[MNT] - Test organizations

lisc/tests/conftest.py

@@ -10,8 +10,8 @@
 from lisc.io.db import create_file_structure
 from lisc.modutils.dependencies import safe_import
 
-from lisc.tests.tdata import create_term_files, create_api_files
-from lisc.tests.tobjs import (TestDB, load_base, load_counts1d, load_counts, load_words,
+from lisc.tests.tfiles import create_term_files, create_api_files
+from lisc.tests.tdata import (TestDB, load_base, load_counts1d, load_counts, load_words,
                               load_arts, load_arts_all, load_tag, load_term, load_meta_dict)
 from lisc.tests.tsettings import TEST_WAIT_TIME, TESTS_PATH, TEST_DB_PATH, TEST_DB_NAME
 
@@ -20,6 +20,8 @@
 ###################################################################################################
 ###################################################################################################
 
+## TEST SETUP
+
 def pytest_configure(config):
 
     # Set backend for matplotlib tests, if mpl is available
@@ -39,6 +41,8 @@ def check_db():
     create_term_files(tdb)
     create_api_files(tdb)
 
+## TEST OBJECTS
+
 @pytest.fixture(scope='function')
 def test_req():
     return Requester(wait_time=TEST_WAIT_TIME)

lisc/tests/tdata.py

@@ -1,37 +1,182 @@
-"""Utilities to create data files for testing."""
+"""Utilties to create tests data and objects."""
 
-import os
+from copy import deepcopy
+from itertools import repeat
 
-from lisc.io.db import check_directory
+from bs4.element import Tag
+
+import numpy as np
+
+from lisc.objects.base import Base
+from lisc.objects import Counts1D, Counts, Words
+from lisc.data import Articles, ArticlesAll, Term
+
+from lisc.io.db import SCDB
+
+from lisc.tests.tsettings import TEST_DB_PATH
 
 ###################################################################################################
 ###################################################################################################
 
-def create_term_files(directory):
-    """Creates some test term files."""
+class TestDB(SCDB):
+    """Overloads the SCDB object as database object for tests."""
+
+    def __init__(self):
+
+        # Initialize from normal database object
+        SCDB.__init__(self, base=TEST_DB_PATH)
+
+def load_tag():
+    """Helper function to create a complex bs4 tag for testing."""
+
+    tag = Tag(name='Out')
+    inn1a = Tag(name='Inn1')
+    inn1b = Tag(name='Inn1')
+
+    inn1a.append('words words')
+    inn1b.append('more words')
+
+    tag.append(inn1a)
+    tag.append(inn1b)
+
+    return tag
+
+def load_term():
+    """Helper function to create a Term object for testing."""
+
+    return Term(label='label', search=['test', 'synonym'],
+                inclusions=['incl', 'incl_synonym'],
+                exclusions=['excl', 'excl_synonym'])
+
+def load_meta_dict():
+    """Helper function to create a dictionary of meta data information."""
+
+    return {
+        'date': '1999-12-31_00:00:00',
+        'log': None,
+        'requester_n_requests': 1,
+        'requester_wait_time': 1,
+        'requester_start_time': '00:00:00 Friday 01 January 2000',
+        'requester_end_time': '00:00:00 Monday 01 January 2000',
+        'requester_logging': None,
+        'db_info_dbname': 'pubmed',
+        'db_info_menuname': 'PubMed',
+        'db_info_description': 'PubMed bibliographic record',
+        'db_info_dbbuild': 'Build-#####',
+        'db_info_count': '123456789',
+        'db_info_lastupdate': '1999/12/31 00:00',
+        'settings_setting1' : True,
+        'settings_setting2' : 42,
+    }
+
+def load_base(add_terms=False, add_clusions=False, add_labels=False, n_terms=2):
+    """Helper function to load Base object for testing."""
+
+    base = Base()
+
+    if add_terms:
+        base.add_terms(repeat_data(['test', 'synonym'], n_terms))
+
+    if add_clusions:
+        base.add_terms(repeat_data(['incl', 'incl_synonym'], n_terms), 'inclusions')
+        base.add_terms(repeat_data(['excl', 'excl_synonym'], n_terms), 'exclusions')
+
+    if add_labels:
+        base.add_labels([val[0] for val in repeat_data(['label'], n_terms)])
+
+    return base
+
+def load_counts1d(add_terms=False, add_data=False, n_terms=2):
+    """Helper function to load Counts1D object for testing."""
+
+    counts1d = Counts1D()
+
+    if add_terms:
+        counts1d.add_terms(repeat_data(['test', 'synonym'], n_terms))
+
+    if add_data:
+        counts1d.counts = np.random.randint(0, 100, (2))
+
+    return counts1d
+
+def load_counts(add_terms=False, add_data=False, n_terms=(2, 2)):
+    """Helper function to load Counts object for testing."""
+
+    counts = Counts()
+
+    if add_terms:
+        counts1d.add_terms(repeat_data(['test', 'synonym'], n_terms[0]), dim='A')
+        counts1d.add_terms(repeat_data(['test', 'synonym'], n_terms[1]), dim='B')
+
+    if add_data:
+        counts.terms['A'].counts = np.random.randint(0, 100, (n_terms[0]))
+        counts.terms['B'].counts = np.random.randint(0, 100, (n_terms[1]))
+        counts.counts = np.random.randint(0, 100, n_terms)
+
+    return counts
+
+def load_words(add_terms=False, add_data=False, n_terms=2):
+    """Helper function to load Words object for testing."""
+
+    words = Words()
+
+    if add_terms:
+        words.add_terms(repeat_data(['test', 'synonym'], n_terms))
+
+    if add_data:
+        arts = load_arts(add_data=True, n_data=2)
+        words.results = [deepcopy(arts) for ind in range(n_terms)]
+
+    return words
+
+def load_arts(add_data=False, n_data=1, add_none=False):
+    """Helper function to load Articles object for testing."""
+
+    arts = Articles(Term('label', ['search'], ['inclusion'], ['exclusion']))
+
+    if add_data:
+        for ind in range(n_data):
 
-    path = check_directory(directory, 'terms')
+            arts.add_data('ids', ind)
+            arts.add_data('titles', 'title')
+            arts.add_data('journals', ['science', 'sc'])
+            arts.add_data('authors', [['ln1', 'fn1', 'in1', 'af1'], ['ln2', 'fn2', 'in2', 'af2']])
+            arts.add_data('words', 'Lots of words data. Just a continuous text.')
+            arts.add_data('keywords', ['lots', 'of', 'keywords'])
+            arts.add_data('years', 2112)
+            arts.add_data('dois', 'doi_str')
 
-    with open(os.path.join(path, 'test_terms.txt'), 'w') as term_file:
-        term_file.write('word\nthing, same')
+    if add_none:
+        arts.dois[-1] = None
+        arts.years[-1] = None
+        arts.authors[-1] = None
+        arts.words[-1] = str()
+        arts.keywords[-1] = list()
 
-    with open(os.path.join(path, 'test_inclusions.txt'), 'w') as incl_file:
-        incl_file.write('need\nrequired')
+    return arts
 
-    with open(os.path.join(path, 'test_exclusions.txt'), 'w') as excl_file:
-        excl_file.write('not\navoid')
+def load_arts_all():
+    """Helper function to load ArticlesAll object for testing."""
 
-    with open(os.path.join(path, 'test_exclusions_line.txt'), 'w') as excl_file2:
-        excl_file2.write('not\n')
+    arts = load_arts(add_data=True, n_data=2)
+    arts_all = ArticlesAll(arts)
 
-    with open(os.path.join(path, 'test_labels.txt'), 'w') as labels_file:
-        labels_file.write('label1\nlabel2')
+    return arts_all
 
+def repeat_data(terms, n_times):
+    """Repeat a list of data, appending index number, a specified number of times.
 
-def create_api_files(directory):
-    """Create test API key file."""
+    Parameters
+    ----------
+    terms : list of str
+        List of elements to repeat.
+    n_times : int
+        Number of times to repeat.
 
-    path = check_directory(directory, 'base')
+    Returns
+    -------
+    list of list of str
+        List of repeated elements.
+    """
 
-    with open(os.path.join(path, 'api_key.txt'), 'w') as term_file:
-        term_file.write('123abc')
+    return [[val + str(ind) for val in vals] for ind, vals in enumerate(repeat(terms, n_times))]

lisc/tests/tfiles.py

@@ -0,0 +1,37 @@
+"""Utilities to create data files for testing."""
+
+import os
+
+from lisc.io.db import check_directory
+
+###################################################################################################
+###################################################################################################
+
+def create_term_files(directory):
+    """Creates some test term files."""
+
+    path = check_directory(directory, 'terms')
+
+    with open(os.path.join(path, 'test_terms.txt'), 'w') as term_file:
+        term_file.write('word\nthing, same')
+
+    with open(os.path.join(path, 'test_inclusions.txt'), 'w') as incl_file:
+        incl_file.write('need\nrequired')
+
+    with open(os.path.join(path, 'test_exclusions.txt'), 'w') as excl_file:
+        excl_file.write('not\navoid')
+
+    with open(os.path.join(path, 'test_exclusions_line.txt'), 'w') as excl_file2:
+        excl_file2.write('not\n')
+
+    with open(os.path.join(path, 'test_labels.txt'), 'w') as labels_file:
+        labels_file.write('label1\nlabel2')
+
+
+def create_api_files(directory):
+    """Create test API key file."""
+
+    path = check_directory(directory, 'base')
+
+    with open(os.path.join(path, 'api_key.txt'), 'w') as term_file:
+        term_file.write('123abc')