Tests fixed

icgc-dcc · Mar 15, 2017 · d95e36f · d95e36f
1 parent ef8887a
commit d95e36f
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Showing 8 changed files with 22 additions and 11 deletions.
diff --git a/egasub/ega/entities/sample.py b/egasub/ega/entities/sample.py
@@ -4,7 +4,7 @@
 class Sample(object):
     def __init__(self,alias,title,description,case_or_control_id,gender_id,organism_part,
                  cell_line,region,phenotype, subject_id, anonymized_name, bio_sample_id,
-                 sample_age, sample_detail, attributes,id_,status=None,ega_accession_id=None):
+                 sample_age, sample_detail, attributes,id_=None,status=None,ega_accession_id=None):
         self.alias = alias
         self.title = title
         self.description  = description
@@ -20,7 +20,7 @@ def __init__(self,alias,title,description,case_or_control_id,gender_id,organism_
         self.sample_age = sample_age
         self.sample_detail = sample_detail
         self.attributes = attributes
-        self.id = id_=None
+        self.id = id_
         self.status = status
         self.ega_accession_id = ega_accession_id
 

diff --git a/tests/submission/test_alignment.py b/tests/submission/test_alignment.py
@@ -29,7 +29,8 @@ def test_alignment():
         'attributes': [],
         'bioSampleId': None,
         'anonymizedName': None,
-        'sampleDetail': None
+        'sampleDetail': None,
+        'egaAccessionId':None
     }
 
     reference_analysis = {
@@ -43,6 +44,7 @@ def test_alignment():
         'analysisTypeId': 0,
         'experimentTypeId' : [0],
         'status': None,
+        'egaAccessionId': None,
         'files': [
             {
                 'unencryptedChecksum': '5e0024389829a7b131fed6476f7e71c4',

diff --git a/tests/submission/test_unaligned.py b/tests/submission/test_unaligned.py
@@ -31,7 +31,8 @@ def test_unaligned():
                     'bioSampleId': None,
                     'anonymizedName': None,
                     'sampleDetail': None,
-                    'status': None
+                    'status': None,
+                    'egaAccessionId': None
                 }
 
     reference_experiment = {
@@ -50,7 +51,8 @@ def test_unaligned():
                     'studyId': None,
                     'libraryStrategyId': 5,
                     'alias': None,
-                    'status': None
+                    'status': None,
+                    'egaAccessionId': None
                 }
 
     reference_run = {
@@ -68,7 +70,8 @@ def test_unaligned():
                     'runFileTypeId': 0,
                     'alias': None,
                     'id': None,
-                    'status': None
+                    'status': None,
+                    'egaAccessionId': None
                 }
 
     assert cmp(unaligned.sample.to_dict(),reference_sample) == 0

diff --git a/tests/submission/test_variation.py b/tests/submission/test_variation.py
@@ -29,7 +29,8 @@ def test_variation():
         'bioSampleId': None,
         'anonymizedName': None,
         'status': None,
-        'sampleDetail': None
+        'sampleDetail': None,
+        'egaAccessionId': None
     }
 
     reference_analysis = {
@@ -43,6 +44,7 @@ def test_variation():
         'analysisTypeId': 1,
         'experimentTypeId' : [0],
         'status': None,
+        'egaAccessionId': None,
         'files': [
             {
                 'unencryptedChecksum': '5e0024389829a7b131fed6476f7e71c4',

diff --git a/tests/test_analysis.py b/tests/test_analysis.py
@@ -72,6 +72,7 @@ def test_to_dict():
         'attributes' : map(lambda attribute: attribute.to_dict(), attributes),
         'chromosomeReferences' : map(lambda ref: ref.to_dict(), chromosome_references),
         'alias' : 'an alias',
-        'status': None
+        'status': None,
+        'egaAccessionId': None
     }, analysis.to_dict()) == 0
 
diff --git a/tests/test_experiment.py b/tests/test_experiment.py
@@ -17,7 +17,8 @@
         'studyId' : 3000,
         'alias' : 'an alias',
         'id' : 22,
-        'status': None
+        'status': None,
+        'egaAccessionId': None
     }
 
 def test_title():

diff --git a/tests/test_run.py b/tests/test_run.py
@@ -28,7 +28,8 @@ def test_to_dict():
             'files' : map(lambda file: file.to_dict(), files),
             'alias' : 'an alias',
             'id' : 22,
-            'status': None
+            'status': None,
+            'egaAccessionId': None
         }, run.to_dict()) == 0
 
 def test_alias():

diff --git a/tests/test_sample.py b/tests/test_sample.py
@@ -71,7 +71,8 @@ def test_to_dict():
             'sampleDetail' : 'some details',
             'attributes' : map(lambda attribute: attribute.to_dict(), attributes),
             'id' : 33,
-            'status': None
+            'status': None,
+            'egaAccessionId':None
         }, sample.to_dict()) == 0