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Jkmarx/remove node group (#1744)
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* Default tool related column to hidden.

* Update to latest ui-grid

* Toggle selection column and input groups.

* Update color array when new tool selected.

* Fix collapse bug.

* Add watcher for when tools are selected.

* Fix unit test.

* Uncomment footertemplate.

* Reorder method according to style guide.

* Remove node group from ui.

* Remove unused variable.

* Remove node-group helper methods.

* Remove lingering node group functionality.

* Fix unit test.

* Remove node_group api.

* Remove unused unit test.

* Remove node group and update migration.
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@jkmarx
jkmarx committed May 26, 2017
1 parent 2249381 commit f7eb940
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Showing 38 changed files with 101 additions and 1,962 deletions.
91 changes: 2 additions & 89 deletions refinery/analysis_manager/views.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@

from .models import AnalysisStatus
from .tasks import run_analysis
from core.models import (Analysis, InvestigationLink, NodeGroup, NodePair,
from core.models import (Analysis, InvestigationLink, NodePair,
NodeRelationship, NodeSet, Workflow,
WorkflowDataInputMap, WorkflowEngine)
from core.utils import get_aware_local_time
Expand Down Expand Up @@ -177,103 +177,16 @@ def run(request):
workflow_uuid = analysis_config['workflowUuid']
study_uuid = analysis_config['studyUuid']
node_set_uuid = analysis_config['nodeSetUuid']
node_group_uuid = analysis_config['nodeGroupUuid']
node_relationship_uuid = analysis_config['nodeRelationshipUuid']
custom_name = analysis_config['name']
except KeyError:
return HttpResponseBadRequest() # 400
# must provide workflow and study UUIDs,
# and either node set UUID or node relationship UUID
if not (workflow_uuid and study_uuid and
(node_set_uuid or node_relationship_uuid or node_group_uuid)):
(node_set_uuid or node_relationship_uuid)):
return HttpResponseBadRequest() # 400

# single-input workflow based node group
if node_group_uuid:
try:
curr_node_group = NodeGroup.objects.get(uuid=node_group_uuid)
except NodeGroup.DoesNotExist:
logger.error("Node Group with UUID '{}' does not exist".format(
node_group_uuid))
return HttpResponse(status='404')
except NodeGroup.MultipleObjectsReturned:
logger.error("Node Group with UUID '{}' returned multiple "
"objects".format(node_group_uuid))
return HttpResponse(status='500')

try:
curr_workflow = Workflow.objects.get(uuid=workflow_uuid)
except Workflow.DoesNotExist:
logger.error("WorkFlow with UUID '{}' does not exist".format(
workflow_uuid))
return HttpResponse(status='404')
except Workflow.MultipleObjectsReturned:
logger.error("WorkFlow with UUID '{}' returns multiple objects"
.format(workflow_uuid))
return HttpResponse(status='500')

try:
study = Study.objects.get(uuid=study_uuid)
except Study.DoesNotExist:
logger.error("Study with UUID '{}' does not exist".format(
study_uuid))
return HttpResponse(status='404')
except Study.MultipleObjectsReturned:
logger.error("Study with UUID '{}' returns multiple objects"
.format(study_uuid))
return HttpResponse(status='500')

investigation_links = InvestigationLink.objects.filter(
investigation__uuid=study.investigation.uuid).order_by(
"version")
if not investigation_links:
logger.error("InvestigationLink with UUID '{}' with does not "
"exist".format(study.investigation.uuid))
return HttpResponse(status='404')

data_set = investigation_links.reverse()[0].data_set
logger.info("Associating analysis with data set %s (%s)",
data_set, data_set.uuid)

# ANALYSIS MODEL
# How to create a simple analysis object
if not custom_name:
temp_name = curr_workflow.name + " " + get_aware_local_time()\
.strftime("%Y-%m-%d @ %H:%M:%S")
else:
temp_name = custom_name

summary_name = "None provided."
analysis = Analysis.objects.create(
summary=summary_name,
name=temp_name,
project=request.user.profile.catch_all_project,
data_set=data_set,
workflow=curr_workflow,
time_start=timezone.now()
)
analysis.set_owner(request.user)

# getting distinct workflow inputs
try:
workflow_data_inputs = curr_workflow.data_inputs.all()[0]
except IndexError:
logger.error("Workflow with UUID '{}' has an index "
"error with inputs".format(workflow_uuid.uuid))
return HttpResponse(status='500')

# NEED TO GET LIST OF FILE_UUIDS from node_group_uuid fields
count = 0
for node_file in curr_node_group.nodes.all():
count += 1
temp_input = WorkflowDataInputMap.objects.create(
workflow_data_input_name=workflow_data_inputs.name,
data_uuid=node_file.uuid,
pair_id=count
)
analysis.workflow_data_input_maps.add(temp_input)
analysis.save()

# single-input workflow
if node_set_uuid:
# TODO: handle DoesNotExist exception
Expand Down
33 changes: 33 additions & 0 deletions refinery/core/migrations/0006_auto_20170524_1554.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import models, migrations


class Migration(migrations.Migration):

dependencies = [
('core', '0005_ontology_data'),
]

operations = [
migrations.AlterUniqueTogether(
name='nodegroup',
unique_together=None,
),
migrations.RemoveField(
model_name='nodegroup',
name='assay',
),
migrations.RemoveField(
model_name='nodegroup',
name='nodes',
),
migrations.RemoveField(
model_name='nodegroup',
name='study',
),
migrations.DeleteModel(
name='NodeGroup',
),
]
34 changes: 0 additions & 34 deletions refinery/core/models.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1888,40 +1888,6 @@ def create_manager_group(sender, instance, created, **kwargs):
post_save.connect(create_manager_group, sender=ExtendedGroup)


class NodeGroup(SharableResource, TemporaryResource):
"""A collection of Nodes representing data files.
Used to save selection state between sessions and to map data files to
workflow inputs.
"""

#: Number of nodes in the NodeSet (provided in POST/PUT/PATCH requests)
node_count = models.IntegerField(default=0)
#: Implicit node is created "on the fly" to support an analysis while
#: explicit node is created by the user to store a particular selection
is_implicit = models.BooleanField(default=False)
study = models.ForeignKey(Study)
assay = models.ForeignKey(Assay)
# The "current selection" node set for the associated study/assay
is_current = models.BooleanField(default=False)
# Nodes in the group, using uuids are foreign-key
nodes = models.ManyToManyField(Node, blank=True,
null=True)

class Meta:
unique_together = ["assay", "name"]
verbose_name = "node group"
permissions = (
('read_%s' % verbose_name, 'Can read %s' % verbose_name),
('share_%s' % verbose_name, 'Can share %s' % verbose_name),
)

def __unicode__(self):
return (
self.name + ("*" if self.is_current else "") + " - " +
self.get_owner_username()
)


class NodeSet(SharableResource, TemporaryResource):
"""A collection of Nodes representing data files.
Used to save selection state between sessions and to map data files to
Expand Down
52 changes: 2 additions & 50 deletions refinery/core/serializers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
from rest_framework import serializers
from rest_framework.validators import UniqueValidator

from .models import DataSet, NodeGroup, Workflow
from data_set_manager.models import Assay, Node, Study
from .models import DataSet, Workflow
from data_set_manager.models import Node
from file_store.models import FileStoreItem


Expand Down Expand Up @@ -46,54 +46,6 @@ def partial_update(self, instance, validated_data):
return instance


class NodeGroupSerializer(serializers.ModelSerializer):
# Slug related field associated uuids with model
nodes = serializers.SlugRelatedField(
many=True, slug_field='uuid',
queryset=Node.objects.all(),
required=False, allow_null=True)
assay = serializers.SlugRelatedField(
queryset=Assay.objects.all(),
slug_field='uuid')
study = serializers.SlugRelatedField(
queryset=Study.objects.all(),
slug_field='uuid')

class Meta:
model = NodeGroup
fields = ('uuid', 'node_count', 'is_implicit', 'study',
'assay', 'is_current', 'nodes', 'name')

def create(self, validated_data):
node_group = NodeGroup.objects.create(
study=validated_data.get('study'),
assay=validated_data.get('assay'),
name=validated_data.get('name'),
is_current=validated_data.get('is_current', False),
)
# Add foreign keys after object is created
if validated_data.get('nodes'):
node_group.nodes.add(*validated_data.get('nodes'))
node_group.node_count = len(validated_data.get('nodes'))
node_group.save()

return node_group

def update(self, instance, validated_data):
"""
Update and return an existing `NodeGroup` instance, given the
validated data.
"""
if validated_data.get('nodes'):
instance.nodes = validated_data.get('nodes', instance.nodes)
instance.node_count = len(validated_data.get('nodes'))

instance.is_current = validated_data.get('is_current',
instance.is_current)
instance.save()
return instance


class WorkflowSerializer(serializers.HyperlinkedModelSerializer):
instance = serializers.HyperlinkedIdentityField(
view_name='workflow-detail')
Expand Down

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