames (list(str)): List of entity names to copy
+        link_existing_entities (boolean): Link all soft conflicts to the entities that already exist.
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/copyEntities
+    """
+
+    uri = "workspaces/{0}/{1}/entities/copy".format(to_namespace, to_workspace)
+    body = {
+        "sourceWorkspace": {
+            "namespace": from_namespace,
+            "name": from_workspace
+        },
+        "entityType": etype,
+        "entityNames": enames
+    }
+    
+    return __post(uri, json=body, params={'linkExistingEntities':
+                                          str(link_existing_entities).lower()})
+
+def get_entities(namespace, workspace, etype):
+    """List entities of given type in a workspace.
+
+    Response content will be in JSON format.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/getEntities
+    """
+    uri = "workspaces/{0}/{1}/entities/{2}".format(namespace, workspace, etype)
+    return __get(uri)
+
+def get_entities_tsv(namespace, workspace, etype, attrs=None, model="firecloud"):
+    """List entities of given type in a workspace as a TSV.
+
+    Similar to get_entities(), but the response is a TSV.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+        attrs (list): list of ordered attribute names to be in downloaded tsv
+        model (str): Data Model type. "firecloud" (default) or "flexible"
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/downloadEntitiesTSV
+    """
+    params = {'model': model}
+    if attrs is not None:
+        params['attributeNames'] = ','.join(attrs)
+    uri = "workspaces/{0}/{1}/entities/{2}/tsv".format(namespace,
+                                                workspace, etype)
+    return __get(uri, params=params)
+
+def get_entity(namespace, workspace, etype, ename):
+    """Request entity information.
+
+    Gets entity metadata and attributes.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+        ename (str): The entity's unique id
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/getEntity
+    """
+    uri = "workspaces/{0}/{1}/entities/{2}/{3}".format(namespace,
+                                            workspace, etype, ename)
+    return __get(uri)
+
+def delete_entities(namespace, workspace, json_body):
+    """Delete entities in a workspace.
+
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        json_body:
+        [
+          {
+            "entityType": "string",
+            "entityName": "string"
+          }
+        ]
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/deleteEntities
+    """
+
+    uri = "workspaces/{0}/{1}/entities/delete".format(namespace, workspace)
+    return __post(uri, json=json_body)
+
+def delete_entity_type(namespace, workspace, etype, ename):
+    """Delete specified entities of a single type in a workspace.
+
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+        ename (str, or iterable of str): unique entity id(s)
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/deleteEntities
+    """
+
+    uri = "workspaces/{0}/{1}/entities/delete".format(namespace, workspace)
+    if isinstance(ename, string_types):
+        body = [{"entityType":etype, "entityName":ename}]
+    elif isinstance(ename, Iterable):
+        body = [{"entityType":etype, "entityName":i} for i in ename]
+
+    return __post(uri, json=body)
+
+def delete_entities_of_type(namespace, workspace, etype):
+    """Delete all entities of a type in a workspace.
+    
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+    
+    Swagger:
+        https://api.firecloud.org/#/Entities/deleteEntitiesOfType
+    """
+    
+    uri = "workspaces/{0}/{1}/entityTypes/{2}".format(namespace, workspace,
+                                                      etype)
+    return __delete(uri)
+
+def delete_participant(namespace, workspace, name):
+    """Delete participant in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): participant_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "participant", name)
+
+def delete_participant_set(namespace, workspace, name):
+    """Delete participant set in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): participant_set_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "participant_set", name)
+
+def delete_sample(namespace, workspace, name):
+    """Delete sample in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): sample_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "sample", name)
+
+def delete_sample_set(namespace, workspace, name):
+    """Delete sample set in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): sample_set_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "sample_set", name)
+
+def delete_pair(namespace, workspace, name):
+    """Delete pair in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): pair_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "pair", name)
+
+def delete_pair_set(namespace, workspace, name):
+    """Delete pair set in a workspace.
+
+    Convenience wrapper for api.delete_entity().
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        name (str, or iterable of str): pair_set_id(s)
+    """
+    return delete_entity_type(namespace, workspace, "pair_set", name)
+
+def get_entities_query(namespace, workspace, etype, page=1, page_size=100,
+                       sort_direction="asc", filter_terms=None,
+                       filter_operator=None, fields=None):
+    """Paginated version of get_entities_with_type.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype (str): Entity type
+        page (int): Page number, 1-indexed
+        page_size (int): Number of entities to return per page
+        sort_direction (str): "asc" or "desc"
+        filter_terms (str): Space-separated list to text match
+        filter_operator (str): "and" or "or" - determines if one or all
+                              filter_terms must have a match. Default: "and"
+        fields (str): Comma-separated list of which fields to populate
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/entityQuery
+
+    """
+
+    # Initial parameters for pagination
+    params = {
+        "page" : page,
+        "pageSize" : page_size,
+        "sortDirection" : sort_direction
+    }
+    if filter_terms:
+        params['filterTerms'] = filter_terms
+    if filter_operator:
+        params['filterOperator'] = filter_operator
+    if fields:
+        params['fields'] = fields
+
+    uri = "workspaces/{0}/{1}/entityQuery/{2}".format(namespace,workspace,etype)
+    return __get(uri, params=params)
+
+def rename_entity(namespace, workspace, etype, ename, name):
+    """Rename entity in a workspace
+    
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype     (str): Entity type
+        ename     (str): Entity name
+        name      (str): New entity name
+    
+    Swagger:
+        https://api.firecloud.org/#/Entities/renameEntity
+    """
+    
+    body = {"name": name}
+    uri = "workspaces/{0}/{1}/entities/{2}/{3}/rename".format(namespace,
+                                                              workspace, etype,
+                                                              ename)
+    return __post(uri, json=body)
+
+def rename_entity_type(namespace, workspace, etype, name):
+    """Rename entity type in a workspace
+    
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype     (str): Entity type
+        name      (str): New entity type name
+    
+    Swagger:
+        https://api.firecloud.org/#/Entities/renameEntityType
+    """
+    
+    body = {"newName": name}
+    uri = "workspaces/{0}/{1}/entityTypes/{2}".format(namespace, workspace,
+                                                      etype)
+    return __patch(uri, json=body)
+
+def rename_entity_type_attribute(namespace, workspace, etype, attr, name):
+    """Change the attribute name for an entity type in a workspace. If the old
+       name doesn't exist the update will fail. If the new name already exists,
+       the update will fail, and no records will be updated.
+    
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype     (str): Entity type
+        attr      (str): Attribute
+        name      (str): New attribute name
+    
+    Swagger:
+        https://api.firecloud.org/#/Entities/rename_entity_attributes
+    """
+    body = {"newAttributeName": name}
+    uri = "workspaces/{0}/{1}/entityTypes/{2}/attributes/{3}".format(namespace,
+                                                                     workspace,
+                                                                     etype,
+                                                                     attr)
+    return __patch(uri, json=body)
+
+def update_entity(namespace, workspace, etype, ename, updates):
+    """ Update entity attributes in a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        etype     (str): Entity type
+        ename     (str): Entity name
+        updates   (list(dict)): List of updates to entity from _attr_set, e.g.
+
+    Swagger:
+        https://api.firecloud.org/#!/Entities/update_entity
+    """
+    headers = _fiss_agent_header({"Content-type":  "application/json"})
+    uri = "{0}workspaces/{1}/{2}/entities/{3}/{4}".format(fcconfig.root_url,
+                                            namespace, workspace, etype, ename)
+
+    # FIXME: create __patch method, akin to __get, __delete etc
+    return __SESSION.patch(uri, headers=headers, json=updates)
+
+###############################
+### 1.2 Method Configurations
+###############################
+
+def list_workspace_configs(namespace, workspace, allRepos=False):
+    """List method configurations in workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        allRepos (bool): list configs for all repos, not just Agora
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/listWorkspaceMethodConfigs
+        DUPLICATE: https://api.firecloud.org/#!/Workspaces/listWorkspaceMethodConfigs
+    """
+    uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
+    return __get(uri, params={'allRepos': allRepos})
+
+def create_workspace_config(namespace, workspace, body):
+    """Create method configuration in workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        body (json) : a filled-in JSON object for the new method config
+                      (e.g. see return value of get_workspace_config)
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/postWorkspaceMethodConfig
+        DUPLICATE: https://api.firecloud.org/#!/Workspaces/postWorkspaceMethodConfig
+    """
+
+    #json_body = {
+    #    "namespace"      : mnamespace,
+    #    "name"           : method,
+    #    "rootEntityType" : root_etype,
+    #    "inputs" : {},
+    #    "outputs" : {},
+    #    "prerequisites" : {}
+    #}
+    uri = "workspaces/{0}/{1}/methodconfigs".format(namespace, workspace)
+    return __post(uri, json=body)
+
+def delete_workspace_config(namespace, workspace, cnamespace, config):
+    """Delete method configuration in workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        mnamespace (str): Method namespace
+        method (str): Method name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/deleteWorkspaceMethodConfig
+    """
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
+                                            workspace, cnamespace, config)
+    return __delete(uri)
+
+def get_workspace_config(namespace, workspace, cnamespace, config):
+    """Get method configuration in workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        cnamespace (str): Config namespace
+        config (str): Config name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/getWorkspaceMethodConfig
+    """
+
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
+                                            workspace, cnamespace, config)
+    return __get(uri)
+
+def overwrite_workspace_config(namespace, workspace, cnamespace, configname, body):
+    """Add or overwrite method configuration in workspace.
+
+    Args:
+        namespace  (str): project to which workspace belongs
+        workspace  (str): Workspace name
+        cnamespace (str): Configuration namespace
+        configname (str): Configuration name
+        body      (json): new body (definition) of the method config
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/overwriteWorkspaceMethodConfig
+    """
+    headers = _fiss_agent_header({"Content-type": "application/json"})
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
+                                        workspace, cnamespace, configname)
+    return __put(uri, headers=headers, json=body)
+
+def update_workspace_config(namespace, workspace, cnamespace, configname, body):
+    """Update method configuration in workspace.
+
+    Args:
+        namespace  (str): project to which workspace belongs
+        workspace  (str): Workspace name
+        cnamespace (str): Configuration namespace
+        configname (str): Configuration name
+        body      (json): new body (definition) of the method config
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/updateWorkspaceMethodConfig
+    """
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}".format(namespace,
+                                        workspace, cnamespace, configname)
+    return __post(uri, json=body)
+
+def validate_config(namespace, workspace, cnamespace, config):
+    """Get syntax validation for a configuration.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        cnamespace (str): Configuration namespace
+        config (str): Configuration name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/validate_method_configuration
+    """
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/validate".format(namespace,
+                                                    workspace, cnamespace, config)
+    return __get(uri)
+
+def rename_workspace_config(namespace, workspace, cnamespace, config,
+                                            new_namespace, new_name):
+    """Rename a method configuration in a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        mnamespace (str): Config namespace
+        config (str): Config name
+        new_namespace (str): Updated config namespace
+        new_name (str): Updated method name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/renameWorkspaceMethodConfig
+    """
+
+    body = {
+        "namespace" : new_namespace,
+        "name"      : new_name,
+        # I have no idea why this is required by FC, but it is...
+        "workspaceName" : {
+            "namespace" : namespace,
+            "name"      : workspace
+        }
+    }
+    uri = "workspaces/{0}/{1}/method_configs/{2}/{3}/rename".format(namespace,
+                                                workspace, cnamespace, config)
+    return __post(uri, json=body)
+
+def copy_config_from_repo(namespace, workspace, from_cnamespace,
+                          from_config, from_snapshot_id, to_cnamespace,
+                          to_config):
+    """Copy a method config from the methods repository to a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        from_cnamespace (str): Source configuration namespace
+        from_config (str): Source configuration name
+        from_snapshot_id (int): Source configuration snapshot_id
+        to_cnamespace (str): Target configuration namespace
+        to_config (str): Target configuration name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/copyFromMethodRepo
+        DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyFromMethodRepo
+    """
+
+    body = {
+        "configurationNamespace"  : from_cnamespace,
+        "configurationName"       : from_config,
+        "configurationSnapshotId" : from_snapshot_id,
+        "destinationNamespace"    : to_cnamespace,
+        "destinationName"         : to_config
+    }
+    uri = "workspaces/{0}/{1}/method_configs/copyFromMethodRepo".format(
+                                                        namespace, workspace)
+    return __post(uri, json=body)
+
+def copy_config_to_repo(namespace, workspace, from_cnamespace,
+                        from_config, to_cnamespace, to_config):
+    """Copy a method config from a workspace to the methods repository.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        from_cnamespace (str): Source configuration namespace
+        from_config (str): Source configuration name
+        to_cnamespace (str): Target configuration namespace
+        to_config (str): Target configuration name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Configurations/copyToMethodRepo
+        DUPLICATE: https://api.firecloud.org/#!/Method_Repository/copyToMethodRepo
+    """
+
+    body = {
+        "configurationNamespace" : to_cnamespace,
+        "configurationName"      : to_config,
+        "sourceNamespace"        : from_cnamespace,
+        "sourceName"             : from_config
+    }
+    uri = "workspaces/{0}/{1}/method_configs/copyToMethodRepo".format(
+                                                    namespace, workspace)
+    return __post(uri, json=body)
+
+###########################
+### 1.3 Method Repository
+###########################
+
+def list_repository_methods(namespace=None, name=None, snapshotId=None):
+    """List method(s) in the methods repository.
+
+    Args:
+        namespace (str): Method Repository namespace
+        name (str): method name
+        snapshotId (int): method snapshot ID
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryMethods
+    """
+    params = {k:v for (k,v) in locals().items() if v is not None}
+    return __get("methods", params=params)
+
+def list_repository_configs(namespace=None, name=None, snapshotId=None):
+    """List configurations in the methods repository.
+
+    Args:
+        namespace (str): Method Repository namespace
+        name (str): config name
+        snapshotId (int): config snapshot ID
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/listMethodRepositoryConfigurations
+    """
+    params = {k:v for (k,v) in locals().items() if v is not None}
+    return __get("configurations", params=params)
+
+def get_config_template(namespace, method, version):
+    """Get the configuration template for a method.
+
+    The method should exist in the methods repository.
+
+    Args:
+        namespace (str): Method's namespace
+        method (str): method name
+        version (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/createMethodTemplate
+    """
+
+    body = {
+        "methodNamespace" : namespace,
+        "methodName"      : method,
+        "methodVersion"   : int(version)
+    }
+    return __post("template", json=body)
+
+def get_inputs_outputs(namespace, method, snapshot_id):
+    """Get a description of the inputs and outputs for a method.
+
+    The method should exist in the methods repository.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        snapshot_id (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/getMethodIO
+    """
+
+    body = {
+        "methodNamespace" : namespace,
+        "methodName"      : method,
+        "methodVersion"   : snapshot_id
+    }
+    return __post("inputsOutputs", json=body)
+
+def get_repository_config(namespace, config, snapshot_id):
+    """Get a method configuration from the methods repository.
+
+    Args:
+        namespace (str): Methods namespace
+        config (str): config name
+        snapshot_id (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/getMethodRepositoryConfiguration
+    """
+    uri = "configurations/{0}/{1}/{2}".format(namespace, config, snapshot_id)
+    return __get(uri)
+
+def get_repository_method(namespace, method, snapshot_id, wdl_only=False):
+    """Get a method definition from the method repository.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        version (int): snapshot_id of the method
+        wdl_only (bool): Exclude metadata
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/get_api_methods_namespace_name_snapshotId
+    """
+    uri = "methods/{0}/{1}/{2}?onlyPayload={3}".format(namespace, method,
+                                                       snapshot_id,
+                                                       str(wdl_only).lower())
+    return __get(uri)
+
+def update_repository_method(namespace, method, synopsis, wdl, doc=None,
+                             comment=""):
+    """Create/Update workflow definition.
+
+    FireCloud will create a new snapshot_id for the given workflow.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        synopsis (str): short (<80 char) description of method
+        wdl (file): Workflow Description Language file
+        doc (file): (Optional) Additional documentation
+        comment (str): (Optional) Comment specific to this snapshot
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/post_api_methods
+
+    """
+    with open(wdl, 'r') as wf:
+        wdl_payload = wf.read()
+    if doc is not None:
+        with open (doc, 'r') as df:
+            doc = df.read()
+
+    body = {
+        "namespace": namespace,
+        "name": method,
+        "entityType": "Workflow",
+        "payload": wdl_payload,
+        "documentation": doc,
+        "synopsis": synopsis,
+        "snapshotComment": comment
+    }
+
+    return __post("methods",
+                  json={key: value for key, value in body.items() if value})
+
+def delete_repository_method(namespace, name, snapshot_id):
+    """Redacts a method and all of its associated configurations.
+
+    The method should exist in the methods repository.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        snapshot_id (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/delete_api_methods_namespace_name_snapshotId
+    """
+    uri = "methods/{0}/{1}/{2}".format(namespace, name, snapshot_id)
+    return __delete(uri)
+
+def delete_repository_config(namespace, name, snapshot_id):
+    """Redacts a configuration and all of its associated configurations.
+
+    The configuration should exist in the methods repository.
+
+    Args:
+        namespace (str): configuration namespace
+        configuration (str): configuration name
+        snapshot_id (int): snapshot_id of the configuration
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/delete_api_configurations_namespace_name_snapshotId
+    """
+    uri = "configurations/{0}/{1}/{2}".format(namespace, name, snapshot_id)
+    return __delete(uri)
+
+def get_repository_method_acl(namespace, method, snapshot_id):
+    """Get permissions for a method.
+
+    The method should exist in the methods repository.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        version (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/getMethodACL
+    """
+    uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
+    return __get(uri)
+
+def update_repository_method_acl(namespace, method, snapshot_id, acl_updates):
+    """Set method permissions.
+
+    The method should exist in the methods repository.
+
+    Args:
+        namespace (str): Methods namespace
+        method (str): method name
+        snapshot_id (int): snapshot_id of the method
+        acl_updates (list(dict)): List of access control updates
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/setMethodACL
+    """
+
+    uri = "methods/{0}/{1}/{2}/permissions".format(namespace,method,snapshot_id)
+    return __post(uri, json=acl_updates)
+
+def get_repository_config_acl(namespace, config, snapshot_id):
+    """Get configuration permissions.
+
+    The configuration should exist in the methods repository.
+
+    Args:
+        namespace (str): Configuration namespace
+        config (str): Configuration name
+        snapshot_id (int): snapshot_id of the method
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/getConfigACL
+    """
+    uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
+                                                    config, snapshot_id)
+    return __get(uri)
+
+def update_repository_config_acl(namespace, config, snapshot_id, acl_updates):
+    """Set configuration permissions.
+
+    The configuration should exist in the methods repository.
+
+    Args:
+        namespace (str): Configuration namespace
+        config (str): Configuration name
+        snapshot_id (int): snapshot_id of the method
+        acl_updates (list(dict)): List of access control updates
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/setConfigACL
+    """
+
+    uri = "configurations/{0}/{1}/{2}/permissions".format(namespace,
+                                                config, snapshot_id)
+    return __post(uri, json=acl_updates)
+
+def get_method_configurations(namespace, method_name):
+    """Get method configurations.
+
+    Given the namespace/name of a method, returns all configurations in
+    the repository that reference that method.
+
+    Args:
+        namespace (str): Method namespace
+        method_name (str): Method name
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/get_api_methods_namespace_name_configurations
+
+    """
+
+    uri = "methods/{0}/{1}/configurations".format(namespace, method_name)
+
+    return __get(uri)
+
+def get_api_methods_definitions():
+    """List method definitions.
+
+    List method definitions - i.e. unique namespace/name pairs -
+    with counts of snapshots and associated configurations
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/get_api_methods_definitions
+
+    """
+
+    uri = "methods/definitions"
+
+    return __get(uri)
+
+
+#################
+### 1.4 Profile
+#################
+
+def list_billing_projects():
+    """list billing projects for a user.
+
+    Swagger:
+        https://api.firecloud.org/#/BillingV2/listUserBillingProjectsV2
+    """
+    return __get("billing/v2")
+
+def get_proxy_group(email=None):
+    """Returns the proxy group email for the current user
+
+    Args:
+        email (str): User email whose proxy group to retrieve
+                     if None uses current user email
+
+    Swagger:
+    https://api.firecloud.org/#/Profile/getProxyGroup
+    """
+    if email is None:
+        email = whoami()
+    uri = "proxyGroup/{}".format(email)
+    return __get(uri)
+
+################
+### 1.5 Status
+################
+
+def get_status():
+    """Request the status of FireCloud services.
+
+    Swagger:
+        https://api.firecloud.org/#!/Status/status
+    """
+    root_url = fcconfig.root_url.rpartition("api")[0]
+    return __get("status", root_url=root_url)
+
+def health():
+    """Health of FireCloud API.
+
+    Swagger:
+        https://api.firecloud.org/#!/Status/health
+    """
+    root_url = fcconfig.root_url.rpartition("api")[0]
+    return __get("health", root_url=root_url)
+
+######################
+### 1.6 Submissions
+######################
+
+def list_submissions(namespace, workspace):
+    """List submissions in FireCloud workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/listSubmissions
+    """
+    uri = "workspaces/{0}/{1}/submissions".format(namespace, workspace)
+    return __get(uri)
+
+def create_submission(wnamespace, workspace, cnamespace, config,
+                      entity=None, etype=None, expression=None,
+                      use_callcache=True, delete_intermediate_output_files=False,
+                      use_reference_disks=False, memory_retry_multiplier=0,
+                      per_workflow_cost_cap=None, workflow_failure_mode="",
+                      user_comment=""):
+    """Submit job in FireCloud workspace.
+
+    Args:
+        wnamespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        cnamespace (str): Method configuration namespace
+        config (str): Method configuration name
+        entity (str): Entity to submit job on. Should be the same type as
+            the root entity type of the method config, unless an
+            expression is used
+        etype (str): Entity type of root_entity
+        expression (str): Instead of using entity as the root entity,
+            evaluate the root entity from this expression.
+        use_callcache (bool): use call cache if applicable (default: true)
+        delete_intermediate_output_files (bool): Whether or not to delete
+            intermediate output files when the workflow completes. See Cromwell
+            docs (https://cromwell.readthedocs.io/en/develop/wf_options/Google)
+            for more information
+        use_reference_disks (bool): Whether or not to use pre-built disks for
+            common genome references
+        memory_retry_multiplier (float): If a task fails due to running out of
+            memory and the task has maxRetries in its runtime attributes, then
+            it will be retried with its memory multiplied by this amount. See
+            Cromwell docs
+            (https://cromwell.readthedocs.io/en/develop/cromwell_features/RetryWithMoreMemory)
+            for more information
+        per_workflow_cost_cap (float): A cost threshold in USD to apply to individual
+            workflows. When the estimated cost is exceeded, the workflow is terminated.
+        workflow_failure_mode (str): What happens after a task fails. Choose from
+            ContinueWhilePossible and NoNewCalls. Defaults to NoNewCalls if not
+            specified. See Cromwell docs
+            (https://cromwell.readthedocs.io/en/develop/execution/ExecutionTwists/#failure-modes)
+            for more information.
+        user_comment: Freeform user defined description, optional (max length
+            1000 characters)
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/createSubmission
+    """
+
+    uri = "workspaces/{0}/{1}/submissions".format(wnamespace, workspace)
+    body = {
+        "methodConfigurationNamespace" : cnamespace,
+        "methodConfigurationName" : config,
+         "useCallCache" : use_callcache
+    }
+
+    if etype:
+        body['entityType'] = etype
+
+    if entity:
+        body['entityName'] = entity
+
+    if expression:
+        body['expression'] = expression
+    
+    if delete_intermediate_output_files:
+        body['deleteIntermediateOutputFiles'] = delete_intermediate_output_files
+    
+    if use_reference_disks:
+        body['useReferenceDisks'] = use_reference_disks
+    
+    if memory_retry_multiplier:
+        body['memoryRetryMultiplier'] = memory_retry_multiplier
+
+    if per_workflow_cost_cap:
+        body['perWorkflowCostCap'] = per_workflow_cost_cap
+    
+    if workflow_failure_mode:
+        body['workflowFailureMode'] = workflow_failure_mode
+    
+    if user_comment:
+        body['userComment'] = user_comment
+
+    return __post(uri, json=body)
+
+def abort_submission(namespace, workspace, submission_id):
+    """Abort running job in a workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        submission_id (str): Submission's unique identifier
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/deleteSubmission
+    """
+    uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
+                                        workspace, submission_id)
+    return __delete(uri)
+
+def get_submission(namespace, workspace, submission_id):
+    """Request submission information.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        submission_id (str): Submission's unique identifier
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/monitorSubmission
+    """
+    uri = "workspaces/{0}/{1}/submissions/{2}".format(namespace,
+                                            workspace, submission_id)
+    return __get(uri)
+
+def get_workflow_metadata(namespace, workspace, submission_id, workflow_id,
+                          include_key=None, exclude_key=None,
+                          expand_sub_workflows=False):
+    """Request the metadata for a workflow in a submission.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        submission_id (str): Submission's unique identifier
+        workflow_id (str): Workflow's unique identifier.
+        include_key (array[str]): When specified, return only these keys in the
+            response. Matches any key in the response, including within nested
+            blocks. May not be used with exclude_key.
+        exclude_key (array[str]): When specified, omit these keys from the
+            response. Matches any key in the response, including within nested
+            blocks. May not be used with include_key.
+        expand_sub_workflows (bool): When true, metadata for sub workflows will
+            be fetched and inserted automatically in the metadata response.
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/workflowMetadata
+    """
+    uri = "workspaces/{0}/{1}/submissions/{2}/workflows/{3}".format(namespace,
+                                            workspace, submission_id, workflow_id)
+    params = {}
+    if include_key is not None:
+        params["includeKey"] = include_key
+    if exclude_key is not None:
+        params["excludeKey"] = exclude_key
+    if expand_sub_workflows:
+        params["expandSubWorkflows"] = expand_sub_workflows
+    return __get(uri, params=params)
+
+def get_workflow_outputs(namespace, workspace, submission_id, workflow_id):
+    """Request the outputs for a workflow in a submission.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        submission_id (str): Submission's unique identifier
+        workflow_id (str): Workflow's unique identifier.
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/workflowOutputsInSubmission
+    """
+    uri = "workspaces/{0}/{1}/".format(namespace, workspace)
+    uri += "submissions/{0}/workflows/{1}/outputs".format(submission_id,
+                                                            workflow_id)
+    return __get(uri)
+
+def get_workflow_cost(namespace, workspace, submission_id, workflow_id):
+    """Request the cost for a workflow in a submission.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        submission_id (str): Submission's unique identifier
+        workflow_id (str): Workflow's unique identifier.
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/workflowCostInSubmission
+    """
+    uri = "workspaces/{0}/{1}/".format(namespace, workspace)
+    uri += "submissions/{0}/workflows/{1}/cost".format(submission_id,
+                                                         workflow_id)
+    return __get(uri)
+
+def get_submission_queue():
+    """ List workflow counts by queueing state.
+
+    Swagger:
+        https://api.firecloud.org/#!/Submissions/workflowQueueStatus
+    """
+    return __get("submissions/queueStatus")
+
+#####################
+### 1.7 Workspaces
+#####################
+
+def list_workspaces(fields=None):
+    """Request list of FireCloud workspaces.
+
+    Args:
+        fields (str): a comma-delimited list of values that limits the
+            response payload to include only those keys and exclude other
+            keys (e.g., to include {"workspace": {"attributes": {...}}},
+            specify "workspace.attributes").
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/listWorkspaces
+    """
+    if fields is None:
+        return __get("workspaces")
+    else:
+        return __get("workspaces", params={"fields": fields})
+
+def get_storage_cost(namespace, workspace):
+    """Request average monthly storage cost for workspace.
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+    Swagger:
+        https://api.firecloud.org/#/WorkspacesV2/getStorageCostEstimateV2
+    """
+    uri = "workspaces/v2/{0}/{1}/storageCostEstimate".format(namespace, workspace)
+    return __get(uri)
+
+def get_bucket_usage(namespace, workspace):
+    """Request google bucket usage for workspace.
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+    """
+    return get_storage_cost(namespace, workspace)
+
+def create_workspace(namespace, name, authorizationDomain="", attributes=None,
+                     noWorkspaceOwner=False, bucketLocation=""):
+    """Create a new FireCloud Workspace.
+
+    Args:
+        namespace (str): The namespace (billing project) the workspace belongs to
+        name (str): The name of the workspace
+        authorizationDomain (str|list): The list of groups in the Authorization
+                                        Domain (empty if no AD is set)
+        attributes (dict): Workspace attributes as key value pairs
+        noWorkspaceOwner (bool): Optional, false if not specified. If true, the
+                                 workspace is created with a Billing Project
+                                 owner but no workspace owner. Requires being a
+                                 Billing Project owner.
+        bucketLocation (str): Region (NOT multi-region) in which bucket
+                              attached to the workspace should be created. If
+                              not provided, the bucket will be created in the
+                              'US' multi-region.
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/createWorkspace
+    """
+
+    if not attributes:
+        attributes = dict()
+
+    body = {
+        "namespace": namespace,
+        "name": name,
+        "attributes": attributes
+    }
+    
+    if authorizationDomain:
+        if isinstance(authorizationDomain, string_types):
+            authDomain = [{"membersGroupName": authorizationDomain}]
+        else:
+            authDomain = [{"membersGroupName": groupName} for groupName in authorizationDomain]
+    else:
+        authDomain = []
+
+    body["authorizationDomain"] = authDomain
+    
+    if noWorkspaceOwner:
+        body["noWorkspaceOwner"] = noWorkspaceOwner
+        
+    if bucketLocation:
+        body["bucketLocation"] = bucketLocation
+
+    return __post("workspaces", json=body)
+
+def delete_workspace(namespace, workspace):
+    """Delete FireCloud Workspace.
+
+    Note: This action is not reversible. Be careful!
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/deleteWorkspace
+    """
+    uri = "workspaces/{0}/{1}".format(namespace, workspace)
+    return __delete(uri)
+
+def get_workspace(namespace, workspace, fields=None):
+    """Request FireCloud Workspace information.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        fields (str): a comma-delimited list of values that limits the
+            response payload to include only those keys and exclude other
+            keys (e.g., to include {"workspace": {"attributes": {...}}},
+            specify "workspace.attributes").
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/getWorkspace
+    """
+    uri = "workspaces/{0}/{1}".format(namespace, workspace)
+    if fields is None:
+        return __get(uri)
+    else:
+        return __get(uri, params={"fields": fields})
+
+def get_workspace_acl(namespace, workspace):
+    """Request FireCloud access aontrol list for workspace.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/getWorkspaceAcl
+    """
+    uri = "workspaces/{0}/{1}/acl".format(namespace, workspace)
+    return __get(uri)
+
+def update_workspace_acl(namespace, workspace, acl_updates, invite_users_not_found=False):
+    """Update workspace access control list.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        acl_updates (list(dict)): Acl updates as dicts with two keys:
+            "email" - Firecloud user email
+            "accessLevel" - one of "OWNER", "READER", "WRITER", "NO ACCESS"
+            Example: {"email":"user1@mail.com", "accessLevel":"WRITER"}
+        invite_users_not_found (bool): true to invite unregistered users, false to ignore
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/updateWorkspaceACL
+    """
+    uri = "{0}workspaces/{1}/{2}/acl?inviteUsersNotFound={3}".format(fcconfig.root_url,
+                                                namespace, workspace, str(invite_users_not_found).lower())
+    headers = _fiss_agent_header({"Content-type":  "application/json"})
+    # FIXME: create __patch method, akin to __get, __delete etc
+    return __SESSION.patch(uri, headers=headers, data=json.dumps(acl_updates))
+
+def clone_workspace(from_namespace, from_workspace, to_namespace, to_workspace,
+                    authorizationDomain="", copyFilesWithPrefix=None, bucketLocation=None):
+    """Clone a FireCloud workspace.
+
+    A clone is a shallow copy of a FireCloud workspace, enabling
+    easy sharing of data, such as TCGA data, without duplication.
+
+    Args:
+        from_namespace (str):  project (namespace) to which source workspace belongs
+        from_workspace (str): Source workspace's name
+        to_namespace (str):  project to which target workspace belongs
+        to_workspace (str): Target workspace's name
+        authorizationDomain: (str) required authorization domains
+        copyFilesWithPrefix: (str) prefix of bucket objects to copy to the destination workspace
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/cloneWorkspace
+    """
+
+    if authorizationDomain:
+        if isinstance(authorizationDomain, string_types):
+            authDomain = [{"membersGroupName": authorizationDomain}]
+        else:
+            authDomain = [{"membersGroupName": authDomain} for authDomain in authorizationDomain]
+    else:
+        authDomain = []
+
+    body = {
+        "namespace": to_namespace,
+        "name": to_workspace,
+        "attributes": dict(),
+        "authorizationDomain": authDomain,
+    }
+    
+    if copyFilesWithPrefix is not None:
+        body["copyFilesWithPrefix"] = copyFilesWithPrefix
+    if bucketLocation is not None:
+        body["bucketLocation"] = bucketLocation
+
+    uri = "workspaces/{0}/{1}/clone".format(from_namespace, from_workspace)
+    return __post(uri, json=body)
+
+def lock_workspace(namespace, workspace):
+    """Lock FireCloud workspace, making it read-only.
+
+    This prevents modifying attributes or submitting workflows
+    in the workspace. Can be undone with unlock_workspace()
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/lockWorkspace
+    """
+    uri = "workspaces/{0}/{1}/lock".format(namespace, workspace)
+    return __put(uri)
+
+def unlock_workspace(namespace, workspace):
+    """Unlock FireCloud workspace.
+
+    Enables modifications to a workspace. See lock_workspace()
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/unlockWorkspace
+    """
+    uri = "workspaces/{0}/{1}/unlock".format(namespace, workspace)
+    return __put(uri)
+
+def update_workspace_attributes(namespace, workspace, attrs):
+    """Update or remove workspace attributes.
+
+    Args:
+        namespace (str): project to which workspace belongs
+        workspace (str): Workspace name
+        attrs (list(dict)): List of update operations for workspace attributes.
+            Use the helper dictionary construction functions to create these:
+
+            _attr_set()       : Set/Update attribute
+            _attr_rem()       : Remove attribute
+            _attr_ladd()      : Add member to list attribute
+            _attr_lrem()      : Remove member from list attribute
+            _attr_vlcreate()  : Create a value-list attribute
+            _attr_erlcreate() : Create an entity-reference list attribute
+
+    Swagger:
+        https://api.firecloud.org/#!/Workspaces/updateAttributes
+    """
+    headers = _fiss_agent_header({"Content-type":  "application/json"})
+    uri = "{0}workspaces/{1}/{2}/updateAttributes".format(fcconfig.root_url,
+                                                        namespace, workspace)
+    body = json.dumps(attrs)
+
+    # FIXME: create __patch method, akin to __get, __delete etc
+    return __SESSION.patch(uri, headers=headers, data=body)
+
+# Helper functions to create attribute update dictionaries
+
+def _attr_set(attr, value):
+    """Create an 'update' dictionary for update_workspace_attributes() and
+    update_entity()"""
+    return {
+        "op"                 : "AddUpdateAttribute",
+        "attributeName"      : attr,
+        "addUpdateAttribute" : value
+   }
+
+def _attr_rem(attr):
+    """Create a 'remove' dictionary for update_workspace_attributes() and
+    update_entity()"""
+    return {
+        "op"             : "RemoveAttribute",
+        "attributeName"  : attr
+    }
+
+def _attr_ladd(attr, value):
+    """Create a 'list add' dictionary for update_workspace_attributes() and
+    update_entity()"""
+    return {
+        "op"                : "AddListMember",
+        "attributeListName" : attr,
+        "newMember"         : value
+    }
+
+def _attr_lrem(attr, value):
+    """Create a 'list remove' dictionary for update_workspace_attributes() and
+    update_entity()"""
+    return {
+        "op"                : "RemoveListMember",
+        "attributeListName" : attr,
+        "removeMember"      : value,
+    }
+
+def _attr_vlcreate(attr):
+    """Create a 'value-list create' dict for update_workspace_attributes() and
+    update_entity()"""
+    return {
+        "op"            : "CreateAttributeValueList",
+        "attributeName" : attr
+    }
+
+def _attr_erlcreate(attr):
+    """Create a 'entity-reference list create' dictionary for
+       update_workspace_attributes() and update_entity()"""
+    return {
+        "op"                : "CreateAttributeEntityReferenceList",
+        "attributeListName" : attr
+    }
+
+#####################
+### 1.8 Groups
+#####################
+
+def get_groups():
+    """Get the list of the groups that the caller is a member of
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/getGroups
+    """
+    return __get('groups')
+
+def get_group(group):
+    """View the members in a group (must be an Admin of the group)
+
+    Args:
+        group (str): Group name
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/getGroup
+    """
+    uri = "groups/{0}".format(group)
+    return __get(uri)
+
+def delete_group(group):
+    """Delete a group that the caller owns
+
+    Args:
+        group (str): Group name
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/deleteGroup
+    """
+    uri = "groups/{0}".format(group)
+    return __delete(uri)
+
+def create_group(group):
+    """Create a new group
+
+    Args:
+        group (str): Group name
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/createGroup
+    """
+    uri = "groups/{0}".format(group)
+    return __post(uri)
+
+def add_user_to_group(group, role, email):
+    """Add a user to a group the caller owns
+
+    Args:
+        group (str): Group name
+        role (str) : Role of user for group; either 'member' or 'admin'
+        email (str): Email of user or group to add
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/addUserToGroup
+    """
+    uri = "groups/{0}/{1}/{2}".format(group, role, email)
+    return __put(uri)
+
+def remove_user_from_group(group, role, email):
+    """Remove a user from a group the caller owns
+
+    Args:
+        group (str): Group name
+        role (str) : Role of user for group; either 'member' or 'admin'
+        email (str): Email of user or group to remove
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/removeUserFromGroup
+    """
+    uri = "groups/{0}/{1}/{2}".format(group, role, email)
+    return __delete(uri)
+
+def request_access_to_group(group):
+    """Request access to a group
+
+    Args:
+        group (str): Group name
+    
+    Swagger:
+        https://api.firecloud.org/#!/Groups/requestAccessToGroup
+    """
+    uri = "groups/{0}/requestAccess".format(group)
+    return __post(uri)