Merge pull request #14 from daisybio/dependency_migration

Dependency migration

Dockerfile

@@ -16,11 +16,11 @@ RUN pip3 --no-cache-dir install -r requirements.txt
 # the mariadb plugin directory seems to be misconfigured
 # bei default. In order to work properly we manually adjust
 # the path.
-ENV MARIADB_PLUGIN_DIR /usr/lib/mariadb/plugin
+ENV MARIADB_PLUGIN_DIR=/usr/lib/mariadb/plugin
 
 # EXPOSE 5000
 # CMD ["python3", "server.py"]
 
 #run the command to start uWSGI
-CMD ["uwsgi", "app.ini"]
+CMD ["gunicorn", "-k", "uvicorn.workers.UvicornWorker", "-b", "0.0.0.0:5000", "-w", "4", "server:connex_app"]
 

TestCases/test_ceRNAInteraction_findAll.py

@@ -1,5 +1,7 @@
 from config import *
-import models, geneInteraction, unittest
+import models, unittest
+with app.app_context(): 
+    import geneInteraction
 from flask import abort
 import sqlalchemy as sa
 from werkzeug.exceptions import HTTPException
@@ -41,9 +43,10 @@ def test_read_all_genes(disease_name=None, ensg_number=None, gene_symbol=None, g
     queries_2 = []
     # if specific disease_name is given:
     if disease_name is not None:
-        run = models.SpongeRun.query.join(models.Dataset, models.Dataset.dataset_ID == models.SpongeRun.dataset_ID) \
-            .filter(models.Dataset.disease_name.like("%" + disease_name + "%")) \
-            .all()
+        with app.app_context():
+            run = models.SpongeRun.query.join(models.Dataset, models.Dataset.dataset_ID == models.SpongeRun.dataset_ID) \
+                .filter(models.Dataset.disease_name.like("%" + disease_name + "%")) \
+                .all()
 
         if len(run) > 0:
             run_IDs = [i.sponge_run_ID for i in run]
@@ -143,7 +146,7 @@ def test_read_all_genes(disease_name=None, ensg_number=None, gene_symbol=None, g
         else:
             # Serialize the data for the response depending on parameter all
             schema = models.GeneInteractionDatasetShortSchema(many=True)
-        return schema.dump(interaction_result).data
+        return schema.dump(interaction_result)
     else:
         abort(404, "No information with given parameters found")
 
@@ -153,66 +156,51 @@ def test_read_all_genes(disease_name=None, ensg_number=None, gene_symbol=None, g
 
 class TestDataset(unittest.TestCase):
 
-    def test_abort_error_disease(self):
+    def setUp(self):
         app.config["TESTING"] = True
         self.app = app.test_client()
+        self.app_context = app.app_context()
+        self.app_context.push()
 
+    def tearDown(self):
+        self.app_context.pop()
+
+    def test_abort_error_disease(self):
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(disease_name="foobar", pValue = None), 404)
 
     def test_abort_error_limit(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(disease_name="foobar", limit = 20000, pValue = None), 404)
 
     def test_abort_error_ensg(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(ensg_number=["ENSGfoobar"], pValue = None), 404)
 
     def test_abort_error_gene_symbol(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(gene_symbol=["foobar"], pValue = None), 404)
 
     def test_abort_error_ensg_and_gene_symbol(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(ensg_number=["ENSGfoobar"],gene_symbol=["foobar"], pValue = None), 404)
 
     def test_abort_error_gene_type(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(gene_type="foobar", pValue = None), 404)
 
     def test_abort_error_no_data(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         with self.assertRaises(HTTPException) as http_error:
             # retrieve current API response to request
             self.assertEqual(geneInteraction.read_all_genes(disease_name="bladder urothelial carcinoma", ensg_number=['ENSG00000023041'], pValue = None), 404)
 
     def test_findAll_disease_and_ensg(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma', ensg_number=['ENSG00000172137','ENSG00000078237'], limit=50, pValue = None)
 
@@ -223,9 +211,6 @@ def test_findAll_disease_and_ensg(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma', gene_symbol=['CALB2','TIGAR'], limit=50, pValue = None)
 
@@ -236,9 +221,6 @@ def test_findAll_disease_and_gene_symbol(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_ensg_pValue_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, pValue=0.5, pValueDirection="<", sorting="pValue")
@@ -251,9 +233,6 @@ def test_findAll_disease_and_ensg_pValue_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_ensg_pValue_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, pValue=0.5, pValueDirection=">", sorting="pValue")
@@ -266,9 +245,6 @@ def test_findAll_disease_and_ensg_pValue_greater(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_pValue_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, pValue=0.5, pValueDirection="<", sorting="pValue")
@@ -281,9 +257,6 @@ def test_findAll_disease_and_gene_symbol_pValue_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_pValue_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, pValue=0.5, pValueDirection=">", sorting="pValue")
@@ -297,9 +270,6 @@ def test_findAll_disease_and_gene_symbol_pValue_greater(self):
 
 
     def test_findAll_disease_and_ensg_correlation_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, correlation=0.2, correlationDirection="<", sorting="correlation", pValue = None)
@@ -312,9 +282,6 @@ def test_findAll_disease_and_ensg_correlation_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_ensg_correlation_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, correlation=0.1, correlationDirection=">", sorting="correlation", pValue = None)
@@ -327,9 +294,6 @@ def test_findAll_disease_and_ensg_correlation_greater(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_correlation_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, correlation=0.2, correlationDirection="<", sorting="correlation",pValue = None)
@@ -342,9 +306,6 @@ def test_findAll_disease_and_gene_symbol_correlation_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_correlation_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, correlation=0.1, correlationDirection=">", sorting="correlation",pValue = None)
@@ -358,9 +319,6 @@ def test_findAll_disease_and_gene_symbol_correlation_greater(self):
 
 
     def test_findAll_disease_and_ensg_mscor_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, mscor=0.02, mscorDirection="<", sorting="mscor",pValue = None)
@@ -373,9 +331,6 @@ def test_findAll_disease_and_ensg_mscor_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_ensg_mscor_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             ensg_number=['ENSG00000172137', 'ENSG00000078237'], limit=50, mscor=0.01, mscorDirection=">", sorting="mscor", pValue = None)
@@ -388,9 +343,6 @@ def test_findAll_disease_and_ensg_mscor_greater(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_mscor_smaller(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, mscor=0.02, mscorDirection="<", sorting="mscor", pValue = None)
@@ -403,9 +355,6 @@ def test_findAll_disease_and_gene_symbol_mscor_smaller(self):
         self.assertEqual(mock_response, api_response)
 
     def test_findAll_disease_and_gene_symbol_mscor_greater(self):
-        app.config["TESTING"] = True
-        self.app = app.test_client()
-
         # retrieve correct database response to request
         mock_response = test_read_all_genes(disease_name='bladder urothelial carcinoma',
                                             gene_symbol=['CALB2', 'TIGAR'], limit=50, mscor=0.01, mscorDirection=">", sorting="mscor", pValue = None)

TestCases/test_ceRNAInteraction_findSpecific.py

@@ -1,5 +1,7 @@
 from config import *
-import models, geneInteraction, unittest
+import models, unittest
+with app.app_context(): 
+    import geneInteraction
 from flask import abort
 import sqlalchemy as sa
 from werkzeug.exceptions import HTTPException
@@ -74,7 +76,7 @@ def test_read_specific_interaction(disease_name=None, ensg_number=None, gene_sym
 
     if len(interaction_result) > 0:
         # Serialize the data for the response depending on parameter all
-        return models.GeneInteractionDatasetShortSchema(many=True).dump(interaction_result).data
+        return models.GeneInteractionDatasetShortSchema(many=True).dump(interaction_result)
     else:
         abort(404, "No information with given parameters found")
 
@@ -84,6 +86,16 @@ def test_read_specific_interaction(disease_name=None, ensg_number=None, gene_sym
 ########################################################################################################################
 
 class TestDataset(unittest.TestCase):
+
+    def setUp(self):
+        app.config["TESTING"] = True
+        self.app = app.test_client()
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
     def test_abort_error_disease(self):
         app.config["TESTING"] = True
         self.app = app.test_client()

TestCases/test_findceRNA.py

@@ -1,11 +1,13 @@
 from config import *
-import models, geneInteraction, unittest
+import models, unittest
+with app.app_context(): 
+    import geneInteraction
 from flask import abort
 from werkzeug.exceptions import HTTPException
 
 def test_read_all_gene_network_analysis(disease_name=None, ensg_number=None, gene_symbol=None, gene_type=None,
                                    minBetweenness=None, minNodeDegree=None, minEigenvector=None,
-                                   sorting=None, descending=True, limit=100, offset=0):
+                                   sorting=None, descending=True, limit=100, offset=0, db_version=2):
     """
     This function responds to a request for /sponge/findceRNA
     and returns all interactions the given identification (ensg_number or gene_symbol) in all available datasets is in involved and satisfies the given filters
@@ -21,6 +23,7 @@ def test_read_all_gene_network_analysis(disease_name=None, ensg_number=None, gen
     :param limit: number of results that shouls be shown
     :param offset: startpoint from where results should be shown
     :return: all ceRNAInteractions in the dataset of interest that satisfy the given filters
+    :db_version: database version
     """
 
     # test limit
@@ -76,6 +79,8 @@ def test_read_all_gene_network_analysis(disease_name=None, ensg_number=None, gen
         queries.append(models.networkAnalysis.eigenvector > minEigenvector)
     if gene_type is not None:
         queries.append(models.Gene.gene_type == gene_type)
+    if db_version is not None: 
+        queries.append(models.Dataset.version == db_version)
 
     # add all sorting if given:
     sort = [models.networkAnalysis.sponge_run_ID]
@@ -105,7 +110,7 @@ def test_read_all_gene_network_analysis(disease_name=None, ensg_number=None, gen
 
     if len(result) > 0:
         schema = models.networkAnalysisSchema(many=True)
-        return schema.dump(result).data
+        return schema.dump(result)
     else:
         abort(404, "Not data found that satisfies the given filters")
 
@@ -114,6 +119,16 @@ def test_read_all_gene_network_analysis(disease_name=None, ensg_number=None, gen
 ########################################################################################################################
 
 class TestDataset(unittest.TestCase):
+
+    def setUp(self):
+        app.config["TESTING"] = True
+        self.app = app.test_client()
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
     def test_abort_error_disease(self):
         app.config["TESTING"] = True
         self.app = app.test_client()
@@ -151,7 +166,7 @@ def test_findceRNA_disease_and_type(self):
         self.app = app.test_client()
 
         # retrieve correct database response to request
-        mock_response = test_read_all_gene_network_analysis(disease_name='bladder urothelial carcinoma', gene_type='protein_coding', limit=50)
+        mock_response = test_read_all_gene_network_analysis(disease_name='bladder urothelial carcinoma', gene_type='protein_coding', limit=50, db_version=1)
 
         # retrieve current API response to request
         api_response = geneInteraction.read_all_gene_network_analysis(disease_name='bladder urothelial carcinoma',

TestCases/test_getDataset.py

@@ -1,5 +1,7 @@
 from config import *
-import models, dataset, unittest
+import models, unittest
+with app.app_context(): 
+    import dataset
 from flask import abort
 from werkzeug.exceptions import HTTPException
 
@@ -25,7 +27,7 @@ def test_read(disease_name=None):
     # Did we find a dataset?
     if len(data) > 0:
         # Serialize the data for the response
-        return models.DatasetSchema(many=True).dump(data).data
+        return models.DatasetSchema(many=True).dump(data)
     else:
         abort(404, 'No data found for name: {disease_name}'.format(disease_name=disease_name))
 
@@ -35,6 +37,15 @@ def test_read(disease_name=None):
 
 class TestDataset(unittest.TestCase):
 
+    def setUp(self):
+        app.config["TESTING"] = True
+        self.app = app.test_client()
+        self.app_context = app.app_context()
+        self.app_context.push()
+
+    def tearDown(self):
+        self.app_context.pop()
+
     def test_get_dataset_information_all(self):
         app.config["TESTING"] = True
         self.app = app.test_client()