deriva 1.7.3__py3-none-any.whl → 1.7.5__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- deriva/config/rollback_annotation.py +1 -1
- deriva/core/__init__.py +1 -1
- deriva/core/datapath.py +55 -55
- deriva/core/ermrest_model.py +702 -186
- deriva/core/hatrac_cli.py +3 -5
- deriva/core/hatrac_store.py +9 -20
- deriva/core/mmo.py +379 -0
- deriva/transfer/download/processors/postprocess/transfer_post_processor.py +2 -2
- deriva/transfer/download/processors/query/base_query_processor.py +2 -1
- deriva/transfer/upload/deriva_upload.py +4 -0
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/METADATA +1 -1
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/RECORD +25 -16
- tests/deriva/core/mmo/__init__.py +0 -0
- tests/deriva/core/mmo/base.py +300 -0
- tests/deriva/core/mmo/test_mmo_drop.py +252 -0
- tests/deriva/core/mmo/test_mmo_find.py +90 -0
- tests/deriva/core/mmo/test_mmo_prune.py +196 -0
- tests/deriva/core/mmo/test_mmo_rename.py +222 -0
- tests/deriva/core/mmo/test_mmo_replace.py +180 -0
- tests/deriva/core/test_datapath.py +52 -26
- tests/deriva/core/test_ermrest_model.py +782 -0
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/LICENSE +0 -0
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/WHEEL +0 -0
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/entry_points.txt +0 -0
- {deriva-1.7.3.dist-info → deriva-1.7.5.dist-info}/top_level.txt +0 -0
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# Tests for the datapath module.
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#
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# Environment variables:
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# DERIVA_PY_TEST_HOSTNAME: hostname of the test server
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# DERIVA_PY_CATALOG: catalog identifier of the reusable test catalog (optional)
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# DERIVA_PY_TEST_CREDENTIAL: user credential, if none, it will attempt to get credential for given hostname (optional)
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# DERIVA_PY_TEST_VERBOSE: set for verbose logging output to stdout (optional)
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import logging
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import os
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import unittest
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from deriva.core import DerivaServer, get_credential, ermrest_model, tag
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logger = logging.getLogger(__name__)
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logger.addHandler(logging.StreamHandler())
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if os.getenv("DERIVA_PY_TEST_VERBOSE"):
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logger.setLevel(logging.DEBUG)
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else:
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logger.setLevel(logging.INFO)
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hostname = os.getenv("DERIVA_PY_TEST_HOSTNAME")
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@unittest.skipUnless(hostname, "Test host not specified")
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class ErmrestModelTests (unittest.TestCase):
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catalog = None
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@classmethod
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def _purgeCatalog(cls):
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model = cls.catalog.getCatalogModel()
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# exclude the 'public' schema
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schemas = [s for s in model.schemas.values() if s.name != 'public']
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# drop all fkeys
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for s in schemas:
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for t in s.tables.values():
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for fk in list(t.foreign_keys):
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fk.drop()
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# drop all tables and schemas
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for s in list(schemas):
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for t in list(s.tables.values()):
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t.drop()
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s.drop()
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@classmethod
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def setUpClass(cls):
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credential = os.getenv("DERIVA_PY_TEST_CREDENTIAL") or get_credential(hostname)
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server = DerivaServer('https', hostname, credentials=credential)
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catalog_id = os.getenv("DERIVA_PY_TEST_CATALOG")
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if catalog_id is not None:
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logger.info(f"Reusing catalog {catalog_id} on host {hostname}")
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cls.catalog = server.connect_ermrest(catalog_id)
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cls._purgeCatalog()
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else:
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cls.catalog = server.create_ermrest_catalog()
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logger.info(f"Created catalog {cls.catalog.catalog_id} on host {hostname}")
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@classmethod
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def tearDownClass(cls):
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if cls.catalog and os.getenv("DERIVA_PY_TEST_CATALOG") is None:
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logger.info(f"Deleting catalog {cls.catalog.catalog_id} on host {hostname}")
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cls.catalog.delete_ermrest_catalog(really=True)
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def setUp(self):
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self.model = self.catalog.getCatalogModel()
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def tearDown(self):
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self._purgeCatalog()
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def _create_schema_with_fkeys(self):
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"""Creates a simple schema of two tables with a fkey relationship from child to parent."""
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# build a single, low-level catalog /schema POST operation
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# should be (slightly) faster and avoids using the client APIs under test in this module
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schema_def = ermrest_model.Schema.define('schema_with_fkeys')
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schema_def["tables"] = {
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"parent": ermrest_model.Table.define(
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'parent',
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column_defs=[
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ermrest_model.Column.define('id', ermrest_model.builtin_types.text),
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ermrest_model.Column.define('id_extra', ermrest_model.builtin_types.text),
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],
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key_defs=[
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ermrest_model.Key.define(['id'], constraint_name='parent_id_key'),
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ermrest_model.Key.define(['id', 'id_extra'], constraint_name='parent_compound_key'),
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]
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),
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"child": ermrest_model.Table.define(
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'child',
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column_defs=[
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ermrest_model.Column.define('parent_id', ermrest_model.builtin_types.text),
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ermrest_model.Column.define('parent_id_extra', ermrest_model.builtin_types.text),
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],
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fkey_defs=[
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ermrest_model.ForeignKey.define(
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['parent_id'], 'schema_with_fkeys', 'parent', ['id']
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),
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ermrest_model.ForeignKey.define(
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['parent_id_extra', 'parent_id'], 'schema_with_fkeys', 'parent', ['id_extra', 'id']
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)
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]
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),
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}
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self.catalog.post('/schema', json=[schema_def])
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# refresh the local state of the model
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self.model = self.catalog.getCatalogModel()
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def test_0a_schema_define_defaults(self):
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sname = "test_schema"
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sdef = ermrest_model.Schema.define(sname)
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self.assertEqual(sdef.get("schema_name"), sname)
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self.assertEqual(sdef.get("comment"), None)
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self.assertEqual(sdef.get("acls"), dict())
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self.assertEqual(sdef.get("annotations"), dict())
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_test_comment = "my comment"
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_test_acls = {
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"insert": ["a"],
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"update": ["b"],
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}
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_test_acl_bindings = {
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}
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_test_annotations = {"tag1": "value1"}
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def test_0b_schema_define_custom(self):
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sname = "test_schema"
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sdef = ermrest_model.Schema.define(sname, self._test_comment, self._test_acls, self._test_annotations)
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self.assertEqual(sdef.get("schema_name"), sname)
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self.assertEqual(sdef.get("comment"), self._test_comment)
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self.assertEqual(sdef.get("acls"), self._test_acls)
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self.assertEqual(sdef.get("annotations"), self._test_annotations)
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def test_1a_column_define_defaults(self):
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cname = "test_column"
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cdef = ermrest_model.Column.define(cname, ermrest_model.builtin_types.text)
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self.assertEqual(cdef.get("name"), cname)
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ctype = cdef.get("type")
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self.assertIsInstance(ctype, dict)
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self.assertEqual(ctype.get("typename"), "text")
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self.assertEqual(cdef.get("nullok"), True)
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self.assertEqual(cdef.get("default"), None)
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self.assertEqual(cdef.get("comment"), None)
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self.assertEqual(cdef.get("acls"), dict())
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self.assertEqual(cdef.get("acl_bindings"), dict())
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self.assertEqual(cdef.get("annotations"), dict())
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def test_1b_column_define_custom(self):
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cname = "test_column"
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nullok = False
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default = "my default"
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cdef = ermrest_model.Column.define(
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cname, ermrest_model.builtin_types.text, nullok, default,
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self._test_comment, self._test_acls, self._test_acl_bindings, self._test_annotations,
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)
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self.assertEqual(cdef.get("name"), cname)
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ctype = cdef.get("type")
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self.assertIsInstance(ctype, dict)
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self.assertEqual(ctype.get("typename"), "text")
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self.assertEqual(cdef.get("nullok"), nullok)
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self.assertEqual(cdef.get("default"), default)
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self.assertEqual(cdef.get("comment"), self._test_comment)
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self.assertEqual(cdef.get("acls"), self._test_acls)
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self.assertEqual(cdef.get("acl_bindings"), self._test_acl_bindings)
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self.assertEqual(cdef.get("annotations"), self._test_annotations)
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def test_1c_key_define_defaults(self):
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cnames = ["id"]
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kdef = ermrest_model.Key.define(cnames)
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self.assertEqual(kdef.get("unique_columns"), cnames)
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self.assertEqual(not kdef.get("names"), True)
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self.assertEqual(kdef.get("comment"), None)
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self.assertEqual(kdef.get("annotations"), dict())
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def test_1d_key_define_custom(self):
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cnames = ["id"]
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constraint_name = "my_constraint"
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kdef = ermrest_model.Key.define(cnames, None, self._test_comment, self._test_annotations, constraint_name)
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self.assertEqual(kdef.get("unique_columns"), cnames)
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self.assertIsInstance(kdef.get("names"), list)
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self.assertIsInstance(kdef.get("names")[0], list)
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self.assertEqual(kdef.get("names")[0][1], constraint_name)
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self.assertEqual(kdef.get("comment"), self._test_comment)
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self.assertEqual(kdef.get("annotations"), self._test_annotations)
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def test_1e_fkey_define_defaults(self):
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fk_colnames = ["fk1"]
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pk_sname = "pk_schema"
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pk_tname = "pk_table"
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pk_colnames = ["RID"]
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fkdef = ermrest_model.ForeignKey.define(
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fk_colnames,
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pk_sname,
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pk_tname,
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pk_colnames,
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)
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self.assertEqual([ c.get("column_name") for c in fkdef.get("foreign_key_columns") ], fk_colnames)
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self.assertEqual([ c.get("column_name") for c in fkdef.get("referenced_columns") ], pk_colnames)
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self.assertEqual(all([ c.get("schema_name") == pk_sname for c in fkdef.get("referenced_columns") ]), True)
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self.assertEqual(all([ c.get("table_name") == pk_tname for c in fkdef.get("referenced_columns") ]), True)
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self.assertEqual(fkdef.get("on_update"), "NO ACTION")
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self.assertEqual(fkdef.get("on_delete"), "NO ACTION")
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self.assertEqual(not fkdef.get("names"), True)
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self.assertEqual(fkdef.get("comment"), None)
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self.assertEqual(fkdef.get("acls"), dict())
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self.assertEqual(fkdef.get("acl_bindings"), dict())
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self.assertEqual(fkdef.get("annotations"), dict())
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def test_1f_fkey_define_custom(self):
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fk_colnames = ["fk1"]
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pk_sname = "pk_schema"
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pk_tname = "pk_table"
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pk_colnames = ["RID"]
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constraint_name = "my_constraint"
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action1 = "CASCADE"
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action2 = "RESTRICT"
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fkdef = ermrest_model.ForeignKey.define(
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fk_colnames,
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pk_sname,
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pk_tname,
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pk_colnames,
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action1,
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action2,
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None,
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self._test_comment,
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self._test_acls,
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self._test_acl_bindings,
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self._test_annotations,
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constraint_name,
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)
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self.assertEqual([ c.get("column_name") for c in fkdef.get("foreign_key_columns") ], fk_colnames)
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self.assertEqual([ c.get("column_name") for c in fkdef.get("referenced_columns") ], pk_colnames)
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self.assertEqual(all([ c.get("schema_name") == pk_sname for c in fkdef.get("referenced_columns") ]), True)
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self.assertEqual(all([ c.get("table_name") == pk_tname for c in fkdef.get("referenced_columns") ]), True)
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self.assertEqual(fkdef.get("on_update"), action1)
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self.assertEqual(fkdef.get("on_delete"), action2)
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self.assertIsInstance(fkdef.get("names"), list)
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self.assertIsInstance(fkdef.get("names")[0], list)
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self.assertEqual(fkdef.get("names")[0][1], constraint_name)
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self.assertEqual(fkdef.get("comment"), self._test_comment)
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self.assertEqual(fkdef.get("acls"), self._test_acls)
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self.assertEqual(fkdef.get("acl_bindings"), self._test_acl_bindings)
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self.assertEqual(fkdef.get("annotations"), self._test_annotations)
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def test_2a_table_define_defaults(self):
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tname = "test_table"
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tdef = ermrest_model.Table.define(
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tname,
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[
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ermrest_model.Column.define("id", ermrest_model.builtin_types.text),
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],
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)
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self.assertEqual(tdef.get("table_name"), tname)
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cdefs = tdef.get("column_definitions")
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self.assertIsInstance(cdefs, list)
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self.assertEqual(len(cdefs), 5 + 1)
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kdefs = tdef.get("keys")
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self.assertIsInstance(kdefs, list)
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self.assertEqual(len(kdefs), 1)
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fkdefs = tdef.get("foreign_keys")
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self.assertIsInstance(fkdefs, list)
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self.assertEqual(len(fkdefs), 2)
|
|
265
|
+
self.assertEqual(tdef.get("comment"), None)
|
|
266
|
+
self.assertEqual(tdef.get("acls"), dict())
|
|
267
|
+
self.assertEqual(tdef.get("acl_bindings"), dict())
|
|
268
|
+
self.assertEqual(tdef.get("annotations"), dict())
|
|
269
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
270
|
+
table = schema.create_table(tdef)
|
|
271
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
272
|
+
|
|
273
|
+
def test_2b_table_define_custom(self):
|
|
274
|
+
tname = "test_table"
|
|
275
|
+
tdef = ermrest_model.Table.define(
|
|
276
|
+
tname,
|
|
277
|
+
[
|
|
278
|
+
ermrest_model.Column.define("id", ermrest_model.builtin_types.text),
|
|
279
|
+
ermrest_model.Column.define("fk1", ermrest_model.builtin_types.text),
|
|
280
|
+
],
|
|
281
|
+
[
|
|
282
|
+
ermrest_model.Key.define(["id"]),
|
|
283
|
+
],
|
|
284
|
+
[
|
|
285
|
+
ermrest_model.ForeignKey.define(["fk1"], "public", "ERMrest_Client", ["RID"]),
|
|
286
|
+
],
|
|
287
|
+
self._test_comment,
|
|
288
|
+
self._test_acls,
|
|
289
|
+
self._test_acl_bindings,
|
|
290
|
+
self._test_annotations,
|
|
291
|
+
provide_system_fkeys=False,
|
|
292
|
+
)
|
|
293
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
294
|
+
cdefs = tdef.get("column_definitions")
|
|
295
|
+
self.assertIsInstance(cdefs, list)
|
|
296
|
+
self.assertEqual(len(cdefs), 5 + 2)
|
|
297
|
+
kdefs = tdef.get("keys")
|
|
298
|
+
self.assertIsInstance(kdefs, list)
|
|
299
|
+
self.assertEqual(len(kdefs), 1 + 1)
|
|
300
|
+
fkdefs = tdef.get("foreign_keys")
|
|
301
|
+
self.assertIsInstance(fkdefs, list)
|
|
302
|
+
self.assertEqual(len(fkdefs), 1)
|
|
303
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
304
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
305
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
306
|
+
self.assertEqual(tdef.get("annotations"), self._test_annotations)
|
|
307
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
308
|
+
table = schema.create_table(tdef)
|
|
309
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
310
|
+
|
|
311
|
+
def test_2c_table_define_with_reference(self):
|
|
312
|
+
tname = "test_table"
|
|
313
|
+
tdef = ermrest_model.Table.define(
|
|
314
|
+
tname,
|
|
315
|
+
[
|
|
316
|
+
ermrest_model.Column.define("id", ermrest_model.builtin_types.text),
|
|
317
|
+
self.model.schemas["public"].tables["ERMrest_Client"],
|
|
318
|
+
],
|
|
319
|
+
[],
|
|
320
|
+
[],
|
|
321
|
+
self._test_comment,
|
|
322
|
+
self._test_acls,
|
|
323
|
+
self._test_acl_bindings,
|
|
324
|
+
self._test_annotations,
|
|
325
|
+
)
|
|
326
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
327
|
+
cdefs = tdef.get("column_definitions")
|
|
328
|
+
self.assertIsInstance(cdefs, list)
|
|
329
|
+
self.assertEqual(len(cdefs), 5 + 2)
|
|
330
|
+
kdefs = tdef.get("keys")
|
|
331
|
+
self.assertIsInstance(kdefs, list)
|
|
332
|
+
self.assertEqual(len(kdefs), 1)
|
|
333
|
+
fkdefs = tdef.get("foreign_keys")
|
|
334
|
+
self.assertIsInstance(fkdefs, list)
|
|
335
|
+
self.assertEqual(len(fkdefs), 2 + 1)
|
|
336
|
+
self.assertEqual(
|
|
337
|
+
{
|
|
338
|
+
(
|
|
339
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
340
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
341
|
+
frozenset(zip(
|
|
342
|
+
( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
343
|
+
( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
344
|
+
))
|
|
345
|
+
)
|
|
346
|
+
for fkdef in fkdefs
|
|
347
|
+
},
|
|
348
|
+
{
|
|
349
|
+
("public", "ERMrest_Client", frozenset([ ("ERMrest_Client", "ID",) ])),
|
|
350
|
+
("public", "ERMrest_Client", frozenset([ ("RCB", "ID",) ])),
|
|
351
|
+
("public", "ERMrest_Client", frozenset([ ("RMB", "ID",) ])),
|
|
352
|
+
}
|
|
353
|
+
)
|
|
354
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
355
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
356
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
357
|
+
self.assertEqual(tdef.get("annotations"), self._test_annotations)
|
|
358
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
359
|
+
table = schema.create_table(tdef)
|
|
360
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
361
|
+
|
|
362
|
+
def test_3a_vocab_define_defaults(self):
|
|
363
|
+
tname = "test_table"
|
|
364
|
+
curie_template = "test:{RID}"
|
|
365
|
+
tdef = ermrest_model.Table.define_vocabulary(
|
|
366
|
+
tname,
|
|
367
|
+
curie_template,
|
|
368
|
+
)
|
|
369
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
370
|
+
cdefs = tdef.get("column_definitions")
|
|
371
|
+
self.assertIsInstance(cdefs, list)
|
|
372
|
+
self.assertEqual(len(cdefs), 5 + 5)
|
|
373
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","ID","Name","Description","Synonyms","URI"})
|
|
374
|
+
cdefs = { c["name"]: c for c in cdefs }
|
|
375
|
+
self.assertEqual(cdefs["ID"]["default"], curie_template)
|
|
376
|
+
self.assertEqual(cdefs["URI"]["default"], '/id/{RID}')
|
|
377
|
+
kdefs = tdef.get("keys")
|
|
378
|
+
self.assertIsInstance(kdefs, list)
|
|
379
|
+
self.assertEqual(len(kdefs), 1 + 3)
|
|
380
|
+
fkdefs = tdef.get("foreign_keys")
|
|
381
|
+
self.assertIsInstance(fkdefs, list)
|
|
382
|
+
self.assertEqual(len(fkdefs), 2)
|
|
383
|
+
self.assertEqual(tdef.get("comment"), None)
|
|
384
|
+
self.assertEqual(tdef.get("acls"), dict())
|
|
385
|
+
self.assertEqual(tdef.get("acl_bindings"), dict())
|
|
386
|
+
self.assertEqual(tdef.get("annotations"), dict())
|
|
387
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
388
|
+
table = schema.create_table(tdef)
|
|
389
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
390
|
+
|
|
391
|
+
def test_3b_vocab_define_custom(self):
|
|
392
|
+
tname = "test_table"
|
|
393
|
+
curie_template = "test:{RID}"
|
|
394
|
+
uri_template = "/id/1/{RID}"
|
|
395
|
+
tdef = ermrest_model.Table.define_vocabulary(
|
|
396
|
+
tname,
|
|
397
|
+
curie_template,
|
|
398
|
+
uri_template,
|
|
399
|
+
[
|
|
400
|
+
ermrest_model.Column.define("fk1", ermrest_model.builtin_types.text),
|
|
401
|
+
],
|
|
402
|
+
[],
|
|
403
|
+
[
|
|
404
|
+
ermrest_model.ForeignKey.define(["fk1"], "public", "ERMrest_Client", ["RID"]),
|
|
405
|
+
],
|
|
406
|
+
self._test_comment,
|
|
407
|
+
self._test_acls,
|
|
408
|
+
self._test_acl_bindings,
|
|
409
|
+
self._test_annotations,
|
|
410
|
+
provide_name_key=False,
|
|
411
|
+
provide_system_fkeys=False,
|
|
412
|
+
)
|
|
413
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
414
|
+
cdefs = tdef.get("column_definitions")
|
|
415
|
+
self.assertIsInstance(cdefs, list)
|
|
416
|
+
self.assertEqual(len(cdefs), 5 + 5 + 1)
|
|
417
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","ID","Name","Description","Synonyms","URI","fk1"})
|
|
418
|
+
cdefs = { c["name"]: c for c in cdefs }
|
|
419
|
+
self.assertEqual(cdefs["ID"]["default"], curie_template)
|
|
420
|
+
self.assertEqual(cdefs["URI"]["default"], uri_template)
|
|
421
|
+
kdefs = tdef.get("keys")
|
|
422
|
+
self.assertIsInstance(kdefs, list)
|
|
423
|
+
self.assertEqual(len(kdefs), 1 + 2)
|
|
424
|
+
fkdefs = tdef.get("foreign_keys")
|
|
425
|
+
self.assertIsInstance(fkdefs, list)
|
|
426
|
+
self.assertEqual(len(fkdefs), 1)
|
|
427
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
428
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
429
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
430
|
+
self.assertEqual(tdef.get("annotations"), self._test_annotations)
|
|
431
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
432
|
+
table = schema.create_table(tdef)
|
|
433
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
434
|
+
|
|
435
|
+
def test_3c_vocab_define_with_reference(self):
|
|
436
|
+
tname = "test_table"
|
|
437
|
+
curie_template = "test:{RID}"
|
|
438
|
+
uri_template = "/id/1/{RID}"
|
|
439
|
+
target = self.model.schemas["public"].tables["ERMrest_Client"]
|
|
440
|
+
self.assertIsInstance(target, ermrest_model.Table)
|
|
441
|
+
tdef = ermrest_model.Table.define_vocabulary(
|
|
442
|
+
tname,
|
|
443
|
+
curie_template,
|
|
444
|
+
uri_template,
|
|
445
|
+
[ target, ],
|
|
446
|
+
[],
|
|
447
|
+
[],
|
|
448
|
+
self._test_comment,
|
|
449
|
+
self._test_acls,
|
|
450
|
+
self._test_acl_bindings,
|
|
451
|
+
self._test_annotations,
|
|
452
|
+
)
|
|
453
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
454
|
+
cdefs = tdef.get("column_definitions")
|
|
455
|
+
self.assertIsInstance(cdefs, list)
|
|
456
|
+
self.assertEqual(len(cdefs), 5 + 5 + 1)
|
|
457
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","ID","Name","Description","Synonyms","URI","ERMrest_Client"})
|
|
458
|
+
kdefs = tdef.get("keys")
|
|
459
|
+
self.assertIsInstance(kdefs, list)
|
|
460
|
+
self.assertEqual(len(kdefs), 1 + 3)
|
|
461
|
+
fkdefs = tdef.get("foreign_keys")
|
|
462
|
+
self.assertIsInstance(fkdefs, list)
|
|
463
|
+
self.assertEqual(len(fkdefs), 2 + 1)
|
|
464
|
+
self.assertEqual(
|
|
465
|
+
{
|
|
466
|
+
(
|
|
467
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
468
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
469
|
+
frozenset(zip(
|
|
470
|
+
( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
471
|
+
( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
472
|
+
))
|
|
473
|
+
)
|
|
474
|
+
for fkdef in fkdefs
|
|
475
|
+
},
|
|
476
|
+
{
|
|
477
|
+
("public", "ERMrest_Client", frozenset([ ("ERMrest_Client", "ID",) ])),
|
|
478
|
+
("public", "ERMrest_Client", frozenset([ ("RCB", "ID",) ])),
|
|
479
|
+
("public", "ERMrest_Client", frozenset([ ("RMB", "ID",) ])),
|
|
480
|
+
}
|
|
481
|
+
)
|
|
482
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
483
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
484
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
485
|
+
self.assertEqual(tdef.get("annotations"), self._test_annotations)
|
|
486
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
487
|
+
table = schema.create_table(tdef)
|
|
488
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
489
|
+
|
|
490
|
+
def test_4a_asset_define_defaults(self):
|
|
491
|
+
tname = "test_table"
|
|
492
|
+
tdef = ermrest_model.Table.define_asset(
|
|
493
|
+
"model_define_schema",
|
|
494
|
+
tname,
|
|
495
|
+
)
|
|
496
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
497
|
+
cdefs = tdef.get("column_definitions")
|
|
498
|
+
self.assertIsInstance(cdefs, list)
|
|
499
|
+
self.assertEqual(len(cdefs), 5 + 5)
|
|
500
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","Filename","Description","Length","MD5","URL"})
|
|
501
|
+
cdefs = { c["name"]: c for c in cdefs }
|
|
502
|
+
kdefs = tdef.get("keys")
|
|
503
|
+
self.assertIsInstance(kdefs, list)
|
|
504
|
+
self.assertEqual(len(kdefs), 1 + 1)
|
|
505
|
+
fkdefs = tdef.get("foreign_keys")
|
|
506
|
+
self.assertIsInstance(fkdefs, list)
|
|
507
|
+
self.assertEqual(len(fkdefs), 2)
|
|
508
|
+
self.assertEqual(tdef.get("acls"), dict())
|
|
509
|
+
self.assertEqual(tdef.get("acl_bindings"), dict())
|
|
510
|
+
self.assertEqual(set(tdef.get("annotations").keys()), {tag.table_display})
|
|
511
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
512
|
+
table = schema.create_table(tdef)
|
|
513
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
514
|
+
|
|
515
|
+
def test_4b_asset_define_custom(self):
|
|
516
|
+
tname = "test_table"
|
|
517
|
+
hatrac_template = "/hatrac/foo/{{{MD5}}}.{{{Filename}}}"
|
|
518
|
+
tdef = ermrest_model.Table.define_asset(
|
|
519
|
+
"model_define_schema",
|
|
520
|
+
tname,
|
|
521
|
+
hatrac_template,
|
|
522
|
+
[
|
|
523
|
+
ermrest_model.Column.define("fk1", ermrest_model.builtin_types.text),
|
|
524
|
+
],
|
|
525
|
+
[],
|
|
526
|
+
[
|
|
527
|
+
ermrest_model.ForeignKey.define(["fk1"], "public", "ERMrest_Client", ["RID"]),
|
|
528
|
+
],
|
|
529
|
+
self._test_comment,
|
|
530
|
+
self._test_acls,
|
|
531
|
+
self._test_acl_bindings,
|
|
532
|
+
self._test_annotations,
|
|
533
|
+
provide_system_fkeys=False,
|
|
534
|
+
)
|
|
535
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
536
|
+
cdefs = tdef.get("column_definitions")
|
|
537
|
+
self.assertIsInstance(cdefs, list)
|
|
538
|
+
self.assertEqual(len(cdefs), 5 + 5 + 1)
|
|
539
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","Filename","Description","Length","MD5","URL","fk1"})
|
|
540
|
+
cdefs = { c["name"]: c for c in cdefs }
|
|
541
|
+
self.assertEqual(cdefs["URL"]["annotations"][tag.asset]["url_pattern"], hatrac_template)
|
|
542
|
+
kdefs = tdef.get("keys")
|
|
543
|
+
self.assertIsInstance(kdefs, list)
|
|
544
|
+
self.assertEqual(len(kdefs), 1 + 1)
|
|
545
|
+
fkdefs = tdef.get("foreign_keys")
|
|
546
|
+
self.assertIsInstance(fkdefs, list)
|
|
547
|
+
self.assertEqual(len(fkdefs), 1)
|
|
548
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
549
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
550
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
551
|
+
annotations = tdef.get("annotations")
|
|
552
|
+
for k, v in self._test_annotations.items():
|
|
553
|
+
self.assertEqual(annotations[k], v)
|
|
554
|
+
self.assertIn(tag.table_display, annotations)
|
|
555
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
556
|
+
table = schema.create_table(tdef)
|
|
557
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
558
|
+
|
|
559
|
+
def test_4c_asset_define_with_reference(self):
|
|
560
|
+
tname = "test_table"
|
|
561
|
+
hatrac_template = "/hatrac/foo/{{{MD5}}}.{{{Filename}}}"
|
|
562
|
+
target = self.model.schemas["public"].tables["ERMrest_Client"]
|
|
563
|
+
self.assertIsInstance(target, ermrest_model.Table)
|
|
564
|
+
tdef = ermrest_model.Table.define_asset(
|
|
565
|
+
"model_define_schema",
|
|
566
|
+
tname,
|
|
567
|
+
hatrac_template,
|
|
568
|
+
[ target, ],
|
|
569
|
+
[],
|
|
570
|
+
[],
|
|
571
|
+
self._test_comment,
|
|
572
|
+
self._test_acls,
|
|
573
|
+
self._test_acl_bindings,
|
|
574
|
+
self._test_annotations,
|
|
575
|
+
)
|
|
576
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
577
|
+
cdefs = tdef.get("column_definitions")
|
|
578
|
+
self.assertIsInstance(cdefs, list)
|
|
579
|
+
self.assertEqual(len(cdefs), 5 + 5 + 1)
|
|
580
|
+
self.assertEqual({ c["name"] for c in cdefs }, {"RID","RCT","RMT","RCB","RMB","Filename","Description","Length","MD5","URL","ERMrest_Client"})
|
|
581
|
+
kdefs = tdef.get("keys")
|
|
582
|
+
self.assertIsInstance(kdefs, list)
|
|
583
|
+
self.assertEqual(len(kdefs), 1 + 1)
|
|
584
|
+
fkdefs = tdef.get("foreign_keys")
|
|
585
|
+
self.assertIsInstance(fkdefs, list)
|
|
586
|
+
self.assertEqual(len(fkdefs), 2 + 1)
|
|
587
|
+
self.assertEqual(
|
|
588
|
+
{
|
|
589
|
+
(
|
|
590
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
591
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
592
|
+
frozenset(zip(
|
|
593
|
+
( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
594
|
+
( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
595
|
+
))
|
|
596
|
+
)
|
|
597
|
+
for fkdef in fkdefs
|
|
598
|
+
},
|
|
599
|
+
{
|
|
600
|
+
("public", "ERMrest_Client", frozenset([ ("ERMrest_Client", "ID",) ])),
|
|
601
|
+
("public", "ERMrest_Client", frozenset([ ("RCB", "ID",) ])),
|
|
602
|
+
("public", "ERMrest_Client", frozenset([ ("RMB", "ID",) ])),
|
|
603
|
+
}
|
|
604
|
+
)
|
|
605
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
606
|
+
self.assertEqual(tdef.get("acls"), self._test_acls)
|
|
607
|
+
self.assertEqual(tdef.get("acl_bindings"), self._test_acl_bindings)
|
|
608
|
+
annotations = tdef.get("annotations")
|
|
609
|
+
for k, v in self._test_annotations.items():
|
|
610
|
+
self.assertEqual(annotations[k], v)
|
|
611
|
+
self.assertIn(tag.table_display, annotations)
|
|
612
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
613
|
+
table = schema.create_table(tdef)
|
|
614
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
615
|
+
|
|
616
|
+
def test_5a_assoctable_define_defaults(self):
|
|
617
|
+
tdef = ermrest_model.Table.define_association(
|
|
618
|
+
[
|
|
619
|
+
self.model.schemas["public"].tables["ERMrest_Client"],
|
|
620
|
+
self.model.schemas["public"].tables["ERMrest_Group"],
|
|
621
|
+
],
|
|
622
|
+
)
|
|
623
|
+
self.assertEqual(tdef.get("table_name"), "ERMrest_Client_ERMrest_Group")
|
|
624
|
+
self.assertEqual(tdef.get("comment"), None)
|
|
625
|
+
cdefs = tdef.get("column_definitions")
|
|
626
|
+
self.assertIsInstance(cdefs, list)
|
|
627
|
+
self.assertEqual(len(cdefs), 5 + 2)
|
|
628
|
+
kdefs = tdef.get("keys")
|
|
629
|
+
self.assertIsInstance(kdefs, list)
|
|
630
|
+
self.assertEqual(
|
|
631
|
+
{ tuple(key["unique_columns"]) for key in kdefs },
|
|
632
|
+
{ ('RID',), ('ERMrest_Client', 'ERMrest_Group') },
|
|
633
|
+
)
|
|
634
|
+
fkdefs = tdef.get("foreign_keys")
|
|
635
|
+
self.assertIsInstance(fkdefs, list)
|
|
636
|
+
self.assertEqual(
|
|
637
|
+
{
|
|
638
|
+
(
|
|
639
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
640
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
641
|
+
frozenset(zip(
|
|
642
|
+
tuple( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
643
|
+
tuple( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
644
|
+
))
|
|
645
|
+
)
|
|
646
|
+
for fkdef in fkdefs
|
|
647
|
+
},
|
|
648
|
+
{
|
|
649
|
+
("public", "ERMrest_Client", frozenset([ ("ERMrest_Client", "ID",) ])),
|
|
650
|
+
("public", "ERMrest_Group", frozenset([ ("ERMrest_Group", "ID",) ])),
|
|
651
|
+
("public", "ERMrest_Client", frozenset([ ("RCB", "ID",) ])),
|
|
652
|
+
("public", "ERMrest_Client", frozenset([ ("RMB", "ID",) ])),
|
|
653
|
+
}
|
|
654
|
+
)
|
|
655
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
656
|
+
table = schema.create_table(tdef)
|
|
657
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
658
|
+
|
|
659
|
+
def test_5b_assoctable_define_custom(self):
|
|
660
|
+
tname = "client_group"
|
|
661
|
+
tdef = ermrest_model.Table.define_association(
|
|
662
|
+
[
|
|
663
|
+
('c_id', self.model.schemas["public"].tables["ERMrest_Client"]),
|
|
664
|
+
('g_id', self.model.schemas["public"].tables["ERMrest_Group"]),
|
|
665
|
+
],
|
|
666
|
+
[],
|
|
667
|
+
tname,
|
|
668
|
+
self._test_comment,
|
|
669
|
+
provide_system_fkeys=False,
|
|
670
|
+
)
|
|
671
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
672
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
673
|
+
cdefs = tdef.get("column_definitions")
|
|
674
|
+
self.assertIsInstance(cdefs, list)
|
|
675
|
+
self.assertEqual(len(cdefs), 5 + 2)
|
|
676
|
+
kdefs = tdef.get("keys")
|
|
677
|
+
self.assertIsInstance(kdefs, list)
|
|
678
|
+
self.assertEqual(
|
|
679
|
+
{ tuple(key["unique_columns"]) for key in kdefs },
|
|
680
|
+
{ ('RID',), ('c_id', 'g_id') },
|
|
681
|
+
)
|
|
682
|
+
fkdefs = tdef.get("foreign_keys")
|
|
683
|
+
self.assertIsInstance(fkdefs, list)
|
|
684
|
+
self.assertEqual(
|
|
685
|
+
{
|
|
686
|
+
(
|
|
687
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
688
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
689
|
+
frozenset(zip(
|
|
690
|
+
tuple( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
691
|
+
tuple( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
692
|
+
))
|
|
693
|
+
)
|
|
694
|
+
for fkdef in fkdefs
|
|
695
|
+
},
|
|
696
|
+
{
|
|
697
|
+
("public", "ERMrest_Client", frozenset([ ("c_id", "ID",) ])),
|
|
698
|
+
("public", "ERMrest_Group", frozenset([ ("g_id", "ID",) ])),
|
|
699
|
+
}
|
|
700
|
+
)
|
|
701
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
702
|
+
table = schema.create_table(tdef)
|
|
703
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
704
|
+
|
|
705
|
+
def test_5c_assoctable_define_with_metadata(self):
|
|
706
|
+
tname = "client_group"
|
|
707
|
+
tdef = ermrest_model.Table.define_association(
|
|
708
|
+
[
|
|
709
|
+
('c_id', self.model.schemas["public"].tables["ERMrest_Client"]),
|
|
710
|
+
('g_id', self.model.schemas["public"].tables["ERMrest_Group"]),
|
|
711
|
+
],
|
|
712
|
+
[
|
|
713
|
+
ermrest_model.Column.define("md1", ermrest_model.builtin_types.text),
|
|
714
|
+
],
|
|
715
|
+
tname,
|
|
716
|
+
self._test_comment,
|
|
717
|
+
)
|
|
718
|
+
self.assertEqual(tdef.get("table_name"), tname)
|
|
719
|
+
self.assertEqual(tdef.get("comment"), self._test_comment)
|
|
720
|
+
cdefs = tdef.get("column_definitions")
|
|
721
|
+
self.assertIsInstance(cdefs, list)
|
|
722
|
+
self.assertEqual(len(cdefs), 5 + 2 + 1)
|
|
723
|
+
kdefs = tdef.get("keys")
|
|
724
|
+
self.assertIsInstance(kdefs, list)
|
|
725
|
+
self.assertEqual(
|
|
726
|
+
{ tuple(key["unique_columns"]) for key in kdefs },
|
|
727
|
+
{ ('RID',), ('c_id', 'g_id') },
|
|
728
|
+
)
|
|
729
|
+
fkdefs = tdef.get("foreign_keys")
|
|
730
|
+
self.assertIsInstance(fkdefs, list)
|
|
731
|
+
self.assertEqual(
|
|
732
|
+
{
|
|
733
|
+
(
|
|
734
|
+
fkdef["referenced_columns"][0]["schema_name"],
|
|
735
|
+
fkdef["referenced_columns"][0]["table_name"],
|
|
736
|
+
frozenset(zip(
|
|
737
|
+
tuple( c["column_name"] for c in fkdef["foreign_key_columns"] ),
|
|
738
|
+
tuple( c["column_name"] for c in fkdef["referenced_columns"] ),
|
|
739
|
+
))
|
|
740
|
+
)
|
|
741
|
+
for fkdef in fkdefs
|
|
742
|
+
},
|
|
743
|
+
{
|
|
744
|
+
("public", "ERMrest_Client", frozenset([ ("c_id", "ID",) ])),
|
|
745
|
+
("public", "ERMrest_Group", frozenset([ ("g_id", "ID",) ])),
|
|
746
|
+
("public", "ERMrest_Client", frozenset([ ("RCB", "ID",) ])),
|
|
747
|
+
("public", "ERMrest_Client", frozenset([ ("RMB", "ID",) ])),
|
|
748
|
+
}
|
|
749
|
+
)
|
|
750
|
+
schema = self.model.create_schema(ermrest_model.Schema.define("model_define_schema"))
|
|
751
|
+
table = schema.create_table(tdef)
|
|
752
|
+
self.assertIsInstance(table, ermrest_model.Table)
|
|
753
|
+
|
|
754
|
+
def test_key_drop_cascading(self):
|
|
755
|
+
self._create_schema_with_fkeys()
|
|
756
|
+
schema = self.model.schemas['schema_with_fkeys']
|
|
757
|
+
self.model.schemas['schema_with_fkeys'].tables['parent'].keys[(schema, 'parent_id_key')].drop(cascade=True)
|
|
758
|
+
|
|
759
|
+
def test_key_reordered_drop_cascading(self):
|
|
760
|
+
self._create_schema_with_fkeys()
|
|
761
|
+
schema = self.model.schemas['schema_with_fkeys']
|
|
762
|
+
self.model.schemas['schema_with_fkeys'].tables['parent'].keys[(schema, 'parent_compound_key')].drop(cascade=True)
|
|
763
|
+
|
|
764
|
+
def test_key_column_drop_cascading(self):
|
|
765
|
+
self._create_schema_with_fkeys()
|
|
766
|
+
self.model.schemas['schema_with_fkeys'].tables['parent'].columns['id'].drop(cascade=True)
|
|
767
|
+
|
|
768
|
+
def test_fkey_column_drop_cascading(self):
|
|
769
|
+
self._create_schema_with_fkeys()
|
|
770
|
+
self.model.schemas['schema_with_fkeys'].tables['child'].columns['parent_id_extra'].drop(cascade=True)
|
|
771
|
+
|
|
772
|
+
def test_table_drop_cascading(self):
|
|
773
|
+
self._create_schema_with_fkeys()
|
|
774
|
+
self.model.schemas['schema_with_fkeys'].tables['parent'].drop(cascade=True)
|
|
775
|
+
|
|
776
|
+
def test_schema_drop_cascading(self):
|
|
777
|
+
self._create_schema_with_fkeys()
|
|
778
|
+
self.model.schemas['schema_with_fkeys'].drop(cascade=True)
|
|
779
|
+
|
|
780
|
+
|
|
781
|
+
if __name__ == '__main__':
|
|
782
|
+
unittest.main()
|