Merge pull request #17 from galaxy-genome-annotation/has_table

Fix has_table error

Author: abretaud

.github/workflows/test.yml

@@ -46,6 +46,7 @@ jobs:
 
   pypi:
     runs-on: ubuntu-latest
+    needs: [lint, py_test]
     name: Deploy release to Pypi
     steps:
     - name: Checkout

README.md

@@ -87,6 +87,9 @@ $ chakin feature load_fasta \
 
 ## History
 
+- 2.3.5
+    - Fix has_table() calls with recent sqlalchemy versions
+
 - 2.3.4
     - Now requires biopython >=1.78
     - Fixes biopython sequence usage in recent biopython

chado/load/__init__.py

@@ -21,7 +21,7 @@
 
 from future import standard_library
 
-from sqlalchemy import Column, Float, ForeignKey, Integer, String, Table
+from sqlalchemy import Column, Float, ForeignKey, Integer, String, Table, inspect
 from sqlalchemy import exc as sa_exc
 
 standard_library.install_aliases()
@@ -824,7 +824,7 @@ def _setup_tables(self, module):
             self.ci.create_cvterm(term='analysis_blast_output_iteration_hits', term_definition='Hits of a blast', cv_name='tripal', db_name='tripal')
             # Tables for blast
             added_table = False
-            if not self.engine.dialect.has_table(self.engine, 'tripal_analysis_blast', schema='public'):
+            if not inspect(self.engine).has_table('tripal_analysis_blast', schema='public'):
                 tripal_analysis_blast_table = Table(
                     'tripal_analysis_blast', self.metadata,
                     Column('db_id', Integer, primary_key=True, nullable=False, default=0, index=True),
@@ -839,7 +839,7 @@ def _setup_tables(self, module):
                 tripal_analysis_blast_table.create(self.engine)
                 added_table = True
 
-            if not self.engine.dialect.has_table(self.engine, 'blast_organisms', schema=self.ci.dbschema):
+            if not inspect(self.engine).has_table('blast_organisms', schema=self.ci.dbschema):
                 blast_organisms_table = Table(
                     'blast_organisms', self.metadata,
                     Column('blast_org_id', Integer, primary_key=True, nullable=False),
@@ -855,7 +855,7 @@ def _setup_tables(self, module):
                     self.ci._reflect_tables()
                     self.model = self.ci.model
 
-            if not self.engine.dialect.has_table(self.engine, 'blast_hit_data', schema=self.ci.dbschema):
+            if not inspect(self.engine).has_table('blast_hit_data', schema=self.ci.dbschema):
                 blast_hit_data_table = Table(
                     'blast_hit_data', self.metadata,
                     Column('analysisfeature_id', Integer, ForeignKey(self.model.analysisfeature.analysisfeature_id, ondelete="CASCADE"), nullable=False, index=True, primary_key=True),

docs/conf.py

@@ -5,6 +5,8 @@
 
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..', 'chado'))
 
+project = "Python-chado"
+
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.napoleon']
 master_doc = 'index'
 

setup.py

@@ -6,7 +6,7 @@
 
 setup(
     name="chado",
-    version='2.3.4',
+    version='2.3.5',
     description="Chado library",
     author="Anthony Bretaudeau",
     author_email="[email protected]",