From b1bbfa832199611ad7e9df7c8077ad93b508df4d Mon Sep 17 00:00:00 2001
From: Nathaniel Kofalt <nathaniel@kofalt.com>
Date: Wed, 7 Sep 2016 14:53:12 -0500
Subject: [PATCH] Add gear suggestion endpoint
---
api/api.py | 1 +
api/dao/containerstorage.py | 14 ++++++++++++++
api/jobs/gears.py | 31 +++++++++++++++++++++++++++++--
api/jobs/handlers.py | 18 +++++++++++++++---
4 files changed, 59 insertions(+), 5 deletions(-)
diff --git a/api/api.py b/api/api.py
index dee8d8e5..b2d19c3a 100644
--- a/api/api.py
+++ b/api/api.py
@@ -125,6 +125,7 @@ routes = [
webapp2_extras.routes.PathPrefixRoute(r'/api/gears', [
webapp2.Route(r'/<:[^/]+>', GearHandler),
webapp2.Route(r'/<:[^/]+>/invocation', GearHandler, handler_method='get_invocation'),
+ webapp2.Route(r'/<:[^/]+>/suggest/<:[^/]+>/<:[^/]+>', GearHandler, handler_method='suggest'),
]),
webapp2.Route(r'/api/rules', RulesHandler),
webapp2.Route(r'/api/groups', grouphandler.GroupHandler, handler_method='get_all', methods=['GET']),
diff --git a/api/dao/containerstorage.py b/api/dao/containerstorage.py
index 175b9f26..37105127 100644
--- a/api/dao/containerstorage.py
+++ b/api/dao/containerstorage.py
@@ -122,3 +122,17 @@ class GroupStorage(ContainerStorage):
},
upsert=True)
+def inflate_container(cr):
+ """
+ Given a container reference, inflate its hierarchy into a map.
+ Eeventually, this might want to deduplicate with logic in hierarchy.py.
+ """
+
+ if cr.type != 'session':
+ raise Exception('Only sessions are supported for inflation right now')
+
+ oid = bson.ObjectId(cr.id)
+ root = ContainerStorage('sessions', True).exec_op('GET', oid, projection={'permissions': 0})
+ root['acquisitions'] = ContainerStorage('acquisitions', True).exec_op('GET', query={'session': oid}, projection={'permissions': 0})
+
+ return root
diff --git a/api/jobs/gears.py b/api/jobs/gears.py
index f236370b..664573f0 100644
--- a/api/jobs/gears.py
+++ b/api/jobs/gears.py
@@ -2,10 +2,15 @@
Gears
"""
+import bson.objectid
+import jsonschema
+from jsonschema import Draft4Validator
+import gear_tools
+
from .. import config
from .jobs import Job
+from ..dao.containerstorage import inflate_container
-import gear_tools
log = config.log
@@ -51,9 +56,31 @@ def get_gear_by_name(name):
# Mongo returns the full document: { '_id' : 'gears', 'gear_list' : [ { .. } ] }, so strip that out
return gear_doc[SINGLETON_KEY][0]
-def get_invocation(gear):
+def get_invocation_schema(gear):
return gear_tools.derive_invocation_schema(gear['manifest'])
+def suggest_container(gear, cr):
+ """
+ Given a container reference, suggest files that would work well for each input on a gear.
+ """
+
+ root = inflate_container(cr)
+ invocation_schema = get_invocation_schema(gear)
+
+ schemas = {}
+ for x in gear['manifest']['inputs']:
+ schema = gear_tools.isolate_file_invocation(invocation_schema, x)
+ schemas[x] = Draft4Validator(schema)
+
+ # It would be nice to have use a visitor here instead of manual key loops.
+ for acq in root['acquisitions']:
+ for f in acq.get('files', []):
+ f['suggested'] = {}
+ for x in schemas:
+ f['suggested'][x] = schemas[x].is_valid({})
+
+ return root
+
def insert_gear(doc):
config.db.singletons.update(
{"_id" : "gears"},
diff --git a/api/jobs/handlers.py b/api/jobs/handlers.py
index b7a52de9..a2ab54a1 100644
--- a/api/jobs/handlers.py
+++ b/api/jobs/handlers.py
@@ -5,11 +5,11 @@ API request handlers for the jobs module
import json
import StringIO
-from ..dao.containerutil import create_filereference_from_dictionary, create_containerreference_from_dictionary, create_containerreference_from_filereference
+from ..dao.containerutil import create_filereference_from_dictionary, create_containerreference_from_dictionary, create_containerreference_from_filereference, ContainerReference
from .. import base
from .. import config
-from .gears import get_gears, get_gear_by_name, get_invocation, remove_gear, upsert_gear
+from .gears import get_gears, get_gear_by_name, get_invocation_schema, remove_gear, upsert_gear, suggest_container
from .jobs import Job
from .queue import Queue
@@ -47,7 +47,19 @@ class GearHandler(base.RequestHandler):
self.abort(403, 'Request requires login')
gear = get_gear_by_name(_id)
- return get_invocation(gear)
+ return get_invocation_schema(gear)
+
+ def suggest(self, _id, cont_name, cid):
+
+ if self.public_request:
+ self.abort(403, 'Request requires login')
+
+ cr = ContainerReference(cont_name, cid)
+ if not self.superuser_request:
+ cr.check_access(self.uid, 'ro')
+
+ gear = get_gear_by_name(_id)
+ return suggest_container(gear, cr)
def post(self, _id):
"""Upsert an entire gear document."""
--
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