Jkmarx/remove old node maps api (#2279)

* Remove node relationship model and references.

* Remove node_set model and references.

* Bump version (#2264)

* Bump version

* Change name to match expectations of on_startup.py

* Update tests to work with new IGV image version

* Update assertion with new Solr mock info

* Assert that `VisualizationError` is raised now that `launch()` is being called directly

* Scottx611x/set workflow tool analysis library_id (#2280)

* Set Analysis.library_id

* Test that WorkflowTool.analysis.library_id is set when we create a Galaxy Library

* Jkmarx/analysis tab url fix (#2276)

* Add facet name.

* Remove error caused from double encoding.

* Refactor facet_name method.

* Update test.

* Remove data_set_query which is not needed.

* Update analysis complete url.

* Update urls to all analysis links.

* Remove consoles.

* Remove self targets, unneccessary.

* Fix typo in `generate_tool_definitions` mgmt command (#2270)

* Mock USER_FILES_COLUMNS (#2282)

Tests pass locally. Fix #2235.

* Remove unused JS global. Fix #1765. (#2283)

* Scottx611x/tool manager test coverage (#2271)

* Add test for case where specified docker image has no version

* Add test coverage for `FileTypeValidationErrors`

* Add test coverage for ToolDefinitions with bad filetypes specified

* Add test coverage for `get_workflows()`

* `get_queryset()` shouldn't return an HTTPResponse;
The exception handling here also might mask the importance of the GuardianError.
Letting it propgate might not be a bad idea since this is one of those "shouldn't happen" scenarios, and knowing that something is wrong asap would be great.

* Fix typos

* Remove comma

* Be more clear as to my intentions with the overriding of this setting

* Factor out commonalities between these tests

* Fix test

* Remove unused JS global. Fix #1765. (#2287)

* Remove extra scrollbar cause by auto class on exterior panel. (#2297)

* Mccalluc/misc travis log cleanup (#2302)

* geckodriver download progress can be 1000 lines in the log

* FF download also wastes space... but what does the unzip?

* Remove "PhantomJS 2.1.1 (Linux 0.0.0): Executed 638 of 648 SUCCESS" messages

* Last commit was in entirely the wrong place to quiet the JS tests
(There should be a better way to make them quiet, but it looks like we choose between this, or a new package like mostly-quiet-grunt

* Adding grep also confuses the result status

* Feels like there should be a better way, but this cleans up the output without confusing the status (#2303)

* Jkmarx/data set 1 cleanup (#2278)

* Remove analysis-launch module.

* Remove from unit test.

* Remove node-relationship module.

* Remove node-mapping module and add third party dependency to refinery.js.

* Clean up data-set-nav and remove references.

* Update unit tests.

* Remove select workflow module.

* Remove igv module.

* Fix typo ,

* Remove solr_table_view.

* Remove analysis view.

* Remove solr_facet view.

* Remove pivot matrix.

* Remove data_set_configurator.

* Remove IGV references.

* Remove the file browser one table and some unneccessary code.

* Remove unneeded code since there's only one view.

* Remove float thread code.

* Remove float thread dependencies.

* Remove matrix styling.

* Remove old help modals, not dealing with provvis.

* Remove tipsy.

* Remove tipsy depenency in angular.

* Remove commented code which references old node sets.

* Remove node_set_manager reference.

* Remove node-set-manager references.

* Remove lingering merge tag.

* Add node set comments.

* Fix comment typo.

* Remove added dependency in wrong location and tracked.

* Fix height error.

* Revert data_set.html.

* Jkmarx/provvis tab integration (#2289)

* Add provvis tab.

* Seperate out provvis module initialization.

* Move ctrls to own file.

* Move directives to own files.

* Remove inialization module, ctrl, & directives to own file.

* Add provvis module.

* Fix page redirect.

* Fix info-panel routing.

* Fix bug with panel groups redirect.

* Better solution to nav tab.

* Add padding to top of infobar.

* Add refinery-base class to btns.

* Remove modal for popover.

* Remove provenance view and template.

* Cosemetic changes.

* Prevent pre-generation from content.js when loading in data-set page.

* Add bootbox.

* Fix height issue.

* Fix missing closed tag.

* Fix outdent.

* Fix tabbing.

refinery/analysis_manager/tests.py

@@ -15,12 +15,10 @@
 from analysis_manager.models import AnalysisStatus
 from analysis_manager.tasks import (_check_galaxy_history_state, _get_analysis,
                                     _get_analysis_status, run_analysis)
-from analysis_manager.utils import (_fetch_node_relationship, _fetch_node_set,
-                                    fetch_objects_required_for_analysis,
+from analysis_manager.utils import (fetch_objects_required_for_analysis,
                                     validate_analysis_config)
 from analysis_manager.views import analysis_status, run
-from core.models import (Analysis, DataSet, NodeRelationship, NodeSet, Project,
-                         Workflow, WorkflowEngine)
+from core.models import Analysis, DataSet, Project, Workflow, WorkflowEngine
 from data_set_manager.models import Assay
 from factory_boy.utils import (create_dataset_with_necessary_models,
                                make_analyses_with_single_dataset)
@@ -190,34 +188,6 @@ def test_fetch_objects_required_for_analyses_bad_dataset(self):
             )
             self.assertIn("Couldn't fetch DataSet", context.exception.message)
 
-    def test_fetch_nodeset_valid_uuid(self):
-        nodeset = NodeSet.objects.create(
-            study=self.study,
-            assay=self.assay
-        )
-        self.assertEqual(
-            nodeset,
-            _fetch_node_set(nodeset.uuid)
-        )
-
-    def test_fetch_nodeset_invalid_uuid(self):
-        with self.assertRaises(RuntimeError):
-            _fetch_node_set(str(uuid.uuid4()))
-
-    def test_fetch_node_relationship_valid_uuid(self):
-        node_relationship = NodeRelationship.objects.create(
-            study=self.study,
-            assay=self.assay
-        )
-        self.assertEqual(
-            node_relationship,
-            _fetch_node_relationship(node_relationship.uuid)
-        )
-
-    def test_fetch_node_relationship_invalid_uuid(self):
-        with self.assertRaises(RuntimeError):
-            _fetch_node_relationship(str(uuid.uuid4()))
-
 
 class AnalysisViewsTests(AnalysisManagerTestBase, ToolManagerTestBase):
     """

refinery/analysis_manager/utils.py

@@ -13,8 +13,7 @@
 import requests
 from requests.packages.urllib3.exceptions import HTTPError
 
-from core.models import (Analysis, NodeRelationship, NodeSet, Study, Workflow,
-                         WorkflowDataInputMap)
+from core.models import Analysis, Study, Workflow, WorkflowDataInputMap
 from core.utils import get_aware_local_time
 import tool_manager
 
@@ -237,50 +236,3 @@ def _create_analysis_name(current_workflow):
         current_workflow.name,
         get_aware_local_time().strftime("%Y-%m-%d @ %H:%M:%S")
     )
-
-
-def _fetch_node_relationship(node_relationship_uuid):
-    """
-    Fetches a NodeRelationship instance from a given UUID
-    :param node_relationship_uuid: UUID String
-    :return: <NodeRelationship>
-    :raises: RuntimeError
-    """
-    try:
-        return NodeRelationship.objects.get(uuid=node_relationship_uuid)
-    except(NodeRelationship.DoesNotExist,
-           NodeRelationship.MultipleObjectsReturned) as e:
-        raise RuntimeError(
-            "Couldn't fetch NodeRelationship from UUID: {} {}"
-            .format(node_relationship_uuid, e)
-        )
-
-
-def _fetch_node_set(node_set_uuid):
-    """
-    Fetches a NodeSet instance from a given UUID
-    :param node_set_uuid: UUID String
-    :return: <NodeSet>
-    :raises: RuntimeError
-    """
-    try:
-        return NodeSet.objects.get(uuid=node_set_uuid)
-    except(NodeSet.DoesNotExist, NodeSet.MultipleObjectsReturned) as e:
-        raise RuntimeError(
-            "Couldn't fetch NodeSet from UUID: {} {}".format(node_set_uuid, e)
-        )
-
-
-def _fetch_solr_uuids(nodeset_instance):
-    """
-    Fetches solr_uuids from a given NodeSet instance
-    :param nodeset_instance: <NodeSet> instance
-    :return: list of UUIDs corresponding to Nodes indexed in Solr
-    """
-    curr_node_dict = json.loads(nodeset_instance.solr_query_components)
-    return get_solr_results(
-        nodeset_instance.solr_query,
-        only_uuids=True,
-        selected_mode=curr_node_dict['documentSelectionBlacklistMode'],
-        selected_nodes=curr_node_dict['documentSelection']
-    )

refinery/config/urls.py

@@ -14,11 +14,9 @@
 from config.utils import RouterCombiner
 from core.api import (AnalysisResource, DataSetResource, ExtendedGroupResource,
                       GroupManagementResource, InvitationResource,
-                      NodePairResource, NodeRelationshipResource, NodeResource,
-                      NodeSetListResource, NodeSetResource, ProjectResource,
-                      StatisticsResource, UserAuthenticationResource,
-                      UserProfileResource, WorkflowInputRelationshipsResource,
-                      WorkflowResource)
+                      NodeResource, ProjectResource, StatisticsResource,
+                      UserAuthenticationResource, UserProfileResource,
+                      WorkflowInputRelationshipsResource, WorkflowResource)
 from core.forms import RegistrationFormWithCustomFields
 from core.models import AuthenticationFormUsernameOrEmail, DataSet
 from core.urls import core_router
@@ -53,10 +51,6 @@
 v1_api.register(DataSetResource())
 v1_api.register(AttributeOrderResource())
 v1_api.register(NodeResource())
-v1_api.register(NodeSetResource())
-v1_api.register(NodeSetListResource())
-v1_api.register(NodePairResource())
-v1_api.register(NodeRelationshipResource())
 v1_api.register(WorkflowResource())
 v1_api.register(WorkflowInputRelationshipsResource())
 v1_api.register(StatisticsResource())

refinery/core/admin.py

@@ -11,8 +11,7 @@
 
 from core.models import (Analysis, AnalysisNodeConnection, AnalysisResult,
                          DataSet, DiskQuota, Download, ExtendedGroup,
-                         InvestigationLink, Invitation, NodePair,
-                         NodeRelationship, NodeSet, Ontology, Project,
+                         InvestigationLink, Invitation, Ontology, Project,
                          SiteProfile, Tutorials, UserProfile, Workflow,
                          WorkflowDataInput, WorkflowDataInputMap,
                          WorkflowEngine, WorkflowFilesDL,
@@ -139,20 +138,6 @@ class ExtendedGroupAdmin(GuardedModelAdmin, ForeignKeyAutocompleteAdmin):
                     'member_list', 'perm_list', 'can_edit']
 
 
-class NodePairAdmin(GuardedModelAdmin, ForeignKeyAutocompleteAdmin):
-    list_display = ['id', 'uuid', 'node1', 'node2', 'group']
-
-
-class NodeRelationshipAdmin(GuardedModelAdmin, ForeignKeyAutocompleteAdmin):
-    list_display = ['__unicode__', 'id', 'type', 'node_set_1',
-                    'node_set_2', 'study', 'assay', 'is_current']
-
-
-class NodeSetAdmin(GuardedModelAdmin, ForeignKeyAutocompleteAdmin):
-    list_display = ['__unicode__', 'id', 'node_count', 'is_implicit',
-                    'study', 'assay', 'is_current']
-
-
 class UserProfileAdmin(GuardedModelAdmin):
     list_display = ['__unicode__', 'id', 'uuid', 'user', 'affiliation',
                     'catch_all_project', 'login_count',
@@ -201,9 +186,6 @@ class SiteProfileAdmin(GuardedModelAdmin):
 admin.site.register(AnalysisResult, AnalysisResultAdmin)
 admin.site.register(AnalysisNodeConnection, AnalysisNodeConnectionAdmin)
 admin.site.register(DiskQuota, DiskQuotaAdmin)
-admin.site.register(NodePair, NodePairAdmin)
-admin.site.register(NodeRelationship, NodeRelationshipAdmin)
-admin.site.register(NodeSet, NodeSetAdmin)
 admin.site.register(Invitation, InvitationAdmin)
 admin.site.register(UserProfile, UserProfileAdmin)
 admin.site.register(Tutorials, TutorialsAdmin)

refinery/core/api.py

@@ -8,7 +8,6 @@
 from datetime import timedelta
 import json
 import logging
-import re
 from sets import Set
 import uuid
 
@@ -33,16 +32,15 @@
 from tastypie.authorization import Authorization
 from tastypie.bundle import Bundle
 from tastypie.constants import ALL, ALL_WITH_RELATIONS
-from tastypie.exceptions import ImmediateHttpResponse, NotFound, Unauthorized
+from tastypie.exceptions import ImmediateHttpResponse, NotFound
 from tastypie.http import (HttpAccepted, HttpBadRequest, HttpCreated,
                            HttpForbidden, HttpGone, HttpMethodNotAllowed,
                            HttpNoContent, HttpNotFound, HttpUnauthorized)
 from tastypie.resources import ModelResource, Resource
 from tastypie.utils import trailing_slash
 
 from core.models import (Analysis, DataSet, ExtendedGroup, GroupManagement,
-                         Invitation, NodePair, NodeRelationship, NodeSet,
-                         Project, ResourceStatistics, Tutorials,
+                         Invitation, Project, ResourceStatistics, Tutorials,
                          UserAuthentication, UserProfile, Workflow,
                          WorkflowInputRelationships)
 from core.utils import get_data_sets_annotations, get_resources_for_user
@@ -1119,193 +1117,6 @@ def dehydrate(self, bundle):
             bundle.data['file_import_status'] = file_item.get_import_status()
         return bundle
 
-        # def get_object_list(self, request):
-        #     """
-        #     Temporarily removed for performance reasons (and not required
-        #     without authorization)
-        #     Get all nodes available to the current user (via dataset)
-        #     Temp workaround due to Node being not Ownable
-        #
-        #     """
-        #     user = request.user
-        #     perm = 'read_%s' % DataSet._meta.module_name
-        #     if (user.is_authenticated()):
-        #         allowed_datasets = get_objects_for_user(user, perm, DataSet)
-        #     else:
-        #         allowed_datasets = get_objects_for_group(
-        #             ExtendedGroup.objects.public_group(), perm, DataSet)
-        #     # get list of node UUIDs that belong to all datasets available to
-        #     # the current user
-        #     all_allowed_studies = []
-        #     for dataset in allowed_datasets:
-        #         dataset_studies = dataset.get_investigation().study_set.all()
-        #         all_allowed_studies.extend(
-        #               [study for study in dataset_studies]
-        #         )
-        #     allowed_nodes = []
-        #     for study in all_allowed_studies:
-        #         allowed_nodes.extend(study.node_set.all().values('uuid'))
-        #     # filter nodes using that list
-        #     return super(NodeResource, self).get_object_list(request).filter(
-        #         uuid__in=[node['uuid'] for node in allowed_nodes])
-
-
-class NodeSetResource(ModelResource):
-    # https://github.com/toastdriven/django-tastypie/pull/538
-    # https://github.com/toastdriven/django-tastypie/issues/526
-    # Once the above has been integrated into a tastypie release branch remove
-    # NodeSetListResource and use "use_in" instead
-    # nodes = fields.ToManyField(NodeResource, 'nodes', use_in="detail" )
-
-    solr_query = fields.CharField(attribute='solr_query', null=True)
-    solr_query_components = fields.CharField(
-        attribute='solr_query_components', null=True)
-    node_count = fields.IntegerField(attribute='node_count', null=True)
-    is_implicit = fields.BooleanField(attribute='is_implicit', default=False)
-    study = fields.ToOneField(StudyResource, 'study')
-    assay = fields.ToOneField(AssayResource, 'assay')
-
-    class Meta:
-        # create node count attribute on the fly - node_count field has to be
-        # defined on resource
-        queryset = NodeSet.objects.all().order_by('-is_current', 'name')
-        resource_name = 'nodeset'
-        detail_uri_name = 'uuid'  # for using UUIDs instead of pk in URIs
-        authentication = SessionAuthentication()
-        authorization = Authorization()
-        fields = [
-            'is_current', 'name', 'summary', 'assay', 'study', 'uuid',
-            'is_implicit', 'node_count', 'solr_query', 'solr_query_components'
-        ]
-        ordering = [
-            'is_current', 'name', 'summary', 'assay', 'study', 'uuid',
-            'is_implicit', 'node_count', 'solr_query', 'solr_query_components'
-        ]
-        allowed_methods = ["get", "post", "put"]
-        filtering = {
-            "study": ALL_WITH_RELATIONS, "assay": ALL_WITH_RELATIONS,
-            "uuid": ALL
-        }
-        # jQuery treats a 201 as an error for data type "JSON"
-        always_return_data = True
-
-    def prepend_urls(self):
-        return [
-            url((r"^(?P<resource_name>%s)/(?P<uuid>" + UUID_RE + r")/$") %
-                self._meta.resource_name,
-                self.wrap_view('dispatch_detail'),
-                name="api_dispatch_detail"),
-        ]
-
-    def obj_create(self, bundle, **kwargs):
-        """Create a new NodeSet instance and assign current user as owner if
-        current user has read permission on the data set referenced by the new
-        NodeSet
-        """
-        # get the Study specified by the UUID in the new NodeSet
-        study_uri = bundle.data['study']
-        match = re.search(
-            UUID_RE,
-            study_uri)
-        study_uuid = match.group()
-        try:
-            study = Study.objects.get(uuid=study_uuid)
-        except Study.DoesNotExist:
-            logger.error("Study '%s' does not exist", study_uuid)
-            self.unauthorized_result(
-                Unauthorized("You are not allowed to create a new NodeSet."))
-        # look up the dataset via InvestigationLink relationship
-        # an investigation is only associated with a single dataset even though
-        # InvestigationLink is a many to many relationship
-        try:
-            dataset = \
-                study.investigation.investigationlink_set.all()[0].data_set
-        except IndexError:
-            logger.error("Data set not found in study '%s'", study.uuid)
-            self.unauthorized_result(
-                Unauthorized("You are not allowed to create a new NodeSet."))
-        permission = "read_%s" % dataset._meta.module_name
-        if not bundle.request.user.has_perm(permission, dataset):
-            self.unauthorized_result(
-                Unauthorized("You are not allowed to create a new NodeSet."))
-        # if user has the read permission on the data set
-        # continue with creating the new NodeSet instance
-        bundle = super(NodeSetResource, self).obj_create(bundle, **kwargs)
-        bundle.obj.set_owner(bundle.request.user)
-        return bundle
-
-
-class NodeSetListResource(ModelResource):
-    study = fields.ToOneField(StudyResource, 'study')
-    assay = fields.ToOneField(AssayResource, 'assay')
-    node_count = fields.IntegerField(attribute='node_count', readonly=True)
-    is_implicit = fields.BooleanField(attribute='is_implicit', default=False)
-
-    class Meta:
-        # create node count attribute on the fly - node_count field has to be
-        # defined on resource
-        queryset = NodeSet.objects.all().order_by('-is_current', 'name')
-        # NG: introduced to get correct resource IDs
-        detail_resource_name = 'nodeset'
-        resource_name = 'nodesetlist'
-        detail_uri_name = 'uuid'  # for using UUIDs instead of pk in URIs
-        authentication = SessionAuthentication()
-        authorization = Authorization()
-        fields = ['is_current', 'name', 'summary', 'assay', 'study', 'uuid']
-        allowed_methods = ["get"]
-        filtering = {"study": ALL_WITH_RELATIONS, "assay": ALL_WITH_RELATIONS}
-        ordering = ['is_current', 'name', 'node_count']
-
-    def dehydrate(self, bundle):
-        # replace resource URI to point to the nodeset resource instead of the
-        # nodesetlist resource
-        bundle.data['resource_uri'] = bundle.data['resource_uri'].replace(
-            self._meta.resource_name, self._meta.detail_resource_name)
-        return bundle
-
-
-class NodePairResource(ModelResource):
-    node1 = fields.ToOneField(NodeResource, 'node1')
-    node2 = fields.ToOneField(NodeResource, 'node2', null=True)
-    group = fields.CharField(attribute='group', null=True)
-
-    class Meta:
-        detail_allowed_methods = ['get', 'post', 'delete', 'put', 'patch']
-        queryset = NodePair.objects.all()
-        detail_resource_name = 'nodepair'
-        resource_name = 'nodepair'
-        detail_uri_name = 'uuid'
-        authentication = SessionAuthentication()
-        authorization = Authorization()
-        # for use with AngularJS $resources: returns newly created object upon
-        # POST (in addition to the location response header)
-        always_return_data = True
-
-
-class NodeRelationshipResource(ModelResource):
-    name = fields.CharField(attribute='name', null=True)
-    type = fields.CharField(attribute='type', null=True)
-    # , full=True), if you need each attribute for each nodepair
-    node_pairs = fields.ToManyField(NodePairResource, 'node_pairs')
-    study = fields.ToOneField(StudyResource, 'study')
-    assay = fields.ToOneField(AssayResource, 'assay')
-
-    class Meta:
-        detail_allowed_methods = ['get', 'post', 'delete', 'put', 'patch']
-        queryset = NodeRelationship.objects.all().order_by('-is_current',
-                                                           'name')
-        detail_resource_name = 'noderelationship'
-        resource_name = 'noderelationship'
-        detail_uri_name = 'uuid'
-        authentication = SessionAuthentication()
-        authorization = Authorization()
-        # for use with AngularJS $resources: returns newly created object upon
-        # POST (in addition to the location response header)
-        always_return_data = True
-        # fields = ['type', 'study', 'assay', 'node_pairs']
-        ordering = ['is_current', 'name', 'type', 'node_pairs']
-        filtering = {'study': ALL_WITH_RELATIONS, 'assay': ALL_WITH_RELATIONS}
-
 
 class StatisticsResource(Resource):
     user = fields.IntegerField(attribute='user')