Merge branch 'sub_queue_and_find_py_venv' into release-0.15.3

Author: sammeier

firecloud/api.py

@@ -273,6 +273,7 @@ def get_entity(namespace, workspace, etype, ename, api_root=PROD_API_ROOT):
                         api_root, namespace, workspace, etype, ename)
     return __get(uri)
 
+
 def delete_entities(namespace, workspace, json_body, api_root=PROD_API_ROOT):
     """Delete entities in a workspace.
 
@@ -812,7 +813,7 @@ def update_repository_method(namespace, method, synopsis,
 
 def delete_repository_method(namespace, name, snapshot_id,
                              api_root=PROD_API_ROOT):
-    """Redact a version of a workflow.
+    """Redacts a method and all of its associated configurations.
 
     The method should exist in the methods repository.
 
@@ -823,10 +824,27 @@ def delete_repository_method(namespace, name, snapshot_id,
         api_root (str): FireCloud API url, if not production
 
     Swagger:
-        UNDOCUMENTED
+        https://api.firecloud.org/#!/Method_Repository/delete_api_methods_namespace_name_snapshotId
     """
-    uri = "{0}/methods/{1}/{2}/{3}".format(api_root, namespace,
-                                           name, snapshot_id)
+    uri = "{0}/methods/{1}/{2}/{3}".format(api_root, namespace, name, snapshot_id)
+    return __delete(uri)
+
+def delete_repository_config(namespace, name, snapshot_id,
+                             api_root=PROD_API_ROOT):
+    """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
+        api_root (str): FireCloud API url, if not production
+
+    Swagger:
+        https://api.firecloud.org/#!/Method_Repository/delete_api_configurations_namespace_name_snapshotId
+    """
+    uri = "{0}/configurations/{1}/{2}/{3}".format(api_root, namespace, name, snapshot_id)
     return __delete(uri)
 
 def get_repository_method_acl(namespace, method,
@@ -1089,7 +1107,7 @@ def list_workspaces(api_root=PROD_API_ROOT):
     """
     return __get(api_root+ "/workspaces")
 
-def create_workspace(namespace, name, protected=False,
+def create_workspace(namespace, name, authorizationDomain = "",
                      attributes=None, api_root=PROD_API_ROOT):
     """Create a new FireCloud Workspace.
 
@@ -1108,12 +1126,15 @@ def create_workspace(namespace, name, protected=False,
     uri = "{0}/workspaces".format(api_root)
     if not attributes:
         attributes = dict()
+    
     body = {
         "namespace": namespace,
         "name": name,
-        "attributes": attributes,
-        "isProtected": protected
+        "attributes": attributes        
     }
+    if authorizationDomain:
+        body["authorizationDomain"] = {"membersGroupName": authorizationDomain}
+
     return __post(uri, json=body)
 
 def delete_workspace(namespace, workspace,api_root=PROD_API_ROOT):

firecloud/fiss.py

@@ -84,7 +84,7 @@ def space_lock(args):
 def space_new(args):
     """ Create a new workspace. """
     r = fapi.create_workspace(args.project, args.workspace,
-                                 args.protected, dict(), args.api_url)
+                                 args.authdomain, dict(), args.api_url)
     fapi._check_response_code(r, 201)
     print_('Created workspace {0}/{1}'.format(args.project, args.workspace))
     if fapi.get_verbosity():
@@ -1528,9 +1528,9 @@ def main(argv=None):
     # Create Workspace
     subp = subparsers.add_parser('space_new', parents=[workspace_parent],
                                         description='Create new workspace')
-    phelp = 'Create a protected (dbGaP-controlled) workspace.'
-    phelp += 'You must have linked NIH credentials for this option.'
-    subp.add_argument('--protected', action='store_true', help=phelp)
+    phelp = 'Limit access to the workspace to a specific authorization domain. '
+    phelp += 'For dbGaP-controlled access (domain name: dbGapAuthorizedUsers) you must have linked NIH credentials to your account.'
+    subp.add_argument('--authdomain', default="", help=phelp)
     subp.set_defaults(func=space_new)
 
     # Determine existence of workspace

firecloud/tests/highlevel_tests.py

@@ -13,16 +13,22 @@
 
 # Context manager to capture stdout when calling another function
 # Source: http://stackoverflow.com/questions/16571150/how-to-capture-stdout-output-from-a-python-function-call
-from cStringIO import StringIO
+# from cStringIO import StringIO
+# replace cStringIO with StringIO for python3 compatibility
+from io import StringIO
 import sys
+import ast
 
 class Capturing(list):
     def __enter__(self):
         self._stdout = sys.stdout
         sys.stdout = self._stringio = StringIO()
         return self
     def __exit__(self, *args):
-        self.extend(self._stringio.getvalue().splitlines())
+        if sys.version_info[0] < 3:
+            self.extend(self._stringio.getvalue().splitlines())
+        else:
+            self.extend(ast.literal_eval(self._stringio.getvalue()).decode().splitlines())
         del self._stringio    # free up some memory
         sys.stdout = self._stdout
 

firecloud/tests/lowlevel_tests.py

@@ -233,10 +233,11 @@ def test_get_submission(self):
         """Test get_submission()."""
         pass
 
-    @unittest.skip("Not Implemented")
     def test_get_submission_queue(self):
         """Test get_submission_queue()."""
-        pass
+        r =  fapi.get_submission_queue()
+        print_(r.status_code, r.content)
+        self.assertEqual(r.status_code, 200)
 
     @unittest.skip("Not Implemented")
     def test_get_workflow_outputs(self):

setup.py

@@ -27,6 +27,7 @@
         'requests',
         'six',
         'yapsy',
+        'nose',
         'pylint==1.7.1'
     ],
     classifiers = [

util/findPython.sh

@@ -1,36 +1,42 @@
 #!/bin/bash
 
-# findPython.sh: help determine installation location for this package,
-#                by identifying existing candidate Python installations
+# config.sh: Help determine installation location for gdctools package,
+#            by identifying existing Python installations as candidates.
 
 InstallDir=
 
-# Use any Python3 installation, or Python2 if >= 2.7
-Python=`type -P python`
-if [ -n "$Python" ] ; then
-    case `python --version 2>&1 | awk '{print $NF}'` in
-        2.7*| 3.*)
-            InstallDir=`dirname $Python`
-            InstallDir=`dirname $InstallDir`
-            ;;
-    esac
+if [ -n "$1" ] ; then
+    PythonExe=$1
+    shift
+else
+    PythonExe=python
 fi
 
+# For convenience, give precedence to well-known directories @ Broad Institute
+BroadDirs="/local/firebrowse/latest /xchip/tcga/Tools/gdac/latest"
+for dir in $BroadDirs ; do
+    if [ -d $dir ] ; then
+        InstallDir=$dir
+        break
+    fi
+done
+
 if [ -z "$InstallDir" ] ; then
-    # Nothing found: for convenience, look for well-known dirs @ Broad Institute
-    BroadDirs="/local/firebrowse/latest /xchip/tcga/Tools/gdac/latest"
-    for dir in $BroadDirs ; do
-        if [ -d $dir ] ; then
-            InstallDir=$dir
-            break
-        fi
-    done
+    if [ -n "$VIRTUAL_ENV" ] ; then
+      InstallDir=$VIRTUAL_ENV
+    else
+      Python=`type -P $PythonExe`
+      if [ -n "$Python" ]; then
+        InstallDir=`dirname $Python`
+        InstallDir=`dirname $InstallDir`
+      fi
+    fi
 fi
 
 if [ -z "$InstallDir" ] ; then
-    echo "Error: could not find an appropriate python installation to use" >&2
+    echo "Error: could not find a $PythonExe installation to use" >&2
     exit 1
 fi
 
 echo "$InstallDir"
-exit 0
+exit 0