Save searches

api/api.py

@@ -13,6 +13,7 @@
 from .handlers.reporthandler        import ReportHandler
 from .handlers.resolvehandler       import ResolveHandler
 from .handlers.roothandler          import RootHandler
+from .handlers.savesearchhandler   import SaveSearchHandler
 from .handlers.schemahandler        import SchemaHandler
 from .handlers.userhandler          import UserHandler
 from .jobs.handlers                 import BatchHandler, JobsHandler, JobHandler, GearsHandler, GearHandler, RulesHandler, RuleHandler
@@ -109,6 +110,12 @@ def prefix(path, routes):
         route('/dataexplorer/search/nodes',             DataExplorerHandler,   h='get_nodes',              m=['POST']),
         route('/dataexplorer/index/fields',             DataExplorerHandler,   h='index_field_names',      m=['POST']),
 
+        # Search Saving
+        route('/savesearches',                            SaveSearchHandler,                                m=['POST']),
+        route('/savesearches',                            SaveSearchHandler,     h='get_all',               m=['GET']),
+        route('/savesearches/<sid:{cid}>',                SaveSearchHandler,                                m=['GET','DELETE']),
+        route('/savesearches/<sid:{cid}>',                SaveSearchHandler,     h='replace_search',        m=['POST']),
+
         # Users
 
         route( '/users',                   UserHandler, h='get_all', m=['GET']),
@@ -233,7 +240,7 @@ def prefix(path, routes):
 
         # Collections / Projects
 
-        prefix('/<cont_name:collections|projects>', [
+        prefix('/<cont_name:collections|projects|savesearches>', [
             prefix('/<cid:{cid}>', [
                 route('/<list_name:permissions>',                          PermissionsListHandler, m=['POST']),
                 route('/<list_name:permissions>/<_id:{uid}>',              PermissionsListHandler, m=['GET', 'PUT', 'DELETE']),

api/config.py

@@ -172,6 +172,7 @@ def apply_env_variables(config):
     'project-update.json',
     'rule-new.json',
     'rule-update.json',
+    'search-input.json',
     'session.json',
     'session-update.json',
     'subject.json',
@@ -228,6 +229,7 @@ def initialize_db():
     # TODO review all indexes
     db.users.create_index('api_key.key')
     db.projects.create_index([('gid', 1), ('name', 1)])
+    db.savesearches.create_index('creator')
     db.sessions.create_index('project')
     db.sessions.create_index('uid')
     db.sessions.create_index('created')

api/dao/containerstorage.py

@@ -1,5 +1,5 @@
 import datetime
-
+import pymongo
 import bson
 import copy
 
@@ -10,7 +10,7 @@
 from ..jobs.jobs import Job
 from ..jobs.queue import Queue
 from ..jobs.rules import copy_site_rules_for_project
-from ..web.errors import APIStorageException, APINotFoundException
+from ..web.errors import APIStorageException, APINotFoundException, APIConflictException
 from .basecontainerstorage import ContainerStorage
 
 log = config.log
@@ -434,3 +434,19 @@ def inflate_job_info(self, analysis):
 
         analysis['job'] = job
         return analysis
+
+class SearchStorage(ContainerStorage):
+
+    def __init__(self):
+        super(SearchStorage, self).__init__('savesearches', use_object_id=True)
+
+    def create_el(self, payload):
+        try:
+            result = self.dbc.insert_one(payload)
+        except pymongo.errors.DuplicateKeyError:
+            raise APIConflictException('Object with id {} already exists.'.format(payload['_id']))
+        return result
+
+    def replace_el(self, search):
+        self.delete_el(search['_id'])
+        return self.create_el(search)

api/dao/containerutil.py

@@ -17,6 +17,7 @@
     'project':     'projects',
     'session':     'sessions',
     'user':        'users',
+    'savesearch':  'savesearches',
 }
 PLURAL_TO_SINGULAR = {p: s for s, p in SINGULAR_TO_PLURAL.iteritems()}
 

api/handlers/listhandler.py

@@ -82,6 +82,7 @@ def initialize_list_configurations():
         'acquisitions': copy.deepcopy(container_default_configurations),
         'collections': copy.deepcopy(container_default_configurations),
         'analyses': copy.deepcopy(container_default_configurations),
+        'savesearches': copy.deepcopy(container_default_configurations),
     }
     # preload the Storage instances for all configurations
     for cont_name, cont_config in list_container_configurations.iteritems():

api/handlers/savesearchhandler.py

@@ -0,0 +1,99 @@
+import bson
+from ast import literal_eval
+from ..web import base
+from .. import config, validators
+from ..auth import require_login
+from ..dao.containerstorage import SearchStorage
+
+from ..auth import groupauth
+from ..dao import noop
+
+
+log = config.log
+storage = SearchStorage()
+
+
+def string_filters(payload):
+	if payload.get('search') and payload['search'].get('filters'):
+		filters = []
+		for filter_ in payload['search'].get('filters',[]):
+			filters.append(str(filter_))
+		payload['search']['filters'] = filters
+	return payload
+
+def unstring_filters(payload):
+	if payload['search'].get('filters'):
+		filters= []
+		for filter_ in payload['search'].get('filters',[]):
+			filters.append(literal_eval(filter_))
+		payload['search']['filters']= filters
+	return payload
+
+class SaveSearchHandler(base.RequestHandler):
+
+	def __init__(self, request=None, response=None):
+		super(SaveSearchHandler, self).__init__(request, response)
+
+	@require_login
+	def post(self):
+		payload = self.request.json_body
+		validators.validate_data(payload, 'search-input.json', 'input', 'POST')
+		payload = string_filters(payload)
+		payload['permissions'] = [{"_id": self.uid, "access": "admin"}]
+		payload['creator'] = self.uid
+		result = storage.create_el(payload)
+		if result.acknowledged:
+			if result.inserted_id:
+				return {'_id': result.inserted_id}
+		else:
+			self.abort(404, 'Search not created')
+
+	def get_all(self):
+		log.debug(self.uid)
+		return storage.get_all_el({}, {'_id': self.uid}, {'label': 1})
+
+	def get(self, sid):
+		result = storage.get_el(sid)
+		if result is None:
+			self.abort(404, 'Element {} not found'.format(sid))
+		unstring_filters(result)
+		return result
+
+	def delete(self, sid):
+		search = storage.get_container(sid)
+		permchecker = groupauth.default(self, search)
+		result = permchecker(storage.exec_op)('DELETE', sid)
+		if result.deleted_count == 1:
+			return {'deleted': result.deleted_count}
+		else:
+			self.abort(404, 'Group {} not removed'.format(sid))
+		return result
+
+	def replace_search(self, sid):
+		payload = self.request.json_body
+		payload = self._scrub_replace(payload)
+		validators.validate_data(payload, 'search-input.json', 'input', 'POST')
+		payload = string_filters(payload)
+		payload['_id'] = bson.ObjectId(sid)
+		search = storage.get_container(sid)
+		payload['permissions'] = search['permissions']
+		permchecker = groupauth.default(self, search)
+		permchecker(noop)('DELETE', sid)
+		result = storage.replace_el(payload)
+		if result.acknowledged:
+			if result.inserted_id:
+				return {'_id': result.inserted_id}
+		return {"hi" : "bye"}
+
+	def _scrub_replace(self, payload):
+		'''
+		Function to turn a search returned from a GET to a legal post/replace
+		'''
+		if payload.get('_id'):
+			del(payload['_id'])
+		if payload.get('permissions'):
+			del(payload['permissions'])
+		if payload.get('creator'):
+			del(payload['creator'])
+		return payload
+

raml/api.raml

@@ -55,3 +55,4 @@ resourceTypes:
 /acquisitions: !include resources/acquisitions.raml
 /projects: !include resources/projects.raml
 /report: !include resources/report.raml
+/savesearches: !include resources/savesearch.raml

raml/examples/input/search-input.json

@@ -0,0 +1,7 @@
+{
+"search": {
+	"return_type": "file",
+	"filters": [{"terms": {"file.type":["nifti"]}}]
+},
+"label" : "Test Search"
+}

raml/examples/output/search-list.json

@@ -0,0 +1,4 @@
+[{
+	"label": "Test Search",
+	"_id": "57e452791cff88b85f9f9c23"
+}]

raml/examples/output/search-output.json

@@ -0,0 +1,10 @@
+{
+	"label": "Test Search",
+	"_id": "57e452791cff88b85f9f9c23",
+	"search": {
+		"return_type": "file",
+		"filters": [{"terms": {"file.type":["nifti"]}}]
+	},
+	"permissions": [{"access": "admin", "_id": "[email protected]"}],
+	"creator": "[email protected]"
+}

raml/resources/savesearch.raml

@@ -0,0 +1,38 @@
+type: container
+get:
+  description: List all saved searches user has access to.
+  responses:
+    200:
+      body:
+        application/json:
+          example: !include ../examples/output/search-list.json
+          schema: !include ../schemas/output/search-list.json
+post:
+  body:
+    application/json:
+      schema: !include ../schemas/input/search-input.json
+/{SearchId}:
+  type: container
+  get:
+    responses:
+      200:
+        body:
+          application/json:
+            schema: !include ../schemas/output/search-output.json
+  post:
+    description: Replace saved search with a new search
+    body:
+          application/json:
+            schema: !include ../schemas/input/search-input.json
+  /permissions:
+    type: permissions-list
+    /{UserId}:
+      type: permissions-item
+  delete:
+    description: Delete a saved search
+    responses:
+      200:
+        body:
+          application/json:
+            schema: !include ../schemas/output/container-delete.json
+            example: !include ../examples/output/container-delete.json

raml/schemas/definitions/search.json

@@ -0,0 +1,46 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "definitions":{
+        "filter" : {
+          "type" :  "object"
+
+        },
+        "search" : {
+          "type": "object",
+          "properties": {
+            "filters": {
+                "type" :      "array",
+                "items" :     {"$ref": "#/definitions/filter"}
+            },
+            "search_string":  {"type" : "string"},
+            "all_data":       {"type": "boolean"},
+            "return_type":    {"enum": ["session", "acquisition", "analysis", "file"]}
+          },
+          "additionalProperties": false,
+          "required": ["return_type"]
+        },
+        "search-input":{
+          "type":       "object",
+          "properties": {
+            "label": {"$ref": "../definitions/container.json#/definitions/label"},
+            "search": {"$ref": "#/definitions/search"}
+          },
+          "additionalProperties": false
+        },
+        "search-output":{
+          "type":         "object",
+          "properties": {
+            "_id":          {"$ref":"../definitions/objectid.json#"},
+            "label":        {"$ref": "../definitions/container.json#/definitions/label"},
+            "creator":          {"$ref":"../definitions/container.json#/definitions/uid"},
+            "created":      {"$ref":"../definitions/created-modified.json#/definitions/created"},
+            "modified":     {"$ref":"../definitions/created-modified.json#/definitions/modified"},
+            "permissions":  {
+                "type":"array",
+                "items":{"$ref":"../definitions/permission.json#/definitions/permission-output-default-required"}
+            },
+            "search":       {"$ref":"#/definitions/search"}    
+          }
+        }
+    }
+}

raml/schemas/input/search-input.json

@@ -0,0 +1,6 @@
+{
+	"$schema": "http://json-schema.org/draft-04/schema#",
+    "title": "Search",
+    "type": "object",
+	"allOf":[{"$ref":"../definitions/search.json#/definitions/search-input"}]
+}

raml/schemas/output/search-list.json

@@ -0,0 +1,11 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"array",
+    "items":{
+        "type":"object",
+        "allOf":[{"$ref":"../definitions/search.json#/definitions/search-output"}],
+        "required":[
+            "_id", "label"
+        ]
+    }
+}

raml/schemas/output/search-output.json

@@ -0,0 +1,8 @@
+{
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type":"object",
+    "allOf":[{"$ref":"../definitions/search.json#/definitions/search-output"}],
+    "required":[
+        "_id", "label", "permissions", "search"
+    ]
+}