Merge pull request #139 from brinkmanlab/dev-merge

Merge dev and cluster-vis

IslandCompare/analysis/integration_tests.py

@@ -1,5 +1,6 @@
 from django.test import TestCase, override_settings
-from genomes.models import Genome
+from genomes.models import Genome, GenomicIsland
+from analysis.models import Analysis
 from django.contrib.auth.models import User
 from django.core.files import File
 from analysis.components import ParsnpPipelineComponent, MauvePipelineComponent, \
@@ -155,10 +156,12 @@ def setUp(self):
         self.test_genome_1 = Genome.objects.create(name=self.test_genome_1_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_1_gbk)
+        self.test_genome_1.save()
 
         self.test_genome_2 = Genome.objects.create(name=self.test_genome_2_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_2_gbk)
+        self.test_genome_2.save()
 
     def test_sigihmm_analysis(self):
         report = {
@@ -175,8 +178,8 @@ def test_sigihmm_analysis(self):
         component.analysis(report)
         component.cleanup()
 
-        self.assertTrue("sigi_gis" in report)
-        self.assertEqual(2, len(report["sigi_gis"]))
+        self.assertTrue(self.test_genome_1.genomicisland_set.filter(method="sigi").exists())
+        self.assertTrue(self.test_genome_2.genomicisland_set.filter(method="sigi").exists())
 
     def tearDown(self):
         for genome in Genome.objects.all():
@@ -202,10 +205,12 @@ def setUp(self):
         self.test_genome_1 = Genome.objects.create(name=self.test_genome_1_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_1_gbk)
+        self.test_genome_1.save()
 
         self.test_genome_2 = Genome.objects.create(name=self.test_genome_2_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_2_gbk)
+        self.test_genome_2.save()
 
     def test_islandpath_analysis(self):
         report = {
@@ -222,10 +227,8 @@ def test_islandpath_analysis(self):
         component.analysis(report)
         component.cleanup()
 
-        self.assertTrue("islandpath_gis" in report)
-        self.assertEqual(2, len(report["islandpath_gis"]))
-        self.assertTrue(self.test_genome_1.id in report["islandpath_gis"])
-        self.assertTrue(self.test_genome_2.id in report["islandpath_gis"])
+        self.assertTrue(self.test_genome_1.genomicisland_set.filter(method="islandpath").exists())
+        self.assertTrue(self.test_genome_2.genomicisland_set.filter(method="islandpath").exists())
 
     def tearDown(self):
         for genome in Genome.objects.all():
@@ -284,6 +287,8 @@ class MashMCLTestCase(TestCase):
     test_username = "username"
     test_user = None
 
+    test_cluster_analysis = None
+
     test_genome_1 = None
     test_genome_1_name = "genome_1"
     test_genome_1_gbk = File(open("../TestFiles/AE009952.gbk"))
@@ -292,32 +297,62 @@ class MashMCLTestCase(TestCase):
     test_genome_2_name = "genome_2"
     test_genome_2_gbk = File(open("../TestFiles/BX936398.gbk"))
 
+    test_gi_1 = None
+    test_gi_2 = None
+
+    report = None
+
     def setUp(self):
         self.test_user = User(username=self.test_username)
         self.test_user.save()
 
+        self.test_cluster_analysis = Analysis(
+            celery_task_id="1",
+            name="test_cluster_analysis",
+            owner=self.test_user
+        )
+        self.test_cluster_analysis.save()
+
         self.test_genome_1 = Genome.objects.create(name=self.test_genome_1_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_1_gbk)
+        self.test_genome_1.save()
 
         self.test_genome_2 = Genome.objects.create(name=self.test_genome_2_name,
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_2_gbk)
-
-    def test_generate_gi_fna(self):
-        component = MashMclClusterPipelineComponent()
-
-        report = {
-            "analysis": 1,
-            "available_dependencies": ["merge_gis", "gbk_paths"],
+        self.test_genome_2.save()
+
+        self.test_cluster_analysis.genomes.add(self.test_genome_1)
+        self.test_cluster_analysis.genomes.add(self.test_genome_2)
+        self.test_cluster_analysis.save()
+
+        self.test_gi_1 = GenomicIsland(
+            method="merge",
+            start=0,
+            end=1000,
+            genome=self.test_genome_1
+        ).save()
+        self.test_gi_2 = GenomicIsland(
+            method="merge",
+            start=0,
+            end=1000,
+            genome=self.test_genome_2
+        ).save()
+
+        self.report = {
+            "analysis": self.test_cluster_analysis.id,
+            "available_dependencies": ["gbk_paths"],
             "gbk_paths": {self.test_genome_1.id: self.test_genome_1.gbk.path,
                           self.test_genome_2.id: self.test_genome_2.gbk.path},
-            "merge_gis": {self.test_genome_1.id: [[0, 1000]],
-                          self.test_genome_2.id: [[0, 1000]]}
+            "pipeline_components": "merge"
         }
 
-        component.setup(report)
-        component.create_gi_fasta_files(report)
+    def test_generate_gi_fna(self):
+        component = MashMclClusterPipelineComponent()
+
+        component.setup(self.report)
+        component.create_gi_fasta_files(self.report)
 
         self.assertTrue(os.path.exists(component.temp_dir_path + "/fna/1/0"))
         self.assertTrue(os.path.exists(component.temp_dir_path + "/fna/2/0"))
@@ -327,25 +362,18 @@ def test_generate_gi_fna(self):
     def test_analysis(self):
         component = MashMclClusterPipelineComponent()
 
-        report = {
-            "analysis": 1,
-            "available_dependencies": ["merge_gis", "gbk_paths"],
-            "gbk_paths": {self.test_genome_1.id: self.test_genome_1.gbk.path,
-                          self.test_genome_2.id: self.test_genome_2.gbk.path},
-            "merge_gis": {self.test_genome_1.id: [[0, 1000]],
-                          self.test_genome_2.id: [[0, 1000]]}
-        }
-
-        component.setup(report)
-        component.analysis(report)
+        component.setup(self.report)
+        component.analysis(self.report)
         component.cleanup()
 
-        self.assertTrue("cluster_gis" in report)
-        self.assertEqual(0, report["cluster_gis"]['numberClusters'])
+        self.assertTrue("numberClusters" in self.report)
+        self.assertTrue(Analysis.objects.get(id=self.report["analysis"]).clusters != "")
 
     def tearDown(self):
         for genome in Genome.objects.all():
             genome.delete()
+        for analysis in Analysis.objects.all():
+            analysis.delete()
 
 
 class RGIComponentIntegrationTestCase(TestCase):
@@ -364,15 +392,14 @@ def setUp(self):
                                                    owner=self.test_user,
                                                    gbk=self.test_genome_1_gbk)
 
-    @skip("Complete writing tests when component is defined and implemented")
     def test_rgi_component(self):
         report = {
             "analysis": 1,
             "available_dependencies": ["gbk_paths"],
             "gbk_paths": {self.test_genome_1.id: self.test_genome_1.gbk.path},
         }
 
-        component = RGIPipelineComponent()#mock.MagicMock(RGIPipelineComponent)
+        component = RGIPipelineComponent()
         component.setup(report)
         component.analysis(report)
         component.cleanup()

IslandCompare/analysis/migrations/0002_auto_20170718_1718.py

@@ -0,0 +1,25 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-07-18 17:18
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('analysis', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='analysis',
+            name='celery_task_id',
+            field=models.CharField(max_length=765),
+        ),
+        migrations.AlterField(
+            model_name='analysiscomponent',
+            name='celery_task_id',
+            field=models.CharField(max_length=765),
+        ),
+    ]

IslandCompare/analysis/migrations/0003_analysis_clusters.py

@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.10.5 on 2017-07-31 17:44
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('analysis', '0002_auto_20170718_1718'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='analysis',
+            name='clusters',
+            field=models.TextField(blank=True),
+        ),
+    ]

IslandCompare/analysis/models.py

@@ -3,8 +3,6 @@
 from genomes.models import Genome
 from django.utils import timezone
 
-# Create your models here.
-
 
 class Analysis(models.Model):
     id = models.AutoField(primary_key=True)
@@ -15,6 +13,7 @@ class Analysis(models.Model):
     start_time = models.DateTimeField(null=True)
     complete_time = models.DateTimeField(null=True)
     owner = models.ForeignKey(User)
+    clusters = models.TextField(blank=True)
 
     class Meta:
         unique_together = ('name', 'owner')

IslandCompare/analysis/pipeline.py

@@ -133,6 +133,8 @@ class Pipeline(object):
     """A list of available dependencies"""
     analysis = None
     """The analysis"""
+    failed_components = None
+    """A list of failed components"""
 
     def __init__(self):
         """
@@ -141,6 +143,7 @@ def __init__(self):
         self.pipeline_components = []
         self.available_dependencies = []
         self.analysis = None
+        self.failed_components = {}
 
     def create_database_entry(self, name, genomes, owner):
         """
@@ -188,7 +191,8 @@ def serialize(pipeline):
             'analysis': pipeline.analysis.id,
             'available_dependencies': pipeline.available_dependencies,
             'pipeline_components': serialized_pipeline_components,
-            'component_param': serialized_pipeline_param
+            'component_param': serialized_pipeline_param,
+            'failed_components': pipeline.failed_components
         }
         return serialized_dict
 
@@ -208,5 +212,6 @@ def deserialize(serialized_dict, pipeline_component_factory):
             )
         pipeline.available_dependencies = serialized_dict['available_dependencies']
         pipeline.analysis = Analysis.objects.get(id=serialized_dict['analysis'])
+        pipeline.failed_components = serialized_dict['failed_components']
 
         return pipeline