Merge branch 'develop' of https://github.com/parklab/refinery-platform …

…into develop

Vagrantfile

@@ -15,7 +15,7 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
   config.vm.network "private_network", ip: "192.168.50.50"
 
   config.vm.provider "virtualbox" do |v|
-    v.memory = 1280
+    v.memory = 1024
     v.cpus = 1
   end
 

refinery/core/api.py

@@ -12,7 +12,8 @@
 from sets import Set
 from django.conf.urls.defaults import url
 from django.contrib.auth.models import User, Group
-from guardian.shortcuts import get_objects_for_user, get_objects_for_group
+from guardian.shortcuts import get_objects_for_user, get_objects_for_group, \
+    get_perms
 from tastypie import fields
 from tastypie.authentication import SessionAuthentication, Authentication
 from tastypie.authorization import Authorization
@@ -241,8 +242,8 @@ def res_sharing(self, request, **kwargs):
         if request.method == 'GET':
             kwargs['sharing'] = True
             return self.process_get(request, res, **kwargs)
-        elif request.method == 'PATCH':
-            data = json.loads(request.raw_post_data)
+        elif request.method == 'PUT':
+            data = json.loads(request.body)
             new_share_list = data['share_list']
 
             groups_shared_with = map(

refinery/core/models.py

@@ -251,8 +251,6 @@ def share(self, group, readonly=True):
         if not readonly:
             assign_perm('change_%s' % self._meta.verbose_name, group, self)
 
-        resource_shared.send(sender=self)
-
     def unshare(self, group):
         remove_perm('read_%s' % self._meta.verbose_name, group, self)
         remove_perm('change_%s' % self._meta.verbose_name, group, self)
@@ -286,6 +284,16 @@ def get_groups(self, changeonly=False, readonly=False):
 
         return groups
 
+    def get_group_ids(self, changeonly=False, readonly=False):
+        groups = get_groups_with_perms(self)
+
+        ids = []
+
+        for group in groups:
+            ids.append(group.id)
+
+        return ids
+
     # TODO: clean this up
     def is_public(self):
         permissions = get_groups_with_perms(self, attach_perms=True)
@@ -305,13 +313,6 @@ class Meta:
         abstract = True
 
 
-def print_shared(sender, **kwargs):
-    logger.info("Sharable Resouce has been shared with sender: %s" % sender)
-
-resource_shared = Signal()
-resource_shared.connect(print_shared)
-
-
 class TemporaryResource:
     '''Mix-in class for temporary resources like NodeSet instances.
 
@@ -487,6 +488,24 @@ def get_file_size(self):
 
         return file_size
 
+    def share(self, group, readonly=True):
+        super(DataSet, self).share(group, readonly)
+        # This might be a hack but I couldn't find an easier solution to about
+        # the import loop. I found this solution here
+        # http://stackoverflow.com/a/7199514/981933
+        from core.search_indexes import DataSetIndex
+        logger.info("Re-index / update data set: %s", self)
+        DataSetIndex().update_object(self, using='core')
+
+    def unshare(self, group):
+        super(DataSet, self).unshare(group)
+        # This might be a hack but I couldn't find an easier solution to about
+        # the import loop. I found this solution here
+        # http://stackoverflow.com/a/7199514/981933
+        from core.search_indexes import DataSetIndex
+        logger.info("Re-index / update data set: %s", self)
+        DataSetIndex().update_object(self, using='core')
+
 
 class InvestigationLink(models.Model):
     data_set = models.ForeignKey(DataSet)

refinery/core/search_indexes.py

@@ -18,10 +18,6 @@
 
 class DataSetIndex(indexes.SearchIndex, indexes.Indexable):
     text = indexes.CharField(document=True, use_template=True)
-    # id of the user who owns this project
-    owner_id = indexes.CharField()
-    # ids of the groups who have read permission for this data set
-    group_ids = indexes.MultiValueField(null=True)
     name = indexes.CharField(model_attr='name', null=True)
     title = indexes.CharField(null=True)
     uuid = indexes.CharField(model_attr='uuid')
@@ -34,6 +30,10 @@ class DataSetIndex(indexes.SearchIndex, indexes.Indexable):
     measurement = indexes.MultiValueField(null=True, faceted=True)
     technology = indexes.MultiValueField(null=True, faceted=True)
 
+    # We only need one multi value field to story every id that has access since
+    # Solr only handles read permissions.
+    access = indexes.MultiValueField(null=True)
+
     # We add this for autocomplete.
     content_auto = indexes.EdgeNgramField(null=True)
 
@@ -53,14 +53,13 @@ def prepare_title(self, object):
     def prepare_content_auto(self, object):
         return object.get_investigation().get_title()
 
-    def prepare_owner_id(self, object):
-        if object.get_owner() is None:
-            return None
-
-        return object.get_owner().id
-
-    def prepare_group_ids(self, object):
-        return [g["id"] for g in object.get_groups()]
+    def prepare_access(self, object):
+        access_list = []
+        if object.get_owner() is not None:
+            access_list.append('u_{}'.format(object.get_owner().id))
+        for group_id in object.get_group_ids():
+            access_list.append('g_{}'.format(group_id))
+        return access_list
 
     def prepare_submitter(self, object):
         investigation = object.get_investigation()
@@ -174,10 +173,7 @@ def prepare(self, data_set):
 
 class ProjectIndex(indexes.SearchIndex, indexes.Indexable):
     text = indexes.CharField(document=True, use_template=True)
-    # id of the user who owns this project
-    owner_id = indexes.CharField()
-    # ids of the groups who have read permission for this data set
-    group_ids = indexes.MultiValueField(null=True)
+    access = indexes.MultiValueField(null=True)
     name = indexes.CharField(model_attr='name', null=True)
     uuid = indexes.CharField(model_attr='uuid')
     summary = indexes.CharField(model_attr='summary')
@@ -192,11 +188,14 @@ class ProjectIndex(indexes.SearchIndex, indexes.Indexable):
     def get_model(self):
         return Project
 
-    def prepare_owner_id(self, object):
-        return object.get_owner().id
-
-    def prepare_group_ids(self, object):
-        return [g["id"] for g in object.get_groups()]
+    def prepare_access(self, object):
+        access_list = []
+        if object.get_owner() is not None:
+            access_list.append('u_{}'.format(object.get_owner().id))
+        for group in object.get_groups():
+            if id in group:
+                access_list.append('g_{}'.format(group.id))
+        return access_list
 
     def index_queryset(self, using=None):
         """Used when the entire index for model is updated."""

refinery/core/urls.py

@@ -7,13 +7,14 @@
 from django.conf.urls.defaults import patterns, url
 
 
-urlpatterns = patterns('core.views',
-    url(r'^$', 'home', name="home" ),        
-    url(r'^about/$', 'about', name="about" ),
-    url(r'^contact/$', 'contact', name="contact" ),
-    url(r'^statistics/$', 'statistics', name="statistics" ),
+urlpatterns = patterns(
+    'core.views',
+    url(r'^$', 'home', name="home"),
+    url(r'^about/$', 'about', name="about"),
+    url(r'^contact/$', 'contact', name="contact"),
+    url(r'^statistics/$', 'statistics', name="statistics"),
     url(r'^users/(?P<query>[\@\.\-\+a-z0-9]+)/$', 'user'),
-        # "name" is required for use with the url tag in templates
+    # "name" is required for use with the url tag in templates
     url(r'^users/(?P<query>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', 'user', name="user"),
     url(r'^users/(?P<uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/edit/$', 'user_edit', name="user_edit"),
     url(r'^groups/(?P<query>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', 'group', name="group"),
@@ -30,14 +31,19 @@
     url(r'^data_sets/(?P<slug>[a-zA-Z0-9\_]+)/$', 'data_set_slug', name="data_set_slug"),
     url(r'^workflows/(?P<uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', 'workflow', name="workflow"),
     url(r'^workflows/(?P<uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/edit/$', 'workflow_edit', name="workflow_edit"),
-    url(r'^workflows/(?P<slug>[a-zA-Z0-9\_]+)/$', 'workflow_slug', name="workflow_slug"),    
+    url(r'^workflows/(?P<slug>[a-zA-Z0-9\_]+)/$', 'workflow_slug', name="workflow_slug"),
     url(r'^workflow_engines/(?P<uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', 'workflow_engine', name="workflow_engine"),
 
     url(r'^data_sets/(?P<ds_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/samples/(?P<study_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/(?P<assay_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/$', 'samples', name="samples"),
-
-    url(r'^solr/igv/$', 'solr_igv' ),
+
+    url(r'^solr/igv/$', 'solr_igv'),
+    url(
+        r'^solr/core/select/$',
+        'solr_core_search',
+        name="solr_core_search"
+    ),
     url(r'^solr/(?P<core>.+)/select/$', 'solr_select', name="solr_select"),
-    
+
     # test solr/search view
     url(r'^data_sets/(?P<ds_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/samples/(?P<study_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/(?P<assay_uuid>[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12})/solr$', 'samples_solr', name="samples"),
 )
@@ -54,6 +60,6 @@ def get_queryset(self):
             context_object_name='datasets',
             paginate_by=15,
             template_name='core/data_sets.html'
-        ))              
+       ))
 )
 """

refinery/core/utils.py

@@ -0,0 +1,9 @@
+import logging
+from core.search_indexes import DataSetIndex
+
+logger = logging.getLogger(__name__)
+
+
+def index_data_set(data_set):
+    logger.debug('Index new data set (uuid: %s)', data_set.uuid)
+    DataSetIndex().update_object(data_set, using='core')