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Merge pull request #27 from biothings/add-support-to-geneset
Add support to geneset.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,259 @@ | ||
| import unittest | ||
| import pytest | ||
| import sys | ||
| import os | ||
| import types | ||
| try: | ||
| from StringIO import StringIO | ||
| except ImportError: | ||
| from io import StringIO | ||
| sys.path.insert(0, os.path.split(os.path.split(os.path.abspath(__file__))[0])[0]) | ||
|
|
||
| try: | ||
| from utils import descore | ||
| except ImportError: | ||
| from tests.utils import descore | ||
|
|
||
| import biothings_client | ||
| sys.stdout.write('"biothings_client {0}" loaded from "{1}"\n'.format(biothings_client.__version__, biothings_client.__file__)) | ||
|
|
||
|
|
||
| class TestGenesetClient(unittest.TestCase): | ||
|
|
||
| def setUp(self): | ||
| self.mgs = biothings_client.get_client("geneset") | ||
|
|
||
| def test_metadata(self): | ||
| meta = self.mgs.metadata() | ||
| self.assertTrue("src" in meta) | ||
| self.assertTrue("stats" in meta) | ||
| self.assertTrue("total" in meta['stats']) | ||
|
|
||
| def test_getgeneset(self): | ||
| gs = self.mgs.getgeneset("WP100") | ||
| self.assertEqual(gs['_id'], "WP100") | ||
| self.assertEqual(gs['name'], 'Glutathione metabolism') | ||
| self.assertEqual(gs['source'], 'wikipathways') | ||
| self.assertEqual(gs['taxid'], '9606') | ||
| self.assertGreaterEqual(len(gs['genes']), 19) | ||
| self.assertEqual(gs['count'], len(gs['genes'])) | ||
|
|
||
| self.assertTrue('wikipathways' in gs) | ||
| self.assertEqual(gs['wikipathways']['id'], "WP100") | ||
| self.assertEqual(gs['wikipathways']['pathway_name'], 'Glutathione metabolism') | ||
| self.assertEqual(gs['wikipathways']['url'], 'http://www.wikipathways.org/instance/WP100_r107114') | ||
| self.assertEqual(gs['wikipathways']['_license'], 'https://www.wikipathways.org/index.php/WikiPathways:License_Terms') | ||
|
|
||
| self.assertTrue(any((gene.get('mygene_id') == '2937' and gene.get('symbol') == 'GSS') for gene in gs['genes'])) | ||
|
|
||
| def test_query_fetch_all(self): | ||
|
|
||
| # pdb-->reactome | ||
| # q=source:reactome | ||
| # _exists_:pdb ---> source:reactome | ||
|
|
||
| # fetch_all won't work when caching is used. | ||
| self.mgs.stop_caching() | ||
| qres = self.mgs.query('source:reactome') | ||
| total = qres['total'] | ||
|
|
||
| qres = self.mgs.query('source:reactome', fields='source,count,name', fetch_all=True) | ||
| self.assertTrue(isinstance(qres, types.GeneratorType)) | ||
| self.assertEqual(total, len(list(qres))) | ||
|
|
||
| def test_query_with_fields_as_list(self): | ||
| qres1 = self.mgs.query("genes.ncbigene:1017", fields="name,source,taxid") | ||
| qres2 = self.mgs.query("genes.ncbigene:1017", fields=["name", "source", "taxid"]) | ||
| self.assertTrue('hits' in qres1) | ||
| self.assertEqual(len(qres1['hits']), 10) | ||
| self.assertEqual(descore(qres1['hits']), descore(qres2['hits'])) | ||
|
|
||
| def test_getgeneset_with_fields(self): | ||
| gs = self.mgs.getgeneset("WP100", fields="name,source,taxid,genes.mygene_id,genes.symbol") | ||
|
|
||
| self.assertTrue('_id' in gs) | ||
| self.assertTrue('name' in gs) | ||
| self.assertTrue('source' in gs) | ||
| self.assertTrue('taxid' in gs) | ||
|
|
||
| self.assertTrue(any((gene.get('mygene_id') == '2937' and gene.get('symbol') == 'GSS') for gene in gs['genes'])) | ||
| self.assertFalse(any(gene.get('name') for gene in gs['genes'])) | ||
|
|
||
| def test_getgenesets(self): | ||
| gs_li = self.mgs.getgenesets([ | ||
| "WP100", | ||
| "WP101", | ||
| 'WP103' | ||
| ]) | ||
|
|
||
| self.assertEqual(len(gs_li), 3) | ||
| self.assertEqual(gs_li[0]['_id'], 'WP100') | ||
| self.assertEqual(gs_li[1]['_id'], 'WP101') | ||
| self.assertEqual(gs_li[2]['_id'], 'WP103') | ||
|
|
||
| def test_query(self): | ||
| qres = self.mgs.query('genes.mygene_id:2937', size=5) | ||
| self.assertTrue('hits' in qres) | ||
| self.assertEqual(len(qres['hits']), 5) | ||
|
|
||
| def test_query_default_fields(self): | ||
| self.mgs.query(q='glucose') | ||
|
|
||
| def test_query_field(self): | ||
| self.mgs.query(q='genes.ncbigene:1017') | ||
|
|
||
| def test_species_filter_plus_query(self): | ||
| dog = self.mgs.query(q='glucose', species='9615') | ||
| self.assertEqual(dog['hits'][0]['taxid'], "9615") | ||
|
|
||
| def test_query_by_id(self): | ||
| query = self.mgs.query(q="_id:WP100") | ||
| self.assertEqual(query['hits'][0]['_id'], "WP100") | ||
|
|
||
| def test_query_by_name(self): | ||
| kinase = self.mgs.query(q='name:kinase') | ||
| self.assertIn('kinase', kinase['hits'][0]['name'].lower()) | ||
|
|
||
| def test_query_by_description(self): | ||
| desc = self.mgs.query(q='description:cytosine deamination') | ||
| self.assertIn('cytosine', desc['hits'][0]['description'].lower()) | ||
| self.assertIn('deamination', desc['hits'][0]['description'].lower()) | ||
|
|
||
| def test_query_by_source_go(self): | ||
| go = self.mgs.query(q='source:go', fields='all') | ||
| self.assertIn('go', go['hits'][0].keys()) | ||
| self.assertEqual(go['hits'][0]['source'], 'go') | ||
|
|
||
| def test_query_by_source_ctd(self): | ||
| ctd = self.mgs.query(q='source:ctd', fields='all') | ||
| self.assertIn('ctd', ctd['hits'][0].keys()) | ||
| self.assertEqual(ctd['hits'][0]['source'], 'ctd') | ||
|
|
||
| def test_query_by_source_msigdb(self): | ||
| msigdb = self.mgs.query(q='source:msigdb', fields='all') | ||
| self.assertIn('msigdb', msigdb['hits'][0].keys()) | ||
| self.assertEqual(msigdb['hits'][0]['source'], 'msigdb') | ||
|
|
||
| @pytest.mark.skip(reason="We removed kegg data source for now") | ||
| def test_query_by_source_kegg(self): | ||
| kegg = self.mgs.query(q='source:kegg', fields='all') | ||
| self.assertIn('kegg', kegg['hits'][0].keys()) | ||
| self.assertEqual(kegg['hits'][0]['source'], 'kegg') | ||
|
|
||
| def test_query_by_source_do(self): | ||
| do = self.mgs.query(q='source:do', fields='all') | ||
| self.assertIn('do', do['hits'][0].keys()) | ||
| self.assertEqual(do['hits'][0]['source'], 'do') | ||
|
|
||
| def test_query_by_source_reactome(self): | ||
| reactome = self.mgs.query(q='source:reactome', fields='all') | ||
| self.assertIn('reactome', reactome['hits'][0].keys()) | ||
| self.assertEqual(reactome['hits'][0]['source'], 'reactome') | ||
|
|
||
| def test_query_by_source_smpdb(self): | ||
| smpdb = self.mgs.query(q='source:smpdb', fields='all') | ||
| self.assertIn('smpdb', smpdb['hits'][0].keys()) | ||
| self.assertEqual(smpdb['hits'][0]['source'], 'smpdb') | ||
|
|
||
| @unittest.skipIf(not biothings_client.caching_avail, "requests_cache not available") | ||
| def test_caching(self): | ||
| def _getgeneset(): | ||
| return self.mgs.getgenesets("WP100") | ||
|
|
||
| def _getgenesets(): | ||
| return self.mgs.getgenesets(["WP100", "WP101"]) | ||
|
|
||
| def _query(): | ||
| return self.mgs.query("wnt", fields="name,count,source,taxid") | ||
|
|
||
| def _querymany(): | ||
| return self.mgs.querymany(["wnt", "jak-stat"], fields="name,count,source,taxid") | ||
|
|
||
| def _cache_request(f): | ||
| current_stdout = sys.stdout | ||
| try: | ||
| out = StringIO() | ||
| sys.stdout = out | ||
| r = f() | ||
| output = out.getvalue().strip() | ||
| finally: | ||
| sys.stdout = current_stdout | ||
|
|
||
| return ('[ from cache ]' in output, r) | ||
|
|
||
| try: | ||
| from_cache, pre_cache_r = _cache_request(_getgeneset) | ||
| self.assertFalse(from_cache) | ||
|
|
||
| if os.path.exists('mgsc.sqlite'): | ||
| os.remove('mgsc.sqlite') | ||
| self.mgs.set_caching('mgsc') | ||
|
|
||
| # populate cache | ||
| from_cache, cache_fill_r = _cache_request(_getgeneset) | ||
| self.assertTrue(os.path.exists('mgsc.sqlite')) | ||
| self.assertFalse(from_cache) | ||
| # is it from the cache? | ||
| from_cache, cached_r = _cache_request(_getgeneset) | ||
| self.assertTrue(from_cache) | ||
|
|
||
| self.mgs.stop_caching() | ||
| # same query should be live - not cached | ||
| from_cache, post_cache_r = _cache_request(_getgeneset) | ||
| self.assertFalse(from_cache) | ||
|
|
||
| self.mgs.set_caching('mgsc') | ||
|
|
||
| # same query should still be sourced from cache | ||
| from_cache, recached_r = _cache_request(_getgeneset) | ||
| self.assertTrue(from_cache) | ||
|
|
||
| self.mgs.clear_cache() | ||
| # cache was cleared, same query should be live | ||
| from_cache, clear_cached_r = _cache_request(_getgeneset) | ||
| self.assertFalse(from_cache) | ||
|
|
||
| # all requests should be identical except the _score, which can vary slightly | ||
| for x in [pre_cache_r, cache_fill_r, cached_r, post_cache_r, recached_r, clear_cached_r]: | ||
| x.pop('_score', None) | ||
|
|
||
| self.assertTrue(all([x == pre_cache_r for x in | ||
| [pre_cache_r, cache_fill_r, cached_r, post_cache_r, recached_r, clear_cached_r]])) | ||
|
|
||
| # test getvariants POST caching | ||
| from_cache, first_getgenes_r = _cache_request(_getgenesets) | ||
| del first_getgenes_r | ||
| self.assertFalse(from_cache) | ||
| # should be from cache this time | ||
| from_cache, second_getgenes_r = _cache_request(_getgenesets) | ||
| del second_getgenes_r | ||
| self.assertTrue(from_cache) | ||
|
|
||
| # test query GET caching | ||
| from_cache, first_query_r = _cache_request(_query) | ||
| del first_query_r | ||
| self.assertFalse(from_cache) | ||
| # should be from cache this time | ||
| from_cache, second_query_r = _cache_request(_query) | ||
| del second_query_r | ||
| self.assertTrue(from_cache) | ||
|
|
||
| # test querymany POST caching | ||
| from_cache, first_querymany_r = _cache_request(_querymany) | ||
| del first_querymany_r | ||
| self.assertFalse(from_cache) | ||
| # should be from cache this time | ||
| from_cache, second_querymany_r = _cache_request(_querymany) | ||
| del second_querymany_r | ||
| self.assertTrue(from_cache) | ||
|
|
||
| finally: | ||
| self.mgs.stop_caching() | ||
| os.remove('mgsc.sqlite') | ||
|
|
||
| def suite(): | ||
| return unittest.defaultTestLoader.loadTestsFromTestCase(TestGenesetClient) | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| unittest.TextTestRunner().run(suite()) |