Unit testing framework (#26)

* added unit test framework

* added unit test framework

* file rename

* variable name update

* pep8 compliance

* pep8 compliance

tests/sampleFile.csv

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+favoriteColor,name
+blue,phil
+green,tom

tests/sampleMeta.csv

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+id,mexico,serbia,favoriteMeat,favoriteFruit
+1,quien,ко,bacon,orange
+2,que,Шта,bacon,banana
+3,donde,где,,

tests/unit/conftest.py

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+import pytest
+import sys
+import logging
+import pandas
+import synapseclient
+
+
+SAMPLE_FILE = "../sampleFile.csv"
+SAMPLE_META = "../sampleMeta.csv"
+
+
+@pytest.fixture(scope='session')
+def syn():
+    syn = synapseclient.login()
+    return syn
+
+
+@pytest.fixture(scope='session')
+def sampleEntities():
+    data = pandas.read_csv(SAMPLE_FILE, header=0, index_col=None)
+    meta = pandas.read_csv(SAMPLE_META, header=0, index_col=None)
+    return {'data': data, 'meta': meta}
+
+
+@pytest.fixture(scope='session')
+def entities(syn, sampleEntities):
+    import uuid  # random project name
+    project = synapseclient.Project(str(uuid.uuid4()))
+    project = syn.store(project)
+    # store sample files
+    _file = synapseclient.File(path=SAMPLE_FILE, name='file1.csv',
+                               parent=project)
+    _file = syn.store(_file)
+    _file2 = synapseclient.File(path=SAMPLE_FILE, name='file2.csv',
+                                parent=project)
+    _file2 = syn.store(_file2)
+    _file3 = synapseclient.File(path=SAMPLE_FILE, name='file3.csv.gz',
+                                parent=project)
+    _file3 = syn.store(_file3)
+    # store a sample metadata file
+    meta = synapseclient.File(path=SAMPLE_META, name='meta', parent=project)
+    meta = syn.store(meta)
+    # store a sample table (same values as sample file)
+    df = sampleEntities['data']
+    cols = synapseclient.as_table_columns(df)
+    schema = synapseclient.Schema(name="table", columns=cols,
+                                  parent=project)
+    schema = syn.store(schema)
+    table = syn.store(synapseclient.Table(schema, df))
+    # store a sample file view
+    entity_view = synapseclient.EntityViewSchema(
+            name='entity_view',
+            parent=project,
+            scopes=[project])
+    entity_view = syn.store(entity_view)
+    ents = {'files': [_file, _file2, _file3],
+            'meta': meta,
+            'schema': schema,
+            'entity_view': entity_view}
+    yield ents
+    syn.delete(project)

tests/unit/test_utils.py

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+import annotator
+import pandas
+
+
+def test_setUp(syn, sampleEntities, entities):
+    """ Set up working environment on Synapse,
+    passes if set-up is successful
+    """
+    assert True
+
+
+def test_synread_csv(syn, sampleEntities, entities):
+    df = annotator.utils.synread(syn, entities['files'][0].id, sortCols=False)
+    pandas.testing.assert_frame_equal(df, sampleEntities['data'],
+                                      check_like=True)
+
+
+def test_synread_table(syn, sampleEntities, entities):
+    df = annotator.utils.synread(syn, entities['schema'].id, sortCols=False)
+    pandas.testing.assert_frame_equal(
+            df.reset_index(drop=True),
+            sampleEntities['data'],
+            check_like=True)
+
+
+def test_synread_entity_view(syn, sampleEntities, entities):
+    df = annotator.utils.synread(
+            syn,
+            entities['entity_view'].id,
+            sortCols=False)
+    assert isinstance(df, pandas.DataFrame)
+
+
+def test_synread_list_csv(syn, sampleEntities, entities):
+    listOfDataFrames = annotator.utils.synread(
+            syn,
+            [f['id'] for f in entities['files']],
+            sortCols=False)
+    pandas.testing.assert_frame_equal(
+            listOfDataFrames[0],
+            sampleEntities['data'],
+            check_like=True)