Merge pull request #52 from DeepRank/issue51

Issue51

Author: NicoRenaud

pdb2sql/many2sql.py

@@ -13,10 +13,30 @@
 class many2sql(pdb2sql):
 
     def __init__(self, pdbfiles, tablenames=None):
-        """Create a sql database containing multiple pdbs."""
+        """Create a sql database containing multiple pdbs.
+
+        Args:
+            pdbfiles(list): list of pdb files or data.
+            tablenames (list): list of table names in string
+                Defaults to None.
+
+        Raises:
+            TypeError: pdbfiles must be a list
+            TypeError: tablenames must be a list
+            TypeError: tablenames must be a list of strings
+        """
 
         if not isinstance(pdbfiles, list):
-            raise ValueError('pdbfiles must be a list')
+            raise TypeError('pdbfiles must be a list')
+
+        if tablenames is not None:
+            if not isinstance(tablenames, list):
+                raise TypeError('tablenames must be a list')
+            else:
+                for i in tablenames:
+                    if not isinstance(i, str):
+                        raise TypeError(f'tablenames must be a list of strings,'
+                            f' {i} is a type of {type(i)}')
 
         self.npdb = len(pdbfiles)
 

test/test_many2sql.py

@@ -1,5 +1,4 @@
 import unittest
-import os
 import numpy as np
 from pathlib import Path
 from pdb2sql import many2sql
@@ -12,53 +11,46 @@
 class TestMany2SQL(unittest.TestCase):
 
     def setUp(self):
-        self.pdb1 = os.fspath(Path(pdb_folder, '1AK4', '1AK4_5w.pdb'))
-        self.pdb2 = os.fspath(Path(pdb_folder, '1AK4', '1AK4_10w.pdb'))
+        pdb1 = Path(pdb_folder, '1AK4', '1AK4_5w.pdb')
+        pdb2 = Path(pdb_folder, '1AK4', '1AK4_10w.pdb')
+        self.pdbs = [pdb1, pdb2]
+        self.tablenames = [str(pdb1), str(pdb2)]
 
     def test_init_from_files(self):
         """Verify init from path."""
-        pdbs = [self.pdb1, self.pdb2]
-        many = many2sql(pdbs, tablenames=pdbs)
+        many = many2sql(self.pdbs, tablenames=self.tablenames)
 
     def test_init_from_pdb_data(self):
         """Verify init from data."""
-        pdbs = [self.pdb1, self.pdb2]
-        sqls = [pdb2sql(p) for p in pdbs]
+        sqls = [pdb2sql(p) for p in self.pdbs]
         data = [db.sql2pdb() for db in sqls]
-        many = many2sql(data, tablenames=pdbs)
+        many = many2sql(data, tablenames=self.tablenames)
 
     def test_init_from_sql(self):
         """Verify default sqls."""
-        pdbs = [self.pdb1, self.pdb2]
-        sqls = [pdb2sql(p) for p in pdbs]
-        many = many2sql(sqls, tablenames=pdbs)
+        sqls = [pdb2sql(p) for p in self.pdbs]
+        many = many2sql(sqls, tablenames=self.tablenames)
 
     def test_call(self):
         """Test call function."""
-        pdbs = [self.pdb1, self.pdb2]
-        many = many2sql(pdbs, tablenames=pdbs)
+        many = many2sql(self.pdbs, tablenames=self.tablenames)
         chainA = many(chainID='A')
 
     def test_get_all(self):
         """Test get_all function."""
-        pdbs = [self.pdb1, self.pdb2]
-        many = many2sql(pdbs, tablenames=pdbs)
+        many = many2sql(self.pdbs, tablenames=self.tablenames)
         data = many.get_all('x,y,z', chainID='A')
 
     def test_get_intersection(self):
         """Test get_all function."""
-        pdbs = [self.pdb1, self.pdb2]
-        many = many2sql(pdbs, tablenames=pdbs)
+        many = many2sql(self.pdbs, tablenames=self.tablenames)
         data = many.get_intersection('x,y,z')
 
     def test_intersect(self):
         """Test get_all function."""
-        pdbs = [self.pdb1, self.pdb2]
-        many = many2sql(pdbs, tablenames=pdbs)
+        many = many2sql(self.pdbs, tablenames=self.tablenames)
         chainA = many.intersect()
 
 
 if __name__ == '__main__':
-    # runner = unittest.TextTestRunner(verbosity=2)
-    # unittest.main(testRunner=runner)
-    unittest.main()
+    unittest.main()