Updated bel obj in tests

belbio · Jan 4, 2018 · d7eefce · d7eefce
1 parent 7bda4d4
commit d7eefce
Show file tree

Hide file tree

Showing 6 changed files with 65 additions and 65 deletions.
diff --git a/tests/lang/test_canonicalize.py b/tests/lang/test_canonicalize.py
@@ -1,8 +1,8 @@
-import bel.lang
+import bel.lang.belobj
 
 from bel.Config import config
 
-bel_obj = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 # TODO Add test for specified canonical_targets - need to make sure BEL.bio API endpoint is updated to handle this querystring arg
 
@@ -13,11 +13,11 @@ def test_canon_one():
 
     expected = 'activity(proteinAbundance(EG:207), molecularActivity(GO:"kinase activity"))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.canonicalize()
+    bo.canonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_canon_two():
@@ -26,11 +26,11 @@ def test_canon_two():
 
     expected = 'activity(proteinAbundance(EG:4615), molecularActivity(GO:"catalytic activity")) directlyIncreases complexAbundance(proteinAbundance(EG:4615), proteinAbundance(EG:3654), proteinAbundance(EG:51135))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.canonicalize()
+    bo.canonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_canon_nested():
@@ -39,11 +39,11 @@ def test_canon_nested():
 
     expected = 'activity(proteinAbundance(EG:4615), molecularActivity(GO:"catalytic activity")) directlyIncreases (complexAbundance(proteinAbundance(EG:4615), proteinAbundance(EG:3654), proteinAbundance(EG:51135)) directlyIncreases complexAbundance(proteinAbundance(EG:4615), proteinAbundance(EG:3654), proteinAbundance(EG:51135)))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.canonicalize()
+    bo.canonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_decanon_one():
@@ -52,11 +52,11 @@ def test_decanon_one():
 
     expected = 'activity(proteinAbundance(HGNC:AKT1), molecularActivity(GO:"kinase activity"))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.decanonicalize()
+    bo.decanonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_decanon_two():
@@ -65,11 +65,11 @@ def test_decanon_two():
 
     expected = 'activity(proteinAbundance(HGNC:MYD88), molecularActivity(GO:"catalytic activity")) directlyIncreases complexAbundance(proteinAbundance(HGNC:MYD88), proteinAbundance(HGNC:IRAK1), proteinAbundance(HGNC:IRAK4))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.decanonicalize()
+    bo.decanonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_decanon_nested():
@@ -78,8 +78,8 @@ def test_decanon_nested():
 
     expected = 'activity(proteinAbundance(HGNC:MYD88), molecularActivity(GO:"catalytic activity")) directlyIncreases (complexAbundance(proteinAbundance(HGNC:MYD88), proteinAbundance(HGNC:IRAK1), proteinAbundance(HGNC:IRAK4)) directlyIncreases complexAbundance(proteinAbundance(HGNC:MYD88), proteinAbundance(HGNC:IRAK1), proteinAbundance(HGNC:IRAK4)))'
 
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    bel_obj.decanonicalize()
+    bo.decanonicalize()
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
diff --git a/tests/lang/test_computed.py b/tests/lang/test_computed.py
@@ -1,7 +1,7 @@
-import bel.lang.bel
+import bel.lang.belobj
 from bel.Config import config
 
-bel_obj = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 
 def test_abundance():
@@ -11,7 +11,7 @@ def test_abundance():
                       'MESHD:Inflammation componentOf bp(MESHD:Inflammation)'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -33,7 +33,7 @@ def test_complex():
                       'ma(tscript) componentOf act(complex(SCOMP:"Nfkb Complex"), ma(tscript))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -58,7 +58,7 @@ def test_composite():
                       'ma(kin) componentOf act(p(HGNC:PRKCA), ma(kin))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -79,7 +79,7 @@ def test_g():
                       'var("c.1521_1523delCTT") componentOf g(REF:NM_000492.3, var("c.1521_1523delCTT"))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -101,7 +101,7 @@ def test_m():
     expected_edges = ['MGI:Mir21 componentOf m(MGI:Mir21)'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -125,7 +125,7 @@ def test_p():
                       'MESHCS:Cytoplasm componentOf loc(MESHCS:Cytoplasm)',
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -145,7 +145,7 @@ def test_r():
                       'HGNC:ENO1 componentOf r(HGNC:ENO1)'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -167,7 +167,7 @@ def test_bp():
                       'ma(kin) componentOf act(p(HGNC:KDR), ma(kin))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -187,7 +187,7 @@ def test_path():
                       'MESH:"Skin Diseases" componentOf path(MESH:"Skin Diseases")'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -209,7 +209,7 @@ def test_act():
                       'ma(GOMF:"transporter activity") componentOf {}'.format(statement)
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -233,7 +233,7 @@ def test_tloc():
                       'toLoc(MESHCL:"Cell Nucleus") componentOf {}'.format(statement)
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -254,7 +254,7 @@ def test_sec():
                       'a(CHEBI:"nitric oxide") componentOf sec(a(CHEBI:"nitric oxide"))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -278,7 +278,7 @@ def test_surf():
                       'complex(p(HGNC:ITGA2), p(HGNC:ITGB1)) componentOf surf(complex(p(HGNC:ITGA2), p(HGNC:ITGB1)))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -303,7 +303,7 @@ def test_deg():
                       'deg(p(HGNC:HBP1)) decreases p(HGNC:HBP1)'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -329,7 +329,7 @@ def test_rxn():
                       'products(a(CHEBI:"hydrogen peroxide"), a(CHEBI:oxygen)) componentOf {}'.format(statement)
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -352,7 +352,7 @@ def test_list():
                       'p(HGNC:MAPK9) componentOf list(p(HGNC:MAPK8), p(HGNC:MAPK9))'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -373,7 +373,7 @@ def test_nested_one():
                       'GO:"apoptotic process" componentOf bp(GO:"apoptotic process")'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:
@@ -395,7 +395,7 @@ def test_nested_two():
                       'CHEBI:EXAMPLE2 componentOf a(CHEBI:EXAMPLE2)'
                       ]
 
-    actual_edges_partials = bel_obj.parse(statement).compute_edges()
+    actual_edges_partials = bo.parse(statement).compute_edges()
     actual_edges = []
 
     for each in actual_edges_partials:

diff --git a/tests/lang/test_orthologize.py b/tests/lang/test_orthologize.py
@@ -1,7 +1,7 @@
-import bel.lang
+import bel.lang.belobj
 from bel.Config import config
 
-bel_obj = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 
 # def test_ortho():
@@ -16,7 +16,7 @@
 #                         ['EG:21858']]
 
 #     for index, (gene, species) in enumerate(gene_species_id_tuples):
-#         result = bel_obj.orthologize(gene, species)
+#         result = bo.orthologize(gene, species)
 #         assert result == list_of_expected[index]
 
 
@@ -25,27 +25,27 @@ def test_ortho_one():
     statement = 'act(p(HGNC:AKT1), ma(GO:"kinase activity"))'
     expected = 'activity(proteinAbundance(MGI:Akt1), molecularActivity(GO:"kinase activity"))'
 
-    bel_obj.parse(statement)
-    bel_obj.orthologize('TAX:10090')
+    bo.parse(statement)
+    bo.orthologize('TAX:10090')
 
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_ortho_two():
 
     statement = 'act(p(HGNC:A1BG), ma(GO:"catalytic activity")) directlyIncreases complex(p(HGNC:ROCK1), p(HGNC:SOD1), p(HGNC:TIMP2))'
     expected = 'activity(proteinAbundance(MGI:A1bg), molecularActivity(GO:"catalytic activity")) directlyIncreases complexAbundance(proteinAbundance(MGI:Rock1), proteinAbundance(MGI:Sod1), proteinAbundance(EG:21858))'
 
-    bel_obj.parse(statement)
-    bel_obj.orthologize('TAX:10090')
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    bo.parse(statement)
+    bo.orthologize('TAX:10090')
+    assert bo.ast.to_string(fmt='long') == expected
 
 
 def test_ortho_nested():
 
     statement = 'act(p(HGNC:A1BG), ma(GO:"catalytic activity")) directlyIncreases (complex(p(HGNC:ROCK1), p(HGNC:SOD1), p(HGNC:TIMP2)) directlyIncreases complex(p(HGNC:ROCK1), p(HGNC:SOD1), p(HGNC:TIMP2)))'
     expected = 'activity(proteinAbundance(MGI:A1bg), molecularActivity(GO:"catalytic activity")) directlyIncreases (complexAbundance(proteinAbundance(MGI:Rock1), proteinAbundance(MGI:Sod1), proteinAbundance(EG:21858)) directlyIncreases complexAbundance(proteinAbundance(MGI:Rock1), proteinAbundance(MGI:Sod1), proteinAbundance(EG:21858)))'
 
-    bel_obj.parse(statement)
-    bel_obj.orthologize('TAX:10090')
-    assert bel_obj.ast.to_string(fmt='long') == expected
+    bo.parse(statement)
+    bo.orthologize('TAX:10090')
+    assert bo.ast.to_string(fmt='long') == expected
diff --git a/tests/lang/test_parse.py b/tests/lang/test_parse.py
@@ -1,30 +1,30 @@
-import bel.lang
+import bel.lang.belobj
 from bel.Config import config
 
-bel_obj = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 
 def test_empty_string():
 
     statement = ''
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    assert bel_obj.ast is None
-    assert 'Please include a valid BEL statement.' in bel_obj.validation_messages[0][1]
+    assert bo.ast is None
+    assert 'Please include a valid BEL statement.' in bo.validation_messages[0][1]
 
 
 def test_bad_string_start():
 
     statement = '$$!@$'
-    bel_obj.parse(statement)
+    bo.parse(statement)
 
-    assert bel_obj.ast is None
-    assert 'Failed parse at position 0.' in bel_obj.validation_messages[0][1]
+    assert bo.ast is None
+    assert 'Failed parse at position 0.' in bo.validation_messages[0][1]
 
 # def test_whitespace_string():
 #
 #     statement = 'a('
-#     parse_obj = bel_obj.parse(statement)
+#     parse_obj = bo.parse(statement)
 #
 #     print(parse_obj.error)
 #     assert isinstance(parse_obj, ParseObject)

diff --git a/tests/lang/test_semantic_checks.py b/tests/lang/test_semantic_checks.py
@@ -1,8 +1,8 @@
 import pytest
-import bel.lang
+import bel.lang.belobj
 from bel.Config import config
 
-bo = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 SPECIFIED_VERSION_UNDERLINED = config['bel']['lang']['default_bel_version']
 

diff --git a/tests/lang/test_syntax_checks.py b/tests/lang/test_syntax_checks.py
@@ -1,7 +1,7 @@
-import bel.lang.bel
+import bel.lang.belobj
 from bel.Config import config
 
-bo = bel.lang.bel.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
+bo = bel.lang.belobj.BEL(config['bel']['lang']['default_bel_version'], config['bel_api']['servers']['api_url'])
 
 SPECIFIED_VERSION_UNDERLINED = config['bel']['lang']['default_bel_version']