Merge pull request #1451 from AlexsLemonade/dev

[HOTFIX] Deploy a couple minor changes to prod

.circleci/config.yml

@@ -329,10 +329,9 @@ workflows:
             branches:
               ignore: /.*/
             tags:
-              # From CirlceCI Docs:
-              # If both only and ignore are specified the only is considered before ignore.
-              only: /v.*/
-              ignore: /v.*-hotfix/
+              # Only run deploys on versions tagged with /v.*/, unless regex
+              # lookahead finds `-hotfix` at the end of the version tag
+              only: /^v((?!-hotfix$).)*$/
 
   hotfix-deploy:
     jobs:

api/data_refinery_api/serializers.py

@@ -604,6 +604,7 @@ class DatasetSerializer(serializers.ModelSerializer):
     start = serializers.NullBooleanField(required=False)
     experiments = DatasetDetailsExperimentSerializer(source='get_experiments', many=True, read_only=True)
     organism_samples = serializers.SerializerMethodField(read_only=True)
+    worker_version = serializers.SerializerMethodField(read_only=True)
 
     def __init__(self, *args, **kwargs):
         super(DatasetSerializer, self).__init__(*args, **kwargs)
@@ -616,6 +617,7 @@ def __init__(self, *args, **kwargs):
                 if 'details' not in kwargs['context']['request'].query_params:
                     self.fields.pop('experiments')
                     self.fields.pop('organism_samples')
+                    self.fields.pop('worker_version')
 
             # only include the field `download_url` if a valid token is specified
             # the token lookup happens in the view.
@@ -646,7 +648,8 @@ class Meta:
                     'experiments',
                     'organism_samples',
                     'download_url',
-                    'quantile_normalize'
+                    'quantile_normalize',
+                    'worker_version'
             )
         extra_kwargs = {
                         'data': {
@@ -693,6 +696,10 @@ class Meta:
                         },
                         'download_url': {
                             'read_only': True,
+                        },
+                        'worker_version': {
+                            'read_only': True,
+                            'help_text': 'Returns the latest version of refine.bio that was used to build this dataset.'
                         }
                     }
 
@@ -722,6 +729,13 @@ def get_organism_samples(self, obj):
 
         return result
 
+    def get_worker_version(self, obj):
+        processor_jobs = obj.processor_jobs.order_by('-created_at').values_list('worker_version', flat=True)
+        if processor_jobs:
+            return processor_jobs[0]
+        else:
+            return None
+
 class APITokenSerializer(serializers.ModelSerializer):
 
     class Meta:

common/data_refinery_common/migrations/0023_fix_platform_names_spaces.py

@@ -0,0 +1,22 @@
+
+from django.db import migrations
+from data_refinery_common.utils import get_supported_rnaseq_platforms
+from django.core.paginator import Paginator
+
+def make_sample_platform_names_readable(apps, schema_editor):
+    Sample = apps.get_model('data_refinery_common', 'Sample')
+
+    for platform_name in get_supported_rnaseq_platforms():
+        munged_platform = platform_name.replace(' ', '')
+        Sample.objects.all().filter(platform_name=munged_platform).update(platform_name=platform_name)
+        print("Updating platform name from \'%s\' to \'%s\'" % (munged_platform, platform_name))
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('data_refinery_common', '0022_auto_20190607_1505'),
+    ]
+
+    operations = [
+        migrations.RunPython(make_sample_platform_names_readable)
+    ]

common/data_refinery_common/migrations/0024_dataset_processor_jobs.py

@@ -0,0 +1,18 @@
+# Generated by Django 2.1.8 on 2019-07-26 18:41
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('data_refinery_common', '0023_fix_platform_names_spaces'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='dataset',
+            name='processor_jobs',
+            field=models.ManyToManyField(through='data_refinery_common.ProcessorJobDatasetAssociation', to='data_refinery_common.ProcessorJob'),
+        ),
+    ]

common/data_refinery_common/models/models.py

@@ -1108,6 +1108,8 @@ class Dataset(models.Model):
     is_processed = models.BooleanField(default=False)  # Result has been made
     is_available = models.BooleanField(default=False)  # Result is ready for delivery
 
+    processor_jobs = models.ManyToManyField('data_refinery_common.ProcessorJob', through='ProcessorJobDataSetAssociation')
+
     # Fail handling
     success = models.NullBooleanField(null=True)
     failure_reason = models.TextField()

foreman/data_refinery_foreman/foreman/management/commands/create_missing_downloader_jobs.py

@@ -55,7 +55,3 @@ def handle(self, *args, **options):
                 break
 
             page = paginator.page(page.next_page_number())
-
-            # 2000 samples queued up every five minutes should be fast
-            # enough and also not thrash the DB.
-            time.sleep(60 * 5)