Revert both (#2283, #2248) ENCD-4020 commits

src/encoded/audit/experiment.py

@@ -2514,19 +2514,18 @@ def audit_experiment_ChIP_control(value, system, files_structure):
         return
 
     num_IgG_controls = 0
-
-    for control_dataset in value['possible_controls']:
-        if not is_control_dataset(control_dataset):
+    for control in value['possible_controls']:
+        if ('target' not in control) or ('control' not in control['target']['investigated_as']):
             detail = 'Experiment {} is ChIP-seq but its control {} is not linked to a target with investigated.as = control'.format(
                 value['@id'],
-                control_dataset['@id'])
+                control['@id'])
             yield AuditFailure('invalid possible_control', detail, level='ERROR')
             return
 
-        if not control_dataset.get('replicates'):
+        if not control.get('replicates'):
             continue
 
-        if 'antibody' in control_dataset.get('replicates')[0]:
+        if 'antibody' in control.get('replicates')[0]:
             num_IgG_controls += 1
 
     # If all of the possible_control experiments are mock IP control experiments
@@ -2535,23 +2534,11 @@ def audit_experiment_ChIP_control(value, system, files_structure):
             # The binding group agreed that ChIP-seqs all should have an input control.
             detail = 'Experiment {} is ChIP-seq and requires at least one input control, as agreed upon by the binding group. {} is not an input control'.format(
                 value['@id'],
-                control_dataset['@id'])
+                control['@id'])
             yield AuditFailure('missing input control', detail, level='NOT_COMPLIANT')
     return
 
 
-def is_control_dataset(dataset):
-    if 'target' not in dataset:
-        return False
-    if (dataset['@type'][0] == 'Experiment'):
-        return 'control' in dataset['target']['investigated_as']
-    else:
-        for target_of_related_dataset in dataset['target']:
-            if 'control' not in target_of_related_dataset['investigated_as']:
-                return False
-    return True
-
-
 def audit_experiment_spikeins(value, system, excluded_types):
     if not check_award_condition(value, [
             "ENCODE3",

src/encoded/schemas/changelogs/experiment.md

@@ -1,9 +1,5 @@
 ## Changelog for experiment.json
 
-### Minor changes since schema version 20
-
-* *possible_controls* property allows specification of any type of Dataset as possible control
-
 ### Schema version 20
 
 * Added *organoid* to biosample_type enums.

src/encoded/schemas/experiment.json

@@ -254,16 +254,16 @@
         },
         "possible_controls": {
             "title": "Controls",
-            "description": "Dataset that contain files that can serve as scientific controls for this experiment.",
+            "description": "Experiments that contain files that can serve as scientific controls for this experiment.",
             "type": "array",
             "default": [],
             "uniqueItems": true,
             "items": {
                 "title": "Control",
-                "description": "A dataset that contains files that can serve as a scientific control for this experiment.",
-                "comment": "See dataset.json for a list of available identifiers. Exact pairing of data files with their controls is done using file relationships.",
+                "description": "An experiment that contains files that can serve as a scientific control for this experiment.",
+                "comment": "See experiment.json for a list of available identifiers. Exact pairing of data files with their controls is done using file relationships.",
                 "type": "string",
-                "linkTo": "Dataset"
+                "linkTo": "Experiment"
             }
         },
         "supersedes": {

src/encoded/tests/test_schema_experiment.py

@@ -29,13 +29,6 @@ def experiment_no_error(testapp, lab, award):
     }
     return item
 
-@pytest.fixture
-def matched_set(testapp, lab, award):
-    item = {
-        'lab': lab['@id'],
-        'award': award['@id']
-    }
-    return item
 
 def test_not_pipeline_error_without_message_ok(testapp, experiment_no_error):
     # internal_status != pipeline error, so an error detail message is not required.
@@ -130,10 +123,3 @@ def test_experiment_submission_date_dependency(testapp, experiment_no_error):
         'date_submitted': '2000-10-10'},
         status=200)
 
-def test_experiment_possible_controls(testapp, experiment_no_error, matched_set):
-    exp = testapp.post_json('/experiment', experiment_no_error).json['@graph'][0]
-    matched_set_control = testapp.post_json('/matched_set', matched_set).json['@graph'][0]
-    testapp.patch_json(
-        exp['@id'], 
-        {'possible_controls': [matched_set_control['@id']]},
-        status=200)

src/encoded/types/dataset.py

@@ -468,6 +468,7 @@ class Series(Dataset, CalculatedSeriesAssay, CalculatedSeriesBiosample, Calculat
         'related_datasets.replicates.library.spikeins_used',
         'related_datasets.replicates.library.treatments',
         'related_datasets.possible_controls',
+        'related_datasets.possible_controls.target',
         'related_datasets.possible_controls.lab',
         'related_datasets.target.organism',
         'related_datasets.references',