Merge pull request #20 from mboudet/master

Fix connection closed error for big files when loading interproscan

Author: abretaud

.github/workflows/test.yml

@@ -8,7 +8,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install flake8
       run: pip install flake8 flake8-import-order
     - name: Flake8
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.8]
         tripal: [0, 1]
     steps:
     - name: Checkout
@@ -53,7 +53,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Python install
       run: pip install -U pip setuptools nose build
     - name: Build a binary wheel and a source tarball

README.md

@@ -87,6 +87,9 @@ $ chakin feature load_fasta \
 
 ## History
 
+- 2.3.8
+    - Fix connection closed error when loading big interproscan files
+
 - 2.3.7
     - Fix loading of expression data when first column header is not empty
 

chado/__init__.py

@@ -54,7 +54,11 @@ def __init__(self, dbhost="localhost", dbname="chado", dbuser="chado", dbpass="c
             engine_url = 'postgresql://%s:%s@%s:%s/%s' % (self.dbuser, self.dbpass, self.dbhost, self.dbport, self.dbname)
 
         if pool_connections:
-            self._engine = create_engine(engine_url)
+            self._engine = create_engine(engine_url, pool_pre_ping=True, connect_args={
+                "keepalives": 1,
+                "keepalives_idle": 30,
+                "keepalives_interval": 10,
+            })
         else:
             # Prevent SQLAlchemy to make a connection pool.
             # Useful for galaxy dynamic options as otherwise it triggers "sorry, too many clients already" errors after a while

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="chado",
-    version='2.3.7',
+    version='2.3.8',
     description="Chado library",
     author="Anthony Bretaudeau",
     author_email="anthony.bretaudeau@inrae.fr",
@@ -25,10 +25,5 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
         "Topic :: Scientific/Engineering",
-        "Programming Language :: Python :: 2",
-        "Programming Language :: Python :: 2.7",
-        "Programming Language :: Python :: 3.4",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
     ])