Merge branch 'master' of https://github.com/HBPMedical/algorithm-repository.git

Author: mbreskvar

dev/docker-compose.yml

@@ -50,7 +50,7 @@ services:
       - db
 
   woken_db_setup:
-    image: "hbpmip/woken-db-setup:1.1.0"
+    image: "hbpmip/woken-db-setup:1.2.1"
     container_name: "woken-db-setup"
     restart: "no"
     environment:

java-rapidminer-knn/tests/docker-compose.yml

@@ -48,7 +48,7 @@ services:
       - db
 
   woken_db_setup:
-    image: "hbpmip/woken-db-setup:1.1.0"
+    image: "hbpmip/woken-db-setup:1.2.1"
     container_name: "woken-db-setup"
     restart: "no"
     environment:

java-rapidminer-naivebayes/tests/docker-compose.yml

@@ -48,7 +48,7 @@ services:
       - db
 
   woken_db_setup:
-    image: "hbpmip/woken-db-setup:1.1.0"
+    image: "hbpmip/woken-db-setup:1.2.1"
     container_name: "woken-db-setup"
     restart: "no"
     environment:

python-anova/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.3
+current_version = 0.4.4
 commit = True
 tag = True
 tag_name = python-anova-{new_version}

python-anova/Dockerfile

@@ -21,7 +21,7 @@ FROM hbpmip/python-mip:0.6.1
 
 MAINTAINER mirco.nasuti@chuv.ch
 
-ENV DOCKER_IMAGE=hbpmip/python-anova:0.4.3 \
+ENV DOCKER_IMAGE=hbpmip/python-anova:0.4.4 \
     FUNCTION=python-anova
 
 COPY requirements.txt /requirements.txt

python-anova/anova.py

@@ -69,7 +69,12 @@ def format_output(statsmodels_dict):
 def compute_anova(dep_var, indep_vars, data, design='factorial'):
     formula = generate_formula(dep_var, indep_vars, design)
     logging.info("Formula: %s" % formula)
-    lm = ols(data=DataFrame(data), formula=formula).fit()
+    data = DataFrame(data)
+
+    if data.empty:
+        raise errors.UserError('SQL returned no data, check your dataset and null values.')
+
+    lm = ols(data=data, formula=formula).fit()
     logging.info(lm.summary())
     return anova_lm(lm)
 

python-anova/tests/docker-compose.yml

@@ -48,7 +48,7 @@ services:
       - db
 
   woken_db_setup:
-    image: "hbpmip/woken-db-setup:1.1.0"
+    image: "hbpmip/woken-db-setup:1.2.1"
     container_name: "woken-db-setup"
     restart: "no"
     environment:

python-anova/tests/unit/test_anova.py

@@ -1,6 +1,9 @@
 import pytest
-from anova import generate_formula
+import mock
+import json
+from anova import generate_formula, main
 from mip_helper import errors
+from mip_helper import testing as t
 
 
 def test_generate_formula():
@@ -9,3 +12,52 @@ def test_generate_formula():
     indep_vars = [{'name': str(i)} for i in range(10)]
     with pytest.raises(errors.UserError):
         generate_formula(dep_var, indep_vars, 'factorial')
+
+
+@mock.patch('anova.io_helper.fetch_data')
+@mock.patch('anova.io_helper.save_results')
+def test_main(mock_save_results, mock_fetch_data):
+    mock_fetch_data.return_value = t.inputs_regression(include_nominal=False)
+    main()
+    result = json.loads(mock_save_results.call_args[0][0])
+    assert t.round_dict(result) == {
+        'Residual': {
+            'F': 'NaN',
+            'PR(>F)': 'NaN',
+            'df': 1.0,
+            'mean_sq': 0.019,
+            'sum_sq': 0.019
+        },
+        'minimentalstate': {
+            'F': 12.831,
+            'PR(>F)': 0.173,
+            'df': 1.0,
+            'mean_sq': 0.248,
+            'sum_sq': 0.248
+        },
+        'subjectage': {
+            'F': 0.958,
+            'PR(>F)': 0.507,
+            'df': 1.0,
+            'mean_sq': 0.019,
+            'sum_sq': 0.019
+        },
+        'subjectage:minimentalstate': {
+            'F': 0.096,
+            'PR(>F)': 0.808,
+            'df': 1.0,
+            'mean_sq': 0.002,
+            'sum_sq': 0.002
+        }
+    }
+
+
+@mock.patch('anova.io_helper.fetch_data')
+@mock.patch('anova.io_helper.save_error')
+@mock.patch('sys.exit')
+def test_main_empty_input(mock_exit, mock_save_error, mock_fetch_data):
+    mock_fetch_data.return_value = t.inputs_regression(limit_to=0)
+    main()
+
+    mock_exit.assert_called_once_with(1)
+    mock_save_error.assert_called_once()

python-correlation-heatmap/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.0
+current_version = 0.4.0
 commit = True
 tag = True
 tag_name = python-correlation-heatmap-{new_version}
@@ -8,3 +8,5 @@ serialize = {major}.{minor}.{patch}
 
 [bumpversion:file:Dockerfile]
 
+[bumpversion:file:Dockerfile.pca]
+

python-correlation-heatmap/Dockerfile

@@ -20,7 +20,7 @@ FROM hbpmip/python-mip:0.6.1
 
 MAINTAINER mirco.nasuti@chuv.ch
 
-ENV DOCKER_IMAGE=hbpmip/python-correlation-heatmap:0.3.0 \
+ENV DOCKER_IMAGE=hbpmip/python-correlation-heatmap:0.4.0 \
     FUNCTION=python-correlation-heatmap
 
 COPY requirements.txt /requirements.txt