From 2b8686621594ead5d8526c7b4847dbd6bead553a Mon Sep 17 00:00:00 2001 From: mboudet Date: Wed, 2 Mar 2022 18:57:56 +0100 Subject: [PATCH 1/6] Fix connection closed error for big files --- chado/__init__.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/chado/__init__.py b/chado/__init__.py index ce6a716..66c5966 100755 --- a/chado/__init__.py +++ b/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 From 1a2ff8890f71fb96637404e9a50e6d033bd8a49f Mon Sep 17 00:00:00 2001 From: mboudet Date: Tue, 8 Mar 2022 17:43:27 +0100 Subject: [PATCH 2/6] Update test.yml --- .github/workflows/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 0d09f06..558bf30 100644 --- a/.github/workflows/test.yml +++ b/.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 From 68bced83fb780a2ca2c2eff394b0f55bb7a685dc Mon Sep 17 00:00:00 2001 From: mboudet Date: Wed, 9 Mar 2022 09:13:14 +0100 Subject: [PATCH 3/6] Update README.md --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 32c1069..ebcfdec 100644 --- a/README.md +++ b/README.md @@ -87,6 +87,9 @@ $ chakin feature load_fasta \ ## History +- 2.3.8 + - Fix connection closed error when loading big interproscan + - 2.3.7 - Fix loading of expression data when first column header is not empty From 6fe53a0faee5ce819603215935abf7e1893dd873 Mon Sep 17 00:00:00 2001 From: mboudet Date: Wed, 9 Mar 2022 09:14:18 +0100 Subject: [PATCH 4/6] Update setup.py --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b2713e6..11f7bf0 100644 --- a/setup.py +++ b/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", @@ -31,4 +31,5 @@ "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", ]) From e6dd0d147050176691ac583070b8d16dd150445f Mon Sep 17 00:00:00 2001 From: mboudet Date: Wed, 9 Mar 2022 09:15:52 +0100 Subject: [PATCH 5/6] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ebcfdec..300755d 100644 --- a/README.md +++ b/README.md @@ -88,7 +88,7 @@ $ chakin feature load_fasta \ ## History - 2.3.8 - - Fix connection closed error when loading big interproscan + - Fix connection closed error when loading big interproscan files - 2.3.7 - Fix loading of expression data when first column header is not empty From e9211ac789443c48ac4f8241ee43a80887228e56 Mon Sep 17 00:00:00 2001 From: mboudet Date: Wed, 9 Mar 2022 11:44:42 +0100 Subject: [PATCH 6/6] Update setup.py --- setup.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/setup.py b/setup.py index 11f7bf0..9aad9f2 100644 --- a/setup.py +++ b/setup.py @@ -25,11 +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", ])