deriva 1.7.10__py3-none-any.whl → 1.7.11__py3-none-any.whl

tests/deriva/core/test_datapath.py

@@ -1,893 +0,0 @@
-# Tests for the datapath module.
-#
-# Environment variables:
-#  DERIVA_PY_TEST_HOSTNAME: hostname of the test server
-#  DERIVA_PY_TEST_CREDENTIAL: user credential, if none, it will attempt to get credentail for given hostname
-#  DERIVA_PY_TEST_VERBOSE: set for verbose logging output to stdout
-
-from copy import deepcopy
-import logging
-from operator import itemgetter
-import os
-import unittest
-from deriva.core import DerivaServer, get_credential, ermrest_model as _em, __version__
-from deriva.core.datapath import *
-
-try:
-    from pandas import DataFrame
-    HAS_PANDAS = True
-except ImportError:
-    HAS_PANDAS = False
-
-TEST_EXP_MAX = 100
-TEST_EXPTYPE_MAX = 10
-TEST_EXP_NAME_FORMAT = "experiment-{}"
-TEST_PROJ_MAX = 1
-TEST_PROJ_INVESTIGATOR = "Smith"
-TEST_PROJ_NUM = 1
-
-SPECIAL_CHARACTERS = '`~!@#$%^&*()_+-={}|[]\\;:"\',./<>?'
-INVALID_IDENTIFIER, INVALID_IDENTIFIER_FIXED = '9 %$ ', '_9____'
-RESERVED_IDENTIFIER = 'column_definitions'
-CONFLICTING_IDENTIFIER, CONFLICTING_IDENTIFIER_FIXED = RESERVED_IDENTIFIER + '1', RESERVED_IDENTIFIER + '2'
-
-SNAME_ISA = 'ISA'
-SNAME_VOCAB = 'Vocab'
-TNAME_PROJECT = 'Project'
-TNAME_EXPERIMENT = 'Experiment'
-TNAME_EXPERIMENT_TYPE = 'Experiment_Type'
-TNAME_EXPERIMENT_COPY = 'Experiment_Copy'
-
-hostname = os.getenv("DERIVA_PY_TEST_HOSTNAME")
-logger = logging.getLogger(__name__)
-if os.getenv("DERIVA_PY_TEST_VERBOSE"):
-    logger.setLevel(logging.DEBUG)
-    logger.addHandler(logging.StreamHandler())
-
-
-def define_test_schema(catalog):
-    """Defines the test schema.
-
-    A 'vocab' schema with an 'experiment_type' term table.
-    An 'isa' schema with an 'experiment' table, with 'type' that references the vocab table.
-    """
-    model = catalog.getCatalogModel()
-    vocab = model.create_schema(_em.Schema.define(SNAME_VOCAB))
-    vocab.create_table(_em.Table.define_vocabulary(TNAME_EXPERIMENT_TYPE, "TEST:{RID}"))
-    isa = model.create_schema(_em.Schema.define(SNAME_ISA))
-
-    # create TNAME_PROJECT table
-    table_def = _em.Table.define(
-        TNAME_PROJECT,
-        column_defs=[
-            _em.Column.define(cname, ctype) for (cname, ctype) in [
-                ('Investigator', _em.builtin_types.text),
-                ('Num', _em.builtin_types.int4),
-                (INVALID_IDENTIFIER, _em.builtin_types.int4),
-                (RESERVED_IDENTIFIER, _em.builtin_types.text),
-                (RESERVED_IDENTIFIER + '1', _em.builtin_types.text)
-            ]
-        ],
-        key_defs=[
-            _em.Key.define(['Investigator', 'Num'])
-        ]
-    )
-    isa.create_table(table_def)
-
-    # experiment table definition helper
-    def exp_table_def(exp_table_name):
-        return _em.Table.define(
-            exp_table_name,
-            column_defs=[
-                _em.Column.define(cname, ctype) for (cname, ctype) in [
-                    ('Name', _em.builtin_types.text),
-                    ('Amount', _em.builtin_types.int4),
-                    ('Time', _em.builtin_types.timestamptz),
-                    ('Type', _em.builtin_types.text),
-                    ('Project Investigator', _em.builtin_types.text),
-                    ('Project_Num', _em.builtin_types.int4),
-                    ('Empty', _em.builtin_types.int4)
-                ]
-            ],
-            key_defs=[
-                _em.Key.define(['Name'])
-            ],
-            fkey_defs=[
-                _em.ForeignKey.define(['Type'], SNAME_VOCAB, TNAME_EXPERIMENT_TYPE, ['ID']),
-                _em.ForeignKey.define(['Project Investigator', 'Project_Num'], SNAME_ISA, TNAME_PROJECT, ['Investigator', 'Num'])
-            ]
-        )
-
-    # create experiment tables
-    isa.create_table(exp_table_def(TNAME_EXPERIMENT))
-    isa.create_table(exp_table_def(TNAME_EXPERIMENT_COPY))
-
-
-def _generate_experiment_entities(types, count):
-    """Generates experiment entities (content only)
-
-    :param types: type entities to be referenced from entities
-    :param count: number of entities to return
-    :return: a list of dict objects (experiment entities)
-    """
-    return [
-        {
-            "Name": TEST_EXP_NAME_FORMAT.format(i),
-            "Amount": i,
-            "Time": "2018-01-{}T01:00:00.0".format(1 + (i % 31)),
-            "Type": types[i % TEST_EXPTYPE_MAX]['ID'],
-            "Project Investigator": TEST_PROJ_INVESTIGATOR,
-            "Project_Num": TEST_PROJ_NUM,
-            "Empty": None
-        }
-        for i in range(count)
-    ]
-
-
-def populate_test_catalog(catalog):
-    """Populate the test catalog."""
-    paths = catalog.getPathBuilder()
-    logger.debug("Inserting project...")
-    proj_table = paths.schemas[SNAME_ISA].tables[TNAME_PROJECT]
-    logger.debug("Inserting investigators...")
-    proj_table.insert([
-        {"Investigator": TEST_PROJ_INVESTIGATOR, "Num": TEST_PROJ_NUM}
-    ])
-    logger.debug("Inserting experiment types...")
-    type_table = paths.schemas[SNAME_VOCAB].tables[TNAME_EXPERIMENT_TYPE]
-    types = type_table.insert([
-        {"Name": "{}".format(name), "Description": "NA"} for name in range(TEST_EXPTYPE_MAX)
-    ], defaults=['ID', 'URI'])
-    logger.debug("Inserting experiments...")
-    exp = paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT]
-    exp.insert(_generate_experiment_entities(types, TEST_EXP_MAX))
-
-
-@unittest.skipUnless(hostname, "Test host not specified")
-class DatapathTests (unittest.TestCase):
-    catalog = None
-
-    @classmethod
-    def setUpClass(cls):
-        logger.debug("setupUpClass begin")
-        credential = os.getenv("DERIVA_PY_TEST_CREDENTIAL") or get_credential(hostname)
-        server = DerivaServer('https', hostname, credentials=credential)
-        cls.catalog = server.create_ermrest_catalog()
-        try:
-            define_test_schema(cls.catalog)
-            populate_test_catalog(cls.catalog)
-        except Exception:
-            # on failure, delete catalog and re-raise exception
-            cls.catalog.delete_ermrest_catalog(really=True)
-            raise
-        logger.debug("setupUpClass done")
-
-    @classmethod
-    def tearDownClass(cls):
-        logger.debug("tearDownClass begin")
-        cls.catalog.delete_ermrest_catalog(really=True)
-        logger.debug("tearDownClass done")
-
-    def setUp(self):
-        self.paths = self.catalog.getPathBuilder()
-        self.project = self.paths.schemas[SNAME_ISA].tables[TNAME_PROJECT]
-        self.experiment = self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT]
-        self.experiment_type = self.paths.schemas[SNAME_VOCAB].tables[TNAME_EXPERIMENT_TYPE]
-        self.experiment_copy = self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT_COPY]
-        self.types = list(self.experiment_type.entities())
-        self.model = self.catalog.getCatalogModel()
-
-    def tearDown(self):
-        try:
-            self.experiment_copy.path.delete()
-        except DataPathException:
-            # suppresses 404 errors when the table is empty
-            pass
-
-    def test_catalog_dir_base(self):
-        self.assertIn('schemas', dir(self.paths))
-
-    def test_schema_dir_base(self):
-        self.assertLess({'_name', 'tables', 'describe'}, set(dir(self.paths.schemas[SNAME_ISA])))
-
-    def test_datapath_dir_base(self):
-        self.assertLess({'aggregates', 'groupby', 'attributes', 'context', 'delete', 'entities', 'filter',
-                         'link', 'table_instances', 'uri'}, set(dir(self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].path)))
-
-    def test_table_dir_base(self):
-        self.assertLess({'aggregates', 'alias', 'groupby', 'attributes', 'describe', 'entities', 'filter', 'insert',
-                         'link', 'path', 'update', 'uri'}, set(dir(self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT])))
-
-    def test_catalog_dir_with_schemas(self):
-        self.assertLess({SNAME_ISA, SNAME_VOCAB}, set(dir(self.paths)))
-
-    def test_schema_dir_with_tables(self):
-        self.assertIn(TNAME_EXPERIMENT, dir(self.paths.ISA))
-
-    def test_table_dir_with_columns(self):
-        self.assertLess({'Name', 'Amount', 'Time', 'Type'}, set(dir(self.paths.ISA.Experiment)))
-
-    def test_dir_path(self):
-        self.assertIn(TNAME_EXPERIMENT, dir(self.paths.ISA.Experiment.path))
-
-    def test_dir_invalid_identifier(self):
-        self.assertIn(INVALID_IDENTIFIER_FIXED, dir(self.project))
-        self.assertIsNotNone(getattr(self.project, INVALID_IDENTIFIER_FIXED))
-
-    def test_dir_conflicting_identifier(self):
-        self.assertIn(CONFLICTING_IDENTIFIER_FIXED, dir(self.project))
-        self.assertIsNotNone(getattr(self.project, CONFLICTING_IDENTIFIER))
-        self.assertIsNotNone(getattr(self.project, CONFLICTING_IDENTIFIER_FIXED))
-
-    def test_describe_schema(self):
-        with self.assertWarns(DeprecationWarning):
-            self.paths.schemas[SNAME_ISA].describe()
-
-    def test_describe_table(self):
-        with self.assertWarns(DeprecationWarning):
-            self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].describe()
-
-    def test_describe_column(self):
-        with self.assertWarns(DeprecationWarning):
-            self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].column_definitions['Name'].describe()
-
-    def test_unfiltered_fetch(self):
-        results = self.experiment.entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-
-    def test_fetch_with_headers(self):
-        headers = {'User-Agent': __name__ + '/' + __version__}
-        results = self.experiment.entities().fetch(headers=headers)
-        self.assertEqual(len(results), TEST_EXP_MAX)
-
-    def test_fetch_with_limit(self):
-        results = self.experiment.entities()
-        limit = TEST_EXP_MAX / 5
-        results.fetch(limit=limit)
-        self.assertEqual(len(results), limit)
-
-    def test_fetch_with_sort(self):
-        results = self.experiment.entities()
-        results.sort(self.experiment.column_definitions['Amount'])
-        self.assertEqual(results[0]['Amount'], 0)
-
-    def test_fetch_attributes_with_sort(self):
-        results = self.experiment.attributes(self.experiment.RID, self.experiment.Amount)
-        results.sort(self.experiment.Amount)
-        self.assertEqual(results[0]['Amount'], 0)
-
-    def test_fetch_all_attributes_with_sort(self):
-        results = self.experiment.attributes(self.experiment)
-        results.sort(self.experiment.Amount)
-        self.assertEqual(results[0]['Amount'], 0)
-
-    def test_fetch_all_attributes_with_sort_desc(self):
-        results = self.experiment.attributes(self.experiment)
-        results.sort(self.experiment.Amount.desc)
-        self.assertEqual(results[0]['Amount'], TEST_EXP_MAX-1)
-
-    def test_fetch_from_path_attributes_with_sort_on_talias(self):
-        path = self.experiment.path
-        results = path.Experiment.attributes(path.Experiment.RID, path.Experiment.Amount)
-        results.sort(path.Experiment.Amount)
-        self.assertEqual(results[0]['Amount'], 0)
-
-    def test_fetch_from_path_attributes_with_sort_on_talias_desc(self):
-        path = self.experiment.path
-        results = path.Experiment.attributes(path.Experiment.RID, path.Experiment.Amount)
-        results.sort(path.Experiment.Amount.desc)
-        self.assertEqual(results[0]['Amount'], TEST_EXP_MAX-1)
-
-    def test_fetch_from_path_all_attributes_with_sort_on_talias(self):
-        path = self.experiment.path
-        results = path.Experiment.attributes(*path.Experiment.column_definitions.values())
-        results.sort(path.Experiment.Amount)
-        self.assertEqual(results[0]['Amount'], 0)
-
-    def test_fetch_from_path_all_attributes_with_sort_on_alias_desc(self):
-        path = self.experiment.path
-        results = path.Experiment.attributes(*path.Experiment.column_definitions.values())
-        results.sort(path.Experiment.Amount.desc)
-        self.assertEqual(results[0]['Amount'], TEST_EXP_MAX-1)
-
-    def test_fetch_all_cols_with_talias(self):
-        path = self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].alias('X').path
-        results = path.attributes(path.X)
-        result = results.fetch(limit=1)[0]
-        self.assertIn('X:RID', result)
-        self.assertIn('X:Name', result)
-
-    def test_fetch_with_talias(self):
-        path = self.paths.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].alias('X').path
-        results = path.attributes(path.X.RID, path.X.Name.alias('typeName'))
-        result = results.fetch(limit=1)[0]
-        self.assertIn('RID', result)
-        self.assertIn('typeName', result)
-
-    def test_attribute_projection(self):
-        results = self.experiment.attributes(
-            self.experiment.column_definitions['Name'],
-            self.experiment.column_definitions['Amount']
-        )
-        result = results.fetch(limit=1)[0]
-        self.assertIn('Name', result)
-        self.assertIn('Amount', result)
-
-    def test_attribute_err_table_attr(self):
-        table_attr = ['_name', '_schema']
-        for attr in table_attr:
-            with self.assertRaises(TypeError):
-                self.experiment.attributes(getattr(self.experiment, attr))
-
-    def test_update_err_no_targets(self):
-        entities = [{'RID': 1234}]
-        with self.assertRaises(ValueError):
-            self.experiment.update(entities)
-
-    def test_aggregate_w_invalid_attributes(self):
-        with self.assertRaises(TypeError):
-            self.experiment.aggregates(Min(self.experiment.column_definitions['Amount']))
-
-    def test_aggregate_w_invalid_renames(self):
-        with self.assertRaises(TypeError):
-            self.experiment.aggregates(
-                self.experiment.column_definitions['Name'],
-                Min(self.experiment.column_definitions['Amount'])
-            )
-
-    def test_aggregate_fns(self):
-        tests = [
-            ('min_amount',      Min,    0),
-            ('max_amount',      Max,    TEST_EXP_MAX-1),
-            ('sum_amount',      Sum,    sum(range(TEST_EXP_MAX))),
-            ('avg_amount',      Avg,    sum(range(TEST_EXP_MAX))/TEST_EXP_MAX),
-            ('cnt_amount',      Cnt,    TEST_EXP_MAX),
-            ('cnt_d_amount',    CntD,   TEST_EXP_MAX),
-            ('array_amount',    Array,  list(range(TEST_EXP_MAX))),
-            ('array_d_amount',  ArrayD, list(range(TEST_EXP_MAX)))
-        ]
-        for name, Fn, value in tests:
-            with self.subTest(name=name):
-                # results = self.experiment.aggregates(**{name: Fn(self.experiment.column_definitions['Amount'])})
-                results = self.experiment.aggregates(Fn(self.experiment.column_definitions['Amount']).alias(name))
-                result = results.fetch()[0]
-                self.assertIn(name, result)
-                self.assertEqual(result[name], value)
-
-    def test_aggregate_w_2_fns(self):
-        results = self.experiment.aggregates(
-            Min(self.experiment.column_definitions['Amount']).alias('min_amount'),
-            Max(self.experiment.column_definitions['Amount']).alias('max_amount')
-        )
-        result = results.fetch()[0]
-        self.assertIn('min_amount', result)
-        self.assertEqual(result['min_amount'], 0)
-        self.assertIn('max_amount', result)
-        self.assertEqual(result['max_amount'], TEST_EXP_MAX-1)
-
-    def test_aggregate_fns_array_star(self):
-        path = self.experiment.path
-        tests = [
-            ('array_table_star',  Array,  self.experiment, self.experiment),
-            ('array_alias_star',  Array,  path,            path.Experiment),
-            ('arrayd_table_star', ArrayD, self.experiment, self.experiment),
-            ('arrayd_alias_star', ArrayD, path,            path.Experiment)
-        ]
-        for name, Fn, path, instance in tests:
-            results = path.aggregates(Fn(instance).alias('arr'))
-            with self.subTest(name=name):
-                result = results.fetch()[0]
-                self.assertIn('arr', result)
-                self.assertEqual(len(result['arr']), TEST_EXP_MAX)
-                self.assertIn('Time', result['arr'][0])
-
-    def test_aggregate_fns_cnt_star(self):
-        path = self.experiment.path
-        tests = [
-            ('cnt_table_star', Cnt, self.experiment, self.experiment),
-            ('cnt_alias_star', Cnt, path,            path.Experiment)
-        ]
-        for name, Fn, path, instance in tests:
-            results = path.aggregates(Fn(instance).alias('cnt'))
-            with self.subTest(name=name):
-                result = results.fetch()[0]
-                self.assertIn('cnt', result)
-                self.assertEqual(result['cnt'], TEST_EXP_MAX)
-
-    def test_attributegroup_fns(self):
-        tests = [
-            ('one group key',     [self.experiment.column_definitions['Type']]),
-            ('two group keys',    [self.experiment.column_definitions['Project_Num'], self.experiment.column_definitions['Type']]),
-            ('aliased group key', [self.experiment.column_definitions['Type'].alias('The Type')])
-        ]
-        for test_name, group_key in tests:
-            with self.subTest(name=test_name):
-                self._do_attributegroup_fn_subtests(group_key)
-
-    def _do_attributegroup_fn_subtests(self, group_key):
-        """Helper method for running common attributegroup subtests for different group keys."""
-        tests = [
-            ('min_amount',      Min,    0),
-            ('max_amount',      Max,    TEST_EXP_MAX-TEST_EXPTYPE_MAX),
-            ('sum_amount',      Sum,    sum(range(0, TEST_EXP_MAX, TEST_EXPTYPE_MAX))),
-            ('avg_amount',      Avg,    sum(range(0, TEST_EXP_MAX, TEST_EXPTYPE_MAX))/TEST_EXPTYPE_MAX),
-            ('cnt_amount',      Cnt,    TEST_EXPTYPE_MAX),
-            ('cnt_d_amount',    CntD,   TEST_EXPTYPE_MAX),
-            ('array_amount',    Array,  list(range(0, TEST_EXP_MAX, TEST_EXPTYPE_MAX))),
-            ('array_d_amount',  ArrayD, list(range(0, TEST_EXP_MAX, TEST_EXPTYPE_MAX)))
-        ]
-        for name, Fn, value in tests:
-            with self.subTest(name=name):
-                results = self.experiment.groupby(*group_key).attributes(
-                    Fn(self.experiment.column_definitions['Amount']).alias(name)).sort(*group_key)
-
-                result = results[0]
-                self.assertEqual(len(results), TEST_EXPTYPE_MAX)
-                self.assertTrue(all(key._name in result for key in group_key))
-                self.assertIn(name, result)
-                self.assertEqual(result[name], value)
-
-    def test_attributegroup_w_bin(self):
-        tests = [
-            ('min/max given',     0,    TEST_EXP_MAX),
-            ('min/max not given', None, None),
-            ('min only given',    0,    None),
-            ('max only given',    None, TEST_EXP_MAX)
-        ]
-        for testname, minval, maxval in tests:
-            with self.subTest(name=testname):
-                self._do_bin_subtests(minval, maxval)
-
-    def _do_bin_subtests(self, minval, maxval):
-        """Helper method for running common binning tests with & without min/max values."""
-        new_name, bin_name = 'TheProj', 'ABin'
-        nbins = int(TEST_EXP_MAX/20)
-        group_key = [
-            self.experiment.column_definitions['Project_Num'].alias(new_name),
-            Bin(self.experiment.column_definitions['Amount'], nbins, minval=minval, maxval=maxval).alias(bin_name)
-        ]
-        tests = [
-            ('min_amount',      Min,    lambda a, b: a >= b[1]),
-            ('max_amount',      Max,    lambda a, b: a <= b[2]),
-            ('sum_amount',      Sum,    lambda a, b: a >= b[1] + b[2]),
-            ('avg_amount',      Avg,    lambda a, b: b[1] <= a <= b[2]),
-            ('cnt_amount',      Cnt,    lambda a, b: a == TEST_EXP_MAX/nbins),
-            ('cnt_d_amount',    CntD,   lambda a, b: a == TEST_EXP_MAX/nbins),
-            ('array_amount',    Array,  lambda a, b: all(b[1] <= a_i <= b[2] for a_i in a)),
-            ('array_d_amount',  ArrayD, lambda a, b: all(b[1] <= a_i <= b[2] for a_i in a))
-        ]
-        for name, Fn, compare in tests:
-            with self.subTest(name=name):
-                results = self.experiment.groupby(*group_key).attributes(
-                    Fn(self.experiment.column_definitions['Amount']).alias(name)).fetch()
-
-                self.assertTrue(all(key._name in results[0] for key in group_key))
-                self.assertIn(name, results[0])
-                for result in results:
-                    bin = result[bin_name]
-                    if not maxval and (bin[0] >= nbins):
-                        # skip the last 2 bins when maxval was resolved; those bins are not aligned like the others
-                        continue
-                    self.assertTrue(compare(result[name], bin))
-
-    def test_attributegroup_w_bin_sort(self):
-        bin_name = 'bin'
-        nbins = int(TEST_EXP_MAX/20)
-        bin = Bin(self.experiment.column_definitions['Amount'], nbins, 0, TEST_EXP_MAX).alias(bin_name)
-        bin_desc = bin.desc
-        asc_fn = lambda n, a, b: a[n] <= b[n]
-        desc_fn = lambda n, a, b: a[n] >= b[n]
-        tests = [
-            ('min_amount', Min, bin,      asc_fn),
-            ('max_amount', Max, bin,      asc_fn),
-            ('sum_amount', Sum, bin,      asc_fn),
-            ('avg_amount', Avg, bin,      asc_fn),
-            ('min_amount', Min, bin_desc, desc_fn),
-            ('max_amount', Max, bin_desc, desc_fn),
-            ('sum_amount', Sum, bin_desc, desc_fn),
-            ('avg_amount', Avg, bin_desc, desc_fn)
-        ]
-        for name, Fn, sort_key, compfn in tests:
-            with self.subTest(name=name):
-                results = self.experiment.groupby(bin).attributes(
-                    Fn(self.experiment.column_definitions['Amount']).alias(name)).sort(sort_key).fetch()
-
-                self.assertIn(bin._name, results[0])
-                self.assertIn(name, results[0])
-                self.assertTrue(compfn(name, results[0], results[1]))
-
-    def test_attributegroup_w_bin_resolution(self):
-        binkey = self.experiment.column_definitions['Empty']
-        binname = 'bin'
-        tests = [
-            ('min_max_valid', 0,    0,      True),
-            ('max_invalid',   0,    None,   False),
-            ('min_invalid',   None, 0,      False),
-            ('both_invalid',  None, None,   False)
-        ]
-        for name, minval, maxval, valid in tests:
-            def _do_query():
-                bin = Bin(binkey, 10, minval, maxval).alias(binname)
-                return self.experiment.groupby(bin).attributes(Avg(binkey).alias(name)).fetch()
-
-            with self.subTest(name=name):
-                if valid:
-                    results = _do_query()
-                    self.assertIn(binname, results[0])
-                    self.assertIn(name, results[0])
-                else:
-                    with self.assertRaises(ValueError):
-                        _do_query()
-
-    def test_link_implicit(self):
-        results = self.experiment.link(self.experiment_type).entities()
-        self.assertEqual(TEST_EXPTYPE_MAX, len(results))
-
-    def test_link_explicit_simple_key(self):
-        results = self.experiment.link(
-            self.experiment_type,
-            on=(self.experiment.Type == self.experiment_type.ID)
-        ).entities()
-        self.assertEqual(TEST_EXPTYPE_MAX, len(results))
-
-    def test_link_explicit_composite_key(self):
-        path = self.experiment.link(
-            self.project,
-            on=(
-                    (self.experiment.Project_Investigator == self.project.Investigator) &
-                    (self.experiment.Project_Num == self.project.Num)
-            )
-        )
-        results = path.entities()
-        self.assertEqual(TEST_PROJ_MAX, len(results))
-
-    def test_link_outbound_fkey(self):
-        fkey_by_pk_table_name = {
-            fkey.pk_table.name: fkey
-            for fkey in self.model.schemas[SNAME_ISA].tables[TNAME_EXPERIMENT].foreign_keys
-        }
-
-        tests = [
-            ('fkey-link-' + TNAME_PROJECT, fkey_by_pk_table_name[TNAME_PROJECT], self.project, TEST_PROJ_MAX),
-            ('fkey-link-' + TNAME_EXPERIMENT_TYPE, fkey_by_pk_table_name[TNAME_EXPERIMENT_TYPE], self.project, TEST_EXPTYPE_MAX)
-        ]
-
-        for name, fkey, table, expected_results_len in tests:
-            with self.subTest(name=name):
-                results = self.experiment.link(table, on=fkey).entities()
-                self.assertEqual(expected_results_len, len(results))
-
-    def test_link_inbound_fkey(self):
-        fkey_by_fk_table_name = {
-            fkey.table.name: fkey
-            for fkey in self.model.schemas[SNAME_VOCAB].tables[TNAME_EXPERIMENT_TYPE].referenced_by
-        }
-
-        tests = [
-            ('fkey-link-' + TNAME_EXPERIMENT, fkey_by_fk_table_name[TNAME_EXPERIMENT], self.project, TEST_EXP_MAX)
-        ]
-
-        for name, fkey, table, expected_results_len in tests:
-            with self.subTest(name=name):
-                results = self.experiment_type.link(table, on=fkey).entities()
-                self.assertEqual(expected_results_len, len(results))
-
-    def test_filter_equality(self):
-        # test with value
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Name'] == TEST_EXP_NAME_FORMAT.format(1)
-        ).entities()
-        self.assertEqual(len(results), 1)
-        # test again with null
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Name'] == None
-        ).entities()
-        self.assertEqual(len(results), 0)
-
-    def test_filter_notequal(self):
-        # test with value
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Amount'] != 0
-        ).entities()
-        self.assertEqual(len(results), TEST_EXP_MAX-1)
-        # test again with null
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Amount'] != None
-        ).entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-
-    def test_filter_inequality(self):
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Amount'] < 10
-        ).entities()
-        self.assertEqual(len(results), 10)
-
-    def test_filter_ciregexp(self):
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:])
-        ).entities()
-        self.assertEqual(len(results), 1)
-
-    @unittest.skipUnless(TEST_EXP_MAX >= 3, "this test was designed for at least 3 elements in the test set")
-    def test_fitler_w_quantifier(self):
-        int_args = [0, int(TEST_EXP_MAX/2), TEST_EXP_MAX-1, TEST_EXP_MAX*2]
-        str_args = [TEST_EXP_NAME_FORMAT.format(i) for i in int_args]
-        for name, cname, Q, args, expectation in [
-            ('any_3_ints', 'Amount', Any, int_args, 3),
-            ('all_1_int', 'Amount', All, [int_args[0]], 1),
-            ('all_3_ints', 'Amount', All, int_args, 0),
-            ('any_3_strs', 'Name', Any, str_args, 3),
-            ('all_1_str', 'Name', All, [str_args[0]], 1),
-            ('all_3_strs', 'Name', All, str_args, 0)
-        ]:
-            with self.subTest(name=name):
-                results = self.experiment.filter(
-                    self.experiment.column_definitions[cname] == Q(*args)
-                ).entities()
-                self.assertEqual(len(results), expectation)
-
-    def test_filter_negation(self):
-        results = self.experiment.filter(
-            ~ (self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:]))
-        ).entities()
-        self.assertEqual(len(results), TEST_EXP_MAX - 1)
-
-    def test_filter_conjunction(self):
-        results = self.experiment.filter(
-            self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:])
-            & (self.experiment.column_definitions['Amount'] == 0)
-        ).entities()
-        self.assertEqual(len(results), 1)
-
-    def test_attribute_deprecated_rename(self):
-        with self.assertRaises(TypeError):
-            self.experiment.attributes(
-                self.experiment.column_definitions['Name'],
-                howmuch=self.experiment.column_definitions['Amount']
-            )
-
-    def test_attribute_rename(self):
-        results = self.experiment.attributes(
-            self.experiment.column_definitions['Name'],
-            self.experiment.column_definitions['Amount'].alias('How many of them ?'),
-            self.experiment.column_definitions['Project_Num'].alias('Project #')
-        )
-        result = results.fetch(limit=1)[0]
-        self.assertIn('Name', result)
-        self.assertIn('How many of them ?', result)
-        self.assertIn('Project #', result)
-
-    def test_attribute_rename_special_chars(self):
-        # first test with only the `:` character present which would trigger a lexical error from ermrest
-        special_character_out_alias = self.experiment._name + ':' + self.experiment.column_definitions['Name']._name
-        results = self.experiment.attributes(self.experiment.column_definitions['Name'].alias(special_character_out_alias))
-        result = results.fetch(limit=1)[0]
-        self.assertIn(special_character_out_alias, result)
-
-        # second test with url unsafe characters present which would trigger a bad request from the web server
-        special_character_out_alias = SPECIAL_CHARACTERS
-        results = self.experiment.attributes(self.experiment.column_definitions['Name'].alias(special_character_out_alias))
-        result = results.fetch(limit=1)[0]
-        self.assertIn(special_character_out_alias, result)
-
-    def test_context(self):
-        path = self.experiment.link(self.experiment_type)
-        results = path.Experiment.entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-
-    def test_path_table_instances(self):
-        path = self.experiment.link(self.experiment_type)
-        results = path.table_instances[TNAME_EXPERIMENT].entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-
-    def test_path_project(self):
-        path = self.experiment.link(self.experiment_type)
-        results = path.Experiment.attributes(
-            path.Experiment,
-            path.Experiment_Type.column_definitions['URI'],
-            path.Experiment_Type.column_definitions['Name'].alias('exptype')
-        )
-        result = results.fetch(limit=1)[0]
-        self.assertIn('Experiment:Name', result)
-        self.assertIn('Experiment:Time', result)
-        self.assertIn('URI', result)
-        self.assertIn('exptype', result)
-
-    @unittest.skipUnless(HAS_PANDAS, "pandas library not available")
-    def test_dataframe(self):
-        results = self.experiment.entities()
-        df = DataFrame(results)
-        self.assertEqual(len(df), TEST_EXP_MAX)
-
-    def test_insert_double_fetch(self):
-        entities = _generate_experiment_entities(self.types, 2)
-        results = self.experiment_copy.insert(entities)
-        rows1 = results.fetch()
-        rows2 = results.fetch()
-        self.assertEqual(rows1, rows2)
-        
-    def test_insert_empty_entities(self):
-        results = self.experiment_copy.insert(None)
-        self.assertEqual(len(results), 0)
-        results = self.experiment_copy.insert([])
-        self.assertEqual(len(results), 0)
-
-    def test_insert_entities_not_iterable(self):
-        with self.assertRaises(TypeError):
-            self.experiment_type.insert(1)
-
-    def test_insert_entities0_not_dict(self):
-        with self.assertRaises(TypeError):
-            self.experiment_type.insert([1])
-        with self.assertRaises(TypeError):
-            self.experiment_type.insert('this is not a dict')
-
-    def test_insert(self):
-        results = self.experiment_copy.insert(_generate_experiment_entities(self.types, 10))
-        self.assertEqual(len(results), 10)
-
-    def test_insert_on_conflict_raise(self):
-        entities = _generate_experiment_entities(self.types, 2)
-        first = entities[0:1]
-        results = self.experiment_copy.insert(first)
-        self.assertEqual(len(results), 1)
-        with self.assertRaises(DataPathException):
-            self.experiment_copy.insert(entities)
-
-    def test_insert_on_conflict_skip(self):
-        entities = _generate_experiment_entities(self.types, 2)
-        first = entities[0:1]
-        results = self.experiment_copy.insert(first)
-        self.assertEqual(len(results), 1)
-        results = self.experiment_copy.insert(entities, on_conflict_skip=True)
-        self.assertEqual(len(results), 1)
-
-    def test_update(self):
-        inserted = self.experiment_copy.insert(_generate_experiment_entities(self.types, 10))
-        self.assertEqual(len(inserted), 10)
-        # now change something in the first result
-        updates = [dict(**inserted[0])]
-        updates[0]['Name'] = '**CHANGED**'
-        updated = self.experiment_copy.update(updates)
-        self.assertEqual(len(updated), 1)
-        self.assertEqual(inserted[0]['RID'], updated[0]['RID'])
-        self.assertNotEqual(inserted[0]['Name'], updated[0]['Name'])
-
-    def test_update_empty_entities(self):
-        results = self.experiment_copy.update(None)
-        self.assertEqual(len(results), 0)
-        results = self.experiment_copy.update([])
-        self.assertEqual(len(results), 0)
-
-    def test_update_entities_not_iterable(self):
-        with self.assertRaises(TypeError):
-            self.experiment_type.update(1)
-
-    def test_update_entities0_not_dict(self):
-        with self.assertRaises(TypeError):
-            self.experiment_type.update([1])
-        with self.assertRaises(TypeError):
-            self.experiment_type.update('this is not a dict')
-
-    def test_delete_whole_path(self):
-        self.experiment_copy.insert(_generate_experiment_entities(self.types, 10))
-        self.assertEqual(len(self.experiment_copy.entities()), 10)
-        self.experiment_copy.path.delete()
-        self.assertEqual(len(self.experiment_copy.entities()), 0)
-
-    def test_delete_filtered_path(self):
-        self.experiment_copy.insert(_generate_experiment_entities(self.types, 10))
-        expression = self.experiment_copy.column_definitions['Name'] == TEST_EXP_NAME_FORMAT.format(1)
-        self.assertEqual(len(self.experiment_copy.filter(expression).entities()), 1)
-        self.experiment_copy.filter(expression).delete()
-        self.assertEqual(len(self.experiment_copy.filter(expression).entities()), 0)
-
-    def test_delete_whole_table(self):
-        self.experiment_copy.insert(_generate_experiment_entities(self.types, 10))
-        self.assertEqual(len(self.experiment_copy.entities()), 10)
-        self.experiment_copy.delete()
-        self.assertEqual(len(self.experiment_copy.entities()), 0)
-
-    def test_nondefaults(self):
-        nondefaults = {'RID', 'RCB', 'RCT'}
-        results = self.experiment.entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-        entities_copy = self.experiment_copy.insert(results, nondefaults=nondefaults, add_system_defaults=False)
-        self.assertEqual(len(results), len(entities_copy), 'entities not copied completely')
-        ig = itemgetter(*nondefaults)
-        for i in range(TEST_EXP_MAX):
-            self.assertEqual(ig(results[i]), ig(entities_copy[i]), 'copied values do not match')
-
-    def test_nondefaults_w_add_sys_defaults(self):
-        nondefaults = {'RID', 'RCB', 'RCT'}
-        results = self.experiment.entities()
-        self.assertEqual(len(results), TEST_EXP_MAX)
-        entities_copy = self.experiment_copy.insert(results, nondefaults=nondefaults)
-        self.assertEqual(len(results), len(entities_copy), 'entities not copied completely')
-        ig = itemgetter(*nondefaults)
-        for i in range(TEST_EXP_MAX):
-            self.assertEqual(ig(results[i]), ig(entities_copy[i]), 'copied values do not match')
-
-    def test_deepcopy_of_paths(self):
-        paths = [
-            self.experiment.path,
-            self.experiment.link(self.experiment_type),
-            self.experiment.link(self.experiment_type, on=(self.experiment.Type == self.experiment_type.ID)),
-            self.experiment.link(
-                self.project,
-                on=(
-                        (self.experiment.Project_Investigator == self.project.Investigator) &
-                        (self.experiment.Project_Num == self.project.Num)
-                )
-            ),
-            self.project.filter(self.project.Num < 1000).link(self.experiment).link(self.experiment_type),
-            self.experiment.alias('Exp').link(self.experiment_type.alias('ExpType')),
-            self.experiment.filter(self.experiment.column_definitions['Name'] == TEST_EXP_NAME_FORMAT.format(1)),
-            self.experiment.filter(self.experiment.column_definitions['Amount'] < 10),
-            self.experiment.filter(
-                self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:])
-            ),
-            self.experiment.filter(
-                ~ (self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:]))
-            ),
-            self.experiment.filter(
-                self.experiment.column_definitions['Name'].ciregexp(TEST_EXP_NAME_FORMAT.format(0)[10:])
-                & (self.experiment.column_definitions['Amount'] == 0)
-            )
-        ]
-        for path in paths:
-            with self.subTest(name=path.uri):
-                cp = deepcopy(path)
-                self.assertNotEqual(path, cp)
-                self.assertEqual(path.uri, cp.uri)
-
-    def test_merge_paths(self):
-        path1 = self.experiment.filter(self.experiment.Amount >= 0)
-        path2 = self.experiment.link(self.experiment_type).filter(self.experiment_type.ID >= '0')
-        path3 = self.experiment.link(self.project).filter(self.project.Num >= 0)
-        original_uri = path1.uri
-
-        # merge paths 1..3
-        path1.merge(path2).merge(path3)
-        self.assertNotEqual(path1.uri, original_uri, "Merged path's URI should have changed from its original URI")
-        self.assertEqual(path1.context._name, path3.context._name, "Context of merged paths should equal far right-hand path's context")
-        self.assertGreater(len(path1.Experiment.entities()), 0, "Should have returned results")
-
-    def test_compose_paths(self):
-        path1 = self.experiment.filter(self.experiment.Amount >= 0)
-        path2 = self.experiment.link(self.experiment_type).filter(self.experiment_type.ID >= '0')
-        path3 = self.experiment.link(self.project).filter(self.project.Num >= 0)
-        original_uri = path1.uri
-
-        # compose paths 1..3
-        path = self.paths.compose(path1, path2, path3)
-        self.assertNotEqual(path, path1, "Compose should have copied the first path rather than mutate it")
-        self.assertNotEqual(path.uri, path1.uri, "Composed path URI should not match the first path URI")
-        self.assertEqual(path1.uri, original_uri, "First path was changed")
-        self.assertNotEqual(path.uri, original_uri, "Merged path's URI should have changed from its original URI")
-        self.assertEqual(path.context._name, path3.context._name, "Context of composed paths should equal far right-hand path's context")
-        self.assertGreater(len(path.Experiment.entities()), 0, "Should have returned results")
-
-    def test_simple_denormalization(self):
-        entities = self.experiment.entities()
-        results = self.experiment.denormalize()
-        self.assertEqual(len(entities), len(results))
-        self.assertNotEqual(entities[0].keys(), results[0].keys())
-        self.assertIn('Type', results[0])
-        self.assertTrue(entities[0]['Type'].startswith('TEST:'))
-        self.assertTrue(results[0]['Type'])
-        self.assertFalse(results[0]['Type'].startswith('TEST:'))
-
-    def test_simple_denormalization_w_entities(self):
-        entities = self.experiment.entities()
-        results = self.experiment.denormalize(heuristic=simple_denormalization_with_whole_entities)
-        self.assertEqual(len(entities), len(results))
-        self.assertLess(len(entities[0].keys()), len(results[0].keys()))
-        self.assertIn('Experiment_Project Investigator_Project_Num_fkey', results[0])
-        self.assertIsInstance(results[0]['Experiment_Project Investigator_Project_Num_fkey'], list)
-        self.assertIsInstance(results[0]['Experiment_Project Investigator_Project_Num_fkey'][0], dict)
-        self.assertIn('RID', results[0]['Experiment_Project Investigator_Project_Num_fkey'][0])
-
-
-if __name__ == '__main__':
-    unittest.main()